Eiko Kuramae

Prof. dr. ir. Eiko Kuramae PhD

Senior Researcher
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Visiting Address

Droevendaalsesteeg 10
6708 PB Wageningen

+31 (0) 317 47 34 00

The Netherlands


My research aims to understand microbiome interactions for soil functioning and microbe-plant co-dependency in sustainable agriculture. We farm microbes involved N and P cycles to nourish plants, improve soil quality and mitigate N2O emissions.


I am a Senior Scientist of the Netherlands Institute of Ecology, as well as a professor of Microbial Community Ecology & Environmental Genomics at Utrecht University. I lead national and international projects, including bilateral programs with Brazil, Uruguay, Colombia, USA, Africa, China and Japan.

My research focuses on unraveling the taxonomic and functional interactions within microbial communities to enhance our understanding of ecosystem functioning, particularly in soil environments. My primary areas of interest include effects of changes in land use and global climate.
To accomplish these goals, I apply cutting-edge tools of omics approaches, bioinformatics, multivariate statistics, and modeling. By examining microbial taxonomic and functional interactions, we can predict the consequences of various changes, including those related to land use, sustainable agriculture (such as tropical agroforestry and biomass production), and cropping regimes.
Through my research, I seek to find practical solutions to pressing real-world issues, such as mitigating greenhouse gas emissions through best management practices for food and production, land restoration, and cultivating crops with beneficial microbial communities.
If you're interested in the complex and captivating world of microbial interactions and their impact on the environment, join me in unraveling the mysteries of microbial communities and discovering practical solutions that can significantly impact on our planet.

Research groups



  • 2012–Present
    Senior Scientist and Project Leader
  • 2020–Present
    Professor of Microbial Community Ecology & Environmental Genomics, Utrecht University
  • 2010–2011
    Scientist, Netherlands Institute of Ecology (NIOO-KNAW)
  • 2009–2011
    Research Scientist, Free University Amsterdam (VU)
  • 2007–2008
    Post-doctoral researcher, Netherlands Institute of Ecology (NIOO-KNAW)
  • 2003–2007
    Post-doctoral researcher, Westerdijk Fungal Biodiversity Centre, Netherlands
  • 2001–2002
    Assistant professor, University of Sao Paulo State (UNESP), Brazil
  • 1996–2000
    Young scientist, University of Sao Paulo State (UNESP), Brazil
  • 1992–1995
    PhD Biological Sciences, Genetics, University of Sao Paulo State (UNESP), Brazil
  • 1991–1992
    Research Scientist, Agroflora S.A. - Seed Company, Brazil
  • 1987–1991
    Agronomist, Brazilian Agriculture Cooperative of Cotia, Brazil


  • 1992–1995
    PhD in Biological Sciences, area: Genetics, University of Sao Paulo State (UNESP) Botucatu, Sao Paulo, Brazil
  • 1989–1991
    MSc Molecular Biology Vrije Universiteit Brussel (VUB), Belgium
  • 1984–1987
    Agronomic Engineering, University of Sao Paulo State (UNESP) Botucatu, Brazil

Editorial board memberships

  • 2021–Present
    The ISME Journal
  • 2020–Present
  • 2014–Present
    Plos One

PhD students

  • 2022–Present
    Lena Faller
    Utrecht University
    Promotors and Copromotors: Eiko Kuramae and George Kowalchuk
  • 2019–Present
    Han Wang
    Utrecht University
    Promotors and Copromotors: Eiko Kuramae and George Kowalchuk
  • 2019–Present
    Cristina Rotoni
    Utrecht Univeristy
    Promotors and Copromotors: Eiko Kuramae and George Kowalchuk
  • 2017–Present
    Letusa Momesso
    Utrecht Univerity
    Promotors and Copromotors: Eiko Kuramae and George Kowalchuk
  • 2021–Present
    Menghui Dong
    Utrecht University
    Promotors and Copromotors: George Kowalchuk and Eiko Kuramae
  • 2018–Present
    Azkia Nurfikari
    Wageningen University
    Promotors and Copromotors: Wietse de Boer and Eiko Kuramae
  • 2014–2022
    Marcio Leite
    Utrecht University
    Promotors and Copromotors: Eiko Kuramae and George Kowalchuk
  • 2019–Present
    Utrecht University
    Promotors and Copromotors: Eiko Kuramae and George Kowalchuk
  • 2014–2019
    Noriko Cassman
    Leiden University
    Promotors and Copromotors: Johannes van Veen and Eiko Kuramae
  • 2014–2018
    Késia S. Lourenço
    Leiden University
    Promotors and Copromotors: Johannes van Veen and Eiko Kuramae
  • 2016–2020
    Ohana Costa
    Leiden University
    Promotors and Copromotors: Jos Raaijmakers and Eiko Kuramae
  • 2012–2015
    Manoeli Lupatini
    Leiden University
    Promotors and Copromotors: Johannes van Veen and Eiko Kuramae
  • 2013–2019
    Thiago R. Schlemper
    Leiden University
    Promotors and Copromotors: Johannes van Veen and Eiko Kuramae
  • 2012–2016
    Yan Yan
    Leiden University
    Promotors and Copromotors: Johannes van Veen and Eiko Kuramae
  • 2011–2015
    Lucas W. Mendes
    University of Sao Paulo, CENA, Brazil
    Promotors and Copromotors: Sui M. Tsai and Eiko Kuramae
  • 2015–2019
    Elaine G. Labanca
    Agronomic Institute of Campinas (IAC), Brazil
    Promotors and Copromotors: Adriana P. D. da Silveira and Eiko Kuramae

Ancillary activities


Peer-reviewed publications

  • Applied Soil Ecology

    Arbuscular mycorrhizal fungi originated from soils with a fertility gradient highlight a strong intraspecies functional variability

    Valentina Marrassini, Laura Ercoli, Eiko Kuramae, George Kowalchuk, Elisa Pellegrino
    Characterization and selection of arbuscular mycorrhizal fungal (AMF) taxa to design inocula tailored to meet a spectrum of needs is a crucial first step to achieve specific beneficial agronomic functions. Commonly, commercial microbial inocula are based on generalist single AM fungal taxa, having low genetic variability and not offering efficiency and stability when applied in agroecosystems. In this study, we investigated the AMF functional variability at inter- and intra-species levels by characterizing colonization traits, host growth, and mineral uptake of single-spore AM fungi isolated from soils with a fertility gradient. Nineteen single-spore cultures, showing high spore density and AMF colonization, were phylogenetically assigned to different isolates of 3 AMF species (i.e. Entrophospora claroidea, Funneliformis mosseae and Archaeospora trappei). A higher functional variability in infectivity and effectiveness was detected among isolates within AMF species (25 % of total variance) than among AMF species. Most of AMF isolates of F. mosseae have a better outcome in terms of plant growth, although with a performance gradient, while the isolates of E. claroidea showed a variable functional pattern, and those of A. trappei a less variable pattern. Overall, isolates originating from the soil of the conventional arable field with higher pH and phosphorous availability promoted the uptake of plant nutrients, while those originating from soils with higher SOM and plant diversity promoted plant growth. On the contrary, the infectivity traits of the AM fungi were more conserved, as they were not affected by the environmental parameters of the soils of origin. Finally, we highlighted that soil pH played an important role in shaping the pattern of AMF functionality. Boosting the isolation and cultivation of AMF taxa, originating from agricultural and natural soils, is shown to be a key step in exploiting AMF diversity and designing the new generation of microbial inoculants.
  • Applied Soil Ecology

    Cultivar governs plant response to inoculation with single isolates and the microbiome associated with arbuscular mycorrhizal fungi

    Cristina Rotoni, Marcio Fernandes Alves Leite, Lina Wong, Cátia S. D. Pinto, Sidney L. Stürmer, Agata Pijl, Eiko Kuramae

    Plant Growth-Promoting Microbes (PGPM) have the potential to enhance sustainable agriculture, but there is still a limited understanding of how the complex interplay between plant genetic variability, the native soil community, and soil nutrients affects PGPM recruitment. To address this challenge, we investigated the impact of bacteria isolates and arbuscular mycorrhizal fungi (AMF) along with their accompany microbiome (AMFc) derived from a wild chrysanthemum on the growth of five different commercial chrysanthemum cultivars (Chic, Chic 45, Chic Cream, Haydar and Barolo), as well as their rhizosphere microbiomes, within a nutrient-rich complex substrate environment. We found 23 bacterial strains capable of producing siderophore, 14 strains capable of producing Indole-3-acetic acid, and 18 strains capable of solubilizing phosphate. The AMFc had six AMF species, and the bacterial and fungal communities associated with AMF belonged to different phyla. Using generalized joint models, we investigated the impact of the three most effective bacterial strains and the AMFc on plant growth (shoot and root dry mass) while integrating information on plant genotype, environment, and microbes. The impact of PGPM inoculation varied from positive to negative effects depending on the cultivar, with Chic Cream showing the highest increase in root biomass after inoculation with both bacterial strain SMF006 (57 %) and AMFc inoculation (79 %). Our study demonstrates that PGPM from wild relative can impact the growth and assembly of the chrysanthemum root microbiome, but this impact is cultivar-dependent. Furthermore, inoculation with a complex AMF containing community (AMFc) induced greater changes in the rhizosphere microbiome than with a single bacterial isolate. Our study shows that inoculation of a complex community of beneficial microbes results in more effective plant growth promotion.

  • Applied Soil Ecology

    Unraveling the impact of protein hydrolysates on rhizosphere microbial communities

    Ohana Costa, Jingjing Chang, Willem van Lith, Eiko Kuramae
    Protein hydrolysates (PHs), derived from enzymatic or chemical protein hydrolysis, are recognized as effective biostimulants for sustainable and environmentally safe crop production. Extensive research has highlighted their benefits and demonstrated their capacity to enhance crop growth and yield under various abiotic stresses, making them increasingly popular in agriculture. To fully unlock the potential of PHs, more research is needed to elucidate their mechanisms of action. This involves understanding plant preferences for different PH sources as well as their impact on rhizosphere microbial communities. This study explored how PHs from plant and animal sources affect plant growth and rhizosphere microbiota across five different plant species. We found variations in plant responses to different PHs, indicating differing plant preferences for nitrogen sources and protein uptake mechanisms among species. There was an increase in beneficial microbial taxa in response to PH application, including Pseudomonas, Paraburkholderia, and Mortierella. Functional analysis also indicated variations in chemoheterotrophy, nitrate respiration and reduction, based on crop species. In conclusion, this research shows the potential of PHs as biostimulants for diverse crops. Their effectiveness is dependent on various factors, including source, production process and plant species, having a positive impact on both plant growth and rhizosphere microbial communities.
  • Journal of Ecology

    Stem decomposition of temperate tree species is determined by stem traits and fungal community composition during early stem decay

    Shanshan Yang, Lourens Poorter, Frank J. Sterck, Johannes H. C. Cornelissen, Richardus S. P. van Logtestijn, Eiko Kuramae, George Kowalchuk, Mariet M. Hefting, Leo Goudzwaard, Chenhui Chang, Ute Sass‐Klaassen
    Dead trees are vital structural elements in forests playing key roles in the carbon and nutrient cycle. Stem traits and fungal community composition are both important drivers of stem decay, and thereby affect ecosystem functioning, but their relative importance for stem decomposition over time remains unclear.To address this issue, we used a common garden decomposition experiment in a Dutch larch forest hosting fresh logs from 13 common temperate tree species. In total, 25 fresh wood and bark traits were measured as indicators of wood accessibility for decomposers, nutritional quality and chemical or physical defence mechanisms. After 1 and 4 years of decay, we assessed the richness and composition of wood-inhabiting fungi using amplicon sequencing and determined the proportional wood density loss.Average proportional wood density loss for the first year was 18.5%, with further decomposition occurring at a rate of 4.3% year−1 for the subsequent 3 years across tree species. Proportional wood density loss varied widely across tree species in the first year (8.7–24.8% year−1) and subsequent years (0–11.3% year−1). The variation was directly driven by initial wood traits during the first decay year, then later directly driven by bark traits and fungal community composition. Moreover, bark traits affected the composition of wood-inhabiting fungi and thereby indirectly affected decomposition rates. Specifically, traits promoting resource acquisition of the living tree, such as wide conduits that increase accessibility and high nutrient concentration, increased initial wood decomposition rates. Fungal community composition, but not fungal richness explained differences in wood decomposition after 4 years of exposure in the field, where fungal communities dominated by brown-rot and white-rot Basidiomycetes were linked to higher wood decomposition rate.Synthesis: Understanding what drives deadwood decomposition through time is important to understand the dynamics of carbon stocks. Here, using a tailor-made experimental design in a temperate forest setting, we have shown that stem trait variation is key to understanding the roles of these drivers; initially, wood traits explained decomposition rates while subsequently, bark traits and fungal decomposer composition drove decomposition rates. These findings inform forest management with a view to selecting tree species to promote carbon storage.
  • Nature Communications

    Enhancing phosphate-solubilising microbial communities through artificial selection

    Lena Faller, Marcio Fernandes Alves Leite, Eiko Kuramae
    Microbial communities, acting as key drivers of ecosystem processes, harbour immense potential for sustainable agriculture practices. Phosphate-solubilising microorganisms, for example, can partially replace conventional phosphate fertilisers, which rely on finite resources. However, understanding the mechanisms and engineering efficient communities poses a significant challenge. In this study, we employ two artificial selection methods, environmental perturbation, and propagation, to construct phosphate-solubilising microbial communities. To assess trait transferability, we investigate the community performance in different media and a hydroponic system with Chrysanthemum indicum. Our findings reveal a distinct subset of phosphate-solubilising bacteria primarily dominated by Klebsiella and Enterobacterales. The propagated communities consistently demonstrate elevated levels of phosphate solubilisation, surpassing the starting soil community by 24.2% in activity. The increased activity of propagated communities remains consistent upon introduction into the hydroponic system. This study shows the efficacy of community-level artificial selection, particularly through propagation, as a tool for successfully modifying microbial communities to enhance phosphate solubilisation.
  • Science of the Total Environment

    Stable isotope probing reveals compositional and functional shifts in active denitrifying communities along the soil profile in an intensive agricultural area

    Shuaimin Chen, Eiko Kuramae, Zhongjun Jia, Binbin Liu
    Denitrifying microbial communities in the vadose zone play an essential role in eliminating the nitrate leached from agricultural practices. This nitrate could otherwise contaminate groundwater and threaten public health. Here, we utilized stable isotope probing combined with amplicon sequencing and functional gene quantification to inspect the composition and function of heterotrophic denitrifying microorganisms along a 9-m soil profile in an intensive agricultural area. Dramatic differences in the composition of the active denitrifiers were uncovered between the surface soil and deep layers of the vadose zone. The main denitrifying bacterial taxa identified from 13C-DNA fractions were Pseudomonadaceae (Pseudomonas), Rhodocyclaceae (Azoarcus), and Burkholderiaceae in the surface soil (0–0.2 m), and were Pseudomonadaceae (Pseudomonas), Burkholderiaceae, Bacillaceae (Bacillus), and Paenibacillaceae (Ammoniphilus) in the deep layers (0.5–9.0 m). Analysis of the functional genes (nirS, nirK, and nosZ) in isotope-labeled DNA revealed an upward nos/nir ratio with increasing soil depth, which may account for the higher nitrous oxide emission potential in the surface soil, as compared to the deeper sand-rich, low organic carbon layers. This study improves our understanding of active denitrifying microbes in the vadose zone and helps in developing techniques to reduce nitrate pollution in groundwater.
  • Soil Biology and Biochemistry

    Threats to the soil microbiome from nanomaterials

    Sensen Chen, Ying Teng, Yongming Luo, Eiko Kuramae, Wenjie Ren
    Soil is the primary sink for released nanomaterials (NMs), but the understanding of the impacts of NMs on the soil microbiome remains fragmented. Moreover, there is currently lack of systematic approaches to evaluate the microbial ecological risks of NMs. In this study, we conducted a global meta-analysis incorporating 2134 paired observations from 107 publications from 2000 to June 2023 to comprehensively assess the effects of NMs on the soil microbiome. Additionally, we developed a machine-learning approach to predict these impacts and identified key contributing features. The results reveal that NMs have significant negative effects on soil microbial diversity (−0.96%), biomass (−14.01%), activity (−3.39%), and function (−14.44%). The impacts of NMs on fungal diversity were greater than those on bacteria. Compared with carbon NMs, metal NMs have more pronounced negative effects on various soil microbial community metrics, with Ag NMs exhibiting the greatest negative impact. Ag NMs exhibited greater negative effects on microbial function than bulk Ag or Ag+. Nanoscale effects played a pivotal role in these adverse effects. These adverse effects are primarily associated with NM type, size and content. Two machine learning models achieved acceptable prediction accuracy in assessing the impact of NMs on the soil microbial community. This study offers an effective approach for the ecological risk assessment of NMs and provides a scientific foundation for the rational and informed application of NMs in the soil environment.
  • Rhizosphere

    Plant grafting

    Maristela Calvente Morais, Luana Ferreira Torres, Eiko Kuramae, Sara Adrián Lopez de Andrade, Paulo Mazzafera
    Grafting, a traditional agricultural technique, holds significant potential for increasing productivity by harnessing the plant microbiome. The microbiome provides adaptability and metabolic diversity, increasing plant capacity to cope with challenging conditions. Although grafting effects on the composition and structure of microbiome on the root endosphere and, consequently, on the aerial endosphere have been reported, the impact on potential functionalities for plant traits remains to be elucidated. Beneficial microbes assembled by plant grafting have significant biotechnological potential to increase plant performance against biotic and abiotic stressors. In view of the optimal use of rootstock-scion combinations, in this review, we focused on recent grafting studies with plant-microbiome underlying mechanisms related to growth promotion, nutrient accessibility, and protection against abiotic and biotic environmental stresses. We provide significant first-hand information to guide future directions and prospects in shaping plant and core microbiome interactions, which helps in sustainable agriculture.
  • Microorganisms

    Carbon and Nutrients from Organic Residues Modulate the Dynamics of Prokaryotic and Fungal Communities

    Késia Lourenço, Heitor Cantarella, Eiko Kuramae
    Inputs of carbon (C) and nutrients from organic residues may select specific microbes and shape the soil microbial community. However, little is known about the abiotic filtering of the same residues with different nutrient concentrations applied to the soil. In our study, we explored how applying organic residue, vinasse, as fertilizer in its natural state (V) versus its concentrated form (CV) impacts soil microbiota. We conducted two field experiments, evaluating soil prokaryotic and fungal communities over 24 and 45 days with vinasse (V or CV) plus N fertilizer. We used 16S rRNA gene and ITS amplicon sequencing. Inorganic N had no significant impact on bacterial and fungal diversity compared to the control. However, the varying concentrations of organic C and nutrients in vinasse significantly influenced the soil microbiome structure, with smaller effects observed for V compared to CV. Prokaryotic and fungal communities were not correlated (co-inertia: RV coefficient = 0.1517, p = 0.9708). Vinasse did not change the total bacterial but increased the total fungal abundance. A higher C input enhanced the prokaryotic but reduced the fungal diversity. Our findings highlight vinasse’s role as an abiotic filter shaping soil microbial communities, with distinct effects on prokaryotic and fungal communities. Vinasse primarily selects fast-growing microorganisms, shedding light on the intricate dynamics between organic residues, nutrient concentrations, and soil microbes.
  • Geoderma

    Stability of ammonia oxidizer communities upon nitrogen fertilizer pulse disturbances is dependent on diversity

    Akari Mitsuta, Nao Ishige, Chikae Tatsumi, Yvonne Musavi Madegwa, Eiko Kuramae, Yoshitaka Uchida

    Diversity of the soil microbial community is an important factor affecting its stability against disturbance. However, the impact of the decline in soil microbial diversity on the stability of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) is not known, particularly considering the repeated soil nutrient disturbances occurring in modern agricultural systems. Here, we conducted a microcosm experiment and modified the soil microbial diversity using the dilution-to-extinction approach to determine the stability and population dynamics of AOB and AOA communities with repeated nitrogen (N) fertilizer application. Our results demonstrated that the AOB community became more abundant and stable against repeated disturbances by N in the treatments with the highest microbial diversity. In contrast, the abundance of AOA decreased following repeated N fertilizer application, regardless of the microbial diversity. Notably, during the initial application phase, AOA displayed a potential for increased abundance in treatments with high soil microbial diversity. These findings highlight that the soil microbial diversity controls the stability of ammonia oxidizers during short-interval repeated N disturbances.

  • Forests

    Fungal Community Succession of Populus grandidentata (Bigtooth Aspen) during Wood Decomposition

    Buck T. Castillo, Rima Franklin, Kevin R. Amses, Marcio Fernandes Alves Leite, Eiko Kuramae, Christopher Michael Gough, Timothy Y James, Lewis Faller, John Syring
    Fungal communities are primary decomposers of detritus, including coarse woody debris (CWD). We investigated the succession of fungal decomposer communities in CWD through different stages of decay in the wide-ranging and early successional tree species Populus grandidentata (bigtooth aspen). We compared shifts in fungal communities over time with concurrent changes in substrate chemistry and in bacterial community composition, the latter deriving from an earlier study of the same system. We found that fungal communities were highly dynamic during the stages of CWD decay, rapidly colonizing standing dead trees and gradually changing in composition until the late stages of decomposed wood were integrated into soil organic matter. Fungal communities were most similar to neighboring stages of decay, with fungal diversity, abundance, and enzyme activity positively related to percent nitrogen, irrespective of decay class. In contrast to other studies, we found that species diversity remained unchanged across decay classes. Differences in enzyme profiles across CWD decay stages mirrored changes in carbon recalcitrance, as B-D-xylosidase, peroxidase, and Leucyl aminopeptidase activity increased as decomposition progressed. Finally, fungal and bacterial gene abundances were stable and increased, respectively, with the extent of CWD decay, suggesting that fungal-driven decomposition was associated with shifting community composition and associated enzyme functions rather than fungal quantities.
  • ISME Communications

    Tomato growth stage modulates bacterial communities across different soil aggregate sizes and disease levels

    Menghui Dong, Eiko Kuramae, Mengli Zhao, Rong Li, Qirong Shen, George Kowalchuk
    Soil aggregates contain distinct physio-chemical properties across different size classes. These differences in micro-habitats support varied microbial communities and modulate the effect of plant on microbiome, which affect soil functions such as disease suppression. However, little is known about how the residents of different soil aggregate size classes are impacted by plants throughout their growth stages. Here, we examined how tomato plants impact soil aggregation and bacterial communities within different soil aggregate size classes. Moreover, we investigated whether aggregate size impacts the distribution of soil pathogen and their potential inhibitors. We collected samples from different tomato growth stages: before-planting, seedling, flowering, and fruiting stage. We measured bacterial density, community composition, and pathogen abundance using qPCR and 16 S rRNA gene sequencing. We found the development of tomato growth stages negatively impacted root-adhering soil aggregation, with a gradual decrease of large macro-aggregates (1–2 mm) and an increase of micro-aggregates (
  • Applied Soil Ecology

    Identification of general features in soil fungal communities modulated by phenolic acids

    Lv Su, Huatai Li, Xiting Sun, Kesu Wang, Xia Shu, Wenting Gao, Yunpeng Liu, Eiko Kuramae, Biao Shen, Ruifu Zhang
    Phenolic acids are mainly released from plant residue decomposition and play important roles in the assembly of the soil microbiome. Understanding the general features of soil microbial communities modulated by phenolic acids could provide fundamental insights into the assembly of the soil microbiome. We analyzed the effects of four phenolic acids (ferulic acid, phthalic acid, salicylic acid and tannic acid) on the soil fungal communities at two concentrations. Despite the application of different phenolic acids to the soil, we were able to identify certain general changes in the fungal communities. We found that the tested phenolic acids significantly increased the deterministic assembly process of the fungal community but decreased the fungal diversity. Moreover, the fungal community structure under each tested phenolic acid treatment was distinct at low concentrations but similar at high concentrations. Salicylic acid had the greatest impacts on the fungal community. In addition, Fusarium and Aspergillus were significantly enriched in the soil amended with all the tested phenolic acids at high concentrations. Our study revealed certain general changes in the soil fungal communities modulated by phenolic acids, which deepened our understanding of the fungal assembly mechanism and provided robust insights for identifying candidate phenolic acid-degrading microbes.
  • Soil Biology and Biochemistry

    Phosphorus-mediated succession of microbial nitrogen, carbon, and sulfur functions in rice-driven saline-alkali soil remediation

    Chunjie Tian, Eiko Kuramae
    Although rice cultivation holds potential for restoring unproductive saline-alkali soils and increasing food production, the mechanisms underlying the relationship between microbial functions and soil element turnover remain unclear. To clarify this relationship, this study investigated the soil physicochemical properties and microbial functions during remediation in saline-alkali soil by rice cultivation over 2, 4, 6, 8, 11, 12, 20, and 23 years. The results indicated rice cultivation markedly improved soil nutrients, soil nutrient stoichiometry, and soil aggregate stability. Additionally, rice cultivation significantly increased the microbial functions involved in nutrient cycling, such as nitrogen fixation, carbon fixation, methanogenesis, dissimilatory sulfate reduction, and thiosulfate oxidation. However, these nitrogen (N), carbon (C), and sulfur (S) cycle-related functions exhibited a similar “increase-peak-decrease” successional pattern with the years of remediation, reaching optimal levels when rice was continuously grown for 11–16 years. Furthermore, correlation analysis demonstrated that the succession of soil microbial N, C, and S functions during saline-alkali soil restoration closely related to changes in soil properties, particularly the availability of phosphorus (P). Therefore, we propose to prioritize the management of P during saline-alkali soil remediation. In conclusion, this study provides a comprehensive understanding of the microbial N, C, and S functions and soil P in the remediation of saline-alkali soils mediated by rice crop.
  • Applied Soil Ecology

    Soil substrate source drives the microbes involved in the degradation of gelatin used as a biostimulant

    Ohana Costa, Agata Pijl, Jos Houbraken, Willem van Lith, Eiko Kuramae
    Plant biostimulants improve crop yield and quality by stimulating plant nutrition processes and enhancing nutrient uptake efficiency, likely reflecting indirect effects mediated by beneficial soil microbes. Gelatin is an emerging plant biostimulant. Culture-dependent studies have identified several species of gelatin-degrading microbes, but the effect of gelatin on soil microbial communities in the absence of the plant microbiome has not been investigated. The objectives of this work were to evaluate changes in the microbial community induced by granulated gelatin amendments in different soils and substrates using high-throughput sequencing and to identify gelatin-hydrolyzing microbes for further application. Sandy soil, potting soil, paper plugs, black peat soil and pH-neutralized black peat soil were amended with gelatin and incubated at room temperature. After 7 and 15 days, samples were collected, DNA was extracted, and the bacterial and fungal communities were assessed by high-throughput sequencing of the 16S rRNA gene and the internal transcribed spacer (ITS) region, respectively. In parallel, microbes were isolated in culture medium. Regression analysis of shifts in the microbial communities demonstrated that the microbes positively impacted by gelatin amendment varied among the substrates, whereas few variations occurred between timepoints. The fungal genera Penicillium, Mortierella, Fusarium and Trichoderma and the bacterial genera Burkholderia, Pseudomonas and Rhodanobacter were among the microbes that increased in relative abundance in response to gelatin amendment. These microbes are efficient enzyme producers and are potential candidates for formulating beneficial microbial consortia that can be applied in tandem with gelatin to enhance its biostimulant activity.
  • European Journal of Agronomy

    Long term co-application of lime and phosphogypsum increases 15 N recovery and reduces 15 N losses by modulating soil nutrient availability, crop growth and N cycle genes

    João William Bossolani, Carlos Alexandre Costa Crusciol, Eduardo Mariano, Mariley de Cássia da Fonseca, Luiz Moretti de Souza, José Roberto Portugal, Nidia Costa, Juliano Carlos Calonego, Eiko Kuramae
    In no-tillage rotation systems, the recovery of nitrogen (N) fertilizer in the soil–plant system is affected by soil fertility and biological changes caused by the surface application of lime (L) and phosphogypsum (PG). Here we assessed the effect of surface-applied L and/or PG on the fate of 15N-labeled fertilizer, soil chemical properties, microbial gene copy number (16 S rRNA of prokaryotes and genes of N cycle) and grain yield of maize (Zea mays L. intercropped with ruzigrass) in rotation with soybean [Glycine max (L.) Merrill] during two growing seasons. We found that applying L improved soil fertility, particularly when combined with PG (LPG treatment), resulting in higher grain yield. Moreover, compared with the control, the recovery of 15N-labeled ammonium sulfate [(15NH4)2SO4] increased in maize and ruzigrass dry matter but decreased in soybean grown on the residue of the first growing season in two treatments (L and LPG). The losses of 15N-labeled fertilizer were highest in the control and PG treatments. A large amount of 15N-labeled fertilizer was found in the deep layers of PG-amended soil, indicating leaching of fertilizer-derived 15N. Conversely, the analysis of soil microbial N cycle genes revealed that the abundances of denitrifiers were highest in the control (no correctives applied), suggesting that the N fertilizer remaining in the soil increased denitrification rates. Surface application of a combination of L and PG is clearly a feasible strategy for increasing soil fertility, 15N recovery from fertilizer, and grain yield while reducing environmental pollution associated with nitrification and denitrification.
  • Bioresource Technology

    Addition of cellulose degrading bacterial agents promoting keystone fungal-mediated cellulose degradation during aerobic composting

    Yingxin Li, Eiko Kuramae, Fahad Nasir, Enze Wang, Zhengang Zhang, Zongmu Yao, Lei Tian, Yu Sun, Shouyang Luo, Lingling Guo, Gaidi Ren, Chunjie Tian
    To excavate a complex co-degradation system for decomposing cellulose more efficiently, cellulose-degrading bacteria, including Bacillus subtilis WF-8, Bacillus licheniformis WF-11, Bacillus Cereus WS-1 and Streptomyces Nogalater WF-10 were added during maize straw and cattle manure aerobic composting. Bacillus and Streptomyces successfully colonized, which improve cellulose degrading ability. Continuous colonization of cellulose-degrading bacteria can promote the fungi to produce more precursors for humus and promote the negative correlation with Ascomycota. In the current study, the addition of cellulose-degrading bacteria has resulted in the rapid development of Mycothermus and Remersonia in the phylum Ascomycota as keystone fungal genera which constitute the foundation of the co-degradation system. Network analysis reveals the complex co-degradation system of efficient cellulose bacteria and mature fungi to treat cellulose in the process of straw aerobic composting mainly related to the influence of total carbon (TC) /total nitrogen (TN) and humic acid (HA)/fulvic acid (FA). This research offers a complex co-degradation system more efficiently to decompose cellulose aiming to maintain the long-term sustainability of agriculture.
  • Pedosphere

    Carbohydrate metabolism bacteria positive effect determines the increasing soil organic carbon during long-term straw fertilization returning

    Yingxin Li, Yu Sun, Eiko Kuramae, Shaoqing Zhang, Enze Wang, Zongmu Yao, Fahad Nasir, Lei Tian, Qiang Gao, Chunjie Tian
    In the context of global efforts to reduce carbon emissions, several studies have examined the effects of agricultural practices like straw returning and fertilization on the sequestration of carbon by microorganisms. However, our understanding of the specific microbial groups and their roles in long-term carbon increase remains limited. Therefore, we conducted a 36-year farmland experiment (1984–2020) to investigate the impact of bacterial carbon metabolism on the augmentation of soil organic carbon. Our findings demonstrated a noteworthy increase in the diversity of microorganisms in farmland as a result of long-term straw returning and the application of mixed chemical fertilizers. However, when we examined the functions of farmland microorganisms involved in carbon metabolism, we observed that the effects of fertilization on carbon metabolism were relatively consistent. This consistency was attributed to a deterministic competitive exclusion process, which minimized differences between treatment groups. On the other hand, the influence of straw addition on carbon metabolism appeared to follow a more random pattern. These changes in microbial activity were closely linked to the down-representation of core metabolic pathways related to carbon metabolism. Notably, long-term fertilization had a negative impact on soil organic carbon levels, while long-term straw fertilization resulted in a positive increase in soil organic carbon. These findings have important implications for enhancing soil organic carbon content and grain yield in regions with typical black soil characteristics.
  • Science of the Total Environment

    Nitrogen input on organic amendments alters the pattern of soil–microbe-plant co-dependence

    João William Bossolani, Marcio Fernandes Alves Leite, Hein F.M. ten Berge, Jaap Bloem, Eiko Kuramae
    The challenges of nitrogen (N) management in agricultural fields include minimizing N losses while maximizing profitability and soil health. Crop residues can alter N and carbon (C) cycle processes in the soil and modulate the responses of the subsequent crop and soil– microbe-plant interactions. Here, we aim to understand how organic amendments with low and high C/N ratio, combined or not with mineral N may change soil bacterial community and their activity in the soil. Organic amendments with different C/N ratios were combined or not with N fertilization as follows: i) unamended soil (control), ii) grass clover silage (GC; low C/N ratio), and iii) wheat straw (WS; high C/N ratio). The organic amendments modulated the bacterial community assemblage and increased microbial activity. WS amendment had the strongest effects on hot water extractable carbon, microbial biomass N and soil respiration, which were linked with changes in bacterial community composition compared with GC-amended and unamended soil. By contrast, N transformation processes in the soil were more pronounced in GC-amended and unamended soil than in WS-amended soil. These responses were stronger in the presence of mineral N input. WS amendment induced greater N immobilization in the soil, even with mineral N input, impairing crop development. Interestingly, N input in unamended soil altered the co-dependence between the soil and the bacterial community to favor a new co-dependence among the soil, plant and microbial activity. In GC-amended soil, N fertilization shifted the dependence of the crop plant from the bacterial community to soil characteristics. Finally, the combined N input with WS amendment (organic carbon input) placed microbial activity at the center of the interrelationships between the bacterial community, plant, and soil. This emphasizes the crucial importance of microorganisms in the functioning of agroecosystems. To achieve higher yields in crops managed with various organic amendments, it is essential to incorporate mineral N management practices. This becomes particularly crucial when the soil amendments have a high C/N ratio.
  • Soil Biology and Biochemistry

    Responses of soil rare and abundant microorganisms to recurring biotic disturbances

    Zhikang Wang, Marcio Fernandes Alves Leite, Mingkai Jiang, Eiko Kuramae, Xiangxiang Fu

    Periodic inoculations of soil-beneficial microbes can increase their populations, but they also act as recurring biotic disturbances on the native microbial community. Soil rare and abundant microorganisms disproportionally shape the community diversity and stability. Uncovering their dynamic responses to recurring biotic disturbances and the underlying driving factors helps improve our understanding of the inoculation effects. Here, we imposed temporally recurring biotic disturbances by inoculating soils with phosphate-solubilizing bacteria, nitrogen-fixing bacteria, and the combination of both, with the overall aim of studying the successive responses of bacterial and fungal subcommunities along a rarity index. Our results showed that, in both bacterial and fungal communities, the relatively rare taxa exhibited higher diversity than the abundant taxa, and the relative abundance of rare taxa increased with recurring disturbances. However, the responses of rare and abundant taxa to inoculations were different between bacteria and fungi and were related to time and inoculation frequency. The rarer bacteria and the more abundant fungi explained most of the effects of inoculations on the resident microbial community. About 20 percent of the microbes changed their rarity categories over time, and most of the changes and interactions occurred within the rarer taxa during the first 45 days. Modeling analyses and co-occurrence networks indicated that microbial interactions, soil biochemical factors, and inoculation time drove the shifts of subcommunities. In summary, relatively rare bacteria and relatively abundant fungi play major roles in understanding the impacts of recurring biotic disturbances, while the conditionality of microbial rarity is dependent on both biotic and abiotic factors.

  • Biology and Fertility of Soils

    Composition, function and succession of bacterial communities in the tomato rhizosphere during continuous cropping

    Lv Su, Huatai Li, Jing Wang, Wenting Gao, Xia Shu, Xiting Sun, Kesu Wang, Yan Duan, Yunpeng Liu, Eiko Kuramae, Ruifu Zhang, Biao Shen

    The bacteria that dominate and become enriched in the rhizosphere during continuous cropping are of increasing interest, as they can greatly adapt to the rhizosphere. However, there are still little knowledge about the general composition and function of these bacteria. In this study, we planted tomatoes in three different soils for three planting cycles and used both high-throughput sequencing and culture-dependent workflows. Despite significant differences in bacterial communities from the initial soils, we observed a similar succession in the rhizosphere bacterial community compositions. We identified certain bacteria that were gradually enriched and potentially beneficial, such as Rhizobium and Flavobacterium. However, some other potentially beneficial bacteria, such as Massilia and Lysobacter, were gradually depleted. Additionally, we found that predicted functions related to xenobiotic biodegradation, nutrient metabolism and antibiotic biosynthesis were enriched in different rhizosphere soils. Beijerinckia fluminensis GR2, which was gradually enriched in all tested soils, significantly inhibited the growth of Ralstonia solanacearum and protected the host from infection. Our study provides new insights into the assembly mechanism of gradually enriched bacteria and their role as plant-beneficial microbes that adapt well to the rhizosphere.

  • Industrial Crops and Products

    Effects of probiotic consortia on plant metabolites are associated with soil indigenous microbiota and fertilization regimes

    Zhikang Wang, Ziyun Chen, Marcio Fernandes Alves Leite, Ziheng Xu, Quan Lin, George Kowalchuk, Xiangxiang Fu, Eiko Kuramae

    Introducing probiotics to soil is a sustainable way to stimulate the production of plant metabolites. However, the soil-resident microbes may compromise the efficiency of probiotics. To date, it remains challenging to integrate the effects of probiotics on plant performance with soil microbiome changes. Using Cyclocarya paliurus (Batal.) Iljinsk as a model medicinal plant and two types of probiotic consortia combined with organic fertilizer at three levels (low: 0.5, medium: 1.0, and high: 1.5 kg·plant−1), we examined the impacts of three fertilization regimes (O: organic fertilizer, OMF: O coupled with Bacillus megaterium and Pseudomonas fluorescens, OCB: O coupled with Azotobacter chroococcum and Azospirillum brasilense) on plant metabolites and nutrient stoichiometry after three-year applications and identified the key soil microbes relating to the accumulation of plant metabolites via generalized joint attribute model (GJAM) analysis. Our results indicated that the concentration of flavonoids reached 36.9 mg·g−1 in OCB treatment at a low level, and 30.0 mg·g−1 in OMF treatment at a medium level, both were significantly higher than that in O treatment (25.8 mg·g−1 on average). Furthermore, the accumulations of metabolites were associated with plant nutrient acquisition and C: N: P stoichiometry. GJAM analysis showed that higher fertilizer levels restricted the influence of probiotic consortia on the variance of plant-soil-microbe system, with fewer differences observed between fertilizer types. Specific soil microbes were predicted as potential indicators that may assist or impede the effects of probiotics on plant metabolite production. The predictions were further tested in a comparative pot experiment, and the effects of common indicators in both pot and field experiments were consistently associated with probiotics’ addition. This study reveals that the effects of probiotics on plant metabolites are associated with fertilization regimes and soil-indigenous microbes. Identifying microbial indicators will help to understand the probiotics' effects and further improve plant productivity.

  • Soil and Tillage Research

    Toward more sustainable tropical agriculture with cover crops

    Carlos Alexandre Costa Crusciol, João William Bossolani, Luiz Moretti de Souza, Marcio Fernandes Alves Leite, George Kowalchuk, Eiko Kuramae

    Cover crops are a potential pathway for ecological cultivation in agricultural systems. In tropical no-till agricultural systems, the maintenance of residues on the soil surface and the addition of nitrogen (N) benefit the growth and grain yield of cash crops as well as the chemical and physical properties of the soil. However, the effects of these management practices on the soil microbiota are largely unknown. Here, we evaluated the effects of the timing of N application as a pulse disturbance and the growth of different cover crop species before maize in rotation on soil properties, maize productivity, and soil bacterial and fungal community diversity and composition. N fertilizer was applied either on live cover crops (palisade grass or ruzigrass), on cover crop straw just before maize seeding or in the maize V4 growth stage. Soils previously cultivated with palisade grass established similar microbial communities regardless of N application timing, with increases in total bacteria, total archaea, nutrients, and the C:N ratio. The soil microbial alpha diversity in treatments with palisade grass did not vary with N application timing, whereas the bacterial and fungal diversities in the treatments with ruzigrass decreased when N was applied to live ruzigrass or maize in the V4 growth stage. We conclude that palisade grass is a more suitable cover crop than ruzigrass, as palisade grass enhanced soil microbial diversity and maize productivity regardless of N application timing. Ruzigrass could be used as an alternative to palisade grass when N is applied during the straw phase. However, considering the entire agricultural system (soil–plant–microbe), ruzigrass is not as efficient as palisade grass in tropical no-till cover crop–maize rotation systems. Palisade grass is a suitable cover crop alternative for enhancing maize productivity, soil chemical properties and nutrient cycling, regardless of the timing of N application. Additionally, this study demonstrates that a holistic approach is valuable for evaluating soil diversity and crop productivity in agricultural systems.

  • Soil Biology and Biochemistry

    Ammonia-oxidizing bacteria and fungal denitrifier diversity are associated with N2O production in tropical soils

    Késia Lourenço, Ohana Costa, Heitor Cantarella, Eiko Kuramae

    Nitrous oxide (N2O) production in tropical soils cultivated with sugarcane is associated with ammonia-oxidizing bacteria (AOB) and fungal denitrifiers. However, the taxonomic identities and the community diversities, compositions, and structures of AOB and fungal denitrifiers in these soils are not known. Here, we examined the effects of applying different concentrations of an organic recycled residue (vinasse: regular non-concentrated or 5.8-fold concentrated) on the dynamics of AOB and fungal denitrifier community diversity and composition and greenhouse gas emissions during the sugarcane cycle in two different seasons, rainy and dry. DNA was extracted from soil samples collected at six timepoints to determine the dynamics of amoA-AOB and nirK-fungal community diversity and composition by amplicon sequencing with gene-specific primers. Bacterial and archaeal amoA, fungal and bacterial nirK, bacterial nirS and nosZ, total bacteria (16S rRNA) and total fungi (18S rRNA) were quantified by real-time PCR, and N2O and CO2 emissions were measured. The genes amoA-AOB and bacterial nirK clade II correlated with N2O emissions, followed by fungal nirK. The application of inorganic nitrogen fertilizer combined with organic residue, regardless of concentration, did not affect the diversity and structure of the AOB and fungal denitrifier communities but increased their abundances and N2O emissions. Nitrosospira sp. was the dominant AOB, while unclassified fungi were the dominant fungal denitrifiers. Furthermore, the community structures of AOB and fungal denitrifiers were affected by season, with dominance of uncultured Nitrosospira and unclassified fungi in the rainy season and the genera Nitrosospira and Chaetomium in the dry season. Nitrosospira, Chaetomium, Talaromyces purpureogenus, and Fusarium seemed to be the main genera governing N2O production in the studied tropical soils. These results highlight the importance of deciphering the main players in N2O production and demonstrate the impact of fertilization on soil microbial N functions.

  • Science of the Total Environment

    Comparison of methane metabolism in the rhizomicrobiomes of wild and related cultivated rice accessions reveals a strong impact of crop domestication

    Lei Tian, Jingjing Chang, Shaohua Shi, Li Ji, Jianfeng Zhang, Yu Sun, Xiaojie Li, Xiujun Li, Hongwei Xie, Yaohui Cai, Dazhou Chen, Jilin Wang, Hans van Veen, Eiko Kuramae, Lam-Son Phan Tran, Chunjie Tian
    Microbial communities from rhizosphere (rhizomicrobiomes) have been significantly impacted by domestication as evidenced by a comparison of the rhizomicrobiomes of wild and related cultivated rice accessions. While there have been many published studies focusing on the structure of the rhizomicrobiome, studies comparing the functional traits of the microbial communities in the rhizospheres of wild rice and cultivated rice accessions are not yet available. In this study, we used metagenomic data from experimental rice plots to analyze the potential functional traits of the microbial communities in the rhizospheres of wild rice accessions originated from Africa and Asia in comparison with their related cultivated rice accessions. The functional potential of rhizosphere microbial communities involved in alanine, aspartate and glutamate metabolism, methane metabolism, carbon fixation pathways, citrate cycle (TCA cycle), pyruvate metabolism and lipopolysaccharide biosynthesis pathways were found to be enriched in the rhizomicrobiomes of wild rice accessions. Notably, methane metabolism in the rhizomicrobiomes of wild and cultivated rice accessions clearly differed. Key enzymes involved in methane production and utilization were overrepresented in the rhizomicrobiome samples obtained from wild rice accessions, suggesting that the rhizomicrobiomes of wild rice maintain a different ecological balance for methane production and utilization compared with those of the related cultivated rice accessions. A novel assessment of the impact of rice domestication on the primary metabolic pathways associated with microbial taxa in the rhizomicrobiomes was performed. Results indicated a strong impact of rice domestication on methane metabolism; a process that represents a critical function of the rhizosphere microbial community of rice. The findings of this study provide important information for future breeding of rice varieties with reduced methane emission during cultivation for sustainable agriculture.
  • Environmental Microbiology

    Stem traits, compartments, and tree species affect fungal communities on decaying wood

    Shanshan Yang, Lourens Poorter, Eiko Kuramae, U. Sass-Klaassen, Marcio Fernandes Alves Leite, Ohana Costa, George Kowalchuk, J.H.C. Cornelissen, J. Van Hal, L. Goudzwaard, M.M. Hefting, R. Van Logtestijn, F.J. Sterck
    Dead wood quantity and quality is important for forest biodiversity, by determining wood-inhabiting fungal assemblages. We therefore evaluated how fungal communities were regulated by stem traits and compartments (i.e. bark, outer- and inner wood) of 14 common temperate tree species. Fresh logs were incubated in a common garden experiment in a forest site in the Netherlands. After 1 and 4 years of decay, the fungal composition of different compartments was assessed using Internal Transcribed Spacer amplicon sequencing. We found that fungal alpha diversity differed significantly across tree species and stem compartments, with bark showing significantly higher fungal diversity than wood. Gymnosperms and Angiosperms hold different fungal communities, and distinct fungi were found between inner wood and other compartments. Stem traits showed significant afterlife effects on fungal communities; traits associated with accessibility (e.g. conduit diameter), stem chemistry (e.g. C, N, lignin) and physical defence (e.g. density) were important factors shaping fungal community structure in decaying stems. Overall, stem traits vary substantially across stem compartments and tree species, thus regulating fungal communities and the long-term carbon dynamics of dead trees.
  • European Journal of Agronomy

    Feasibility of early fertilization of maize with 15N application to preceding cover crop

    Letusa Momesso Marques, Carlos Alexandre Costa Crusciol, C. A. C. Nascimento, Rogerio P. Soratto, L.P. Canisares, Luiz Moretti de Souza, C.A. Rosolem, Paulo C.O. Trivelin, Eiko Kuramae, Heitor Cantarella
    Early nitrogen (N) application on live cover crops or their residues is a potential alternative for supplying N demand while enhancing the yield of subsequent cash crops in tropical regions. The objective of applying N on live forage grasses or their residues to no-till (NT) systems is to promote the gradual release of N via straw decomposition to the subsequent crop. However, the N use efficiency by the subsequent crop under early fertilization has not been determined in the end of growing season. The aim of this study was to evaluate whether the most cultivated tropical forage grasses can supply the N demand and enhance the grain yields of maize via the N recovery when N is applied with different timings than the conventional method. A 3-year field experiment was performed using palisade grass [(Urochloa brizantha (syn. Brachiaria)] and ruzigrass (U. ruziziensis) as cover crops with four N application timings to agricultural system: (i) no-N, zero N application; (ii) CC+N, 120 kg N ha−1 applied on live cover crops 35 days before maize seeding; (iii) St+N, 120 kg N ha−1 applied on cover crops straw 1 day before seeding; and (iii) Nv4, conventional method of sidedress N application at the maize V4 (four leaf) growth stage. Except control, all N treatments received 40 kg N ha−1at maize seeding, totalizing 160 kg N ha−1. Straw decomposition and cover crop N accumulation were greater in the treatments in which N fertilizer was applied on palisade grass compared with ruzigrass. High maize yields were achieved with N application on palisade grass or its residues or according to the conventional method, with yields of 13.2, 13.2 and 13.6 Mg ha−1, respectively. Similarly, high maize yields were obtained when N was applied on ruzigrass residues or according to the conventional method (12.1 and 11.8 Mg ha−1, respectively). However, regardless of cover crop species, N recovery was highest when N fertilizer was applied via the conventional method. Additionally, most of the N in maize at harvest came from the soil when N fertilizer was applied to live palisade grass. Thus, best recovery of N fertilizer in the grain occurred in maize fertilized using the conventional method. Our results indicate that agricultural systems characterized by high dry matter from palisade grass have the potential to recycle and supply N to subsequent maize. Although palisade grass combined with early N fertilizer application may enhance maize response and yield, the current conventional method of N fertilizer application on maize allows higher recovery from N fertilizer while increasing the maize yield in tropical food production.
  • Science of the Total Environment

    A review on the impact of domestication of the rhizosphere of grain crops and a perspective on the potential role of the rhizosphere microbial community for sustainable rice crop production

    Jingjing Chang, Hans van Veen, Chunjie Tian, Eiko Kuramae
    The rhizosphere-associated microbiome impacts plant performance and tolerance to abiotic and biotic stresses. Despite increasing recognition of the enormous functional role of the rhizomicrobiome on the survival of wild plant species growing under harsh environmental conditions, such as nutrient, water, temperature, and pathogen stresses, the utilization of the rhizosphere microbial community in domesticated rice production systems has been limited. Better insight into how this role of the rhizomicrobiome for the performance and survival of wild plants has been changed during domestication and development of present domesticated crops, may help to assess the potential of the rhizomicrobial community to improve the sustainable production of these crops. Here, we review the current knowledge of the effect of domestication on the microbial rhizosphere community of rice and other crops by comparing its diversity, structure, and function in wild versus domesticated species. We also examine the existing information on the impact of the plant on their physico-chemical environment. We propose that a holobiont approach should be explored in future studies by combining detailed analysis of the dynamics of the physicochemical microenvironment surrounding roots to systematically investigate the microenvironment–plant–rhizomicrobe interactions during rice domestication, and suggest focusing on the use of beneficial microbes (arbuscular mycorrhizal fungi and Nitrogen fixers), denitrifiers and methane consumers to improve the sustainable production of rice.
  • FEMS Microbiology Ecology

    Rhizosphere microbiome response to host genetic variability

    Cristina Rotoni, Marcio Fernandes Alves Leite, Agata Pijl, Eiko Kuramae
    Rhizosphere microbial community composition is strongly influenced by plant species and cultivar. However, our understanding of the impact of plant cultivar genetic variability on microbial assembly composition remains limited. Here, we took advantage of vegetatively propagated chrysanthemum (Chrysanthemum indicum L.) as a plant model and induced roots in five commercial cultivars: Barolo, Chic, Chic 45, Chic Cream and Haydar. We observed strong rhizosphere selection for the bacterial community but weaker selection for the fungal community. The genetic distance between cultivars explained 42.83% of the total dissimilarity between the bacteria selected by the different cultivars. By contrast, rhizosphere fungal selection was not significantly linked to plant genetic dissimilarity. Each chrysanthemum cultivar selected unique bacterial and fungal genera in the rhizosphere. We also observed a trade-off in the rhizosphere selection of bacteria and fungi in which the cultivar with the strongest selection of fungal communities showed the weakest bacterial selection. Finally, bacterial and fungal family taxonomic groups consistently selected by all cultivars were identified (bacteria Chitinophagaceae, Beijerinckiaceae and Acidobacteriaceae, and fungi Pseudeurotiaceae and Chrysozymaceae). Taken together, our findings suggest that chrysanthemum cultivars select distinct rhizosphere microbiomes and share a common core of microbes partially explained by the genetic dissimilarity between cultivars.
  • Biology and Fertility of Soils

    Potassium phosphite enhanced the suppressive capacity of the soil microbiome against the tomato pathogen Ralstonia solanacearum

    Lv Su, H. Feng, X. Mo, J. Sun, P. Qiu, Y. Liu, R. Zhang, Eiko Kuramae, Ben Shen, Qirong Shen
    High-throughput sequencing, culture-dependent workflows, and microbiome transfer experiments reveal whether potassium phosphite (KP), an environmentally acceptable agricultural chemical, could specifically enrich the antagonistic bacterial community that inhibited the growth of the pathogen Ralstonia solanacearum. The application of KP enriched the potential antagonistic bacteria Paenibacillus and Streptomyces in soil, but depleted most dominant genera belonging to gram negative bacteria, such as Pseudomonas, Massilia, and Flavobacterium on day 7. Moreover, the KP-modulated soil microbiome suppressed R. solanacearum growth in soil. The predicted functions related to the synthesis of antagonistic substances, such as streptomycin, and the predicted functions related to tellurite resistance and nickel transport system were significantly enriched, but the synthesis of lipopolysaccharide (distinct component lipopolysaccharide in gram negative bacteria) were significantly depleted in the KP-treated soils. In addition, the copy numbers of specific sequences for Streptomyces coelicoflavus and Paenibacillus favisporus were significantly increased in the soil amended with KP, inhibited the growth of R. solanacearum, and had a higher tolerance of KP than R. solanacearum. Our study linked the application of fertilizers to the enrichment of antagonistic bacteria, which could support future work that aims to precisely regulate the soil microbiome to protect the host from infection by soil-borne pathogens.
  • Microorganisms


    Ohana Costa, Mattias De Hollander, Eiko Kuramae, Paul Bodelier

    The increase in sequencing capacity has amplified the number of taxonomically unclassified sequences in most databases. The classification of such sequences demands phylogenetic tree construction and comparison to currently classified sequences, a process that demands the processing of large amounts of data and use of several different software. Here, we present PhyloFunDB, a pipeline for extracting, processing, and inferring phylogenetic trees from specific functional genes. The goal of our work is to decrease processing time and facilitate the grouping of sequences that can be used for improved taxonomic classification of functional gene datasets.

  • Plant Disease

    Potassium phosphite enhances the antagonistic capability of Bacillus amyloliquefaciens to manage tomato bacterial wilt

    Lv Su, P. Qiu, Zhiying Fang, J. Sun, X. Mo, Y. Liu, Eiko Kuramae, R. Zhang, Ben Shen, Qirong Shen
    Bacterial wilt caused by Ralstonia solanacearum is a distributed and worldwide soil-borne disease. The application of biocontrol microbes or agricultural chemicals has been widely used to manage tomato bacterial wilt. However, whether and how agricultural chemicals affect the antagonistic ability of biocontrol microbes is still unknown. Here, we combined potassium phosphite (K-Phite), an environmentally friendly agricultural chemical, and the biocontrol agent Bacillus amyloliquefaciens QPF8 (strain F8) to manage tomato bacterial wilt disease. First, K-Phite at a concentration of 0.05% (w/v) could significantly inhibit the growth of Ralstonia solanacearum. Second, 0.05% K-Phite enhanced the antagonistic capability of B. amyloliquefaciens F8. Third, the greenhouse soil experiments showed that the control efficiency for tomato bacterial wilt in the combined treatment was significantly higher than that of the application of B. amyloliquefaciens F8 or K-Phite alone. Overall, our results highlighted a novel strategy for the control of tomato bacterial wilt disease via application and revealed a new integrated pattern depending on the enhancement of the antagonistic capability of biocontrol microbes by K-Phite.
  • Science of the Total Environment

    Eucalypt species drive rhizosphere bacterial and fungal community assembly but soil phosphorus availability rearranges the microbiome

    R.G. Bulgarelli, Marcio Fernandes Alves Leite, Mattias De Hollander, P. Mazzafera, Sara Adrián Lopez de Andrade, Eiko Kuramae
    Soil phosphorus (P) availability may limit plant growth and alter root-soil interactions and rhizosphere microbial community composition. The composition of the rhizosphere microbial community can also be shaped by plant genotype. In this study, we examined the rhizosphere microbial communities of young plants of 24 species of eucalypts (22 Eucalyptus and two Corymbia species) under low or sufficient soil P availability. The taxonomic diversity of the rhizosphere bacterial and fungal communities was assessed by 16S and 18S rRNA gene amplicon sequencing. The taxonomic modifications in response to low P availability were evaluated by principal component analysis, and co-inertia analysis was performed to identify associations between bacterial and fungal community structures and parameters related to plant growth and nutritional status under low and sufficient soil P availability. The sequencing results showed that while both soil P availability and eucalypt species influenced the microbial community assembly, eucalypt species was the stronger determinant. However, when the plants are subjected to low P-availability, the rhizosphere selection became strongest. In response to low P, the bacterial and fungal communities in the rhizosphere of some species showed significant changes, whereas in others remained relatively constant under low and sufficient P. Co-inertia analyses revealed a significant co-dependence between plant nutrient contents and bacterial and fungal community composition only under sufficient P. By contrast, under low P, bacterial community composition was related to plant biomass production. In conclusion, our study shows that eucalypt species identity was the main factor modulating rhizosphere microbial community composition; significant shifts due to P availability were observed only for some eucalypt species.
  • FEMS Microbiology Ecology

    Effect of strigolactones on recruitment of the rice root-associated microbiome

    Bora Kim, Johan A. Westerhuis, Age K. Smilde, Kristýna Floková, Afnan Suleiman, Eiko Kuramae, Harro J. Bouwmeester, Anouk Zancarini
    Strigolactones are endogenous plant hormones regulating plant development and are exuded into the rhizosphere when plants experience nutrient deficiency. There, they promote the mutualistic association of plants with arbuscular mycorrhizal fungi that help the plant with the uptake of nutrients from the soil. This shows that plants actively establish—through the exudation of strigolactones—mutualistic interactions with microbes to overcome inadequate nutrition. The signaling function of strigolactones could possibly extend to other microbial partners, but the effect of strigolactones on the global root and rhizosphere microbiome remains poorly understood. Therefore, we analyzed the bacterial and fungal microbial communities of 16 rice genotypes differing in their root strigolactone exudation. Using multivariate analyses, distinctive differences in the microbiome composition were uncovered depending on strigolactone exudation. Moreover, the results of regression modeling showed that structural differences in the exuded strigolactones affected different sets of microbes. In particular, orobanchol was linked to the relative abundance of Burkholderia–Caballeronia–Paraburkholderia and Acidobacteria that potentially solubilize phosphate, while 4-deoxyorobanchol was associated with the genera Dyella and Umbelopsis. With this research, we provide new insight into the role of strigolactones in the interplay between plants and microbes in the rhizosphere.
  • Fungal Systematics and Evolution

    Fusarium diversity associated with the Sorghum-Striga interaction in Ethiopia

    Lorenzo Lombard, R. Van Doorn, Ewald Groenewald, Taye Tessema, Eiko Kuramae, D.W. Etolo, Jos M. Raaijmakers, Pedro W. Crous
    Sorghum production is seriously threatened by the root parasitic weeds (RPWs) Striga hermonthica and Striga asiatica in sub-Saharan Africa. Research has shown that Striga control depends on eliminating its seed reserves in soil. Several species of the genus Fusarium (Nectriaceae, Hypocreales), which have been isolated from diseased Striga plants have proven to be highly pathogenic to all developmental stages of these RPWs. In the present study 439 isolates of Fusarium spp. were found associated with soils from Sorghum growing fields, Sorghum rhizosphere, or as endophytes with Sorghum roots and seeds, or as endophytes of Striga stems and seeds. Based on multi-locus phylogenies of combinations of CaM, tef1, rpb1 and rpb2 alignments, and morphological characteristics, 42 species were identified, including three species that are newly described, namely F. extenuatum and F. tangerinum from Sorghum soils, and F. pentaseptatum from seed of Striga hermonthica. Using a previously published AFLP-derived marker that is specific to detect isolates of F. oxysporum f.sp.strigae, an effective soil-borne biocontrol agent against Striga, we also detected the gene in several other Fusarium species. As these isolates were all associated with the Striga/Sorghum pathosystem, the possibility of horizontal gene transfer among these fusaria will be of interest to further investigate in future.
  • Microorganisms

    Current Challenges and Pitfalls in Soil Metagenomics

    Marcio Fernandes Alves Leite, Sarah W.E.B. van den Broek, Eiko Kuramae

    Soil microbial communities are essential components of agroecological ecosystems that influence soil fertility, nutrient turnover, and plant productivity. Metagenomics data are increasingly easy to obtain, but studies of soil metagenomics face three key challenges: (1) accounting for soil physicochemical properties; (2) incorporating untreated controls; and (3) sharing data. Accounting for soil physicochemical properties is crucial for better understanding the changes in soil microbial community composition, mechanisms, and abundance. Untreated controls provide a good baseline to measure changes in soil microbial communities and separate treatment effects from random effects. Sharing data increases reproducibility and enables meta-analyses, which are important for investigating overall effects. To overcome these challenges, we suggest establishing standard guidelines for the design of experiments for studying soil metagenomics. Addressing these challenges will promote a better understanding of soil microbial community composition and function, which we can exploit to enhance soil quality, health, and fertility.

  • Brazilian Journal of Development

    Vinasse and straw retention decrease fungal diversity and pathogenicity in sugarcane soil

    Victoria Romancini Toledo, Rita de Cássia Félix Alvarez, Eiko Kuramae, Mattias De Hollander, Raffaela Rossetto, Elisângela de Souza Loureiro, Paulo Eduardo Teodoro, Gisele Herbst Vazquez, J.H.P. Americo-Pinheiro, Siu Mui Tsai, Acácio A. Navarrete
    This study focused on the effects of vinasse (V), a by-product of the sugar-ethanol industry, combined with mineral nitrogen fertilizer (N) and straw retention on the fungal community diversity, composition, and structure in a sugarcane-cultivated soil. The experiment consisted of a combination of V, mineral N and sugarcane-straw blanket. Soil samples were collected at 7, 157, and 217 days after planting, corresponding to maximum carbon dioxide emissions from soil after three repeated applications of fertilizers into the soil. Across 57 soil metagenomics datasets, it was revealed that the application the V in combination with N fertilizer and straw retention decreased the diversity, evenness and richness of fungi at the community level in soil. Analysis of the soil fungal community composition based on the 20 genera most abundant revealed decrease for Blastomyces, Melampsora, and Penicillium after the third application of V in combination with N fertilizer and straw blanket. An opposite response was revealed for Amauroascus, Cantharellus, Chrysosporium, Clavaria, Morchella, Puccinia, and Tuber in soil under this treatment. Shifts in fungal community composition were followed by increases in mycorrhizal and decomposers soil-borne fungi and decrease in potentially pathogenic fungi, but not by changes in community structure. Based on these results, it is possible to attest that repeated applications of V in combination with N fertilizer and sugarcane-straw blankets affect ecological aspects of the soil fungal community composition and potential functions played by fungi in sugarcane soil, which are essentials to ecosystem function and sustainable management of agricultural ecosystems.
  • mSystems

    Variations of Bacterial and Diazotrophic Community Assemblies throughout the Soil Profile in Distinct Paddy Soil Types and Their Contributions to Soil Functionality

    Xiaomi Wang, Ying Teng, Wenjie Ren, Yuntao Li, Teng Yang, Yan Chen, Ling Zhao, Huimin Zhang, Eiko Kuramae

    Soil microbiota plays fundamental roles in maintaining ecosystem functions and services, including biogeochemical processes and plant productivity. Despite the ubiquity of soil microorganisms from the topsoil to deeper layers, their vertical distribution and contribution to element cycling in subsoils remain poorly understood. Here, nine soil profiles (0 to 135 cm) were collected at the local scale (within 300 km) from two canonical paddy soil types (Fe-accumuli and Hapli stagnic anthrosols), representing redoximorphic and oxidative soil types, respectively. Variations with depth in edaphic characteristics and soil bacterial and diazotrophic community assemblies and their associations with element cycling were explored. The results revealed that nitrogen and iron status were the most distinguishing edaphic characteristics of the two soil types throughout the soil profile. The acidic Fe-accumuli stagnic anthrosols were characterized by lower concentrations of free iron oxides and total iron in topsoil and ammonia in deeper layers compared with the Hapli stagnic anthrosols. The bacterial and diazotrophic community assemblies were mainly shaped by soil depth, followed by soil type. Random forest analysis revealed that nitrogen and iron cycling were strongly correlated in Fe-accumuli stagnic anthrosol, whereas in Hapli soil, available sulfur was the most important variable predicting both nitrogen and iron cycling. The distinctive biogeochemical processes could be explained by the differences in enrichment of microbial taxa between the two soil types. The main discriminant clades were the iron-oxidizing denitrifier Rhodanobacter, Actinobacteria, and diazotrophic taxa (iron-reducing Geobacter, Nitrospirillum, and Burkholderia) in Fe-accumuli stagnic anthrosol and the sulfur-reducing diazotroph Desulfobacca in Hapli stagnic anthrosol. IMPORTANCE Rice paddy ecosystems support nearly half of the global population and harbor remarkably diverse microbiomes and functions in a variety of soil types. Diazotrophs provide significant bioavailable nitrogen in paddy soil, priming nitrogen transformation and other biogeochemical processes. This study provides a novel perspective on the vertical distribution of bacterial and diazotrophic communities in two hydragric anthrosols. Microbiome analysis revealed divergent biogeochemical processes in the two paddy soil types, with a dominance of nitrogen-iron cycling processes in Fe-accumuli stagnic anthrosol and sulfur-nitrogen-iron coupling in Hapli stagnic anthrosol. This study advances our understanding of the multiple significant roles played by soil microorganisms, especially diazotrophs, in biogeochemical element cycles, which have important ecological and biogeochemical ramifications.

  • Applied and Environmental Microbiology

    The Stochastic Assembly of Nitrobacter winogradskyi-Selected Microbiomes with Heterotrophs from Sewage Sludge or Grassland Soil

    (Riks) H.J. Laanbroek, Noriko Cassman, Roos Keijzer, Eiko Kuramae

    Chemolitho-autotrophic microorganisms like the nitrite-oxidizing Nitrobacter winogradskyi create an environment for heterotrophic microorganisms that profit from the production of organic compounds. It was hypothesized that the assembly of a community of heterotrophic microorganisms around N. winogradskyi depends on the ecosystem from which the heterotrophs are picked. To test this hypothesis, pure cultures of N. winogradskyi were grown in continuously nitrite-fed bioreactors in a mineral medium free of added organic carbon that had been inoculated with diluted sewage sludge or with a suspension from a grassland soil. Samples for chemical and 16S rRNA gene amplicon analyses were taken after each volume change in the bioreactor. At the end of the enrichment runs, samples for shotgun metagenomics were also collected. Already after two volume changes, the transformations in community structure became less dynamic. The enrichment of heterotrophs from both sewage and soil was highly stochastic and yielded different dominant genera in most of the enrichment runs that were independent of the origin of the inoculum. Hence, the hypothesis had to be refuted. Notwithstanding the large variation in taxonomic community structure among the enrichments, the functional compositions of the communities were statistically not different between soil- and sludge-based enrichments. IMPORTANCE In the process of aerobic nitrification, nitrite-oxidizing bacteria together with ammonia-oxidizing microorganisms convert mineral nitrogen from its most reduced appearance, i.e., ammonium, into its most oxidized form, i.e., nitrate. Because the form of mineral nitrogen has large environmental implications, nitrite-oxidizing bacteria such as Nitrobacter winogradskyi play a central role in the global biogeochemical nitrogen cycle. In addition to this central role, the autotrophic nitrite-oxidizing bacteria also play a fundamental role in the global carbon cycle. They form the basis of heterotrophic food webs, in which the assimilated carbon is recycled. Little is known about the heterotrophic microorganisms that participate in these food webs, let alone their assembly in different ecosystems. This study showed that the assembly of microbial food webs by N. winogradskyi was a highly stochastic process and independent of the origin of the heterotrophic microorganisms, but the functional characteristics of the different food webs were similar.

  • Global Change Biology

    Microbiome resilience of Amazonian forests:

    Marcio Fernandes Alves Leite, Binbin Liu, Ernesto Gómez Cardozo, Hulda Rocha e Silva, Ronildson Lima Luz, Karol Henry Mavisoy Muchavisoy, Flávio Henrique Reis Moraes, Guillaume X. Rousseau, George Kowalchuk, Christoph Gehring, Eiko Kuramae
    An alarming and increasing deforestation rate threatens Amazon tropical ecosystems and subsequent degradation due to frequent fires. Agroforestry systems (AFS) may offer a sustainable alternative, reportedly mimicking the plant–soil interactions of the natural mature forest (MF). However, the role of microbial community in tropical AFS remains largely unknown. This knowledge is crucial for evaluating the sustainability of AFS and practices given the key role of microbes in the aboveground–belowground interactions. The current study, by comparing different AFS and successions of secondary and MFs, showed that AFS fostered distinct groups of bacterial community, diverging from the MFs, likely a result of management practices while secondary forests converged to the same soil microbiome found in the MF, by favoring the same groups of fungi. Model simulations reveal that AFS would require profound changes in aboveground biomass and in soil factors to reach the same microbiome found in MFs. In summary, AFS practices did not result in ecosystems mimicking natural for-est plant–soil interactions but rather reshaped the ecosystem to a completely dif-ferent relation between aboveground biomass, soil abiotic properties, and the soil microbiome.
  • Agriculture, Ecosystems and Environment

    Forage grasses steer soil nitrogen processes, microbial populations, and microbiome composition in a long-term tropical agriculture system

    Letusa Momesso Marques, Carlos Alexandre Costa Crusciol, Marcio Fernandes Alves Leite, João William Bossolani, Eiko Kuramae
    Forage grasses used in cropping no-till systems in tropical regions alter soil chemical properties, but their long-term impact on soil microbial processes of the nitrogen (N) cycle and microbial community abundance, composition and structure are unknown. Here, microbial functions related to nitrogen fixation, nitrification and denitrification as well as bacterial, archaeal and fungal populations were evaluated in a long-term field experiment in which tropical forage grasses palisade grass (Urochloa brizantha (Hochst. Ex A. Rich.) R.D. Webster) and ruzigrass (U. ruziziensis (R. Germ. and C.M. Evrard) Crins) were cultivated with or without N fertilization. Uncultivated soil was used as a control. Forage grasses, especially palisade grass, increased soil bacterial and fungal abundances, whereas the archaeal population was highest in uncultivated soil. In soils cultivated with forage grasses, N fertilization favored N-cycle-related genes; however, cultivation of palisade grass increased the abundances of amoA bacteria (AOB) and amoA archaea (AOA) genes associated with soil nitrification and decreased the abundances of genes nirS, nirK and nosZ genes related to denitrification, compared to ruzigrass and control, regardless of N input. In addition, abundances of total bacteria and total fungi were associated with the N cycle and plant biomass in soils cultivated with forage grasses. Forage cultivation clearly benefitted the soil nutrient environment (S-SO42-, Mg2+, total-C and -N, N-NO3- and N-NH4+) and microbiome (bacteria and fungi) compared with uncultivated soil. In soil cultivated with palisade grass, the microbial community composition was unresponsive to N addition. The high N uptake by palisade grass supports the competitive advantage of this plant species over microorganisms for N sources. Our results suggest that palisade grass has advantages over ruzigrass for use in agriculture systems, regardless of N input.
  • Geoderma

    Optimizing cover crop and fertilizer timing for high maize yield and nitrogen cycle control

    Letusa Momesso Marques, Carlos Alexandre Costa Crusciol, Heitor Cantarella, Katiuca S. Tanaka, George Kowalchuk, Eiko Kuramae
    Residues of cover crop grasses release nitrogen (N) to subsequent crops, which can contribute to sustainable agricultural management and prevent increases in N-loss-related microorganisms. Moreover, applying N fertilizer to cover crops can enhance the N-use efficiency and yields of subsequent cash crops and tighten the N cycle in the soil. However, the long-term effects of N fertilization of cover crops on soil microbiota and the N cycle in tropical grass-crop no-till systems are unknown. The aim of this study was to evaluate the long-term effects of the timing of N fertilization of cover crops or maize on crop yields, total microbial abundances and N-cycle gene abundances at the time of maize harvest. We carried out a field experiment with two cover crops (palisade grass (Urochloa brizantha) and ruzigrass (U. ruziziensis) fertilized with 120 kg N ha−1 (ammonium sulfate) at one of three times: (i) broadcast over the green cover crops at 35 days before maize seeding (35 DBS), (ii) broadcast over the cover crop straw residues at 1 day before maize seeding (1 DBS), and (iii) as side-dressing at the maize V4 growth stage according to the conventional method (band-applied 0.05 m from the maize row). A control treatment without N application was also carried out for both cover crop species. Except for the control, 40 kg N ha−1 as ammonium sulfate was subsurface band-applied in all treatments 0.05–0.10 m from the maize row at maize seeding, corresponding to 160 kg N ha−1. The total bacterial, archaeal and fungal abundances and abundances of microbial genes encoding enzymes of the N cycle in the soil were quantified by real-time PCR at the maize harvest stage. Overall, maize yield increased significantly in all N fertilizer applications (average 13 Mg ha−1) compared with the control (6 Mg ha−1) over three growing seasons, with maize following palisade grass having the highest yield. The abundances of archaea and fungi in soil were highest under palisade grass that received N at 35 DBS, with values of 4.6 × 106 and 1.7 × 107 gene copies/g of dry soil, respectively. Both cover crop straw production and N release to the soil were positively correlated with the total microbe densities. When ruzigrass was the cover crop, low N enhanced nifH abundance. Archaeal amoA abundance was positively correlated with cover crop biomass and N release regardless of the N treatment and was highest under palisade grass. Bacterial amoA, nirK, and nirS abundances were highest in soil under ruzigrass and were not linked to cover crop biomass mineralization. We conclude that N fertilizer should be applied using the currently recommended method (40 and 120 kg N ha−1 at seeding and side-dressed in maize, respectively) following palisade grass to achieve high maize yield while controlling the level of N loss from tropical soil via nitrification and denitrification.
  • Microbiome

    Nitrogen, manganese, iron, and carbon resource acquisition are potential functions of the wild rice Oryza rufipogon core rhizomicrobiome

    Jingjing Chang, Lei Tian, Marcio Fernandes Alves Leite, Yu Sun, Shaohua Shi, Shangqi Xu, Jilin Wang, Hongping Chen, Dazhou Chen, Jianfeng Zhang, Chunjie Tian, Eiko Kuramae

    BACKGROUND: The assembly of the rhizomicrobiome, i.e., the microbiome in the soil adhering to the root, is influenced by soil conditions. Here, we investigated the core rhizomicrobiome of a wild plant species transplanted to an identical soil type with small differences in chemical factors and the impact of these soil chemistry differences on the core microbiome after long-term cultivation. We sampled three natural reserve populations of wild rice (i.e., in situ) and three populations of transplanted in situ wild rice grown ex situ for more than 40 years to determine the core wild rice rhizomicrobiome.

    RESULTS: Generalized joint attribute modeling (GJAM) identified a total of 44 amplicon sequence variants (ASVs) composing the core wild rice rhizomicrobiome, including 35 bacterial ASVs belonging to the phyla Actinobacteria, Chloroflexi, Firmicutes, and Nitrospirae and 9 fungal ASVs belonging to the phyla Ascomycota, Basidiomycota, and Rozellomycota. Nine core bacterial ASVs belonging to the genera Haliangium, Anaeromyxobacter, Bradyrhizobium, and Bacillus were more abundant in the rhizosphere of ex situ wild rice than in the rhizosphere of in situ wild rice. The main ecological functions of the core microbiome were nitrogen fixation, manganese oxidation, aerobic chemoheterotrophy, chemoheterotrophy, and iron respiration, suggesting roles of the core rhizomicrobiome in improving nutrient resource acquisition for rice growth. The function of the core rhizosphere bacterial community was significantly (p < 0.05) shaped by electrical conductivity, total nitrogen, and available phosphorus present in the soil adhering to the roots.

    CONCLUSION: We discovered that nitrogen, manganese, iron, and carbon resource acquisition are potential functions of the core rhizomicrobiome of the wild rice Oryza rufipogon. Our findings suggest that further potential utilization of the core rhizomicrobiome should consider the effects of soil properties on the abundances of different genera. Video Abstract.

  • Studies in Mycology

    Fusarium: more than a node or a foot-shaped basal cell

    Pedro W. Crous, Lorenzo Lombard, Marcelo Sandoval, Keith A. Seifert, H.-J. Schroers, P. Chaverri, J. Gené, J. Guarro, Y. Hirooka, K. Bensch, Gert H. J. Kema, Sandra C Lamprecht, L. Cai, Amy Y Rossman, M. Stadler, R.C. Summerbell, J.W. Taylor, Sebastian Ploch, C.M. Visagie, N. Yilmaz, J.C. Frisvad, A.M. Abdel-Azeem, J. Abdollahzadeh, Alireza Abdolrasouli, A. Akulov, J.F. Alberts, J.P.M. Araújo, H. A. Ariyawansa, Mounes Bakhshi, M. Bendiksby, A. Ben Hadj Amor, Jadson D. P. Bezerra, Teun Boekhout, M.P.S. Câmara, Mauricio Carbia, G. Cardinali, Rafael F. Castañeda-Ruiz, A. Celis, V. Chaturvedi, Jérôme Collemare, D. Croll, U. Damm, C.A. Decock, Ronald P. de Vries, Chibundu N. Ezekiel, Xin-Lei Fan, N.B. Fernández, Ester Gaya, C.D. González, D. Gramaje, Ewald Groenewald, M. Grube, M. Guevara-Suarez, V.K. Gupta, V. Guarnaccia, A Haddaji, Ferry Hagen, Danny Haelewaters, K. Hansen, A. Hashimoto, Margarita Ines Hernandez Restrepo, Jos Houbraken, V. Hubka, Kevin D. Hyde, T. Iturriaga, R. Jeewon, Peter R. Johnston, Ž. Jurjević, I Karalti, L Korsten, Eiko Kuramae, I. Kušan, R Labuda, D.P. Lawrence, H.B. Lee, C. Lechat, H.Y. Li, Y.A. Litovka, Sajeewa S. N. Maharachchikumbura, Y. Marin-Felix, B. Matio Kemkuignou, N. Matočec, Alistair R. McTaggart, P. Mlčoch, L. Mugnai, C. Nakashima, R. Henrik Nilsson, Sara Raouia Noumeur, I.N. Pavlov, M.P. Peralta, Alan J. L. Phillips, J. I. Pitt, G. Polizzi, W. Quaedvlieg, Kunhiraman C. Rajeshkumar, S. Restrepo, A. Rhaiem, J. Robert, Vincent Robert, A.M. Rodrigues, C. Salgado-Salazar, Robert A. Samson, A.C.S. Santos, Roger G. Shivas, Cristina M. Souza-Motta, G.Y. Sun, Wijnand J. Swart, S. Szoke, Y.P. Tan, J.E. Taylor, Paul W. J. Taylor, P.V. Tiago, K.Z. Váczy, N. van de Wiele, N.A. van der Merwe, G.J.M. Verkley, W.A.S. Vieira, A. Vizzini, Bevan S. Weir, Nalin N. Wijayawardene, J.W. Xia, M. de Jesús Yáñez-Morales, A. Yurkov, J C Zamora, R. Zare, C.L. Zhang, M. Thines
    Recent publications have argued that there are potentially serious consequences for researchers in recognising distinct genera in the terminal fusarioid clade of the family Nectriaceae. Thus, an alternate hypothesis, namely a very broad concept of the genus Fusarium was proposed. In doing so, however, a significant body of data that supports distinct genera in Nectriaceae based on morphology, biology, and phylogeny is disregarded. A DNA phylogeny based on 19 orthologous protein-coding genes was presented to support a very broad concept of Fusarium at the F1 node in Nectriaceae. Here, we demonstrate that re-analyses of this dataset show that all 19 genes support the F3 node that represents Fusarium sensu stricto as defined by F. sambucinum (sexual morph synonym Gibberella pulicaris). The backbone of the phylogeny is resolved by the concatenated alignment, but only six of the 19 genes fully support the F1 node, representing the broad circumscription of Fusarium. Furthermore, a re-analysis of the concatenated dataset revealed alternate topologies in different phylogenetic algorithms, highlighting the deep divergence and unresolved placement of various Nectriaceae lineages proposed as members of Fusarium. Species of Fusarium s. str. are characterised by Gibberella sexual morphs, asexual morphs with thin- or thick-walled macroconidia that have variously shaped apical and basal cells, and trichothecene mycotoxin production, which separates them from other fusarioid genera. Here we show that the Wollenweber concept of Fusarium presently accounts for 20 segregate genera with clear-cut synapomorphic traits, and that fusarioid macroconidia represent a character that has been gained or lost multiple times throughout Nectriaceae. Thus, the very broad circumscription of Fusarium is blurry and without apparent synapomorphies, and does not include all genera with fusarium-like macroconidia, which are spread throughout Nectriaceae (e.g., Cosmosporella, Macroconia, Microcera). In this study four new genera are introduced, along with 18 new species and 16 new combinations. These names convey information about relationships, morphology, and ecological preference that would otherwise be lost in a broader definition of Fusarium. To assist users to correctly identify fusarioid genera and species, we introduce a new online identification database, Fusarioid-ID, accessible at www.fusarium.org. The database comprises partial sequences from multiple genes commonly used to identify fusarioid taxa (act1, CaM, his3, rpb1, rpb2, tef1, tub2, ITS, and LSU). In this paper, we also present a nomenclator of names that have been introduced in Fusarium up to January 2021 as well as their current status, types, and diagnostic DNA barcode data. In this study, researchers from 46 countries, representing taxonomists, plant pathologists, medical mycologists, quarantine officials, regulatory agencies, and students, strongly support the application and use of a more precisely delimited Fusarium (= Gibberella) concept to accommodate taxa from the robust monophyletic node F3 on the basis of a well-defined and unique combination of morphological and biochemical features. This F3 node includes, among others, species of the F. fujikuroi, F. incarnatum-equiseti, F. oxysporum, and F. sambucinum species complexes, but not species of Bisifusarium [F. dimerum species complex (SC)], Cyanonectria (F. buxicola SC), Geejayessia (F. staphyleae SC), Neocosmospora (F. solani SC) or Rectifusarium (F. ventricosum SC). The present study represents the first step to generating a new online monograph of Fusarium and allied fusarioid genera (www.fusarium.org).
  • Environmental Microbiome

    Facilitation in the soil microbiome does not necessarily lead to niche expansion

    X. Zhou, Marcio Fernandes Alves Leite, Z. Zhang, L. Tian, J. Chang, L. Ma, X. Li, Hans van Veen, Chunjie Tian, Eiko Kuramae
    The soil microbiome drives soil ecosystem function, and soil microbial functionality is directly linked to interactions between microbes and the soil environment. However, the context-dependent interactions in the soil microbiome remain largely unknown.

    Using latent variable models (LVMs), we disentangle the biotic and abiotic interactions of soil bacteria, fungi and environmental factors using the Qinghai-Tibetan Plateau soil ecosystem as a model. Our results show that soil bacteria and fungi not only interact with each other but also shift from competition to facilitation or vice versa depending on environmental variation; that is, the nature of their interactions is context-dependent.

    Overall, elevation is the environmental gradient that most promotes facilitative interactions among microbes but is not a major driver of soil microbial community composition, as evidenced by variance partitioning. The larger the tolerance of a microbe to a specific environmental gradient, the lesser likely it is to interact with other soil microbes, which suggests that facilitation does not necessarily lead to niche expansion.
  • Journal of Microbiological Methods

    The influence of agar brands and micronutrients in the growth optimization of Granulicella sp. (Acidobacteriota)

    Ohana Costa, Eiko Kuramae
    Acidobacteriota are highly abundant in soils, however, few cultured representatives are available. The purity of the reagents can influence microbial growth in laboratory conditions and successful isolation. Here we investigated the impact of different agar brands in culture medium and advocate that agar origin should be carefully considered for Acidobacteriota strains growth and microbial isolation.
  • Nutrient Cycling in Agroecosystems

    Early nitrogen supply as an alternative management for a cover crop-maize sequence under a no-till system

    Letusa Momesso Marques, Carlos Alexandre Costa Crusciol, Rogerio P. Soratto, C. A. C. Nascimento, C.A. Rosolem, Luiz Moretti de Souza, Eiko Kuramae, Heitor Cantarella
  • Bragantia

    Sugarcane pre-sprouted seedlings produced with beneficial bacteria and arbuscular mycorrhizal fungi

    L. Rossetto, G.M.F. Pierangeli, Eiko Kuramae, Mariana Sampaio Xavier, M.A.P. Cipriano, A.P.D. da Silveira
  • Applied and Environmental Microbiology

    Succession of the Resident Soil Microbial Community in Response to Periodic Inoculations

    Zhe Wang, Ziyun Chen, George Kowalchuk, Ziheng Xu, Xiangxiang Fu, Eiko Kuramae
  • Soil Biology & Biochemistry

    Modulation of the soil microbiome by long-term Ca-based soil amendments boosts soil organic carbon and physicochemical quality in a tropical no-till crop rotation system

    João William Bossolani, Carlos Alexandre Costa Crusciol, Marcio Fernandes Alves Leite, L.F. Merloti, Luiz Moretti de Souza, I.M. Pascoaloto, Eiko Kuramae
  • Geochimica et Cosmochimica Acta

    The influence of soil chemistry on branched tetraether lipids in mid- and high latitude soils: implications for brGDGT- based paleothermometry

    C. de Jonge, Eiko Kuramae, Dajana Radujković, J.T. Weedon, Ivan A Janssens, F Peterse
    Branched glycerol dialkyl glycerol tetraethers (BrGDGTs) are a suite of orphan bacterial membrane lipids commonly used as paleo-environmental proxies for mean annual air temperature (MAT) and pH. Recent calibrations between the Methylation of Branched Tetraethers index (MBT′5ME) and MAT, based on modern surface soils (including peats), show a considerable amount of scatter, especially in mid- and high latitude soils, suggesting that brGDGT signals are influenced by additional environmental and/or biological controls at these sites. Here we test the impact of soil chemical gradients and bacterial community changes (16S rDNA sequence-based) on brGDGT distributions at two grasslands sites (Ossenkampen [NL], ForHot [IS]), and one agricultural site (Craibstone [UK]). In addition to the variation in soil chemistry, the ForHot site experiences belowground warming. Of the studied edaphic parameters, soil pH is the primary factor that explains simultaneous changes in both the bacterial community composition and the brGDGT distribution. Variations in the MBT′5ME at two sites without soil warming indeed correlate strongly to soil pH (r = 0.9–1.0, pH = 4.5–7.3), whereas pH explains part of the variation in the MBT′5ME at the site with soil warming (mean soil temperature ranging between 5 and 14 °C). At all sites, soil pH is positively related with the same brGDGTs (Ib, IIb, IIIb, IIIc, IIa′, IIb′, IIc′, IIIa′, IIb′, IIIc′) and influences the ratio between main brGDGT compounds Ia, IIa and IIIa, impacting the MBT′5ME values. This change in brGDGT distributions coincides with a change in the composition of the bacterial community at all sites. The bacterial clades that vary at the three experimental sites (specifically Acidobacteria subgroups 1, 2, 3, 6, 22) have previously been shown to also respond to soil pH on a global scale. As soil pH changes on geological timescales, the impact of changing pH on the MBT′5ME paleothermometer should be considered when performing paleoclimate studies.
  • Microorganisms

    Self-crossing leads to weak co-variation of the bacterial and fungal communities in the rice rhizosphere

    J. Chang, S. Shi, L. Tian, Marcio Fernandes Alves Leite, C. Chang, Li Ji, L. Ma, Chunjie Tian, Eiko Kuramae
  • Plant and Soil

    Rice domestication influences the composition and function of the rhizosphere bacterial chemotaxis systems

    Y. Sun, L. Tian, J. Chang, S. Shi, Jianfeng Zhang, H. Xie, Yuanfeng Cai, Dazhou Chen, Eiko Kuramae, Hans van Veen, W. Li, L.P. Tran, Chunjie Tian
    Specific soil bacteria can sense and respond to the selective rhizosphere recruitment of root exudates using unique systems of chemotaxis that mediate plant-microbe and microbe-microbe interactions. This study investigates how the bacterial chemotaxis systems have been impacted by selection during the domestication of rice (Oryza species).

    Shotgun metagenomic sequencing and 16S rRNA gene amplicon sequencing were performed to investigate the bacterial chemotaxis systems and chemotactic bacteria in the rhizospheres of wild and cultivated rice. Metabolomics analysis was performed to examine the root metabolites of different accessions of rice.

    The bacterial chemotaxis genes exhibited a higher abundance in the rhizospheres of wild rice than cultivated rice, and that the compositional profile of chemotaxis genes was distinctly different between types of rice. Differential selection of chemotaxis systems was at least partially driven by changes in the metabolite profiles of rice roots that were affected by domestication. A core group of chemotactic bacteria was also identified, and specific chemotactic bacteria were found to function as hub taxa in the rhizosphere bacterial community.

    The present study provides novel insights into the composition and function of the bacterial chemotaxis systems in the rhizospheres of wild and domesticated rice. It also provides a new perspective on the impact of rice domestication on the assembly of rhizomicrobiome.
  • Forest Ecology and Management

    Microbial inoculants modulate growth traits, nutrients acquisition and bioactive compounds accumulation of Cyclocarya paliurus (Batal.) Iljinskaja under degraded field condition

    Zhe Wang, Ziheng Xu, Ziyun Chen, George A. Kowalchuk, Xiangxiang Fu, Eiko Kuramae
    Cyclocarya paliurus (Batal.) Iljinsk is an important medicinal plant for treating chronic diseases, but it is difficult to obtain high yields when growing on low-fertility soil. Inoculation with soil beneficial microorganism has suggested an effective means of stimulating plant growth and secondary metabolite production, but effect on plant performance when competing degraded field condition remains unclear. We combined controlled laboratory experiments with field trials to investigate the effects of co-inoculation with phyto-stimulatory strains (Azospirillum brasilense and Pseudomonas fluorescens) and nutrient-enhancing strains (Bacillus megaterium and Azotobacter chroococcum). Bacteria were applied with organic fertilizer at different fertilizer levels, and we tracked effects on soil nutrient availability as well as C. paliurus morphological traits, photosynthesis, growth and bioactive compounds during cultivation on barren land. Amendment of beneficial microbes with organic fertilizer enhanced the soil nutrient availability with high fertilizer showing greatest stimulation under controlled conditions, with the medium fertilizer giving best results in improving plant performance in the field. All fertilization regimes expanded the 3D root architecture, and bacterial additions increased the proportion of lateral roots compared to a single organic fertilizer treatment, which led to higher nutrient uptake. Inoculations at medium fertilizing level modified the root system and increased the photosynthesis rate, nutrient acquisition and plant growth. The co-inoculation with B. megaterium and P. fluorescens at medium fertilizer level stimulated the accumulation of flavonoids and polysaccharides, while co-inoculation with A. chroococcum and A. brasilense at low fertilizing level facilitated the production of flavonoids and triterpenoids. The biosynthesis of secondary metabolites exhibited strong correlations with leaf C/N and C/P ratios. Thus, manipulation of bioactive compounds in C. paliurus leaves can be affected by internal nutrient balance, which is associated with reformed root system morphology that modulated by bacterial inoculation.
  • European Journal of Agronomy

    Beneficial microbial species and metabolites alleviate soybean oxidative damage and increase grain yield during short dry spells

    Luiz Moretti de Souza, Carlos Alexandre Costa Crusciol, João William Bossolani, Juliano Carlos Calonego, A. Moreira, A. Garcia, Letusa Momesso Marques, Eiko Kuramae, M. Hungria
    Short dry spells are an important grain yield constraint in tropical regions. Plant growth-promoting bacteria (PGPB) and their metabolites can mitigate the impact of drought stress by promoting changes in plant metabolism, physiology, and biochemistry. However, the effects of PGPB on soybean [Glycine max (L.) Merril] under drought stress in tropical regions have not been established. The experiments were carried out under tropical field conditions with short dry spells. Therefore, in this study we used a three-factorial trial to evaluate the effects of bacterial consortium consisting of N2-fixing Bradyrhizobium japonicum (strain SEMIA 5079) and Bradyrhizobium diazoefficiens (strain SEMIA 5080), the biocontrol agent Bacillus subtilis (strain QST 713), and the plant growth-promoting Azospirillum brasilense (strains Ab-V5 and Ab-V6) with or without application of microbial secondary metabolites (MSM, rhizobial metabolites enriched in lipo-chitooligosaccharides (LCOs)) during two growing seasons. Photosynthetic pigments, gas exchange parameters, antioxidant enzyme activity and proline concentrations in leaves, nodulation, plant growth development and grain yield were evaluated. The bacterial consortium comprising Bradyrhizobium spp., A. brasilense strains and MSM application increased the contents of chlorophyll a (14.5 %), chlorophyll b (30.8 %), total chlorophyll (17.2 %), and total carotenoids (27.3 %) compared with Bradyrhizobium spp. treatment alone. This consortium also increased the net photosynthetic rate (17.7 %), stomatal conductance (56.5 %), internal CO2 concentration in the substomatal chamber (8.3 %), and transpiration (44 %) compared with plants that received the standard inoculation (Bradyrhizobium spp. only), while reducing the leaf contents of hydrogen peroxide (−18.8 %) and proline (−29.4 %), lipid peroxidation (−15.9 %), and the activities of superoxide dismutase (−18.2 %), catalase (−21.2 %), and ascorbate peroxidase (−19.1 %). Taken together, the results indicate that a beneficial bacterial consortium comprising Bradyrhizobium spp. and A. brasilense strains combined with MSM application can alleviate oxidative damage during dry spells. Furthermore, this consortium improved soybean nodulation, plant growth development, and grain yield by up to 12.2 %.
  • Frontiers in Soil Science

    Combined use of vinasse and nitrogen as fertilizers affects nitrification, ammonification and denitrification by prokaryotes

    M.G. Chaves, Andressa M. Venturini, L.F. Merloti, D.J. Barros, Raffaela Rossetto, Eiko Kuramae, S.M. Tsai, Acácio A. Navarrete
  • Microorganisms

    Plant-Growth Endophytic Bacteria Improve Nutrient Use Efficiency and Modulate Foliar N-Metabolites in Sugarcane Seedling

    M.A.P. Cipriano, Raquel de Paula Freitas Iório Iório, Mauricio Rocha Dimitrov, Sara Adrián Lopez de Andrade, Eiko Kuramae, A.P.D. da Silveira
  • Science of the Total Environment

    Rearranging the sugarcane holobiont via plant growth-promoting bacteria and nitrogen input

    Marcio Fernandes Alves Leite, Mauricio Rocha Dimitrov, Raquel de Paula Freitas Iório Iório, Mattias De Hollander, M.A.P. Cipriano, Sara Adrián Lopez de Andrade, A.P.D. da Silveira, Eiko Kuramae
    The development and productivity of plants are governed by their genetic background, nutrient input, and the microbial communities they host, i.e. the holobiont. Accordingly, engineering beneficial root microbiomes has emerged as a novel and sustainable approach to crop production with reduced nutrient input. Here, we tested the effects of six bacterial strains isolated from sugarcane stalks on sugarcane growth and physiology as well as the dynamics of prokaryote community assembly in the rhizosphere and root endosphere under two N fertilization regimes. All six strains, Paraburkholderia caribensis IAC/BECa 88, Kosakonia oryzae IAC/BECa 90, Kosakonia radicincitans IAC/BECa 95, Paraburkholderia tropica IAC/BECa 135, Pseudomonas fluorescens IAC/BECa 141 and Herbaspirillum frisingense IAC/BECa 152, increased in shoot and root dry mass, and influenced the concentration and accumulation of important macro- and micronutrients. However, N input reduced the impact of inoculation by shifting the sugarcane microbiome (rhizosphere and root endosphere) and weakening the co-dependence between soil microbes and sugarcane biomass and nutrients. The results show that these beneficial microbes improved plant nutrient uptake conditioned to a reduced N nutrient input. Therefore, reduced fertilization is not only desirable consequence of bacterial inoculation but essential for higher impact of these beneficial bacteria on the sugarcane microbiome.
  • Microorganisms

    On-site blackwater treatment fosters microbial groups and functions to efficiently and robustly recover carbon and nutrients

    Eiko Kuramae, Mauricio Rocha Dimitrov, Gustavo Ribeiro da Silva, Adriano Reis Lucheta, L.W. Mendes, Ronildson Lima Luz, Louise E.M. Vet, Tania Vasconcelos Fernandes
    Background: Wastewater is considered as a renewable resource water and energy. An advantage of decentralized sanitation systems is the separation of the blackwater (BW) stream, which is highly contaminated with human pathogens, from the remaining household water. However, the composition and functions of the microbial community in BW are not known. In this study, we used shotgun metagenomics to assess the dynamics of microbial community structure and function throughout a new BW anaerobic digestion system installed at The Netherlands Institute of Ecology. Samples from the influent (BW), primary effluent (anaerobic digested BW), sludge and final effluent of the pilot upflow anaerobic sludge blanket (UASB) reactor and microalgae pilot tubular photobioreactor (PBR) were analyzed.

    Results: Our results showed a decrease in microbial richness and diversity followed by a decrease in functional complexity and co-occurrence along the different modules of the bioreactor. The microbial diversity and function decrease were reflected both changes in substrate composition and wash conditions. The most prevalent core functions in influent (BW) were related to metabolism of carbohydrates, response to chemicals and drugs, and nitrogen. The core functions in anaerobic digested BW and upflow anaerobic sludge blanket reactor were related to response to stress, viral processes and iron-sulfur metabolism. Methanogenesis-related functions were most abundant in upflow anaerobic sludge blanket reactor. Effluent from tubular photobioreactor presented high abundances of functions related to nitrogen utilization, metal ion binding and antibiotic biosynthetic processes. Interestingly, the abundance of sequences related to ‘pathogenesis’ decreased from influent BW to SP1 to effluent from tubular photobioreactor. Our wastewater treatment system also decreased potential microbial functions related to pathogenesis.

    Conclusions: The new sanitation system studied here fosters microbial groups and functions that allow the system to efficiently and robustly recover carbon and nutrients while reducing pathogenic groups, ultimately generating a final effluent safe for discharge and reuse.
  • Journal of Soil Science and Plant Nutrition

    Bacterial consortium and microbial metabolites increase grain quality and soybean yield

    Luiz Moretti de Souza, C.A.C. Cruciol, J.W. Bossolani, Letusa Momesso Marques, A. Garcia, Eiko Kuramae, M. Hungria
    The effects of Bradyrhizobium inoculation on soybean growth and productivity are well known, but plant responses to consortia of other beneficial microbes and microbial molecules have not yet been well explored. Therefore, the main aim of this study was to evaluate the effect of different combinations of beneficial bacteria with and without microbial secondary metabolites (MSM) on two soybean cultivars in three cropping seasons under tropical field conditions. The bacterial consortia consisted of Bradyrhizobium japonicum (strain SEMIA 5079) plus Bradyrhizobium diazoefficiens (strain SEMIA 5080) inoculated with different combinations of Bacillus subtilis (strain QST 713), Azospirillum brasilense (strains Ab-V5 and Ab-V6), and MSM (metabolites enriched in lipo-chitooligosaccharides (LCOs) extracted from B. diazoefficiens (strain USDA 110) and from Rhizobium tropici (strain CIAT 889)). Standard inoculation of Bradyrhizobium combined with Azospirillum brasilense and microbial secondary metabolites increased leaf total N (7.1%), total P (11.1%), and N-ureide (16.5%); nodule number (NN, 26%) and dry weight (NDW, 22%); root (RDW, 15.4%) and shoot dry weight (SDW, 6%); 100-seed weight (3.7%); grain yield (up to 516 kg ha−1); grain crude protein concentration (2.4%); and the agronomic efficiency index (AEI) (11%). Inoculation with bacterial consortia and metabolites increased grain yield and quality, representing a promising technology for sustainable soybean cropping in tropical regions.
  • FEMS Microbiology Letters

    Unraveling the xylanolytic potential of Acidobacteria bacterium AB60 from Cerrado soils

    G. Rodrigues, O. Pinto, L. Schroeder, G. Fernandes, Ohana Costa, B. Quirino, Eiko Kuramae, C. Barreto
    The presence of genes for glycosyl hydrolases in many Acidobacteria genomes indicates an important role in the degradation of plant cell wall material. Acidobacteria bacterium AB60 was obtained from Cerrado oligotrophic soil in Brazil, where this phylum is abundant. The 16S rRNA gene analyses showed that AB60 was closely related to the genera Occallatibacter and Telmatobacter. However, AB60 grew on xylan as carbon source, which was not observed in Occallatibacter species; but growth was not detected on medium containing carboxymethyl cellulose, as observed in Telmatobacter. Nevertheless, the genome analysis of AB60 revealed genes for the enzymes involved in cellulose as well as xylan degradation. In addition to enzymes involved in xylan degradation, α-l-rhamnosidase was detected in the cultures of AB60. Functional screening of a small-insert genomic library did not identify any clones capable of carboxymethyl cellulose degradation, but open reading frames coding α-l-arabinofuranosidase and α-l-rhamnosidase were present in clones showing xylan degradation halos. Both enzymes act on the lateral chains of heteropolymers such as pectin and some hemicelluloses. These results indicate that the hydrolysis of α-linked sugars may offer a metabolic niche for slow-growing Acidobacteria, allowing them to co-exist with other plant-degrading microbes that hydrolyze β-linked sugars from cellulose or hemicellulose backbones.
  • Archives of Microbiology

    Microbial N‑cycling gene abundance is affected by cover crop specie and development stage in an integrated cropping system

    K.F. Rocha, Eiko Kuramae, B.M.F. Borges, Marcio Fernandes Alves Leite, C.A. Rosolem
    Grasses of the Urochloa genus have been widely used in crop-livestock integration systems or as cover crops in no-till systems such as in rotation with maize. Some species of Urochloa have mechanisms to reduce nitrification. However, the responses of microbial functions in crop-rotation systems with grasses and its consequence on soil N dynamics are not well-understood. In this study, the soil nitrification potential and the abundance of ammonifying microorganisms, total bacteria and total archaea (16S rRNA gene), nitrogen-fixing bacteria (NFB, nifH), ammonia-oxidizing bacteria (AOB, amoA) and archaea (AOA, amoA) were assessed in soil cultivated with ruzigrass (Urochloa ruziziensis), palisade grass (Urochloa brizantha) and Guinea grass (Panicum maximum). The abundance of ammonifying microorganisms was not affected by ruzigrass. Ruzigrass increased the soil nitrification potential compared with palisade and Guinea grass. Ruzigrass increased the abundance of N-fixing microorganisms at the middle and late growth stages. The abundances of nitrifying microorganisms and N-fixers in soil were positively correlated with the soil N–NH4+ content. Thus, biological nitrogen fixation might be an important input of N in systems of rotational production of maize with forage grasses. The abundance of microorganisms related to ammonification, nitrification and nitrogen fixing and ammonia-oxidizing archea was related to the development stage of the forage grass.
  • Microorganisms

    Bacterial Tomato Pathogen Ralstonia solanacearum Invasion Modulates Rhizosphere Compounds and Facilitates the Cascade Effect of Fungal Pathogen Fusarium solani

    Lv Su, L. Zhang, P. Qiu, D. Nie, Eiko Kuramae, Ben Shen, Qirong Shen
    Soil-borne pathogen invasions can significantly change the microbial communities of the host rhizosphere. However, whether bacterial Ralstonia solanacearum pathogen invasion influences the abundance of fungal pathogens remains unclear. In this study, we combined high-throughput sequencing, qPCR, liquid chromatography and soil culture experiments to analyze the rhizosphere fungal composition, co-occurrence of fungal communities, copy numbers of functional genes, contents of phenolic acids and their associations in healthy and bacterial wilt-diseased tomato plants. We found that R. solanacearum invasion increased the abundance of the soil-borne pathogen Fusarium solani. The concentrations of three phenolic acids in the rhizosphere soil of bacterial wilt-diseased tomato plants were significantly higher than those in the rhizosphere soil of healthy tomato plants. In addition, the increased concentrations of phenolic acids significantly stimulated F. solani growth in the soil. Furthermore, a simple fungal network with fewer links, nodes and hubs (highly connected nodes) was found in the diseased tomato plant rhizosphere. These results indicate that once the symptom of bacterial wilt disease is observed in tomato, the roots of the wilt-diseased tomato plants need to be removed in a timely manner to prevent the enrichment of other fungal soil-borne pathogens. These findings provide some ecological clues for the mixed co-occurrence of bacterial wilt disease and other fungal soil-borne diseases.
  • Agronomy Journal

    Effects of growth-promoting bacteria on soybean root activity, plant development and yield

    Luiz Moretti de Souza, Carlos Alexandre Costa Crusciol, Eiko Kuramae, J.W. Bossolani, A. Moreira, N.R. Costa, C.J. Alves, I.M. Pascoaloto, A.B.L. Rondina, M. Hungria
    Rhizobia and other plant growth-promoting rhizobacteria (PGPR) have been broadly used as inoculants in agriculture, resulting in morphofunctional improvements in roots and grain yield. This study was carried out during two cropping seasons under field and greenhouse conditions in Brazil to verify the effects of inoculation of two soybean cultivars with PGPR and secondary microbial metabolites (SMMs) on root activity and nodulation, plant development, and grain yield. Inoculation and co-inoculation treatments consisted of Bradyrhizobium japonicum strain SEMIA 5079 and B. diazoefficiens strain SEMIA 5080 inoculated together, in combination with Bacillus subtilis strain QST 713, Azospirillum brasilense strains Ab-V5 and Ab-V6, and SMMs extracted from B. diazoefficiens strain USDA 110 and Rhizobium tropici strain CIAT 889. Root systems were evaluated by direct (optical reading) and indirect (rubidium nitrate application, 85RbNO3) methods. Increases of up to 1.6% in root diameter (0.01- to 0.5-mm class), 28.5% in length, 19.7% in root volume, 17.8% in root surface area, 29% in the number of nodules, 27.2% in nodule dry weight, 13.5% in root dry weight, and 3.8% in shoot dry weight. Greater exploration and activity within and between rows following inoculation at up to 40 and 10 cm in depth, respectively, were observed in plants co-inoculated with the standard inoculation (only Bradyrhizobium spp.) + SMMs + A. brasilense, resulting in a yield increase of 485 kg ha−1. The results emphasize the biotechnological potential of using secondary metabolites of rhizobia with inoculants containing rhizobia and PGPR to improve the growth and soybean yield in tropical conditions.
  • Microorganisms

    Responses of Acidobacteria Granulicella sp. WH15 to high carbon revealed by integrated omics analyses

    Ohana Costa, Marcelo Zerillo, D. Zühlke, Anna Kielak, Agata Pijl, K. Riedel, Eiko Kuramae
    The phylum Acidobacteria is widely distributed in soils, but few representatives have been cultured. In general, Acidobacteria are oligotrophs and exhibit slow growth under laboratory conditions. We sequenced the genome of Granulicella sp. WH15, a strain obtained from decaying wood, and determined the bacterial transcriptome and proteome under growth in poor medium with a low or high concentration of sugar. We detected the presence of 217 carbohydrate-associated enzymes in the genome of strain WH15. Integrated analysis of the transcriptomic and proteomic profiles showed that high sugar triggered a stress response. As part of this response, transcripts related to cell wall stress, such as sigma factor σW and toxin–antitoxin (TA) systems, were upregulated, as were several proteins involved in detoxification and repair, including MdtA and OprM. KEGG metabolic pathway analysis indicated the repression of carbon metabolism (especially the pentose phosphate pathway) and the reduction of protein synthesis, carbohydrate metabolism, and cell division, suggesting the arrest of cell activity and growth. In summary, the stress response of Granulicella sp. WH15 induced by the presence of a high sugar concentration in the medium resulted in the intensification of secretion functions to eliminate toxic compounds and the reallocation of resources to cell maintenance instead of growth.
  • Frontiers in Environmental Science

    Microbial functional diversity in vineyard soils: sulfur metabolism and links with grapevine plants and wine quality

    S. Mocali, Eiko Kuramae, George Kowalchuk, F. Fornasier, S. Priori
    The quality of the vineyard soils has a direct impact on grapes and wine quality and represents a key component of the “Terroir concept”. However, information on the impact of soil microbiota on grapevine plants and wine quality are generally lacking. In fact, over the last few years most of the attempts made to correlate soil microbial communities and wine quality were limited by overlooking both the functional traits of soil microbiota and the spatial variability of vineyards soils. In this work, we used a functional gene microarray approach (GeoChip) and soil enzymatic analyses to assess the soil microbial community functional potential related to the different wine quality. In order to minimize the soil variability, this work was conducted at a “within-vineyard” scale, comparing two similar soils (BRO11 and BRO12) previously identified with respect to pedological and hydrological properties within a single vineyard in Central Tuscany and that yielded highly contrasting wine quality upon cultivation of the same Sangiovese cultivar (BRO12 exhibited the higher quality). Our results showed an enrichment of Actinobacteria in BRO12, whereas Alfa- and Gamma-Proteobacteria were more abundant in BRO11, where an enrichment of bacteria involved in N fixation and denitrification occurred. Overall, the GeoChip output revealed a greater biological activity in BRO11 but a significant enrichment of sulfur-oxidation genes in BRO12 compared to BRO11 soil, where a higher level of arylsulfatase activity was also detected. Moreover, the low content of sulfates and available nitrogen found in BRO12 suggested that the reduced availability of sulfates for vine plants might limit the reduced glutathione (GSH) synthesis, which plays an important role in aroma protection in musts and wines. In conclusion, in addition to nitrogen availability, we propose that soil microbial sulfur metabolism may also play a key role in shaping plant physiology, grapes and wine quality. Overall, these results support the existence of a “microbial functional terroir” effect as a determining factor in vineyard-scale variation among wine grapes.
  • Soil Biology & Biochemistry

    You must choose, but choose wisely

    Marcio Fernandes Alves Leite, Eiko Kuramae
    Soil microbial community data produced by next-generation sequencing platforms has introduced a new era in microbial ecology studies but poses a challenge for data analysis: huge tables with highly sparse data combined with methodological limitations leading to biased analyses. Methodological studies have attempted to improve data interpretation via data transformation and/or rarefaction but usually neglect the assumptions required for an appropriate analysis. Advances in both mathematics and computation are now making model-based approaches feasible, especially latent variable modeling (LVM). LVM is a cornerstone of modern unsupervised learning that permits the evaluation of evolutionary, temporal, and count structure in a unified approach that directly incorporates the data distribution. Despite these advantages, LVM is rarely applied in data analyses of the soil microbiome. Here, we review available methods to handle the characteristics of soil microbial data obtained from next-generation sequencing and advocate for model-based approaches. We focus on the importance of assumption checking for guiding the selection of the most appropriate method of data analysis. We also provide future directions by advocating for the consideration of the dataset produced by sequencing as a representation of microbial detections instead of abundances and for the adoption of hierarchical models to convert these detections into estimated abundances prior to evaluating the microbial community. In summary, we show that model assessment is important for qualifying interpretations and can further guide refinements in subsequent analyses. We have only begun to understand the factors regulating soil microbial communities and the impacts of this microbiota on the environment/ecosystem. Understanding the assumptions of new methods is essential to fully harness their power to test hypotheses using high-throughput sequencing data.
  • 2020

    Methods to Identify Soil Microbial Bioindicators of Sustainable Management of Bioenergy Crops

    Acácio A. Navarrete, R.C. Bonassi, J.H.P. Americo-Pinheiro, G.H. Vazquez, L.W. Mendes, E.S. Loureiro, Eiko Kuramae, S.M. Tsai
    Here we describe a suite of methods to identify potential taxonomic and functional soil microbial indicators of soil quality and plant health in biofuel crops in various areas and land types. This approach draws on tools to assess microbial diversity, greenhouse gas fluxes, and soil physicochemical properties in bioenergy cropping systems. Integrative statistical models are then used to identify potential microbial indicators for sustainable management of bioenergy crops.
  • Nutrient Cycling in Agroecosystems

    Upland rice yield enhanced by early nitrogen fertilization on previous palisade grass

    Letusa Momesso Marques, Carlos Alexandre Costa Crusciol, Rogerio P. Soratto, Katiuca S. Tanaka, Claudio H. M. Costa, Heitor Cantarella, Eiko Kuramae
    High grain yields of upland rice (Oryza sativa L.) can be achieved in no-tillage systems. However, managing nitrogen (N) fertilization for rice in succession to forage grasses is a challenge because forage residues change N cycling and increase microbial immobilization of N, thereby reducing N availability to the subsequent cash crop. In the present study, two field experiments were conducted to determine if applying all or part of the N fertilizer on preceding palisade grass (Urochloa brizantha) and ruzigrass (Urochloa ruziziensis) or their desiccated residues immediately before rice seeding can supply N to the subsequent rice crop. Forage biomass yield (8–16 Mg ha− 1), N accumulation, and N supply to the subsequent upland rice were highest when all of the N fertilizer was applied on forage grasses at 50, 40 or 35 days before rice seeding (DBS), as opposed to the conventional split application at rice seeding and at tillering. On average, the grain yield of upland rice was 54% higher in succession to palisade grass compared with ruzigrass. The grain yield of rice was higher when N was applied to palisade grass at 35 DBS and ruzigrass at 50 DBS, reaching 5.0 Mg ha− 1 and 3.7 Mg ha− 1, respectively. However, applying N to ruzigrass was less effective for increasing upland rice yields since the yields did not differ from the treatments with the conventional split application. Adjusting the time of N application to forage grasses to increase the grain yields of subsequent upland rice is a sustainable alternative that can promote the economic viability of upland rice production.
  • Frontiers In Sustainable Food Systems

    Can Palisade and Guinea Grass Sowing Time in Intercropping Systems Affect Soybean Yield and Soil Chemical Properties?

    Nidia Costa, M. Andreotti, Carlos Alexandre Costa Crusciol, Cristiano M. Pariz, J.W. Bossolani, André M. Castilhos, C. A. C. Nascimento, C.G.R. Lima, C.S.B. Bonini, Eiko Kuramae
    In tropical regions, intercropping systems under no-tillage improve biomass quantity, soil conservation, and cash crop productivity. However, the optimal sowing time for forage species in these cropping systems is unknown. The objective of this study was to evaluate the effects of two sowing times of palisade and guinea grass on forage production and quality, soybean yield and soil chemical properties. Palisade and guinea grasses were sown for intercropping with maize or after maize silage harvest (hereafter succession) in an experiment carried out over three crop seasons. We evaluated forage dry matter production, pasture nutritive values, straw nutrient content, soybean leaf nutrients, yield, and soil fertility. The highest dry matter production was 8.1 Mg ha−1 for guinea grass in the intercropping system (sum of 3 cuts). Sowing forage after maize silage harvest provided 4% more crude protein compared with intercropping, regardless of grass species. Soybean yield was over 1.0 Mg ha−1 higher when soybean was cropped in succession compared with intercropping; however, the effects of the two forage grasses on soybean production were similar. Soil pH, calcium and magnesium content, cation exchange capacity, and base saturation were higher in the intercropping systems than in the succession systems, particularly when guinea grass was cultivated. Sowing guinea grass after maize harvest provided better forage quality, nutrient cycling, soybean yields, and soil chemical properties in tropical conditions.
  • Microorganisms

    Sorghum Growth Promotion by Paraburkholderia tropica and Herbaspirillum frisingense: Putative Mechanisms Revealed by Genomics and Metagenomics

    Eiko Kuramae, S. Derksen, Thiago Schlemper, Mauricio Rocha Dimitrov, Ohana Costa, A.P.D. da Silveira
    Bacteria from the genera Paraburkholderia and Herbaspirillum can promote the growth of Sorghum bicolor, but the underlying mechanisms are not yet known. In a pot experiment, sorghum plants grown on sterilized substrate were inoculated with Paraburkholderia tropica strain IAC/BECa 135 and Herbaspirillum frisingense strain IAC/BECa 152 under phosphate-deficient conditions. These strains significantly increased Sorghum bicolor cultivar SRN-39 root and shoot biomass. Shotgun metagenomic analysis of the rhizosphere revealed successful colonization by both strains; however, the incidence of colonization was higher in plants inoculated with P. tropica strain IAC/BECa 135 than in those inoculated with H. frisingense strain IAC/BECa 152. Conversely, plants inoculated with H. frisingense strain IAC/BECa 152 showed the highest increase in biomass. Genomic analysis of the two inoculants implied a high degree of rhizosphere fitness of P. tropica strain IAC/BECa 135 through environmental signal processing, biofilm formation, and nutrient acquisition. Both genomes contained genes related to plant growth-promoting bacterial (PGPB) traits, including genes related to indole-3-acetate (IAA) synthesis, nitrogen fixation, nodulation, siderophore production, and phosphate solubilization, although the P. tropica strain IAC/BECa 135 genome contained a slightly more extensive repertoire. This study provides evidence that complementary mechanisms of growth promotion in Sorghum might occur, i.e., that P. tropica strain IAC/BECa 135 acts in the rhizosphere and increases the availability of nutrients, while H. frisingense strain IAC/BECa 152 influences plant hormone signaling. While the functional and taxonomic profiles of the rhizobiomes were similar in all treatments, significant differences in plant biomass were observed, indicating that the rhizobiome and the endophytic microbial community may play equally important roles in the complicated plant-microbial interplay underlying increased host plant growth
  • Applied Soil Ecology

    The modulation of sugarcane growth and nutritional profile under aluminum stress is dependent on beneficial endophytic bacteria and plantlet origin

    Elaine Regina Godoy Labanca, Sara Adrián Lopez de Andrade, Eiko Kuramae, A.P.D. da Silveira
    Plant growth-promoting bacteria (PGPB) are claimed to not only improve plant fitness but also alleviate plant stress. In this study, we evaluated the effect of five PGPB strains on plantlet growth and nutrient and aluminum (Al) uptake under acid soil conditions characterized by low P and K nutrient availability and high metal and aluminum (Al) bioavailability, which may represent a stress condition for crop plants. The PGPB strains were inoculated in sugarcane plantlets produced by meristem tissue culture (MCPs) or one-bud stalks (O-BSPs) and cultivated in soil at 37% Al saturation and pH 4.0. Biomass accumulation and Al and nutrient content in roots and shoots were determined after 30 days of growth. Bacterial inoculation increased root and shoot biomass. However, the magnitudes of these increases were dependent on bacterial strain and plantlet origin. The inoculated plantlets exhibited increased Al content and shifts in Al allocation and calcium (Ca) and boron (B) content among different plant parts (root or shoot), and these changes also depended on plantlet origin and the inoculated strain. The higher Ca uptake of inoculated MCPs and higher B uptake of inoculated O-BSPs may have contributed to reducing the damage caused by excessive Al content. The beneficial microbes also caused changes in plant uptake of micronutrients and slightly reduced macronutrient content. Pseudomonas fluorescens (IAC/BECa 141), Kosakonia radicincitans (IAC/BECa 95), Paraburkholderia tropica (IAC/BECa 135) and Herbaspirillum frisingense (IAC/BECa 152) showed potential for alleviating Al stress in sugarcane plantlets.
  • Microbiome

    Cultivation-independent and cultivation-dependent metagenomes reveal genetic and enzymatic potential of microbial community involved in the degradation of a complex microbial polymer

    Ohana Costa, Mattias De Hollander, Agata Pijl, Binbin Liu, Eiko Kuramae
    Cultivation-independent methods, including metagenomics, are tools for the exploration and discovery of biotechnological compounds produced by microbes in natural environments. Glycoside hydrolases (GHs) enzymes are extremely desired and important in the industry of production for goods and biofuel and removal of problematic biofilms and exopolysaccharide (EPS). Biofilms and EPS are complex, requiring a wide range of enzymes for a complete degradation. The aim of this study was to identify potential GH microbial producers and GH genes with biotechnological potential, using EPS-complex structure (WH15EPS) of Acidobacteria Granulicella sp. strain WH15 as an enrichment factor, in cultivation-independent and cultivation-dependent methods. We performed stable isotope probing (SIP) combined with metagenomics on topsoil litter amended with WH15EPS and coupled solid culture-EPS amended medium with metagenomics.

    SIP metagenome analysis of the soil litter demonstrated that phyla Proteobacteria, Actinobacteria, Acidobacteria, and Planctomycetes were the most abundant in WH15EPS amended and unamended treatments. The enrichment cultures in solid culture medium coupled to metagenomics demonstrated an enrichment in Proteobacteria, and the metagenome assembly of this enrichment cultures resulted in 4 metagenome-assembled genomes (MAGs) of microbes with low identity (42–86%) to known microorganisms. Among all carbohydrate-active enzymes (CAZymes) retrieved genes, glycoside transferase (GT) was the most abundant family, either in culture-independent or culture-based metagenome datasets. Within the glycoside hydrolases (GHs), GH13 was the most abundant family in both metagenome datasets. In the “heavy” fraction of the culture-independent metagenome SIP dataset, GH109 (α-N-acetylgalactosaminidases), GH117 (agarases), GH50 (agarases), GH32 (invertases and inulinases), GH17 (endoglucanases), and GH71 (mutanases) families were more abundant in comparison with the controls. Those GH families are affiliated to microorganism that are probably capable to degrade WH15EPS and potentially applicable for biofilm deconstruction. Subsequent in culture-based metagenome, the assembled 4 MAGs (unclassified Proteobacteria) also contained GH families of interest, involving mannosidases, lysozymes, galactosidases, and chitinases.

    We demonstrated that functional diversity induced by the presence of WH15EPS in both culture-independent and culture-dependent approaches was enriched in GHs, such as amylases and endoglucanases that could be applied in chemical, pharmaceutical, and food industrial sectors. Furthermore, WH15EPS may be used for the investigation and isolation of yet unknown taxa, such as unclassified Proteobacteria and Planctomycetes, increasing the number of current cultured bacterial representatives with potential biotechnological traits.
  • Resources, Conservation and Recycling

    From toilet to agriculture

    Afnan Suleiman, Késia Lourenço, C Clark, Ronildson Lima Luz, Gustavo H.R. Silva, Louise E.M. Vet, Heitor Cantarella, Tania Vasconcelos Fernandes, Eiko Kuramae
    Human activities are pushing earth beyond its natural limits, so recycling nutrients is mandatory. Microalgae are highly effective in nutrient recovery and have strong potential as a sustainable wastewater treatment technology. Here, nutrients from black water (toilet wastewater) were recovered as microalgal biomass, which was dried and assessed as a fertilizer in pot experiments compared with inorganic fertilizer. We deciphered the effects of microalgal biomass as a biofertilizer on plant growth and quality and the biological processes linked to greenhouse gas (GHG) emissions. In addition, we elucidated the assembly of the active microbiome in bulk soil and rhizosphere during barley development. Microalgal biomass application and inorganic fertilizer (NPK) resulted in similar plant productivity (16.6 g pot−1). Cumulative nitrous oxide (N2O) emissions were 4.6-fold higher in the treatment amended with microalgal fertilizer (3.1% of applied N) than that with inorganic fertilizer (0.5% of applied N). Nitrification by bacteria was likely the main pathway responsible for N2O emissions (R2 = 0.7, p ≤ 0.001). The application of nitrogen fertilizers affected the structures of both the active bacterial and protozoan communities, but these effects were less obvious than the strong plant effect, as the recruited microbiota varied among different plant developmental stages. Both treatments enriched similar bacterial and protozoan taxonomic orders but with different distributions through time across the plant developmental stages. Furthermore, the bacterial community showed a clear trend of resilience from the beginning of the experiment until harvest, which was not observed for protozoa. Our results indicate that the use of microalgal biomass as a fertilizer is a viable option for recycling nutrients from wastewater into plant production.
  • Scientific Reports

    Peat substrate amended with chitin modulates the N-cycle, siderophore and chitinase responses in the lettuce rhizobiome

    C. de Tender, B. Mesuere, F. van der Jeugt, Annelies Haegeman, T. Ruttink, Bart Vandecasteele, P. Dawyndt, J. Debode, Eiko Kuramae
  • Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology

    Exploitation of new endophytic bacteria and their ability to promote sugarcane growth and nitrogen nutrition

    A.P.D. da Silveira, Raquel de Paula Freitas Iório Iório, F.C.C. Marcos, A.O. Fernandes, S.A.C.D. De Souza, Eiko Kuramae, M.A.P. Cipriano
    Few studies have evaluated endophytic bacteria in relation to plant growth promotion, nitrogen uptake and biological control. The aim of this study was to molecularly and physiologically characterize thirteen endophytic bacteria strains, evaluate their biological control properties and their ability to promote plant growth and plant N nutrition. All the strains produced indole acetic acid and promoted increase of plant biomass, N accumulative amount and N-use efficiency index. None of the strains carries the nifH gene. Four strains stimulated plant nitrate reductase activity, four solubilized phosphate, nine produced siderophores and none produced HCN. Seven strains inhibited Bipolaris sacchari growth and one was antagonistic to Ceratocystis paradoxa. The pathogens were inhibited by the production of diffusible and volatile metabolites by the bacterial strains. Moreover, this is the first study to demonstrate the effect of Delftia acidovorans on sugarcane plant growth, nitrogen metabolism improvement and antagonism to B. sacchari. The most efficient strains in promoting plant growth and exhibiting antagonistic activities towards fungal pathogens were Herbaspirillum frinsingense (IAC-BECa-152) and three Pantoea dispersa strains (IAC-BECa-128, IAC-BECa-129, and IAC-BECa-132). These bacteria show potential to be used as inoculants for sustainable agricultural management, mainly at the seedling production phase.
  • Environmental Microbiology

    Nitrification inhibitors effectively target N2O-producing Nitrosospira spp. in tropical soil

    Noriko Cassman, Johnny Soares, Agata Pijl, Késia Lourenço, Hans van Veen, Heitor Cantarella, Eiko Kuramae
    The nitrification inhibitors (NIs) 3,4‐dimethylpyrazole (DMPP) and dicyandiamide (DCD) can effectively reduce N2O emissions; however, which species are targeted and the effect of these NIs on the microbial nitrifier community is still unclear. Here, we identified the ammonia oxidizing bacteria (AOB) species linked to N2O emissions and evaluated the effects of urea and urea with DCD and DMPP on the nitrifying community in a 258 day field experiment under sugarcane. Using an amoA AOB amplicon sequencing approach and mining a previous dataset of 16S rRNA sequences, we characterized the most likely N2O‐producing AOB as a Nitrosospira spp. and identified Nitrosospira (AOB), Nitrososphaera (archaeal ammonia oxidizer) and Nitrospira (nitrite‐oxidizer) as the most abundant, present nitrifiers. The fertilizer treatments had no effect on the alpha and beta diversities of the AOB communities. Interestingly, we found three clusters of co‐varying variables with nitrifier operational taxonomic units (OTUs): the N2O‐producing AOB Nitrosospira with N2O, NO3−, NH4+, water‐filled pore space (WFPS) and pH; AOA Nitrososphaera with NO3−, NH4+ and pH; and AOA Nitrososphaera and NOB Nitrospira with NH4+, which suggests different drivers. These results support the co‐occurrence of non‐N2O‐producing Nitrososphaera and Nitrospira in the unfertilized soils and the promotion of N2O‐producing Nitrosospira under urea fertilization. Further, we suggest that DMPP is a more effective NI than DCD in tropical soil under sugarcane.
  • Frontiers in Microbiology

    Wood Decay Characteristics and Interspecific Interactions Control Bacterial Community Succession in Populus grandidentata (Bigtooth Aspen)

    Eiko Kuramae, Marcio Fernandes Alves Leite, Afnan Suleiman, Christopher Michael Gough, Buck Castillo, Lewis Faller, Rima Franklin, John Syring
    Few studies have investigated bacterial community succession and the role of bacterial decomposition over a continuum of wood decay. Here, we identified how (i) the diversity and abundance of bacteria changed along a chronosequence of decay in Populus grandidentata (bigtooth aspen); (ii) bacterial community succession was dependent on the physical and chemical characteristics of the wood; (iii) interspecific bacterial interactions may mediate community structure. 459 taxa were identified through Illumina sequencing of 16S rRNA amplicons from samples taken along a continuum of decay, representing standing dead trees, downed wood, and soil. Community diversity increased as decomposition progressed, peaking in the most decomposed trees. While a small proportion of taxa displayed a significant pattern in regards to decay status of the host log, many bacterial taxa followed a stochastic distribution. Changes in the water availability and chemical composition of standing dead and downed trees and soil were strongly coupled with shifts in bacterial communities. Nitrogen was a major driver of succession and nitrogen-fixing taxa of the order Rhizobiales were abundant early in decomposition. Recently downed logs shared 65% of their bacterial abundance with the microbiomes of standing dead trees while only sharing 16% with soil. As decay proceeds, bacterial communities appear to respond less to shifting resource availability and more to interspecific bacterial interactions – we report an increase in both the proportion (+9.3%) and the intensity (+62.3%) of interspecific interactions in later stages of decomposition, suggesting the emergence of a more complex community structure as wood decay progresses.
  • ISME Journal

    Legacy of land use history determines reprogramming of plant physiology by soil microbiome

    Xiogang Li, Alexandre Jousset, Wietse de Boer, Victor Carrion Bravo, Taolin Zhang, Xingxiang Wang, Eiko Kuramae
    Microorganisms associated with roots are thought to be part of the so-called extended plant phenotypes with roles in the acquisition of nutrients, production of growth hormones, and defense against diseases. Since the crops selectively enrich most rhizosphere microbes out of the bulk soil, we hypothesized that changes in the composition of bulk soil communities caused by agricultural management affect the extended plant phenotype. In the current study, we performed shotgun metagenome sequencing of the rhizosphere microbiome of the peanut (Arachis hypogaea) and metatranscriptome analysis of the roots of peanut plants grown in the soil with different management histories, peanut monocropping and crop rotation. We found that the past planting record had a significant effect on the assembly of the microbial community in the peanut rhizosphere, indicating a soil memory effect. Monocropping resulted in a reduction of the rhizosphere microbial diversity, an enrichment of several rare species, and a reduced representation of traits related to plant performance, such as nutrients metabolism and phytohormone biosynthesis. Furthermore, peanut plants in monocropped soil exhibited a significant reduction in growth coinciding with a down-regulation of genes related to hormone production, mainly auxin and cytokinin, and up-regulation of genes related to the abscisic acid, salicylic acid, jasmonic acid, and ethylene pathways. These findings suggest that land use history affects crop rhizosphere microbiomes and plant physiology.
  • Brazilian Journal of Microbiology

    Assessing nickel tolerance of bacteria isolated from serpentine soils

    F. Costa, Maria Wanna Figueiredo Sena Macedo, A. Araujo, Catia Rodrigues, Eiko Kuramae, S. Alcanfor, M. Pessoa-Filho, C. Barreto
    Serpentine soils present unique characteristics such as a low Ca/Mg ratio, low concentration of nutrients, and a high concentration of heavy metals, especially nickel. Soil bacterial isolates from an ultramafic complex located in the tropical savanna known as the Brazilian Cerrado were studied. Nickel-tolerant bacteria were obtained, and their ability to remove nickel from a culture medium was assessed. Bacterial isolates presented higher tolerance to nickel salts than previously reported for bacteria obtained from serpentine environments in other regions of the world. In addition, the quantification of nickel in cell pellets indicated that at least four isolates may adsorb soluble forms of nickel. It is expected that information gathered in this study will support future efforts to exploit serpentine soil bacteria for biotechnological processes involving nickel decontamination from environmental samples.
  • Soil Biology & Biochemistry

    Environmental filtering: A case of bacterial community assembly in soil

    Yan Yan, Peter G.L. Klinkhamer, Hans van Veen, Eiko Kuramae
    Soil has a strong effect on the assembly of bacterial communities, as revealed by studies in which sterilized soil is inoculated with dilution series of bacterial suspensions from the same soil. However, the impact of soil on the assembly of bacterial communities after inoculation with suspensions from different soils is not clear. Here, we explored environmental filtering of bacterial community assembly. Diluted suspensions from different soils harboring different bacterial diversities were used to cross-inoculate three pre-sterilized soils. The main differences in the abiotic factors of the soils were organic matter, ammonium, nitrate, and phosphorus content, pH and the C:N ratio. We used 16S rRNA gene amplicon sequencing to determine the bacterial community structure of the suspensions and the soils. When the different diluted suspensions were used to inoculate their native soils, the regrown soil bacterial communities clustered together; by contrast, the communities were separated when the same suspensions were used to inoculate soils other than their native soils. The diversity indices of the suspensions decreased significantly upon dilution. The strength of selection of bacterial communities by soil was stronger for the 10−1 diluted soil samples than for the 10−9 diluted soil samples. Thus, differences in abiotic factors shape and explain the variation in bacterial community assemblage among these soils.
  • Science of the Total Environment

    Strategies to mitigate the nitrous oxide emissions from nitrogen fertilizer applied with organic fertilizers in sugarcane

    Késia Lourenço, Raffaela Rossetto, A.C. Vitti, Z.F. Montezano, Johnny Soares, R.M. Sousa, J.B. Carmo, Eiko Kuramae, Heitor Cantarella
    Vinasse is a major byproduct of the sugarcane biofuel industry, recycled in the fields. However, there is evidence that the application of vinasse with mineral nitrogen (N) fertilizers in sugarcane enhances the emission of greenhouse gases (GHGs). Therefore, strategies are needed to decrease the environmental impacts caused by both inputs. We carried out three sugarcane field experiments by applying N fertilizer (ammonium nitrate) with types of vinasses (concentrated-CV and standard-V) in different combinations (vinasses with N fertilizer and vinasses one month before or after mineral N fertilization). The gases nitrous oxide (N2O), carbon dioxide (CO2), and methane (CH4) were measured in one experiment fertilized in the beginning (fall/winter = dry season) and two experiments fertilized in the end (spring = rainy season) of the harvest season. Sugarcane fields were sinks rather than sources of CH4, while total carbon emitted as CO2 was similar between seasons and treatments. The effect of mineral fertilization and vinasses (CV and V) on N2O emissions was highly dependent on soil moisture (rain events). The N2O-N fertilizer emission factor (EF) varied from 0.07% to 0.51%, whereas the average EF of V and CV were 0.66% and 0.34%, respectively. On average across the three experiments, the combination of vinasse (CV or V) with N fertilizer increased the N2O emissions 2.9-fold compared to that of N fertilizer alone. For CV + N, the EF was 0.94% of the applied N and 0.23% of the ammonium nitrate-N, and for V + N (EF = 0.47%), increased emissions were observed in two out of three experiments. The strategy of anticipating or postponing vinasse application by one month with respect to mineral N reduced the N2O emissions by 51% for CV, but not for V. Therefore, to avoid boosting N2O emissions, we suggest applying vinasses (CV and V) before or after mineral N fertilization.
  • Science of the Total Environment

    Organic amendment strengthens interkingdom associations in the soil and rhizosphere of barley (Hordeum vulgare)

    Afnan Suleiman, Paula Harkes, Sven J.J. van den Elsen, M. Holterman, Gerard Korthals, J. Helder, Eiko Kuramae
    Anthropogenic modification of soil systems has diverse impacts on food web interactions and ecosystem functioning. To understand the positive, neutral or adverse effects of agricultural practices on the associations of community members of soil microbes and microfaunal biomes, we characterized the effects of different fertilization types (organic, inorganic and a combination of organic and inorganic) on the food web active communities in the bulk soil and rhizosphere compartments in field conditions. We examined the influence of fertilization on (i) individual groups (bacteria, protozoa and fungi as microbe representatives and metazoans as microfauna representatives) and (ii) inter-kingdom interactions (focusing on the interactions between bacteria and eukaryotic groups) both neglecting and considering environmental factors in our analysis in combination with the microbial compositional data. Our results revealed different patterns of biota communities under organic versus inorganic fertilization, which shaped food web associations in both the bulk and rhizosphere compartments. Overall, organic fertilization increased the complexity of microbial–microfaunal ecological associations with inter- and intra- connections among categories of primary decomposers (bacteria and fungi) and predators (protozoa and microfauna) and differences in potential function in the soil food web in both the bulk and rhizosphere compartments. Furthermore, the inter-connections between primary decomposers and predators in bulk soil were more pronounced when environmental factors were considered. We suggest that organic fertilization selects bacterial orders with different potential ecological functions and interactions as survival, predation and cooperation due to more complex environment than those of inorganic or combined fertilization. Our findings support the importance of a comprehensive understanding of trophic food web patterns for soil management systems.
  • Microbial Ecology

    Moisture is more important than Temperature for Assembly of Both Potentially Active and Whole Prokaryotic Communities in Subtropical Grassland

    Manoeli Lupatini, Afnan Suleiman, Rodrigo Jacques, Victor Satler Pylro, Hans van Veen, Eiko Kuramae, Luiz Roesch
    Moisture and temperature play important roles in the assembly and functioning of prokaryotic communities in soil. However, how moisture and temperature regulate the function of niche- versus neutral-based processes during the assembly of these communities has not been examined considering both the total microbial community and the sole active portion with potential for growth in native subtropical grassland. We set up a well-controlled microcosm-based experiment to investigate the individual and combined effects of moisture and temperature on soil prokaryotic communities by simulating subtropical seasons in grassland. The prokaryotic populations with potential for growth and the total prokaryotic community were assessed by 16S rRNA transcript and 16S rRNA gene analyses, respectively. Moisture was the major factor influencing community diversity and structure, with a considerable effect of this factor on the total community. The prokaryotic populations with potential for growth and the total communities were influenced by the same assembly rules, with the niche-based mechanism being more influential in communities under dry condition. Our results provide new information regarding moisture and temperature in microbial communities of soil and elucidate how coexisting prokaryotic populations, under different physiological statuses, are shaped in native subtropical grassland soil.
  • Nature Communications

    Fungal-bacterial diversity and microbiome complexity predict ecosystem functioning

    Cameron Wagg, Klaus Schlaeppi, S. Banerjee, Eiko Kuramae, Marcel G. A. van der Heijden
  • 2019


    Eiko Kuramae, Ohana Costa
    16S rRNA gene sequence surveys and environmental shotgun metagenomic analyses have revealed that Acidobacteria are a highly diverse phylum residing in a wide range of habitats around the globe. Despite this high abundance and diversity, information on their physiology and ecological function remains scarce, mainly due to the low number of cultured Acidobacteria representatives and their slow growth in vitro under standard laboratory conditions. Here, we summarize the characteristics of the Acidobacteria subdivisions that have been described, methods of Acidobacteria isolation, and genomic and metagenomic features of Acidobacteria, including the presence of phage and mobile elements, carbon, nitrogen and sulphur metabolism, exopolysaccharide production, and the roles of Acidobacteria in soil ecosystems.
  • PeerJ

    Bacterial community composition and diversity of two different forms of an organic residue of bioenergy crop

    M.A.P. Cipriano, Afnan Suleiman, A.P.D. da Silveira, J.B. Carmo, Eiko Kuramae
    The use of residue of sugarcane ethanol industry named vinasse in fertirrigation is an established and widespread practice in Brazil. Both non-concentrated vinasse (NCV) and concentrated vinasse (CV) are used in fertirrigation, particularly to replace the potassium fertilizer. Although studies on the chemical and organic composition of vinasse and their impact on nitrous oxide emissions when applied in soil have been carried out, no studies have evaluated the microbial community composition and diversity in different forms of vinasse. We assessed the bacterial community composition of NCV and CV by non-culturable and culturable approaches. The non-culturable bacterial community was assessed by next generation sequencing of the 16S rRNA gene and culturable community by isolation of bacterial strains and molecular and biochemical characterization. Additionally, we assessed in the bacterial strains the presence of genes of nitrogen cycle nitrification and denitrification pathways. The microbial community based on 16S rRNA sequences of NCV was overrepresented by Bacilli and Negativicutes while CV was mainly represented by Bacilli class. The isolated strains from the two types of vinasse belong to class Bacilli, similar to Lysinibacillus, encode for nirK gene related to denitrification pathway. This study highlights the bacterial microbial composition particularly in CV what residue is currently recycled and recommended as a sustainable practice in sugarcane cultivation in the tropics.
  • Scientific Reports

    Conventional &amp; organic soil management as divergent drivers of resident and active fractions of major soil food web constituents

    Paula Harkes, Afnan Suleiman, Sven J.J. van den Elsen, J. De Haan, M. Holterman, Eiko Kuramae, J. Helder
    Conventional agricultural production systems, typified by large inputs of mineral fertilizers and pesticides, reduce soil biodiversity and may negatively affect ecosystem services such as carbon fixation, nutrient cycling and disease suppressiveness. Organic soil management is thought to contribute to a more diverse and stable soil food web, but data detailing this effect are sparse and fragmented. We set out to map both the resident (rDNA) and the active (rRNA) fractions of bacterial, fungal, protozoan and metazoan communities under various soil management regimes in two distinct soil types with barley as the main crop. Contrasts between resident and active communities explained 22%, 14%, 21% and 25% of the variance within the bacterial, fungal, protozoan, and metazoan communities. As the active fractions of organismal groups define the actual ecological functioning of soils, our findings underline the relevance of characterizing both resident and active pools. All four major organismal groups were affected by soil management (p < 0.01), and most taxa showed both an increased presence and an enlarged activity under the organic regime. Hence, a prolonged organic soil management not only impacts the primary decomposers, bacteria and fungi, but also major representatives of the next trophic level, protists and metazoa.
  • Science of the Total Environment

    Long-term farming systems modulate multi-trophic responses

    Manoeli Lupatini, Gerard Korthals, Luiz Roesch, Eiko Kuramae
    Soil microbiome and multi-trophic relationships are essential for the stability and functioning of agroecosystems. However, little is known about how farming systems and alternative methods for controlling plant pathogens modulate microbial communities, soil mesofauna and plant productivity. In this study, we assessed the composition of eukaryotic microbial groups using a high-throughput sequencing approach (18S rRNA gene marker), the populations of parasitic and free-living nematodes, plant productivity and their inter-relationships in long-term conventional and organic farming systems. The diversity of the fungal community increased in the organic farming system compared to the conventional farming system, whereas the diversity of the protist community was similar between the two farming systems. Compared to conventional farming, organic farming increased the population of free-living nematodes and suppressed plant parasitic nematodes belonging to Meloidogynidae and Pratylenchidae. Fungal diversity and community structure appeared to be related to nematode suppression in the system receiving organic fertilizer, which was characterized by component microbial groups known to be involved in the suppression of soil pathogens. Unraveling the microbiome and multi-trophic interactions in different farming systems may permit the management of the soil environment toward more sustainable control of plant pathogens.
  • Frontiers in Microbiology

    Microbial extracellular polymeric substances – ecological functions and impact on soil aggregation

    A wide range of microorganisms produce extracellular polymeric substances (EPS), highly hydrated polymers that are mainly composed of polysaccharides, proteins and DNA. EPS are fundamental for microbial life and provide an ideal environment for chemical reactions, nutrient entrapment and protection against environmental stresses such as salinity and drought. Microbial EPS can enhance the aggregation of soil particles and benefit plants by maintaining the moisture of the environment and trapping nutrients. In addition, EPS have unique characteristics, such as biocompatibility, gelling and thickening capabilities, with industrial applications. However, despite decades of research on the industrial potential of EPS, only a few polymers are widely used in different areas, especially in agriculture. This review provides an overview of current knowledge on the ecological functions of microbial extracellular polymeric substances (EPS) and their application in agricultural soils to improve soil particle aggregation, an important factor for soil structure, health and fertility.
  • Microbial Ecology

    Co-variation of bacterial and fungal communities in different sorghum cultivars and growth stages is soil dependent

    Thiago Schlemper, Hans van Veen, Eiko Kuramae
    Rhizosphere microbial community composition can be influenced by different biotic and abiotic factors. We investigated the composition and co-variation of rhizosphere bacterial and fungal communities from two sorghum genotypes (BRS330 and SRN-39) in three different plant growth stages (emergence of the second leaf, (day10), vegetative to reproductive differentiation point (day 35), and at the last visible emerged leaf (day 50)) in two different soil types, Clue field (CF) and Vredepeel (VD). We observed that either bacterial or fungal community had its composition stronger influenced by soil followed by plant growth stage and cultivar. However, the influence of plant growth stage was higher on fungal community composition than on the bacterial community composition. Furthermore, we showed that sorghum rhizosphere bacterial and fungal communities can affect each other’s composition and structure. The decrease in relative abundance of the fungus genus Gibberella over plant growth stages was followed by decrease of the bacterial families Oxalobacteracea and Sphingobacteriacea. Although cultivar effect was not the major responsible for bacterial and fungal community composition, cultivar SRN-39 showed to promote a stronger co-variance between bacterial and fungal communities.
  • Frontiers in Microbiology

    Nitrosospira sp. govern nitrous oxide emissions in a tropical soil amended with residues of bioenergy crop

    Késia Lourenço, Noriko Cassman, Agata Pijl, Hans van Veen, Heitor Cantarella, Eiko Kuramae
    Organic vinasse, a residue produced during bioethanol production, increases nitrous oxide (N2O) emissions when applied with inorganic nitrogen (N) fertilizer in soil. The present study investigated the role of the ammonia-oxidizing bacteria (AOB) community on the N2O emissions in soils amended with organic vinasse (CV: concentrated and V: non-concentrated) plus inorganic N fertilizer. Soil samples and N2O emissions were evaluated at 11, 19, and 45 days after fertilizer application, and the bacterial and archaea gene (amoA) encoding the ammonia monooxygenase enzyme, bacterial denitrifier (nirK, nirS, and nosZ) genes and total bacteria were quantified by real time PCR. We also employed a deep amoA amplicon sequencing approach to evaluate the effect of treatment on the community structure and diversity of the soil AOB community. Both vinasse types applied with inorganic N application increased the total N2O emissions and the abundance of AOB. Nitrosospira sp. was the dominant AOB in the soil and was correlated with N2O emissions. However, the diversity and the community structure of AOB did not change with vinasse and inorganic N fertilizer amendment. The results highlight the importance of residues and fertilizer management in sustainable agriculture and can be used as a reference and an input tool to determine good management practices for organic fertilization.
  • PeerJ

    Effect of Burkholderia tropica and Herbaspirillum frisingense strains on sorghum growth is plant genotype dependent

    Thiago Schlemper, Mauricio Rocha Dimitrov, Frederico Silva Gutierrez, Hans van Veen, A.P.D. da Silveira, Eiko Kuramae
    Sorghum is a multipurpose crop that is cultivated worldwide. Plant growth-promoting bacteria (PGPB) have important roles in enhancing sorghum biomass and nutrient uptake and suppressing plant pathogens. The aim of this research was to test the effects of the endophytic bacterial species Kosakonia radicincitans strain IAC/BECa 99, Enterobacter asburiae strain IAC/BECa 128, Pseudomonas fluorescens strain IAC/BECa 141, Burkholderia tropica strain IAC/BECa 135 and Herbaspirillum frisingense strain IAC/BECa 152 on the growth and root architecture of four sorghum cultivars (SRN-39, Shanqui-Red, BRS330, BRS509), with different uses and strigolactone profiles. We hypothesized that the different bacterial species would trigger different growth plant responses in different sorghum cultivars. Burkholderia tropica and H. frisingense significantly increased the plant biomass of cultivars SRN-39 and BRS330. Moreover, cultivar BRS330 inoculated with either strain displayed isolates significant decrease in average root diameter. This study shows that Burkholderia tropica strain IAC/BECa 135 and H. frisingense strain IAC/BECa 152 are promising PGPB strains for use as inocula for sustainable sorghum cultivation.
  • Science of the Total Environment

    Recycling organic residues in agriculture impacts soil-borne microbial community structure, function and N2O emissions.

    Afnan Suleiman, Késia Lourenço, Leonardo Pitombo, L.W. Mendes, Luiz Roesch, Agata Pijl, J.B. do Carmo, Heitor Cantarella, Eiko Kuramae
    Recycling residues is a sustainable alternative to improve soil structure and increase the stock of nutrients. However, information about the magnitude and duration of disturbances caused by crop and industrial wastes on soil microbial community structure and function is still scarce. The objective of this study was to investigate how added residues from industry and crops together with nitrogen (N) fertiliser affect the microbial community structure and function, and nitrous oxide (N2O) emissions. The experimental sugarcane field had the following treatments: (I) control with nitrogen, phosphorus, and potassium (NPK), (II) sugarcane straw with NPK, (III) vinasse (by-product of ethanol industry) with NP, and (IV) vinasse plus sugarcane straw with NP. Soil samples were collected on days 1, 3, 6, 11, 24 and 46 of the experiment for DNA extraction and metagenome sequencing. N2O emissions were also measured. Treatments with straw and vinasse residues induced changes in soil microbial composition and potential functions. The change in the microbial community was highest in the treatments with straw addition with functions related to decomposition of different ranges of C-compounds overrepresented while in vinasse treatment, the functions related to spore-producing microorganisms were overrepresented. Furthermore, all additional residues increased microorganisms related to the nitrogen metabolism and vinasse with straw had a synergetic effect on the highest N2O emissions. The results highlight the importance of residues and fertiliser management in sustainable agriculture.
  • FEMS Microbiology Ecology

    Native bacteria promote plant growth under drought stress condition without impacting the rhizomicrobiome

    E. Armada, Marcio Fernandes Alves Leite, Maria Almudena Medina Penafiel, R. Azcón, Eiko Kuramae
    Inoculation of plants with beneficial plant growth-promoting bacteria (PGPB) emerges a valuable strategy for ecosystem recovery. However, drought conditions might compromise plant-microbe interactions especially in semiarid regions. This study highlights the effect of native PGPB after one-year inoculation on autochthonous shrubs growth and rhizosphere microbial community composition and activity under drought stress conditions. We inoculated three plant species of semiarid Mediterranean zones, Thymus vulgaris, Santolina chamaecyparissus and Lavandula dentata with a Bacillus thuringiensis strain IAM 12077 and, evaluated the impact on plant biomass, plant nutrient contents, arbuscular mycorrhiza fungi (AMF) colonization, soil rhizosphere microbial activity, and both the bacterial and fungal communities. Inoculation with strain IAM 12077 improved the ability of all three plants species to uptake nutrients from the soil, promoted L. dentata shoot growth (>65.8%), and doubled the AMF root colonization of S. chamaecyparissus. Inoculation did not change the rhizosphere microbial community. Moreover, changes in rhizosphere microbial activity were mainly plant species-specific and strongly associated with plant nutrients. In conclusion, the strain IAM 12077 induced positive effects on plant growth and nutrient acquisition with no impact on the rhizosphere microbiome, indicating a rhizosphere microbial community resilient to native bacteria inoculation.
  • Microbiome

    Resilience of the resident soil microbiome to organic and inorganic amendment disturbances and to temporary bacterial invasion

    Késia Lourenço, Afnan Suleiman, Agata Pijl, Hans van Veen, Heitor Cantarella, Eiko Kuramae
    Vinasse, a by-product of sugarcane ethanol production, is recycled by sugarcane plantations as a fertilizer due to its rich nutrient content. However, the impacts of the chemical and microbial composition of vinasse on soil microbiome dynamics are unknown. Here, we evaluate the recovery of the native soil microbiome after multiple disturbances caused by the application of organic vinasse residue, inorganic nitrogen, or a combination of both during the sugarcane crop-growing season (389 days). Additionally, we evaluated the resistance of the resident soil microbial community to the vinasse microbiome.

    Vinasse applied alone or 30 days prior to N resulted in similar changes in the soil microbial community. Furthermore, the impact of the application of vinasse together with N fertilizer on the soil microbial community differed from that of N fertilizer alone. Organic vinasse is a source of microbes, nutrients, and organic matter, and the combination of these factors drove the changes in the resident soil microbial community. However, these changes were restricted to a short period of time due to the capacity of the soil community to recover. The invasive bacteria present in the vinasse microbiome were unable to survive in the soil conditions and disappeared after 31 days, with the exception of the Acetobacteraceae (native in the soil) and Lactobacillaceae families.

    Our analysis showed that the resident soil microbial community was not resistant to vinasse and inorganic N application but was highly resilient.
  • Biotechnology for Biofuels

    Genome-resolved metagenomics of sugarcane vinasse bacteria

    Noriko Cassman, Késia Lourenço, Janaina Braga do Carmo, Heitor Cantarella, Eiko Kuramae
    The production of 1 L of ethanol from sugarcane generates up to 12 L of vinasse, which is a liquid waste containing an as-yet uncharacterized microbial assemblage. Most vinasse is destined for use as a fertilizer on the sugarcane fields because of the high organic and K content; however, increased N2O emissions have been observed when vinasse is co-applied with inorganic N fertilizers. Here we aimed to characterize the microbial assemblage of vinasse to determine the gene potential of vinasse microbes for contributing to negative environmental effects during fertirrigation and/or to the obstruction of bioethanol fermentation.

    We measured chemical characteristics and extracted total DNA from six vinasse batches taken over 1.5 years from a bioethanol and sugar mill in Sao Paulo State. The vinasse microbial assemblage was characterized by low alpha diversity with 5–15 species across the six vinasses. The core genus was Lactobacillus. The top six represented bacterial genera across the samples were Lactobacillus, Megasphaera and Mitsuokella (Phylum Firmicutes, 35–97% of sample reads); Arcobacter and Alcaligenes (Phylum Proteobacteria, 0–40%); Dysgonomonas (Phylum Bacteroidetes, 0–53%); and Bifidobacterium (Phylum Actinobacteria, 0–18%). Potential genes for denitrification but not nitrification were identified in the vinasse metagenomes, with putative nirK and nosZ genes the most represented. Binning resulted in 38 large bins with between 36.0 and 99.3% completeness, and five small mobile element bins. Of the large bins, 53% could be classified at the phylum level as Firmicutes, 15% as Proteobacteria, 13% as unknown phyla, 13% as Bacteroidetes and 6% as Actinobacteria. The large bins spanned a range of potential denitrifiers; moreover, the genetic repertoires of all the large bins included the presence of genes involved in acetate, CO2, ethanol, H2O2, and lactose metabolism; for many of the large bins, genes related to the metabolism of mannitol, xylose, butyric acid, cellulose, sucrose, “3-hydroxy” fatty acids and antibiotic resistance were present based on the annotations. In total, 21 vinasse bacterial draft genomes were submitted to the genome repository.

    Identification of the gene repertoires of vinasse bacteria and assemblages supported the idea that organic carbon and nitrogen present in vinasse together with microbiological variation of vinasse might lead to varying patterns of N2O emissions during fertirrigation. Furthermore, we uncovered draft genomes of novel strains of known bioethanol contaminants, as well as draft genomes unknown at the phylum level. This study will aid efforts to improve bioethanol production efficiency and sugarcane agriculture sustainability.
  • Frontiers in Microbiology

    Comparative Genomics of Smut Pathogens: Insights From Orphans and Positively Selected Genes Into Host Specialization

    J. Benevenuto, N.S. Texeira-Silva, Eiko Kuramae, D. Croll, C.B.M. Vitorello
    Host specialization is a key evolutionary process for the diversification and emergence of new pathogens. However, the molecular determinants of host range are poorly understood. Smut fungi are biotrophic pathogens that have distinct and narrow host ranges based on largely unknown genetic determinants. Hence, we aimed to expand comparative genomics analyses of smut fungi by including more species infecting different hosts and to define orphans and positively selected genes to gain further insights into the genetics basis of host specialization. We analyzed nine lineages of smut fungi isolated from eight crop and non-crop hosts: maize, barley, sugarcane, wheat, oats, Zizania latifolia (Manchurian rice), Echinochloa colona (a wild grass), and Persicaria sp. (a wild dicot plant). We assembled two new genomes: Ustilago hordei (strain Uhor01) isolated from oats and U. tritici (strain CBS 119.19) isolated from wheat. The smut genomes were of small sizes, ranging from 18.38 to 24.63 Mb. U. hordei species experienced genome expansions due to the proliferation of transposable elements and the amount of these elements varied among the two strains. Phylogenetic analysis confirmed that Ustilago is not a monophyletic genus and, furthermore, detected misclassification of the U. tritici specimen. The comparison between smut pathogens of crop and non-crop hosts did not reveal distinct signatures, suggesting that host domestication did not play a dominant role in shaping the evolution of smuts. We found that host specialization in smut fungi likely has a complex genetic basis: different functional categories were enriched in orphans and lineage-specific selected genes. The diversification and gain/loss of effector genes are probably the most important determinants of host specificity.
  • GCB Bioenergy

    Dominance of bacterial ammonium oxidizers and fungal denitrifiers in the complex nitrogen cycle pathways related to nitrous oxide emission

    Késia Lourenço, Mauricio Rocha Dimitrov, Agata Pijl, Johnny Soares, J.B. do Carmo, Hans van Veen, Heitor Cantarella, Eiko Kuramae
    Organic compounds and mineral nitrogen (N) usually increase nitrous oxide (N2O) emissions. Vinasse, a by‐product of bio‐ethanol production that is rich in carbon, nitrogen, and potassium, is recycled in sugarcane fields as a bio‐fertilizer. Vinasse can contribute significantly to N2O emissions when applied with N in sugarcane plantations, a common practice. However, the biological processes involved in N2O emissions under this management practice are unknown. This study investigated the roles of nitrification and denitrification in N2O emissions from straw‐covered soils amended with different vinasses (CV: concentrated and V: nonconcentrated) before or at the same time as mineral fertilizers at different time points of the sugarcane cycle in two seasons. N2O emissions were evaluated for 90 days, the period that occurs most of the N2O emission from fertilizers; the microbial genes encoding enzymes involved in N2O production (archaeal and bacterial amoA, fungal and bacterial nirK, and bacterial nirS and nosZ), total bacteria, and total fungi were quantified by real‐time PCR. The application of CV and V in conjunction with mineral N resulted in higher N2O emissions than the application of N fertilizer alone. The strategy of vinasse application 30 days before mineral N reduced N2O emissions by 65% for CV, but not for V. Independent of rainy or dry season, the microbial processes were nitrification by ammonia‐oxidizing bacteria (AOB) and archaea and denitrification by bacteria and fungi. The contributions of each process differed and depended on soil moisture, soil pH, and N sources. We concluded that amoA‐AOB was the most important gene related to N2O emissions, which indicates that nitrification by AOB is the main microbial‐driven process linked to N2O emissions in tropical soil. Interestingly, fungal nirK was also significantly correlated with N2O emissions, suggesting that denitrification by fungi contributes to N2O emission in soils receiving straw and vinasse application.

    Citing Literature
  • Frontiers in Microbiology

    Soil microbiome is more heterogeneous in organic than in conventional farming system

    Manoeli Lupatini, Gerard Korthals, Mattias De Hollander, Thierry K.S. Janssens, Eiko Kuramae
    Organic farming system and sustainable management of soil pathogens aim at reducing the use of agricultural chemicals in order to improve ecosystem health. Despite the essential role of microbial communities in agro-ecosystems, we still have limited understanding of the complex response of microbial diversity and composition to organic and conventional farming systems and to alternative methods for controlling plant pathogens. In this study we assessed the microbial community structure, diversity and richness using 16S rRNA gene next generation sequences and report that conventional and organic farming systems had major influence on soil microbial diversity and community composition while the effects of the soil health treatments (sustainable alternatives for chemical control) in both farming systems were of smaller magnitude. Organically managed system increased taxonomic and phylogenetic richness, diversity and heterogeneity of the soil microbiota when compared with conventional farming system. The composition of microbial communities, but not the diversity nor heterogeneity, were altered by soil health treatments. Soil health treatments exhibited an overrepresentation of specific microbial taxa which are known to be involved in soil suppressiveness to pathogens (plant-parasitic nematodes and soil-borne fungi). Our results provide a comprehensive survey on the response of microbial communities to different agricultural systems and to soil treatments for controlling plant pathogens and give novel insights to improve the sustainability of agro-ecosystems by means of beneficial microorganisms.
  • Pedosphere

    Amazonian Dark Earth and its Black Carbon Particles Harbor Different Fungal Abundance and Diversity

    Adriano Reis Lucheta, F.S. Souza Cannavan, S.M. Tsai, Eiko Kuramae
    Amazonian Dark Earth (ADE) is a highly fertile soil of anthropogenic origin characterized by higher amount of charred black carbon (BC). ADE is considered a fertility model, however knowledge about the fungal community structure and diversity inhabiting ADE and BC is scarce. Fungal community structure and diversity of ADE and BC from four sites under different land use (three agricultural systems and a secondary pristine forest) in the Brazilian Central Amazon was evaluated by 18S rRNA gene pyrosequencing. Fungal communities in ADE and BC were dissimilar and showed differential abundances of fungal Operational Taxonomic Units (OTUs). Estimated fungal species richness (ACE and Chao-1) and diversity (Shannon and Simpson's reciprocal) indices were higher in ADE than BC in all agricultural areas. No differences were observed in the same estimators in ADE and BC samples under secondary forest. Pezizomycotina fungi, and OTUs assigned to Cordyceps confragosa, Acremonium vitellinum, Camarops microspora and Hirsutella rhossiliensis were more abundant in BC particles than in ADE. This study is a breakthrough in understanding the fungal communities in BC particles from ADE and can also be valuable in future studies considering biochar application in soil.
  • PeerJ

    Successive DNA extractions improve characterization of soil microbial communities

    Mauricio Rocha Dimitrov, Annelies Veraart, Mattias De Hollander, H. Smidt, Hans van Veen, Eiko Kuramae
    Currently, characterization of soil microbial communities relies heavily on the use of molecular approaches. Independently of the approach used, soil DNA extraction is a crucial step, and success of downstream procedures will depend on how well DNA extraction was performed. Often, studies describing and comparing soil microbial communities are based on a single DNA extraction, which may not lead to a representative recovery of DNA from all organisms present in the soil. The use of successive DNA extractions might improve soil microbial characterization, but the benefit of this approach has only been limitedly studied. To determine whether successive DNA extractions of the same soil sample would lead to different observations in terms of microbial abundance and community composition, we performed three successive extractions, with two widely used commercial kits, on a range of clay and sandy soils. Successive extractions increased DNA yield considerably (1–374%), as well as total bacterial and fungal abundances in most of the soil samples. Analysis of the 16S and 18S ribosomal RNA genes using 454-pyrosequencing, revealed that microbial community composition (taxonomic groups) observed in the successive DNA extractions were similar. However, successive DNA extractions did reveal several additional microbial groups. For some soil samples, shifts in microbial community composition were observed, mainly due to shifts in relative abundance of a number of microbial groups. Our results highlight that performing successive DNA extractions optimize DNA yield, and can lead to a better picture of overall community composition.
  • Scientific Reports

    Characterization of novel Acidobacteria exopolysaccharides with potential industrial and ecological applications

    Anna Kielak, T.C. Castellane, J.C. Campanharo, L.A. Colnago, Ohana Costa, M.L. Corradi da Silva, Hans van Veen, Eliana G.M. Lemos, Eiko Kuramae
    Acidobacteria have been described as one of the most abundant and ubiquitous bacterial phyla in soil.
    However, factors contributing to this ecological success are not well elucidated mainly due to difficulties
    in bacterial isolation. Acidobacteria may be able to survive for long periods in soil due to protection
    provided by secreted extracellular polymeric substances that include exopolysaccharides (EPSs).
    Here we present the first study to characterize EPSs derived from two strains of Acidobacteria from
    subdivision 1 belonging to Granulicella sp. EPS are unique heteropolysaccharides containing mannose,
    glucose, galactose and xylose as major components, and are modified with carboxyl and methoxyl
    functional groups that we characterized by Fourier transform infrared (FTIR) spectroscopy. Both
    EPS compounds we identified can efficiently emulsify various oils (sunflower seed, diesel, and liquid
    paraffin) and hydrocarbons (toluene and hexane). Moreover, the emulsions are more thermostable over
    time than those of commercialized xanthan. Acidobacterial EPS can now be explored as a source of
    biopolymers that may be attractive and valuable for industrial applications due to their natural origin,
    sustainability, biodegradability and low toxicity.
  • FEMS Microbiology Ecology

    Rhizobacterial community structure differences among sorghum cultivars in different growth stages and soils

    Thiago Schlemper, Marcio Fernandes Alves Leite, Adriano Reis Lucheta, M. Shimels, Harro J. Bouwmeester, Hans van Veen, Eiko Kuramae
    Plant genotype selects the rhizosphere microbiome. The success of plant–microbe interactions is dependent on factors that directly or indirectly influence the plant rhizosphere microbial composition. We investigated the rhizosphere bacterial community composition of seven different sorghum cultivars in two different soil types (abandoned (CF) and agricultural (VD)). The rhizosphere bacterial community was evaluated at four different plant growth stages: emergence of the second (day 10) and third leaves (day 20), the transition between the vegetative and reproductive stages (day 35), and the emergence of the last visible leaf (day 50). At early stages (days 10 and 20), the sorghum rhizosphere bacterial community composition was mainly driven by soil type, whereas at late stages (days 35 and 50), the bacterial community composition was also affected by the sorghum genotype. Although this effect of sorghum genotype was small, different sorghum cultivars assembled significantly different bacterial community compositions. In CF soil, the striga-resistant cultivar had significantly higher relative abundances of Acidobacteria GP1, Burkholderia, Cupriavidus (Burkholderiaceae), Acidovorax and Albidiferax (Comamonadaceae) than the other six cultivars. This study is the first to simultaneously investigate the contributions of plant genotype, plant growth stage and soil type in shaping sorghum rhizosphere bacterial community composition.
  • Scientific Reports

    Methanogens predominate in natural corrosion protective layers on metal sheet piles.

    Nardy Kip, S. Jansen, Marcio Fernandes Alves Leite, Mattias De Hollander, M. Afanasyev, Eiko Kuramae, Hans van Veen
    Microorganisms are able to cause, but also to inhibit or protect against corrosion. Corrosion inhibition by microbial processes may be due to the formation of mineral deposition layers on metal objects. Such deposition layers have been found in archaeological studies on ancient metal objects, buried in soil, which were hardly corroded. Recent field investigations showed that natural mineral deposition layers can be found on sheet piles in soil. We investigated the microbial communities of these deposition layers and the adjacent soil. Our data, from five different sampling sites, all show striking differences between microbial communities of the deposition layer versus the adjacent soil over the depth profile. Bacterial species dominated in top soil while archaeal sequences increased in abundance with depth. All mineral deposition layers from the steel surface were dominated by Euryarchaeota, of which almost all sequences were phylogenetically related with the Methanobacteria genus. The mineral layer consisted of carbonate precipitates. Based on 16S rDNA gene sequencing data we hypothesize that the methanogens directly extract electrons from the metal surface, thereby, initially inducing mild corrosion, but simultaneously, inducing carbonate precipitation. This, will cause encrustation of the archaea, which drastically slow down their activity and create a natural protective layer against further corrosion.
  • Scientific Reports

    Organic nitrogen rearranges both structure and activity of the soil-borne microbial seedbank

    Marcio Fernandes Alves Leite, Yao Pan, J. Bloem, Hein F.M. ten Berge, Eiko Kuramae
    Use of organic amendments is a valuable strategy for crop production. However, it remains unclear how organic amendments shape both soil microbial community structure and activity, and how these changes impact nutrient mineralization rates. We evaluated the effect of various organic amendments, which range in Carbon/Nitrogen (C/N) ratio and degradability, on the soil microbiome in a mesocosm study at 32, 69 and 132 days. Soil samples were collected to determine community structure (assessed by 16S and 18S rRNA gene sequences), microbial biomass (fungi and bacteria), microbial activity (leucine incorporation and active hyphal length), and carbon and nitrogen mineralization rates. We considered the microbial soil DNA as the microbial seedbank. High C/N ratio favored fungal presence, while low C/N favored dominance of bacterial populations. Our results suggest that organic amendments shape the soil microbial community structure through a feedback mechanism by which microbial activity responds to changing organic inputs and rearranges composition of the microbial seedbank. We hypothesize that the microbial seedbank composition responds to changing organic inputs according to the resistance and resilience of individual species, while changes in microbial activity may result in increases or decreases in availability of various soil nutrients that affect plant nutrient uptake.
  • ISME Journal

    Functional traits dominate the diversity-related selection of bacterial communities in the rhizosphere

    Yan Yan, Eiko Kuramae, Mattias De Hollander, P.G.L. Klinkhamer, Hans van Veen
    We studied the impact of community diversity on the selection of bacterial communities in the rhizosphere by comparing the composition and the functional traits of these communities in soil and rhizosphere. Differences in diversity were established by inoculating into sterilized soils diluted suspensions of the same soil. We used 16S ribosomal RNA amplicon sequencing to determine the taxonomical structure of the bacterial communities and a shotgun metagenomics approach to investigate the potential functional diversity of the communities. By comparing the bacterial communities in soil and rhizosphere, the selective power of the plant was observed both at the taxonomic and functional level, although the diversity indices of soil and rhizosphere samples showed a highly variable, irregular pattern. Lesser variation, that is, more homogenization, was found for both the taxonomic structure and the functional profile of the rhizosphere communities as compared to the communities of the bulk soil. Network analysis revealed stronger interactions among bacterial operational taxonomic units in the rhizosphere than in the soil. The enrichment processes in the rhizosphere selected microbes with particular functional genes related to transporters, the Embden–Meyerhof–Parnas pathway and hydrogen metabolism. This selection was not random across bacteria with these functional traits, but it was species specific. Overall, this suggests that functional traits are a key to the assembly of bacterial rhizosphere communities.
  • FEMS Microbiology Ecology

    Lettuce and rhizosphere microbiome responses to growth promoting Pseudomonas species under field conditions

    M.A.P. Cipriano, Manoeli Lupatini, L. Santos, M. da Silva, Luiz Roesch, S. Destefano, S. Freitas, Eiko Kuramae
    Plant growth promoting rhizobacteria (PGPR) are well described and recommended for several crops worldwide. However, one of the most common problems in PGPR research is the difficulty in obtaining reproducible results. Furthermore, few studies have evaluated plant growth promotion and soil microbial community composition due to bacterial inoculation under field conditions. Here we evaluated the effect of 54 Pseudomonas strains on lettuce (Lactuca sativa) growth. The 12 most promising strains were phylogenetically and physiologically characterized for plant growth-promoting traits including phosphate solubilization, hormone production and antagonism to pathogen compounds and their effect on plant growth under farm field conditions. Additionally, the impact of beneficial strains on the rhizospheric bacterial community was evaluated for inoculated plants. The strains IAC-RBcr4 and IAC-RBru1, with different plant growth promoting traits, improved lettuce plant biomass yields up to 30%. These two strains also impacted rhizosphere bacterial groups including Isosphaera and Pirellula (phylum Planctomycetes) and Acidothermus, Pseudolabrys and Singusphaera (phylum Actinobacteria). This is the first study to demonstrate consistent results for the effects of Pseudomonas strains on lettuce growth promotion for seedlings and plants grown under tropical field conditions.
  • Fungal Biology

    Phylogenetic relationships of Rhizoctonia fungi within the Cantharellales

    D. Gonzalez, M. Rodriguez-Carres, Teun Boekhout, Joost Stalpers, Eiko Kuramae, A.K. Nakatani, Rytas Vilgalys, M.A. Cubeta
    Phylogenetic relationships of Rhizoctonia fungi within the order Cantharellales were studied using sequence data from portions of the ribosomal DNA cluster regions ITS-LSU, rpb2, tef1, and atp6 for 50 taxa, and public sequence data from the rpb2 locus for 165 taxa. Data sets were analysed individually and combined using Maximum Parsimony, Maximum Likelihood, and Bayesian Phylogenetic Inference methods. All analyses supported the monophyly of the family Ceratobasidiaceae, which comprises the genera Ceratobasidium and Thanatephorus. Multi-locus analysis revealed 10 well-supported monophyletic groups that were consistent with previous separation into anastomosis groups based on hyphal fusion criteria. This analysis coupled with analyses of a larger sample of 165 rpb2 sequences of fungi in the Cantharellales supported a sister relationship between the Botryobasidiaceae and Ceratobasidiaceae and a sister relationship of the Tulasnellaceae with the rest of the Cantharellales. The inclusion of additional sequence data did not clarify incongruences observed in previous studies of Rhizoctonia fungi in the Cantharellales based on analyses of a single or multiple genes. The diversity of ecological and morphological characters associated with these fungi requires further investigation on character evolution for re-evaluating homologous and homoplasious characters.
  • Soil Biology & Biochemistry

    Temporal variability of soil microbial communities after application of dicyandiamide-treated swine slurry and mineral fertilizers

    Afnan Suleiman, Rogerio Gonzatto, Celso Aita, Manoeli Lupatini, Rodrigo Jacques, Eiko Kuramae, Zaida Antoniolli, Luiz Roesch
    In modern agriculture, mineral and organic fertilization account for most of the global anthropogenic N2O emissions. A strategy to prevent or to reduce emissions of greenhouse gases such as N2O is the use of nitrification inhibitors, which temporarily inhibit the microbial conversion of soil ammonium to nitrate. However, information about the magnitude and duration of disturbance caused by organic fertilization with nitrification inhibitor on the microbial community is lacking. Here we examined N dynamics and how potentially active soil microbial communities changed through time by the addition of dicyandiamide-treated swine slurry and mineral fertilizers. A field experiment (corn/cereal succession under no-tillage system) was carried out using the following treatments: (I) unfertilized control, (II) surface application of mineral nutrients, (III) surface application of swine slurry, and (IV) surface application of swine slurry with dicyandiamide. Soil samples were collected at 0, 3, 6, 11, 25 and 50 days after start of experiment. Total RNA was extracted, synthesized to cDNA and used as template to amplify and sequence the 16S rRNA. Nitrous oxide emissions were also quantified. The organic fertilizers were the main drivers on changes in microbial community structure. Slurry application decreased microbial diversity and changed the microbial structure temporarily but the metabolically active microbial community was resilient, recovering to the original status 50 days post-fertilization. Dicyandiamide reduced the N2O emissions and did not affect the metabolically active microbial community in the nitrification pathway i.e. no impact on nitrifiers.
  • Scientific Reports

    Nitrous oxide emission related to ammonia-oxidizing bacteria and mitigation options from N fertilization in a tropical soil

    Johnny Soares, Noriko Cassman, Anna Kielak, Agata Pijl, J.B. do Carmo, Késia Lourenço, (Riks) H.J. Laanbroek, Heitor Cantarella, Eiko Kuramae
    Nitrous oxide (N2O) from nitrogen fertilizers applied to sugarcane has high environmental impact on ethanol production. This study aimed to determine the main microbial processes responsible for the N2O emissions from soil fertilized with different N sources, to identify options to mitigate N2O emissions, and to determine the impacts of the N sources on the soil microbiome. In a field experiment, nitrogen was applied as calcium nitrate, urea, urea with dicyandiamide or 3,4 dimethylpyrazone phosphate nitrification inhibitors (NIs), and urea coated with polymer and sulfur (PSCU). Urea caused the highest N2O emissions (1.7% of N applied) and PSCU did not reduce cumulative N2O emissions compared to urea. NIs reduced N2O emissions (95%) compared to urea and had emissions comparable to those of the control (no N). Similarly, calcium nitrate resulted in very low N2O emissions. Interestingly, N2O emissions were significantly correlated only with bacterial amoA, but not with denitrification gene (nirK, nirS, nosZ) abundances, suggesting that ammonia-oxidizing bacteria, via the nitrification pathway, were the main contributors to N2O emissions. Moreover, the treatments had little effect on microbial composition or diversity. We suggest nitrate-based fertilizers or the addition of NIs in NH4+-N based fertilizers as viable options for reducing N2O emissions in tropical soils and lessening the environmental impact of biofuel produced from sugarcane.
  • FEMS Microbiology Letters

    Optimized medium culture for Acidobacteia subdivision 1 strains

    J.C. Campanharo, Anna Kielak, T.C. Castellane, Eiko Kuramae, Eliana G.M. Lemos
    The members of subdivision 1 Acidobacterium were grown at different pH values in a new medium formulation named PSYL 5 includes sucrose, as a carbon source and other compounds (such as KH2PO4 and MgSO4.7H2O). Growth rate was nearly constant at pH 5 and declined at pH 3–4 and 6–7. However, it was found that the effects involving good C/N ratios and pH on the growth of members of subdivision 1 Acidobacterium were significant, and the strongest effect was given by this conditions at pH 5. In additional, incubation results of 48, 72, 96 and 120 h were relatively shorter as compared to other media earlier described for members of subdivision 1 of the phylum Acidobacteria on solid laboratory media.
  • Microbial Ecology

    Fungal community assembly in the Amazonian Dark Earth

    Adriano Reis Lucheta, F.S. Souza Cannavan, Luiz Roesch, S.M. Tsai, Eiko Kuramae
    Here, we compare the fungal community composition and diversity in Amazonian Dark Earth (ADE) and the respective non-anthropogenic origin adjacent (ADJ) soils from four different sites in Brazilian Central Amazon using pyrosequencing of 18S ribosomal RNA (rRNA) gene. Fungal community composition in ADE soils were more similar to each other than their ADJ soils, except for only one site. Phosphorus and aluminum saturation were the main soil chemical factors contributing to ADE and ADJ fungal community dissimilarities. Differences in fungal richness were not observed between ADE and ADJ soil pairs regarding to the most sites. In general, the most dominant subphyla present in the soils were Pezizomycotina, Agaricomycotina, and Mortierellomycotina. The most abundant operational taxonomic units (OTUs) in ADE showed similarities with the entomopathogenic fungus Cordyceps confragosa and the saprobes Fomitopsis pinicola, Acremonium vitellinum, and Mortierellaceae sp., whereas OTUs similar to Aspergillus niger, Lithothelium septemseptatum, Heliocephala gracillis, and Pestalosphaeria sp. were more abundant in ADJ soils. Differences in fungal community composition were associated to soil chemical factors in ADE (P, Ca, Zn, Mg, organic matter, sum of bases, and base saturation) and ADJ (Al, potential acidity, Al saturation, B, and Fe) soils. These results contribute to a deeper view of the fungi communities in ADE and open new perspectives for entomopathogenic fungi studies.
  • Archives of Microbiology

    Acidobacteria strains from subdivision 1 act as plant growth-promoting bacteria

    Anna Kielak, M.A.P. Cipriano, Eiko Kuramae
    Acidobacteria is one of the most abundant phyla in soils and has been detected in rhizosphere mainly based on cultivation-independent approaches such as 16S rRNA gene survey. Although putative interaction of Acidobacteria with plants was suggested, so far no plant–bacterial interactions were shown. Therefore, we performed several in vitro tests to evaluate Acidobacteria–plant interactions and the possible mechanisms involved in such interaction. We observed that Arabidopsis thaliana inoculated with three strains belonging to Acidobacteria subdivision 1 showed increase in biomass of roots and shoots as well as morphological changes in root system. Our results indicate that the plant hormone indole-3-acetic acid production and iron acquisition are plausibly involved in the plant and Acidobacteria interactions. Here, we confirm for the first time that Acidobacteria can actively interact with plants and act as plant growth-promoting bacteria. In addition, we show that Acidobacteria strains produce exopolysaccharide which supports the adhesion of bacteria to the root surfaces.
  • Global Change Biology Bioenergy

    Exploring soil microbial 16S rRNA sequence data to increase carbon yield and nitrogen efficiency of a bioenergy crop

    Leonardo Pitombo, J.B. do Carmo, Mattias De Hollander, R. Rosetto, M.V. Lopez, Heitor Cantarella, Eiko Kuramae
    Crop residues returned to the soil are important for the preservation of soil quality, health, and biodiversity, and they increase agriculture sustainability by recycling nutrients. Sugarcane is a bioenergy crop that produces huge amounts of straw (also known as trash) every year. In addition to straw, the ethanol industry also generates large volumes of vinasse, a liquid residue of ethanol production, which is recycled in sugarcane fields as fertilizer. However, both straw and vinasse have an impact on N2O fluxes from the soil. Nitrous oxide is a greenhouse gas that is a primary concern in biofuel sustainability. Because bacteria and archaea are the main drivers of N redox processes in soil, in this study we propose the identification of taxa related with N2O fluxes by combining functional responses (N2O release) and the abundance of these microorganisms in soil. Using a large-scale in situ experiment with ten treatments, an intensive gas monitoring approach, high-throughput sequencing of soil microbial 16S rRNA gene and powerful statistical methods, we identified microbes related to N2O fluxes in soil with sugarcane crops. In addition to the classical denitrifiers, we identified taxa within the phylum Firmicutes and mostly uncharacterized taxa recently described as important drivers of N2O consumption. Treatments with straw and vinasse also allowed the identification of taxa with potential biotechnological properties that might improve the sustainability of bioethanol by increasing C yields and improving N efficiency in sugarcane fields.
  • Frontiers in Microbiology

    Bacterial community succession in pine-wood decomposition

    Anna Kielak, Tanja Scheublin, L.W. Mendes, Hans van Veen, Eiko Kuramae
    BACKGROUND: Though bacteria and fungi are common inhabitants of decaying wood, little is known about the relationship between bacterial and fungal community dynamics during natural wood decay. Based on previous studies involving inoculated wood blocks, strong fungal selection on bacteria abundance and community composition was expected to occur during natural wood decay. Here we focused on bacterial and fungal community compositions in pine wood samples collected from dead trees in different stages of decomposition. We showed that bacterial communities undergo less drastic changes than fungal communities during wood decay. Furthermore, we found that bacterial community assembly was a stochastic process at initial stage of wood decay and became more deterministic in later stages, likely due to environmental factors. Moreover, composition of bacterial communities did not respond to the changes in the major fungal species present in the wood but rather to the stage of decay reflected by the wood density. We concluded that the shifts in the bacterial communities were a result of the changes in wood properties during decomposition and largely independent of the composition of the wood-decaying fungal communities.
  • Scientific Reports

    Plant and soil fungal but not soil bacterial communities are linked in long-term fertilized grassland.

    Noriko Cassman, Marcio Fernandes Alves Leite, Yao Pan, Mattias De Hollander, Hans van Veen, Eiko Kuramae

    Inorganic fertilization and mowing alter soil factors with subsequent effects–direct and indirect - on above- and below-ground communities. We explored direct and indirect effects of long-term fertilization (N, P, NPK, Liming) and twice yearly mowing on the plant, bacterial and fungal communities and soil factors. We analyzed co-variation using 16S and 18S rRNA genes surveys, and plant frequency and edaphic factors across treatments. The plant and fungal communities were distinct in the NPK and L treatments, while the bacterial communities and soil factors were distinct in the N and L treatments. Plant community diversity and evenness had low diversity in the NPK and high diversity in the liming treatment, while the diversity and evenness of the bacterial and fungal communities did not differ across treatments, except of higher diversity and evenness in the liming treatment for the bacteria. We found significant co-structures between communities based on plant and fungal comparisons but not between plant and bacterial nor bacterial and fungal comparisons. Our results suggested that the plant and fungal communities are more tightly linked than either community with the bacterial community in fertilized soils. We found co-varying plant, bacterial and fungal taxa in different treatments that may indicate ecological interactions.
  • Frontiers in Microbiology

    The ecology of Acidobacteria: moving beyond genes and genomes

    Anna Kielak, C. Barreto, George Kowalchuk, Hans van Veen, Eiko Kuramae
    The phylum Acidobacteria is one of the most widespread and abundant on the planet, yet remarkably our knowledge of the role of these diverse organisms in the functioning of terrestrial ecosystems remains surprisingly rudimentary. This blatant knowledge gap stems to a large degree from the difficulties associated with the cultivation of these bacteria by classical means. Given the phylogenetic breadth of the Acidobacteria, which is similar to the metabolically diverse Proteobacteria, it is clear that detailed and functional descriptions of acidobacterial assemblages are necessary. Fortunately, recent advances are providing a glimpse into the ecology of members of the phylum Acidobacteria. These include novel cultivation and enrichment strategies, genomic characterization and analyses of metagenomic DNA from environmental samples. Here, we couple the data from these complementary approaches for a better understanding of their role in the environment, thereby providing some initial insights into the ecology of this important phylum. All cultured acidobacterial type species are heterotrophic, and members of subdivisions 1, 3, and 4 appear to be more versatile in carbohydrate utilization. Genomic and metagenomic data predict a number of ecologically relevant capabilities for some acidobacteria, including the ability to: use of nitrite as N source, respond to soil macro-, micro nutrients and soil acidity, express multiple active transporters, degrade gellan gum and produce exopolysaccharide (EPS). Although these predicted properties allude to a competitive life style in soil, only very few of these prediction shave been confirmed via physiological studies. The increased availability of genomic and physiological information, coupled to distribution data in field surveys and experiments, should direct future progress in unraveling the ecology of this important but still enigmatic phylum.
  • Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology

    Verrucomicrobial community structure and size as indicators for changes in chemical factors linked to soil fertility

    Acácio A. Navarrete, T. Soares, R. Rosetto, Hans van Veen, S.M. Tsai, Eiko Kuramae
    Here we show that verrucomicrobial community structure and abundance are extremely sensitive to changes in chemical factors linked to soil fertility. Terminal restriction fragment length polymorphism fingerprint and real-time quantitative PCR assay were used to analyze changes in verrucomicrobial communities associated with contrasting soil nutrient conditions in tropical regions. In case study Model I (“Slash-and-burn deforestation”) the verrucomicrobial community structures revealed disparate patterns in nutrient-enriched soils after slash-and-burn deforestation and natural nutrient-poor soils under an adjacent primary forest in the Amazonia (R = 0.819, P = 0.002). The relative proportion of Verrucomicrobia declined in response to increased soil fertility after slash-and-burn deforestation, accounting on average, for 4 and 2 % of the total bacterial signal, in natural nutrient-poor forest soils and nutrient-enriched deforested soils, respectively. In case study Model II (“Management practices for sugarcane”) disparate patterns were revealed in sugarcane rhizosphere sampled on optimal and deficient soil fertility for sugarcane (R = 0.786, P = 0.002). Verrucomicrobial community abundance in sugarcane rhizosphere was negatively correlated with soil fertility, accounting for 2 and 5 % of the total bacterial signal, under optimal and deficient soil fertility conditions for sugarcane, respectively. In nutrient-enriched soils, verrucomicrobial community structures were related to soil factors linked to soil fertility, such as total nitrogen, phosphorus, potassium and sum of bases, i.e., the sum of calcium, magnesium and potassium contents. We conclude that community structure and abundance represent important ecological aspects in soil verrucomicrobial communities for tracking the changes in chemical factors linked to soil fertility under tropical environmental conditions.
  • Microbial Ecology

    Soil-borne microbiome: linking diversity to function

    L.W. Mendes, S.M. Tsai, Acácio A. Navarrete, Mattias De Hollander, Hans van Veen, Eiko Kuramae
    Soil microorganisms are sensitive to environment
    disturbances, and such alterations have consequences on microbial
    diversity and functions. Our hypothesis is that alpha
    diversity of microbial communities and functional diversity
    decrease from undisturbed to disturbed soils, with consequences
    for functional redundancy in the soil ecosystem. To
    test this hypothesis, we used soil DNA shotgun metagenomics
    approach to assess the soil microbiome in a chronosequence
    of land-use from a native tropical forest, followed by deforestation
    and cultivation of soybean croplands and pasture in
    different seasons. Agriculture and pasture soils were among
    the most diverse and presented higher functional redundancy,
    which is important to maintain the ecosystemfunctioning after
    the forest conversion. On the other hand, the ecosystem equilibrium
    in forest is maintained based on a lower alpha diversity
    but higher abundance of microorganisms. Our results
    indicate that land-use change alters the structure and composition
    of microbial communities; however, ecosystem
    functionality is overcome by different strategies based on the
    abundance and diversity of the communities.
  • Molecular Ecology

    Soil microbiome responses to the short-term effects of Amazonian deforestation

    A.A. Navarrete, S.M. Tsai, L.W. Mendes, K. Faust, Mattias De Hollander, Noriko Cassman, Jeroen Raes, Hans van Veen, Eiko Kuramae

    Slash-and-burn clearing of forest typically results in increase in soil nutrient availability.However, the impact of these nutrients on the soil microbiome is not known. Using next generation sequencing of 16S rRNA gene and shotgun metagenomic DNA,we compared the structure and the potential functions of bacterial community in forest soils to deforested  soils in the Amazon region and related the differences to soil chemical factors.
    Deforestation decreased soil organic matter content and factors linked to soil acidity and raised soil pH, base saturation and exchangeable bases. Concomitant to expected changes in soil chemical factors, we observed an increase in the alpha diversity of the bacterial microbiota and relative abundances of putative copiotrophic bacteria such as Actinomycetales and a decrease in the relative abundances of bacterial taxa such as Chlamydiae, Planctomycetes and Verrucomicrobia in the deforested soils. We did not observe an increase in genes related to microbial nutrient metabolism in deforested soils. However,
    we did observe changes in community functions such as increases in DNA repair, protein processing, modification, degradation and folding functions, and these functions might reflect adaptation to changes in soil characteristics due to forest clear-cutting and burning. In addition, there were changes in the composition of the bacterial groups associated with metabolism-related functions. Co-occurrence microbial network analysis identified distinct phylogenetic patterns for forest and deforested soils and suggested relationships between Planctomycetes and aluminium content, and Actinobacteria and nitrogen sources in Amazon soils. The results support taxonomic and functional adaptations in the soil bacterial community following deforestation. We hypothesize that these microbial adaptations may serve as a buffer to drastic changes in soil fertility after slashand-burning deforestation in the Amazon region.

  • Frontiers in Plant Science

    Context dependency and saturating effects of loss of rare soil microbes on plant productivity

    (Gera) W.H.G. Hol, Wietse de Boer, Mattias De Hollander, Eiko Kuramae, Annelein Meisner, Wim H. van der Putten
    Land use intensification is associated with loss of biodiversity and altered ecosystem functioning. Until now most studies on the relationship between biodiversity and ecosystem functioning focused on random loss of species, while loss of rare species that usually are the first to disappear received less attention. Here we test if the effect of rare microbial species loss on plant productivity depends on the origin of the microbial soil community. Soils were sampled from three land use types at two farms. Microbial communities with increasing loss of rare species were created by inoculating sterilized soils with serially diluted soil suspensions. After 8 months of incubation, the effects of the different soil communities on abiotic soil properties, soil processes, microbial community composition, and plant productivity was measured. Dilution treatments resulted in increasing species loss, which was in relation to abundance of bacteria in the original field soil, without affecting most of the other soil parameters and processes. Microbial species loss affected plant biomass positively, negatively or not at all, depending on soil origin, but not on land use history. Even within fields the effects of dilution on plant biomass varied between replicates, suggesting heterogeneity in microbial community composition. The effects of medium and severe species loss on plant biomass were similar, pointing toward a saturating effect of species loss. We conclude that changes in the composition of the soil microbial community, including rare species loss, can affect plant productivity, depending on the composition of the initial microbial community. Future work on the relation between function and species loss effects should address this variation by including multiple sampling origins.
  • Applied and Environmental Microbiology

    Revisiting the dilution procedure used to manipulate microbial biodiversity in terrestrial systems revisited

    Yan Yan, Eiko Kuramae, P.G.L. Klinkhamer, Hans van Veen
    It is hard to assess experimentally the importance of microbial diversity in soil for the functioning of terrestrial ecosystems. An approach that is often used to make such assessment is the so-called dilution method. This method is based on the assumption that the biodiversity of the microbial community is reduced after dilution of a soil suspension and that the reduced diversity persists after incubation of more or less diluted inocula in soil. However, little is known about how the communities develop in soil after inoculation. In this study, serial dilutions of a soil suspension were made and reinoculated into the original soil previously sterilized by gamma irradiation. We determined the structure of the microbial communities in the suspensions and in the inoculated soils using 454-pyrosequencing of 16S rRNA genes. Upon dilution, several diversity indices showed that, indeed, the diversity of the bacterial communities in the suspensions decreased dramatically, with Proteobacteria as the dominant phylum of bacteria detected in all dilutions. The structure of the microbial community was changed considerably in soil, with Proteobacteria, Bacteroidetes, and Verrucomicrobia as the dominant groups in most diluted samples, indicating the importance of soil-related mechanisms operating in the assembly of the communities. We found unique operational taxonomic units (OTUs) even in the highest dilution in both the suspensions and the incubated soil samples. We conclude that the dilution approach reduces the diversity of microbial communities in soil samples but that it does not allow accurate predictions of the community assemblage during incubation of (diluted) suspensions in soil.
  • Ecology

    Non-random species loss in bacterial communities reduces antifungal volatile production

    (Gera) W.H.G. Hol, Paolina Garbeva, Cees Hordijk, M.P.J. Hundscheid, P.J.A. Klein Gunnewiek, Maaike Van Agtmaal, Eiko Kuramae, Wietse de Boer
    The contribution of low-abundance microbial species to soil ecosystems is easily overlooked because there is considerable overlap between metabolic abilities (functional redundancy) of dominant and subordinate microbial species. Here we studied how loss of less abundant soil bacteria affected the production of antifungal volatiles, an important factor in the natural control of soil-borne pathogenic fungi. We provide novel empirical evidence that the loss of soil bacterial species leads to a decline in the production of volatiles that suppress root pathogens. By using dilution-to-extinction for seven different soils we created bacterial communities with a decreasing number of species and grew them under carbon-limited conditions. Communities with high bacterial species richness produced volatiles that strongly reduced the hyphal growth of the pathogen Fusarium oxysporum. For most soil origins loss of bacterial species resulted in loss of antifungal volatile production. Analysis of the volatiles revealed that several known antifungal compounds were only produced in the more diverse bacterial communities. Our results suggest that less abundant bacterial species play an important role in antifungal volatile production by soil bacterial communities and, consequently, in the natural suppression of soil-borne pathogens.

    Read More: http://www.esajournals.org/doi/abs/10.1890/14-2359.1
  • Microbial Ecology

    Amazonian Dark Earth and plant species from the Amazon region contribute to shape rhizosphere bacterial communities

    A. Barbosa Lima, F.S. Souza Cannavan, A.A. Navarrete, Eiko Kuramae, W.G. Teixeira, S.M. Tsai
    Amazonian Dark Earths (ADE) or Terra Preta de Índio formed in the past by pre-Columbian populations are highly sustained fertile soils supported by microbial communities that differ from those extant in adjacent soils. These soils are found in the Amazon region and are considered as a model soil when compared to the surrounding and background soils. The aim of this study was to assess the effects of ADE and its surrounding soil on the rhizosphere bacterial communities of two leguminous plant species that frequently occur in the Amazon region in forest sites (Mimosa debilis) and open areas (Senna alata). Bacterial community structure was evaluated using terminal restriction fragment length polymorphism (T-RFLP) and bacterial community composition by V4 16S rRNA gene region pyrosequencing. T-RFLP analysis showed effect of soil types and plant species on rhizosphere bacterial community structure. Differential abundance of bacterial phyla, such as Acidobacteria, Actinobacteria, Verrucomicrobia, and Firmicutes, revealed that soil type contributes to shape the bacterial communities. Furthermore, bacterial phyla such as Firmicutes and Nitrospira were mostly influenced by plant species. Plant roots influenced several soil chemical properties, especially when plants were grown in ADE. These results showed that differences observed in rhizosphere bacterial community structure and composition can be influenced by plant species and soil fertility due to variation in soil attributes.
  • Applied Soil Ecology

    Land-use system shapes soil bacterial communities in Southeastern Amazon region

    L.W. Mendes, Maria Julia de L. Brossi, Eiko Kuramae, S.M. Tsai
    The expansion of the agriculture has become the main agent of disturbance in the Amazon region, and such alteration has consequences on soil microbial communities, which represent the majority of biodiversity in terrestrial ecosystems. In this study we assessed the effects of land-use changes on physicochemical soil properties and, consequently, on the bacterial communities in soils from Southeastern Amazon, Brazil. Soil samples were collected in four distinct land-use systems, i.e. native forest, deforested area, agricultural and pasture fields. The soil bacterial community abundance, structure and composition were addressed using qPCR, one molecular marker (T-RFLP) and high-throughput sequencing of the bacterial 16S rRNA gene, respectively. Obtained data were analyzed using multivariate techniques. We found that the type of land-use had a primary effect on the soil bacterial communities, whereas parameters such as pH, C, N, NO3− and K content significantly correlated to overall community structures. We observed that the abundance and taxonomic diversity of the bacterial 16S rRNA changed to a higher extent according to the land-use system, but they also showed significant temporal turnover within sites. From the total 27 bacterial phyla identified, 12 presented clearly differential distribution across the four land-use systems. Comparison among all sites revealed Acidobacteria and Chlamydiae to be higher abundant in forest soil, Actinobacteria in deforested site, Nitrospira and Deinococcus-Thermus in agriculture and Firmicutes in pasture. When data of specific phyla were correlated to specific soil properties, we demonstrated that parameters such as Al saturation index, Al, base saturation index, Mg and Ca presented correlation with the most number of bacterial groups detected. Thus, we suggest that several soil parameters besides pH should be taken into account when assessing the impacts of land-use change on the microbial communities.
  • ISME Journal

    Taxonomical and functional microbial community selection in soybean rhizosphere

    L.W. Mendes, Eiko Kuramae, A.A. Navarrete, Hans van Veen, S.M. Tsai
    This study addressed the selection of the rhizospheric microbial community from the bulk soil reservoir under agricultural management of soybean in Amazon forest soils. We used a shotgun metagenomics approach to investigate the taxonomic and functional diversities of microbial communities in the bulk soil and in the rhizosphere of soybean plants and tested the validity of neutral and niche theories to explain the rhizosphere community assembly processes. Our results showed a clear selection at both taxonomic and functional levels operating in the assembly of the soybean rhizosphere community. The taxonomic analysis revealed that the rhizosphere community is a subset of the bulk soil community. Species abundance in rhizosphere fits the log-normal distribution model, which is an indicator of the occurrence of niche-based processes. In addition, the data indicate that the rhizosphere community is selected based on functional cores related to the metabolisms of nitrogen, iron, phosphorus and potassium, which are related to benefits to the plant, such as growth promotion and nutrition. The network analysis including bacterial groups and functions was less complex in rhizosphere, suggesting the specialization of some specific metabolic pathways. We conclude that the assembly of the microbial community in the rhizosphere is based on niche-based processes as a result of the selection power of the plant and other environmental factors.
  • FEMS Microbiology Ecology

    Impact of long term N, P, K and NPK fertilization on the composition and potential functions of bacterial community in grassland soil

    Y Pan, Noriko Cassman, Mattias De Hollander, L.W. Mendes, H Korevaar, R.H.E.M. Geerts, Hans van Veen, Eiko Kuramae
    Soil abiotic and biotic interactions govern important ecosystem processes. However, the mechanisms behind these interactions are complex, and the links between specific environmental factors, microbial community structures, and functions are not well understood. Here, we applied DNA shotgun metagenomic techniques to investigate the effect of inorganic fertilizers N, P, K, and NPK on the bacterial community composition and potential functions in grassland soils in a 54-year experiment. Differences in total and available nutrients were found in the treatment soils; interestingly, Al, As, Mg, and Mn contents were variable in N, P, K, and NPK treatments. Bacterial community compositions shifted and Actinobacteria were overrepresented under the four fertilization treatments compared to the control. Redundancy analysis of the soil parameters and the bacterial community profiles showed that Mg, total N, Cd, and Al were linked to community variation. Using correlation analysis, Acidobacteria, Bacteroidetes, and Verrucomicrobia were linked similarly to soil parameters, and Actinobacteria and Proteobacteria were linked separately to different suites of parameters. Surprisingly, we found no fertilizers effect on microbial functional profiles which supports functional redundancy as a mechanism for stabilization of functions during changes in microbial composition. We suggest that functional profiles are more resistant to environmental changes than community compositions in the grassland ecosystem.
  • Environmental Microbiology

    Sulphur-oxidising and Sulphate-reducing Communities in Brazilian Mangrove Sediments

    Maryeimy Varon-Lopez, A.C.F Dias, C.C. Fasanella, A. Durrer, I.S. Melo, Eiko Kuramae, Fernando Dini Andreote
    Mangrove soils are anaerobic environments rich in sulphate and organic matter. Although the sulphur cycle is one of the major actors in this ecosystem, little is known regarding the sulphur bacteria communities in mangrove soils. We investigated the abundance, composition and diversity of sulphur-oxidizing (SOB) and sulphate-reducing (SRB) bacteria in sediments from three Brazilian mangrove communities: two contaminated, one with oil (OilMgv) and one with urban waste and sludge (AntMgv), and one pristine (PrsMgv). The community structures were assessed using quantitative real-time polymerase chain reaction (qPCR), polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and clone libraries, using genes for the enzymes adenosine-5′-phosphosulphate reductase (aprA) and sulphite reductase (Dsr) (dsrB). The abundance for qPCR showed the ratio dsrB/aprA to be variable among mangroves and higher according to the gradient observed for oil contamination in the OilMgv. The PCR-DGGE patterns analysed by Nonmetric Multidimensional Scaling revealed differences among the structures of the three mangrove communities. The clone libraries showed that Betaproteobacteria, Gammaproteobacteria and Deltaproteobacteria were the most abundant groups associated with sulphur cycling in mangrove sediments. We conclude that the microbial SOB and SRB communities in mangrove soils are different in each mangrove forest and that such microbial communities could possibly be used as a proxy for contamination in mangrove forests.
  • The Scientific World Journal

    Soil-borne microbial functional structure across different land uses

    Eiko Kuramae, J. Zhou, George Kowalchuk, Hans van Veen
    Land use change alters the structure and composition of microbial communities. However, the links between environmental factors and microbial functions are not well understood. Here we interrogated the functional structure of soil microbial communities across different land uses. In a multivariate regression tree analysis of soil physicochemical properties and genes detected by functional microarrays, the main factor that explained the different microbial community functional structures was C : N ratio. C : N ratio showed a significant positive correlation with clay and soil pH. Fields with low C : N ratio had an overrepresentation of genes for carbon degradation, carbon fixation, metal reductase, and organic remediation categories, while fields with high C : N ratio had an overrepresentation of genes encoding dissimilatory sulfate reductase, methane oxidation, nitrification, and nitrogen fixation. The most abundant genes related to carbon degradation comprised bacterial and fungal cellulases; bacterial and fungal chitinases; fungal laccases; and bacterial, fungal, and oomycete polygalacturonases. The high number of genes related to organic remediation was probably driven by high phosphate content, while the high number of genes for nitrification was probably explained by high total nitrogen content. The functional gene diversity found in different soils did not group the sites accordingly to land management. Rather, the soil factors, C : N ratio, phosphate, and total N, were the main factors driving the differences in functional genes across the fields examined.
  • Frontiers in Environmental Science

    Network topology reveals high connectance levels and few key microbial genera within soils

    Manoeli Lupatini, Afnan Suleiman, Rodrigo Jacques, Z. Antoniolli, A. de Siqueira Ferreira, Eiko Kuramae, Luiz Roesch
    Microbes have a central role in soil global biogeochemical process, yet specific microbe–microbe relationships are largely unknown. Analytical approaches as network analysis may shed new lights in understanding of microbial ecology and environmental microbiology. We investigated the soil bacterial community interactions through cultivation-independent methods in several land uses common in two Brazilian biomes. Using correlation network analysis we identified bacterial genera that presented important microbial associations within the soil community. The associations revealed non-randomly structured microbial communities and clusters of operational taxonomic units (OTUs) that reflected relevant bacterial relationships. Possible keystone genera were found in each soil. Irrespective of the biome or land use studied only a small portion of OTUs showed positive or negative interaction with other members of the soil bacterial community. The more interactive genera were also more abundant however, within those genera, the abundance was not related to taxon importance as measured by the Betweenness Centrality (BC). Most of the soil bacterial genera were important to the overall connectance of the network, whereas only few genera play a key role as connectors, mainly belonged to phyla Proteobacteria and Actinobacteria. Finally it was observed that each land use presented a different set of keystone genera and that no keystone genus presented a generalized distribution. Taking into account that species interactions could be more important to soil processes than species richness and abundance, especially in complex ecosystems, this approach might represent a step forward in microbial ecology beyond the conventional studies of microbial richness and abundance.
  • PLoS One

    Soil-Borne Bacterial Structure and Diversity Does Not Reflect Community Activity in Pampa Biome

    Manoeli Lupatini, Afnan Suleiman, Rodrigo Jacques, Z. Antoniolli, Eiko Kuramae, F. Camargo, Luiz Roesch
    The Pampa biome is considered one of the main hotspots of the world’s biodiversity and it is estimated that half of its original vegetation was removed and converted to agricultural land and tree plantations. Although an increasing amount of knowledge is being assembled regarding the response of soil bacterial communities to land use change, to the associated plant community and to soil properties, our understanding about how these interactions affect the microbial community from the Brazilian Pampa is still poor and incomplete. In this study, we hypothesized that the same soil type from the same geographic region but under distinct land use present dissimilar soil bacterial communities. To test this hypothesis, we assessed the soil bacterial communities from four land-uses within the same soil type by 454-pyrosequencing of 16S rRNA gene and by soil microbial activity analyzes. We found that the same soil type under different land uses harbor similar (but not equal) bacterial communities and the differences were controlled by many microbial taxa. No differences regarding diversity and richness between natural areas and areas under anthropogenic disturbance were detected. However, the measures of microbial activity did not converge with the 16S rRNA data supporting the idea that the coupling between functioning and composition of bacterial communities is not necessarily correlated.
  • FEMS Microbiology Ecology

    Structural and functional variation in soil fungal communities associated with litter bags containing maize

    Eiko Kuramae, R.H.E. Hillekens, Mattias De Hollander, Marcel G. A. van der Heijden, M. Van den Berg, N.M. Van Straalen, George Kowalchuk
  • FEMS Microbiology Ecology

    Acidobacterial community responses to agricultural management of soybean in Amazon forest soils

    A.A. Navarrete, Eiko Kuramae, Mattias De Hollander, Agata Pijl, Hans van Veen, S.M. Tsai
    This study focused on the impact of land-use changes and agricultural management of soybean in Amazon forest soils on the abundance and composition of the acidobacterial community. Quantitative real-time PCR (q-PCR) assays and pyrosequencing of 16S rRNA gene were applied to study the acidobacterial community in bulk soil samples from soybean croplands and adjacent native forests, and mesocosm soil samples from soybean rhizosphere. Based on qPCR measurements, Acidobacteria accounted for 23% in forest soils, 18% in cropland soils, and 14% in soybean rhizosphere of the total bacterial signals. From the 16S rRNA gene sequences of Bacteria domain, the phylum Acidobacteria represented 28% of the sequences from forest soils, 16% from cropland soils, and 17% from soybean rhizosphere. Acidobacteria subgroups 1–8, 10, 11, 13, 17, 18, 22, and 25 were detected with subgroup 1 as dominant among them. Subgroups 4, 6, and 7 were significantly higher in cropland soils than in forest soils, which subgroups responded to decrease in soil aluminum. Subgroups 6 and 7 responded to high content of soil Ca, Mg, Mn, and B. These results showed a differential response of the Acidobacteria subgroups to abiotic soil factors, and open the possibilities to explore acidobacterial subgroups as early-warning bioindicators of agricultural soil management effects in the Amazon area.
  • PLoS One

    Tracking fungal community responses to maize plants by DNA- and RNA-based pyrosequencing

    Eiko Kuramae, E. Verbruggen, R.H.E. Hillekens, Mattias De Hollander, W.F.M. Röling, Marcel G. A. van der Heijden, George Kowalchuk
    We assessed soil fungal diversity and community structure at two sampling times (t1 = 47 days and t2 = 104 days of plant age) in pots associated with four maize cultivars, including two genetically modified (GM) cultivars by high-throughput pyrosequencing of the 18S rRNA gene using DNA and RNA templates. We detected no significant differences in soil fungal diversity and community structure associated with different plant cultivars. However, DNA-based analyses yielded lower fungal OTU richness as compared to RNA-based analyses. Clear differences in fungal community structure were also observed in relation to sampling time and the nucleic acid pool targeted (DNA versus RNA). The most abundant soil fungi, as recovered by DNA-based methods, did not necessary represent the most “active” fungi (as recovered via RNA). Interestingly, RNA-derived community compositions at t1 were highly similar to DNA-derived communities at t2, based on presence/absence measures of OTUs. We recovered large proportions of fungal sequences belonging to arbuscular mycorrhizal fungi and Basidiomycota, especially at the RNA level, suggesting that these important and potentially beneficial fungi are not affected by the plant cultivars nor by GM traits (Bt toxin production). Our results suggest that even though DNA- and RNA-derived soil fungal communities can be very different at a given time, RNA composition may have a predictive power of fungal community development through time.
  • Applied and Environmental Microbiology

    Testing Potential Effects of Maize Expressing the Bacillus thuringiensis Cry1Ab Endotoxin (Bt Maize) on Mycorrhizal Fungal Communities via DNA- and RNA-Based Pyrosequencing and Molecular Fingerprinting

    E. Verbruggen, Eiko Kuramae, R.H.E. Hillekens, Mattias De Hollander, E.T. Kiers, W.F.M. Roling, George Kowalchuk, Marcel G. A. van der Heijden
    The cultivation of genetically modified (GM) crops has increased significantly over the last decades. However, concerns have been raised that some GM traits may negatively affect beneficial soil biota, such as arbuscular mycorrhizal fungi (AMF), potentially leading to alterations in soil functioning. Here, we test two maize varieties expressing the Bacillus thuringiensis Cry1Ab endotoxin (Bt maize) for their effects on soil AM fungal communities. We target both fungal DNA and RNA, which is new for AM fungi, and we use two strategies as an inclusive and robust way of detecting community differences: (i) 454 pyrosequencing using general fungal rRNA gene-directed primers and (ii) terminal restriction fragment length polymorphism (T-RFLP) profiling using AM fungus-specific markers. Potential GM-induced effects were compared to the normal natural variation of AM fungal communities across 15 different agricultural fields. AM fungi were found to be abundant in the experiment, accounting for 8% and 21% of total recovered DNA- and RNA-derived fungal sequences, respectively, after 104 days of plant growth. RNA- and DNA-based sequence analyses yielded most of the same AM fungal lineages. Our research yielded three major conclusions. First, no consistent differences were detected between AM fungal communities associated with GM plants and non-GM plants. Second, temporal variation in AMF community composition (between two measured time points) was bigger than GM trait-induced variation. Third, natural variation of AMF communities across 15 agricultural fields in The Netherlands, as well as within-field temporal variation, was much higher than GM-induced variation. In conclusion, we found no indication that Bt maize cultivation poses a risk for AMF.
  • FEMS Microbiology Ecology

    Soil characteristics more strongly influence soil bacterial communities than land-use type

    Eiko Kuramae, E. Yergeau, Lina Wong, Agata Pijl, Hans van Veen, George Kowalchuk
    To gain insight into the factors driving the structure of bacterial communities in soil, we applied real-time PCR, PCR-denaturing gradient gel electrophoreses, and phylogenetic microarray approaches targeting the 16S rRNA gene across a range of different land usages in the Netherlands. We observed that the main differences in the bacterial communities were not related to land-use type, but rather to soil factors. An exception was the bacterial community of pine forest soils (PFS), which was clearly different from all other sites. PFS had lowest bacterial abundance, lowest numbers of operational taxonomic units (OTUs), lowest soil pH, and highest C : N ratios. C : N ratio strongly influenced bacterial community structure and was the main factor separating PFS from other fields. For the sites other than PFS, phosphate was the most important factor explaining the differences in bacterial communities across fields. Firmicutes were the most dominant group in almost all fields, except in PFS and deciduous forest soils (DFS). In PFS, Alphaproteobacteria was most represented, while in DFS, Firmicutes and Gammaproteobacteria were both highly represented. Interestingly, Bacillii and Clostridium OTUs correlated with pH and phosphate, which might explain their high abundance across many of the Dutch soils. Numerous bacterial groups were highly correlated with specific soil factors, suggesting that they might be useful as indicators of soil status.
  • FEMS Microbiology Ecology

    Soil and plant factors driving the community of soil-borne microorganisms across chronosequences of secondary succession of chalk grasslands with neutral pH

    Eiko Kuramae, H.A. Gamper, Hans van Veen, George Kowalchuk
    Although soil pH has been shown to be an important factor driving microbial communities, relatively little is known about the other potentially important factors that shape soil-borne microbial community structure. This study examined plant and microbial communities across a series of neutral pH fields (pH=7.0–7.5) representing a chronosequence of secondary succession after former arable fields were taken out of production. These fields ranged from 17 to >66 years since the time of abandonment, and an adjacent arable field was included as a reference. Hierarchical clustering analysis, nonmetric multidimensional scaling and analysis of similarity of 52 different plant species showed that the plant community composition was significantly different in the different chronosequences, and that plant species richness and diversity increased with time since abandonment. The microbial community structure, as analyzed by phylogenetic microarrays (PhyloChips), was significantly different in arable field and the early succession stage, but no distinct microbial communities were observed for the intermediate and the late succession stages. The most determinant factors in shaping the soil-borne microbial communities were phosphorous and NH4+. Plant community composition and diversity did not have a significant effect on the belowground microbial community structure or diversity.
  • BMC Plant Biology

    An EST-based analysis identifies new genes and reveals distinctive gene expression features of Coffea arabica and Coffea canephora

    J.M.C. Mondego, R.O. Vidal, M.F. Carazzolle, E.K. Tokuda, L.P. Parizzi, G.G.L. Costa, L.F.P. Pereira, A.C. Andrade, Carlos A. Colombo, L.G.E. Vieira, G.A.G. Pereira, Eiko Kuramae
    Background: Coffee is one of the world’s most important crops; it is consumed worldwide and plays a significant role in the economy of producing countries. Coffea arabica and C. canephora are responsible for 70 and 30% of commercial production, respectively. C. arabica is an allotetraploid from a recent hybridization of the diploid species, C. canephora and C. eugenioides. C. arabica has lower genetic diversity and results in a higher quality beverage than C. canephora. Research initiatives have been launched to produce genomic and transcriptomic data about Coffea spp. as a strategy to improve breeding efficiency. Results: Assembling the expressed sequence tags (ESTs) of C. arabica and C. canephora produced by the Brazilian Coffee Genome Project and the Nestlé-Cornell Consortium revealed 32,007 clusters of C. arabica and 16,665 clusters of C. canephora. We detected different GC3 profiles between these species that are related to their genome structure and mating system. BLAST analysis revealed similarities between coffee and grape (Vitis vinifera) genes. Using KA/KS analysis, we identified coffee genes under purifying and positive selection. Protein domain and gene ontology analyses suggested differences between Coffea spp. data, mainly in relation to complex sugar synthases and nucleotide binding proteins. OrthoMCL was used to identify specific and prevalent coffee protein families when compared to five other plant species. Among the interesting families annotated are new cystatins, glycine-rich proteins and RALF-like peptides. Hierarchical clustering was used to independently group C. arabica and C. canephora expression clusters according to expression data extracted from EST libraries, resulting in the identification of differentially expressed genes. Based on these results, we emphasize gene annotation and discuss plant defenses, abiotic stress and cup quality-related functional categories. Conclusion: We present the first comprehensive genome-wide transcript profile study of C. arabica and C. canephora, which can be freely assessed by the scientific community at http://www.lge.ibi.unicamp.br/ coffea. Our data reveal the presence of species-specific/prevalent genes in coffee that may help to explain particular characteristics of these two crops. The identification of differentially expressed transcripts offers a starting point for the correlation between gene expression profiles and Coffea spp. developmental traits, providing valuable insights for coffee breeding and biotechnology, especially concerning sugar metabolism and stress tolerance
  • Molecular Plant-Microbe Interactions

    Effects of jasmonic acid, ethylene, and salicylic acid signaling on the rhizosphere bacterial community of Arabidopsis thaliana.

    R.F. Doornbos, B.P.J. Geraats, Eiko Kuramae, L.C. van Loon, P. Bakker
    Systemically induced resistance is a promising strategy to control plant diseases, as it affects numerous pathogens. However, since induced resistance reduces one or both growth and activity of plant pathogens, the indigenous microflora may also be affected by an enhanced defensive state of the plant. The aim of this study was to elucidate how much the bacterial rhizosphere microflora of Arabidopsis is affected by induced systemic resistance (ISR) or systemic acquired resistance (SAR). Therefore, the bacterial microflora of wild-type plants and plants affected in their defense signaling was compared. Additionally, ISR was induced by application of methyl jasmonate and SAR by treatment with salicylic acid or benzothiadiazole. As a comparative model, we also used wild type and ethylene-insensitive tobacco. Some of the Arabidopsis genotypes affected in defense signaling showed altered numbers of culturable bacteria in their rhizospheres; however, effects were dependent on soil type. Effects of plant genotype on rhizosphere bacterial community structure could not be related to plant defense because chemical activation of ISR or SAR had no significant effects on density and structure of the rhizosphere bacterial community. These findings support the notion that control of plant diseases by elicitation of systemic resistance will not significantly affect the resident soil bacterial microflora.
  • FEMS Microbiology Ecology

    Phylogenetic and metagenomic analysis of Verrucomicrobia in former agricultural grassland soil

    Anna Kielak, J.L.M. Rodrigues, Eiko Kuramae, P.S.G. Chain, Hans van Veen, George Kowalchuk
    The bacterial phylum Verrucomicrobia has a widespread distribution, and is known to be one of the most common and diverse phyla in soil habitats. However, members of this phylum have typically been recalcitrant to cultivation methods, hampering the study of this presumably important bacterial group. In this study, we examine the phylogenetic diversity of the Verrucomicrobia in a former agricultural field and gain access to genomic information via a metagenomic approach. We examined Verrucomicrobia-like 16S rRNA gene sequences recovered from general bacterial and phylum-specific libraries, revealing a dominance of subdivisions 1 and 2. A PCR-based screening method was developed to identify inserts containing verrucomicrobial 16S rRNA genes within a large-insert metagenomic library, and upon the screening of 28 800 clones, four fosmids were identified as containing verrucomicrobial genomic DNA. Full-length sequencing of fosmid inserts and gene annotation identified a total of 98 ORFs, representing a range of functions. No conservation of gene order was observed adjacent to the ribosomal operons. Fosmid inserts were further analysed for tetranucleotide frequencies to identify remnants of past horizontal gene transfer events. The metagenomic approach utilized proved suitable for the recovery of verrucomicrobial genomic DNA, thereby providing a window into the genomes of members of this important, yet poorly characterised, bacterial phylum.
  • ISME Journal

    Microbial secondary succession in a chronosequence of chalk grasslands

    Eiko Kuramae, H.A. Gamper, E. Yergeau, Y.M. Piceno, Eoin L. Brodie, T.Z. DeSantis, G.L. Andersen, Hans van Veen, George Kowalchuk
    Although secondary succession has been studied extensively, we have little knowledge of the succession of soil-borne microbial communities. In this study, we therefore examined the structures of the microbial communities across two separate chronosequences of chalk grasslands in Limburg, the Netherlands, which are at different stages of secondary succession after being abandoned for between 17 and >66 years. Arable fields were also included in the investigation as non-abandoned references. Changes in the soil-borne microbial communities, as determined by phylogenetic microarray and quantitative PCR methodologies, were correlated with the prevailing environmental conditions related to vegetation and soil biochemistry. We observed clear patterns of microbial secondary succession related to soil age, pH and phosphate status, as exemplified by the overrepresentation of Verrucomicrobia, Acidobacteria, Gemmatimonadetes, and α-, δ- and ε-Proteobacteria at late successional stages. Moreover, effects of secondary succession versus changes in soil pH could be resolved, with pH significantly altering the trajectory of microbial succession.
  • FEMS Yeast Research

    Promiscuous mitochondria in Cryptococcus gattii

    M. Bovers, Ferry Hagen, Eiko Kuramae, Teun Boekhout
    Cryptococcus gattii is a primary pathogenic basidiomycetous yeast comprising four genotypic groups. Here we present data on two mitochondrial loci (MtLrRNA and ATP6). Two of the genotypic groups, namely amplified fragment length polymorphism (AFLP)5/VGIII and AFLP6/VGII, formed monophyletic lineages. The AFLP4/VGI genotypic group, however, possessed five different mitochondrial genotypes that did not form a monophyletic lineage. The majority of these isolates contained mitochondrial genomes that are partially identical to those found in isolates belonging to AFLP6/VGII, which is causing the ongoing and expanding Vancouver Island outbreak. Two out of four AFLP7/VGIV isolates contained an AFLP4/VGI allele of MtLrRNA. These observations are best explained by assuming a process of mitochondrial recombination. If this is true, mitochondrial recombination seems possible between cells belonging to different genotypic groups of C. gattii, especially between AFLP6/VGII or AFLP7/VGIV and AFLP4/VGI. We also have to assume that mitochondria, most likely, were transferred from cells belonging to AFLP6/VGII to AFLP4/VGI. As such a process of mitochondrial recombination is only possible after cell-cell conjugation, this may also allow the further exchange of genetic material, for example nuclear or plasmid in nature, between different genotypes of C. gattii. This may be relevant as it may provide a possible mechanism contributing to the modulation of virulence attributes of isolates, such as has been observed in the ongoing Vancouver Island outbreak of C. gattii.
  • Summa Phytopathologica

    Characterization of Xanthomonas axonopodis pv. phaseoli isolates

    W.M.C. Nunes, M.J. Corazza, S.A.C.D. De Souza, S.M. Tsai, Eiko Kuramae
    A simple, quick and easy protocol was standardized for extraction of total DNA of the bacteria Xanthomonas axonopodis pv. phaseoli. The DNA obtained by this method had high quality and the quantity was enough for the Random Amplified Polymorphic DNA (RAPD) reactions with random primers, and Polymerase Chain Reaction (PCR) with primers of the hypersensitivity and pathogenicity gene (hrp). The DNA obtained was free of contamination by proteins or carbohydrates. The ratio 260nm/380nm of the DNA extracted ranged from 1.7 to 1.8. The hrp gene cluster is required by bacterial plant pathogen to produce symptoms on susceptible hosts and hypersensitive reaction on resistant hosts. This gene has been found in different bacteria as well as in Xanthomonas campestris pv. vesicatoria (9). The primers RST21 and RST22 (9) were used to amplify the hrp gene of nine different isolates of Xanthomonas axonopodis pv. phaseoli from Botucatu, São Paulo State, Brazil, and one isolate, "Davis". PCR amplified products were obtained in all isolates pathogenic to beans.
  • Fungal Genetics and Biology

    Six monophyletic lineages identified within Cryptococcus neoformans and Cryptococcus gattii by multi-locus sequence typing

    M. Bovers, Ferry Hagen, Eiko Kuramae, Teun Boekhout
    Cryptococcus neoformans and Cryptococcus gattii are closely related pathogenic basidiomycetous yeasts in which six haploid genotypic groups have been distinguished. The two haploid genotypic groups of C. neoformans have been described as variety grubii and variety neoformans. The four C. gattii genotypic groups have, however, not been described as separate taxa. One hundred and seventeen isolates representing all six haploid genotypic groups were selected for multi-locus sequence typing using six loci to investigate if the isolates consistently formed monophyletic lineages. Two monophyletic lineages, corresponding to varieties grubii and neoformans, were consistently present within C. neoformans, supporting the current classification. In addition, four monophyletic lineages corresponding to the previously described genotypic groups were consistently found within C. gattii, indicating that these lineages should be considered different taxa as well.
  • Emerging Infectious Diseases

    AIDS patient death caused by novel Cryptococcus neoformans × C. gattii Hybrid

    M. Bovers, Ferry Hagen, Eiko Kuramae, H.L. Hoogveld, F. Dromer, G. St-Germain, Teun Boekhout
  • BMC Evolutionary Biology

    Cophenetic correlation analysis as a strategy to select phylogenetically informative proteins: an example from the fungal kingdom

    Eiko Kuramae, Vincent Robert, C. Echavarri-Erasun, Teun Boekhout
    The construction of robust and well resolved phylogenetic trees is important for our understanding of many, if not all biological processes, including speciation and origin of higher taxa, genome evolution, metabolic diversification, multicellularity, origin of life styles, pathogenicity and so on. Many older phylogenies were not well supported due to insufficient phylogenetic signal present in the single or few genes used in phylogenetic reconstructions. Importantly, single gene phylogenies were not always found to be congruent. The phylogenetic signal may, therefore, be increased by enlarging the number of genes included in phylogenetic studies. Unfortunately, concatenation of many genes does not take into consideration the evolutionary history of each individual gene. Here, we describe an approach to select informative phylogenetic proteins to be used in the Tree of Life (TOL) and barcoding projects by comparing the cophenetic correlation coefficients (CCC) among individual protein distance matrices of proteins, using the fungi as an example. The method demonstrated that the quality and number of concatenated proteins is important for a reliable estimation of TOL. Approximately 40–45 concatenated proteins seem needed to resolve fungal TOL. Results In total 4852 orthologous proteins (KOGs) were assigned among 33 fungal genomes from the Asco- and Basidiomycota and 70 of these represented single copy proteins. The individual protein distance matrices based on 531 concatenated proteins that has been used for phylogeny reconstruction before [14] were compared one with another in order to select those with the highest CCC, which then was used as a reference. This reference distance matrix was compared with those of the 70 single copy proteins s Conclusion This study provides candidate protein sequences to be considered as phylogenetic markers in different branches of fungal TOL. The selection procedure described here will be useful to select informative protein sequences to resolve branches of TOL that contain few or no species with completely sequenced genomes. The robust phylogenetic trees resulting from this method may contribute to our understanding of organismal diversification processes. The method proposed can be extended easily to other b
  • Proceedings of the National Academy of Sciences of the United States of America

    Dandruff-associated Malassezia genomes reveal convergent and divergent virulence traits shared with plant and human fungal pathogens

    J. Xu, C. Saunders, P. Hu, R.A. Grant, Teun Boekhout, Eiko Kuramae, J.W. Kronstad, Y.M. DeAngelis, N.L. Reeder, K.R. Johnstone, M. Leland, A.M. Fieno, W.M. Begley, Y. Sun, M.P. Lacey, T. Chaudhary, T. Keough, L. Chu, R. Sears, B. Yuan, T.L. Dawson Jr.
    Fungi in the genus Malassezia are ubiquitous skin residents of humans and other warm-blooded animals. Malassezia are involved in disorders including dandruff and seborrheic dermatitis, which together affect >50% of humans. Despite the importance of Malassezia in common skin diseases, remarkably little is known at the molecular level. We describe the genome, secretory proteome, and expression of selected genes of Malassezia globosa. Further, we report a comparative survey of the genome and secretory proteome of Malassezia restricta, a close relative implicated in similar skin disorders. Adaptation to the skin environment and associated pathogenicity may be due to unique metabolic limitations and capabilities. For example, the lipid dependence of M. globosa can be explained by the apparent absence of a fatty acid synthase gene. The inability to synthesize fatty acids may be complemented by the presence of multiple secreted lipases to aid in harvesting host lipids. In addition, an abundance of genes encoding secreted hydrolases (e.g., lipases, phospholipases, aspartyl proteases, and acid sphingomyelinases) was found in the M. globosa genome. In contrast, the phylogenetically closely related plant pathogen Ustilago maydis encodes a different arsenal of extracellular hydrolases with more copies of glycosyl hydrolase genes. M. globosa shares a similar arsenal of extracellular hydrolases with the phylogenetically distant human pathogen, Candida albicans, which occupies a similar niche, indicating the importance of host-specific adaptation. The M. globosa genome sequence also revealed the presence of mating-type genes, providing an indication that Malassezia may be capable of sex.
  • European Journal of Plant Pathology

    rDNA-based characterization of a new binucleate Rhizoctonia spp. causing root rot on kale in Brazil

    Eiko Kuramae, A.L. Buzeto, A.K. Nakatani, Nilton Souza
    In this paper we present the first report of the occurrence of a binucleate Rhizoctonia spp. causing hypocotyl and root rot in kale in Brazil. Rhizoctonia spp. were isolated from kale (Brassica oleracea var. acephala) with symptoms of hypocotyl and root rot. The isolates, characterized as binucleate Rhizoctonia spp., did not show an anastomosis reaction with any of the binucleate Rhizoctonia spp. testers used. The pathogenicity of the isolates was tested under greenhouse conditions; all isolates were pathogenic and showed different symptom severities on kale. The ITS-5.8S rDNA sequences of kale isolates and 50 testers (25 binucleate Rhizoctonia spp. and 25 Rhizoctonia solani) were compared in order to characterize the genetic identity of Rhizoctonia spp. infecting kale. The kale isolates showed genetic identities ranging from 99.3 to 99.8% and were phylogenetically closely related to CAG 7 (AF354084), with identities of 98.5 and 98.7%. It is suggested that the binucleate Rhizoctonia spp. causing hypocotyl and root rot on kale Brazil comprises a new AG not yet described.
  • Summa Phytopathologica

    Citomorphological, cultural, molecular and pathogenical characterization of Rhizoctonia solani Kühn associated with rice in Tocantins, Brazil

    E.C. Souza, Eiko Kuramae, A.K. Nakatani, M.A. Basseto, A.S. Prabhu, P.C. Ceresini
    In Tocantins State, Northern Brazil, the incidence of Rhizoctonia sheath blight on rice is important, causing significant yield losses on rice crops under irrigation. The main objective of this research was to determine the anastomosis group (AG) of R. solani associated with rice in that area, testing the hypothesis that these isolates are from the AG-1 IA, which is also associated with the soybean leaf blight occurring in wet areas of Northern Brazil. All the four rice isolates were characterized, by hyphal fusion, as AG-1 IA. By cultural characterization, based on basal temperatures for mycelial growth (minimum, optimum and maximum), the rice isolates had growth profile similar to the tester isolates AG-1 IA, AG-1 IB and AG-1 IC. The rice isolates were characterized as autotrophic for thiamine, as well as the AG testers AG-1 IA, IB, IC, AG-4 HGI and the soybean leaf blight isolate SJ-047. The pathogenicity test on rice IRGA-409 and the cross pathogenicity on soybean IAC-18 (susceptible to the leaf blight disease) indicated that, besides causing sheath blight, these rice isolates also cause leaf blight on soybean. Similarly, the soybean isolates SJ-047 was pathogenic to rice. The sequences from the ITS-5.8S region of rDNA from the rice isolates were similar to sequences of AG-1 IA deposited at GenBank® - NCBI. The ITS-rDNA phylogeny indicated a common phylogenetic group formed by these rice isolates, the isolate SJ-047 and the tester AG-1 IA. Thus, based on cytomorphological, cultural, phylogenetics and pathogenic attributes, the hypothesis that the rice isolates of R. solani from Tocantins all belong to the AG-1 IA was confirmed, besides the indication that these isolates can also cause soybean foliar blight.
  • 2006

    Conflicting phylogenetic position of Schizosaccharomyces pombe

    Eiko Kuramae, Vincent Robert, Berend Snel, Teun Boekhout
    The phylogenetic position of the fission yeast Schizosaccharomyces pombe in the fungal Tree of Life is still controversial. Three alternative phylogenetic positions have been proposed in the literature, namely (1) a position basal to the Hemiascomycetes and Euascomycetes, (2) a position as a sister group to the Euascomycetes with the Hemiascomycetes as a basal branch, or (3) a sister group to the Hemiascomycetes with Euascomycetes as a basal branch. Here we compared 91 clusters of orthologous proteins containing a single orthologue that are shared by 19 eukaryote genomes. The major part of these 91 orthologues supports a phylogenetic position of S. pombe as a basal lineage among the Ascomycota, thus supporting the second proposition. Interestingly, part of the orthologous proteins supported a fourth, not yet described alternative, in which S. pombe is basal to both Basidiomycota and Ascomycota. Both topologies of phylogenetic trees are well supported. We believe that both reflect correctly the phylogenetic history of the species concerned. This apparent paradox may point to a heterogeneous nuclear genome of the fungi. Importantly, this needs to be taken in consideration for a correct understanding of the fungal Tree of Life. © 2006 Elsevier Inc. All rights reserved.
  • FEMS Yeast Research

    Unique hybrids between the fungal pathogens Cryptococcus neoformans and Cryptococcus gattii

    M. Bovers, Ferry Hagen, Eiko Kuramae, M.R. Diaz, L. Spanjaard, F. Dromer, H.L. Hoogveld, Teun Boekhout
    Cryptococcus neoformans and Cryptococcus gattii are yeasts that cause meningoencephalitis, but that differ in host range and geographical distribution. Cryptococcus neoformans occurs world-wide and mostly infects immunocompromised patients, whereas C. gattii occurs mainly in (sub)tropical regions and infects healthy individuals. Anomalous C. neoformans strains were isolated from patients. These strains were found to be monokaryotic, and diploid or aneuploid. Amplified Fragment Length Polymorphism (AFLP) and sequence analyses indicated that AFLP genotypes 2 (C. neoformans) and 4 (C. gattii) were present. The strains were serologically BD. Mating- and serotype-specific PCR reactions showed that the strains were MATa-serotype D/MATa-serotype B. This study is the first to describe naturally occurring hybrids between C. neoformans and C. gattii. [KEYWORDS: Cryptococcus neoformans ; Cryptococcus gattii ; BD hybrid ; recurrent meningitis]
  • 2006

    Phylogenomics reveal a robust fungal tree of life

    Eiko Kuramae, Vincent Robert, Berend Snel, Michael Weiß, Teun Boekhout
    Our understanding of the tree of life (TOL) is still fragmentary. Until recently, molecular phylogeneticists have built trees based on ribosomal RNA sequences and selected protein sequences, which, however, usually suffered from lack of support for the deeper branches and inconsistencies probably due to limited subsampling of the entire genome. Now, phylogenetic hypotheses can be based on the analysis of full genomes. We used available complete genome data as well as the eukaryote orthologous group (KOG) proteins to reconstruct with confidence basal branches of the fungal TOL. Phylogenetic analysis of a core of 531 KOGs shared among 21 fungal genomes, three animal genomes and one plant genome showed a single tree with high support resulting from four different methods of phylogenetic reconstruction. The single tree that we inferred from our dataset showed excellent nodal support for each branch, suggesting that it reflects the true phylogenetic relationships of the species involved.
  • Genome Research

    Analysis and functional annotation of an expressed sequence tag collection for tropical crop sugarcane

    André L. Vettore, Felipe R. da Silva, Edson L. Kemper, Glaucia M. Souza, Aline M. da Silva, Maria Inês T. Ferro, Flavio Henrique-Silva, Éder A. Giglioti, Manoel V.F. Lemos, Luiz L. Coutinho, Marina P. Nobrega, Helaine Carrer, Suzelei C. França, Maurício Bacci, Maria Helena S. Goldman, Suely L. Gomes, Luiz R. Nunes, Luis E.A. Camargo, Walter J. Siqueira, Marie Anne Van Sluys, Otavio H. Thiemann, Eiko Kuramae, Roberto V. Santelli, Celso L. Marino, Maria L.P.N. Targon, Jesus A. Ferro, Henrique C.S. Silveira, Danyelle C. Marini, Eliana G.M. Lemos, Claudia B. Monteiro-Vitorello, José H.M. Tambor, Dirce M. Carraro, Patrícia G. Roberto, Vanderlei G. Martins, Gustavo H. Goldman, Regina C. de Oliveira, Daniela Truffi, Carlos A. Colombo, Magdalena Rossi, Paula G. de Araujo, Susana A. Sculaccio, Aline Angella, Marleide M.A. Lima, Vicente E. de Rosa, Fábio Siviero, Virginia E. Coscrato, Marcos Machado, Laurent Grivet, Sonia M.Z. Di Mauro, Francisco G. Nobrega, Carlos F.M. Menck, Marilia D.V. Braga, Guilherme P. Telles, Frank A.A. Cara, Guilherme Pedrosa, João Meidanis, Paulo Arruda

    To contribute to our understanding of the genome complexity of sugarcane, we undertook a large-scale expressed sequence tag (EST) program. More than 260,000 cDNA clones were partially sequenced from 26 standard cDNA libraries generated from different sugarcane tissues. After the processing of the sequences, 237,954 high-quality ESTs were identified. These ESTs were assembled into 43,141 putative transcripts. Of the assembled sequences, 35.6% presented no matches with existing sequences in public databases. A global analysis of the whole SUCEST data set indicated that 14,409 assembled sequences (33% of the total) contained at least one cDNA clone with a full-length insert. Annotation of the 43,141 assembled sequences associated almost 50% of the putative identified sugarcane genes with protein metabolism, cellular communication/signal transduction, bioenergetics, and stress responses. Inspection of the translated assembled sequences for conserved protein domains revealed 40,821 amino acid sequences with 1415 Pfam domains. Reassembling the consensus sequences of the 43,141 transcripts revealed a 22% redundancy in the first assembling. This indicated that possibly 33,620 unique genes had been identified and indicated that >90% of the sugarcane expressed genes were tagged.

  • Journal of Bacteriology

    Comparative analyses of the complete genome sequences of Pierce's disease and citrus variegated chlorosis strains of Xylella fastidiosa

    Marie Anne Van Sluys, N.M.C. Oliveira, Claudia B. Monteiro-Vitorello, C. Y. Miyaki, L. R. Furlan, Luis E.A. Camargo, A. C. R. da Silva, D. H. Moon, M. A. Takita, Eliana G.M. Lemos, Marcos Machado, Maria Inês T. Ferro, Felipe R. da Silva, Maria Helena S. Goldman, Gustavo H. Goldman, Manoel V.F. Lemos, H. El-Dorry, S.M. Tsai, Helaine Carrer, Dirce M. Carraro, Regina C. de Oliveira, Luiz R. Nunes, Walter J. Siqueira, Luiz L. Coutinho, E. T. Kimura, E. S. Ferro, R. Harakava, Eiko Kuramae, Celso L. Marino, Éder A. Giglioti, I. L. Abreu, L. M.C. Alves, A. M. Do Amaral, G. S. Baia, S. R. Blanco, A.R. Monteiro de Souza Brito, Fabiana de Souza Cannavan, A. V. Celestino, A. F. Da Cunha, R. C. Fenille, Jesus A. Ferro, E. F. Formighieri, L. T. Kishi, S. G. Leoni, Ana Raquel Oliveira Santos, Vicente E. de Rosa, F. T. Sassaki, J. A. D. Sena, A. C. Souza, Daniela Truffi, F. Tsukumo, G. M. Yanai, L. G. Zaros, E. L. Civerolo, A. J. G. Simpson, N. F. Almeida, J. C. Setubal, J. P. Kitajima

    Xylella fastidiosa is a xylem-dwelling, insect-transmitted, gamma-proteobacterium that causes diseases in many plants, including grapevine, citrus, periwinkle, almond, oleander, and coffee. X. fastidiosa has an unusually broad host range, has an extensive geographical distribution throughout the American continent, and induces diverse disease phenotypes. Previous molecular analyses indicated three distinct groups of X. fastidiosa isolates that were expected to be genetically divergent. Here we report the genome sequence of X. fastidiosa (Temecula strain), isolated from a naturally infected grapevine with Pierce's disease (PD) in a wine-grapegrowing region of California. Comparative analyses with a previously sequenced X. fastidiosa strain responsible for citrus variegated chlorosis (CVC) revealed that 98% of the PD X. fastidiosa Temecula genes are shared with the CVC X. fastidiosa strain 9a5c genes. Furthermore, the average amino acid identity of the open reading frames in the strains is 95.7%. Genomic differences are limited to phage-associated chromosomal rearrangements and deletions that also account for the strain-specific genes present in each genome. Genomic islands, one in each genome, were identified, and their presence in other X. fastidiosa strains was analyzed. We conclude that these two organisms have identical metabolic functions and are likely to use a common set of genes in plant colonization and pathogenesis, permitting convergence of functional genomic strategies.

  • Genetics and Molecular Biology

    Identification of 14-3-3-like protein in sugarcane (Saccharum officinarum)

    Eiko Kuramae, R. C. Fenille, Vicente E. de Rosa

    In a search of the sugarcane expressed sequence tag (SUCEST) database we located three full-length cDNAs (SCCCLR1022D05.g, SCCCRZ1001D02.g and SCBFLR1026E02.g) encoding the 14-3-3 proteins from sugarcane (Saccharum officinarum). The encoded proteins were identified based on the clustering of the expressed sequence tags and were shown to encode proteins similar to 14-3-3 proteins of other monocotyledonous plants. Cluster SCCCLR1022D05.g was 99% similar to the maize 14-3-3-like protein (gi1345587) while cluster SCCCRZ1001D02.g shared 96% and SCBFLR1026E02.g 94% similarity with the 14-3-3 protein of rice (gi7435022). Although 14-3-3 proteins have been reported to be specific to particular species, tissue or organ from which they were isolated, all three sugarcane clusters were found to be expressed in several tissues.

  • Revisão Anual de Patologia de Plantas (RAPP)

    Projeto Genoma da Xylella fastidiosa

Projects & collaborations


  • Deciphering the role of fungal denitrifiers in N2O production from soils

    Project 2022–Present
    The goal of this project is to decipher the role of fungal denitrifiers in N2O production from soils under sustainable management practices. Here we apply mesocosms experiments combined with SIP and meta-omics approaches targeting the functional genes of N cycle. In addition, we design primers for fungal denitrifiers based on complete fungal genomes and soil metagenomics data.  
  • Succession of microbial functions in degraded saline soil restoration

    Project 2022–Present
    The global saline-alkali land area has already exceeded 1.1 billion hectares. China has about 100 million hectares. Rice cultivation has been used as an effective strategy to amend saline-alkaline lands in northeastern Songnen Plain in China since the 1950s. However, it is not known the role of microbial functions during succession of soil restoration. The aim of this project is to fundamental understanding the microbial functions succession during the saline soil restoration.
    rice in salt soil
  • PhyloFunDB

    Project 2020–Present
    PhyloFunDB. This project aims at creating and maintaining phylogenetically validated reference databases of various microbial functional genes and creating the tools to make the databases available for the scientific community
    Pipeline for analyses of functional genes.
  • Long-term Ca-based amendments impact on microbiome and N processes in the rhizosphere and soil in tropical no-till intercropping system

    Project 2019–Present
    Unsustainable agricultural management practices such as non-conservationist tillage and overuse of fertilizers result in soil acidity and, in turn, soil degradation due to reduced carbon (C) concentrations and nutrient availability and increased aluminum toxicity. Application of lime (L) and phosphogypsum (PG) can overcome these constraints and improve soil quality, but the long-term effects of these amendments on both abiotic and biotic soil properties are not known, particularly when applied in combination. Here, we evaluate the effects of L (acidity corrective), PG (soil conditioner), and their combination (LPG) on soil organic matter (SOM) transformations, soil chemical and physical properties, microbiome assembly, N uptake by intercropped plants, maize yield, archaeal and bacterial abundances, and N cycle genes in the maize and ruzigrass rhizospheres in a long-term field experiment in tropical soil with a no-till maize and forage ruzigrass intercropping system. 
  • The role of beneficial microbe in soil aggregation

    Project 2019–Present
    The aim of this project is to determine the ecological relationship between bacteria and soil aggregates. We inoculate individual beneficial bacteria and different microbial communities from different natural soils in simulated Mars soil, attempting to explain their improvement in soil aggregate stability by bacterial exudates (EPS), necromass and microbial functional traits.
    Aggregate in Mars simulated soil by Acidobacteria WH15 (photo: Jan Dijksterhuis)
  • Fiber2Fiber

    Project 2018
    This project aims at degrading asbestos fibers using a combination of plants, fungi and bacteria.
    Fungi and bacteria with asbestos fibers
  • Forage grasses cover crops of rice and maize to steer nitrogen processes and microbiome to mitigate greenhouse gases emissions in long-term tropical agriculture system

    Project 2018–Present
    The aim of this research is to understand how cover crop species combined with different times of N application affect the cover crop straw, nutrition and productivity of cash crop, soil chemical properties and soil microbial composition and function in a holistic approach of the entire agricultural system under tropical no-till system. Focus is on microbiome that immediately respond to the N application disturbances and in a long period to the plant cultivation, N inputs and soil properties changes. We use 3-year field experiment with palisade grass and ruzigrass cover crops and subsequent maize cash crop combined with different N management strategies to quantify the microbial genes of the N cycle and the bacterial and fungal communities’ structure and composition in the agricultural system.
  • Microbial Farming to increase plant productivity

    Project 2018–Present
    Plant-growth promoting microbes (PGPM) are a viable alternative to traditional fertilizers for enhancing plant productivity and improving soil quality without environmental pollution. The use of PGPM in agriculture has been hampered by a lack of reproducible results and the difficulty of transferring this technology to the field. This inconsistent success primarily reflects competition or resistance of the original soil microbiome to inoculants, as well as the negative effects of management practices such as fertilization on plant interactions with the soil microbiome and the efficiency of ecosystem services delivered by PGPM. We were the first to circumvent this problem under field conditions by manipulating the soil microbiome to successfully obtain consistent, positive effects of inoculated microbes on plant productivity (Cipriano et al., 2016;https://doi.org/10.1093/femsec/fiw197). However, the influence of the indigenous soil microbiome on plants remains largely unknown. We propose to investigate this tripartite, PGPM-plant-soil microbiome interaction in plant quality and productivity using state-of-the-art ‘omics’ and bioinformatics approaches to investigate facilitation (positive interactions) and competition (negative interactions) by both microbes and PGPM within the plant realized niche following gradients of both soil diversity and nutrient availability. This research will facilitate the development of innovative methods for agricultural and horticultural starting material production using PGPM for sustainable crop production by combining techniques to reduce nutrient input and enhance the efficiency and long-lasting effects of PGPM. This research proposal will integrate approaches to obtain a fundamental understanding of these tripartite interactions in a smart microbiome engineered plant production system for sustainable high-quality crop production.
    Soil microbial farming to increase plant productivity: reducing nutrient inputs to increase plant-microbe interactions and managing soil microbial diversity
  • Phosphorus use efficiency in Eucalyptus and the microbiome involved

    Project 2018–Present
    Soil phosphorus (P) availability may limit plant growth and alter root-soil interactions and rhizosphere microbial community composition. The composition of the rhizosphere microbial community can also be shaped by plant genotype. In this project we examine the rhizosphere bacterial and fungal including Arbuscular Mycorhizal Fungi (AMF) communities of young plants of 24 species of eucalypts (22 Eucalyptus and two Corymbia species) under low or sufficient soil P availability.
  • Harnessing the rhizosphere microbiome to enhance plant productivity

    Project 2015–Present
    In Bio-Based Economy, plant materials are an essential resource for new industrial and sustainable applications. To ensure the production of sufficient plant biomass there is a need of mineral fertilizers. However, intensive fertilization causes leaching and run-off of nutrients, reduction in biodiversity, production of greenhouse gasses, global warming and changes in soil pH leading to environmental degradation. A key challenge is to intensify agricultural production methods in a way that minimizes harmful environmental effects of fertilizers. Therefore, there is an urgent need for new strategies that optimize plant growth and minimize abiotic and biotic factors that adversely affect plant growth and quality. The plant microbiome, i.e. the collective microbial communities associated with plants, harbors various fungal and bacterial genera that have beneficial effects on plant growth and health. Several bacterial genera promote plant growth and induce systemic resistance in plants against pathogens as well as insect pests. Recent 'omics'-based studies revealed that specific rhizobacteria cause substantial transcriptional changes in plants, leading to elevated levels of specific plant genes expression. Brazilian sugarcane production system is being developed towards to sustainable manner by recycling straw and vinasse (byproduct of ethanol industry), which combined practices allow less mineral fertilizers to be added into soil. In addition, the use of beneficial bacteria, such as plant growth promoting bacteria (PGPB) isolated from sugarcane rhizosphere has shown to increase plant growth and health under controlled situation. However, detailed investigation and fundamental understanding of the effect of these PGPB in different sugarcane genotypes in different soils containing different microbial community are urgent need. Therefore, this proposal aims to: (i) determine the effect of different soil microbial community composition on sugarcane growth inoculated with PGPB; (ii) identify the PGPB traits and genes involved in plant growth promotion; (iii) identify the plant traits and genes involved in plant growth promotion induced by PGPB. Potential applications of this proposal will be (i) the identified PGPB traits and genes to ensure or enhance plant biomass, yield and quality; (ii) the identified genotype-specific genes induced by PGPB responsible for enhancing plant productivity. The proposed project will provide new insights into mechanisms, traits and genes underlying PGPB-plant interactions and will yield new leads and tools to ensure/enhance sugarcane biomass for bio-based economy
  • ClipsMicro: Climate proof soils by steering soil and residue microbiomes

    Project 2022–2028
    To mitigate climate change, global agricultural soils needs to store more carbon and emit less greenhouse gasses (GHG). In ClipsMicro, together with partners in agro-business, this is realised by steering soil microbes by application of novel, refined compost and crops that can reduce emissions of GHG.
    Soil from 70 year composting trial
  • REPHORM - REcycled PHOsphorus Resolved by Microbes

    Project 2022–Present
    Sufficient Phosphorus (P) and Iron (Fe) supply is essential for crop production. Most of the P and Fe in soil is not readily available for the plant, making agriculture depending on inorganic fertilizers mainly derived from depletable resources. An alternative to this unsustainable practice is to use recycled compounds recovered during wastewater treatment. This project focuses on the use of the two recycled compounds struvite (MgNH4PO4·6H2O) and vivianite (Fe3(PO4)2·8H2O) which are both insoluble and hard to synchronize with the nutrient needs during early plant development. To increase efficient nutrient release of these recycled sources, we propose the use of microbes that can solubilize P and release siderophore, both recognized traits of plant growth promoting microbes. Several plant growth-promoting microbes have been isolated, but their transfer to agriculture, so far, resulted in an inconsistent success, due to competition or resistance of the resident soil microbiome to inoculants. This project will circumvent this challenge by steering the local microbiome with the addition of recycled nutrients and will further optimize the microbiome by microbial community breeding. Overall, this project will focus on identifying microbial community members with struvite and vivianite solubilizing function, optimizing these communities, determining the role of these communities on increasing the nutrient release as well as monitoring the recruitment of these beneficial microbes in the rhizosphere and the effect on plant growth.
  • Farming microbial community for plant probiotic - MicroProFarm

    Project 2020–Present
    A current challenge for modern agriculture is to meet the food production needs for an increasing global population while improving resource use efficiency and attenuating impacts on human health and environment. In order to maximize reliability and stability in agriculture, optimization of crop management and resource use efficiency have been considered the best approaches for a sustainable increase of crop yields under variable agro-ecological conditions, environments and years. For this purpose, one interesting and sustainable method is the use of natural plant biostimulants, a diverse class of products and microorganisms that enhance plant growth and other plant parameters, such as flowering, fruit set, crop productivity and nutrient use efficiency. In this context, several studies already demonstrated that plant biostimulants can induce morpho-anatomical, biochemical, physiological and molecular plant responses, not only improving crop productivity but also promoting protection against abiotic stresses, such as drought and salinity. Among the different biostimulant classes there are protein hydrolysates (PH), mixtures of polypeptides, oligopeptides and aminoacids originated from partially hydrolyzed animal and vegetal tissues. Even though the effect of PH were already observed in diverse crops, the mechanisms and behind their action are still scarcely studied, and their action can vary depending on their origin, characteristics, crop species, cultivars, growing conditions, time and mode of applications, among other parameters. The objective of this project is to evaluate the effect of protein hydrolysates in the growth, nutrient content and microbial communities of crops, if microbes are responsible for these effects, which are the mechanisms and if such effects are long-lasting.
    Impact of protein biostimulants in a variety of crops
  • Restoring degraded lands with microbial inoculants

    Project 2019–Present
    Land degradation usually leads to a reduction in soil fertility, decline of plant productivity, and loss of biodiversity. Introducing beneficial microbial inoculants to degraded lands represents a promising and sustainable strategy. The aim of this project is to reveal the ecological roles of microbial inoculants and soil-resident microbial community in restoring both belowground biodiversity and aboveground productivity in the degraded land.
    Degraded land
  • Insectloop: Microbes involved in the decomposition of rest-streams of insect production

    Project 2018–2022
    This is a sub-project of a WUR-NIOO project entitled "Closing the loop: exploiting sustainable insect production to improve soil, crop and animal health", coordinated by Prof. Marcel Dicke. Insects can transform waste streams into high-value proteins for food and feed. Consequently, insects provide valuable contributions to a circular economy. The project aims to investigate the valorisation of the rest-stream of insect production, i.e. moulting skins and faeces (‘frass’) to enhance soil health and crop health (https://doi.org/10.1016/j.tplants.2022.01.007).
    In the NIOO project, we study the decomposition rate of frass and moulting skins of three insects species (black soldier fly, mealworm, cricket) in arable soil as well as the composition of the fungal and bacterial decomposers. In addition, we study if the insect materials, which are rich in chitin, can be used to control soil-borne fungal plant diseases.
    Bioassay with insect materials
  • Promise

    Project 2017–2022
    The long-term goal of the programme is to improve the livelihood of smallholder farmers in sub-Saharan Africa, by increasing the productivity of sorghum:
    Field trial Ethiopia 2021 - Taye Tessema (EIAR)
  • Physiological and ecological strategies of Acidobacteria

    Project 2016–2020
    Acidobacteria is among the most abundant phylum in soils, however, their physiological capabilities and co-occurrence with soil inhabitants are still unknown.
  • Unravelling the mechanisms underlying health and productivity promoting agricultural practices by fine-mapping rhizosphere communities

    Project 2015–2019
    Plant species shape their own rhizosphere community, and on its turn selected soil biota shape the growth and development of plants.
    Plant species shape their own rhizosphere community, and on its turn selected soil biota shape the growth and development of plants.
  • Microbial Networks controlling soil greenhouse gases emissions

    Project 2014–2019
    Soils are considered principally non-renewable resources. Soil ecosystem services have a large impact on numerous societal demands and are of high economic importance. Within the area of sustainable agriculture, it is expected that agricultural production will increasingly rely on the natural nutrient retention and recycling capabilities of soil. This project seeks to provide a fundamental scientific understanding of soil functioning and the resulting ecosystem services in Brazilian and Dutch bio-economies based on innovative microbial ecology and soil science studies. Focus is in sugarcane crop production systems by linking soil microbial composition and functioning, waste residues recycling, fertilizers, soil factors and greenhouse gases (GHG) emissions through integrating and complementing the strong expertise of Brazilian and Dutch researchers from different areas of agronomy, soil sciences, plant nutrition, biogeochemistry, soil ecology, microbial ecology, ecological genomics, molecular ecology and bioinformatics. We will quantify the microbial functional groups and microbial abundance of C and N cycle genes and measure GHG emissions (CO2, CH4 and N2O) from soils during the productive cycle of the plant under different management practices and verify the temporal and spatial variability of these emissions in the evaluated treatments with different concentrations of sugarcane vinasse residue combined with N mineral fertilizers in combination with straw additions, and determine the conditions under which such GHG emissions can be counteracted, or minimized most. The proposed project will enhance fundamental scientific understanding of the interactive role of the microbial networks operating in soil and the consequences of bio-based agricultural management practices for the functioning of soil systems.
    Microbial Networks in control of greenhouse gases emissions in Bio-based agriculture-MiniBag


Is agroforestry a suitable solution for the restoration of the Amazon forest?

Nitrogen, manganese, iron, and carbon resource acquisition are potential functions of the wild rice Oryza rufipogon core rhizomicrobiome

Forest floor microbes produce tough biofilm breaker