Droevendaalsesteeg 10
6708 PB Wageningen
The Netherlands
Over
Molecular technician working for the Microbial and Animal Ecology department.
Biografie
Ir. Agata Pijl graduated as a biotechnology technician in 1992 at the Hogeschool Rotterdam e.o. After this she studied biology at WageningenUR and graduated in 1995. She started working at the NIOO in 2000 for the Department of Microbial Ecology and also in 2003 for the Department of Animal Ecology. Here work now involves all kind of moleculair techniques in the projects of Eiko Kuramae, Marcel Visser, Kees van Oers and Melissah Rowe.
Onderzoeksgroepen
Publicaties
Peer-reviewed publicaties
Mix-method toolbox for monitoring greenhouse gas production and microbiome responses to soil amendments
https://doi.org/10.1016/j.mex.2024.102699In this study, we adopt an interdisciplinary approach, integrating agronomic field experiments with soil chemistry, molecular biology techniques, and statistics to investigate the impact of organic residue amendments, such as vinasse (a by-product of sugarcane ethanol production), on soil microbiome and greenhouse gas (GHG) production. The research investigates the effects of distinct disturbances, including organic residue application alone or combined with inorganic N fertilizer on the environment. The methods assess soil microbiome dynamics (composition and function), GHG emissions, and plant productivity. Detailed steps for field experimental setup, soil sampling, soil chemical analyses, determination of bacterial and fungal community diversity, quantification of genes related to nitrification and denitrification pathways, measurement and analysis of gas fluxes (N2O, CH4, and CO2), and determination of plant productivity are provided. The outcomes of the methods are detailed in our publications (Lourenço et al., 2018a; Lourenço et al., 2018b; Lourenço et al., 2019; Lourenço et al., 2020). Additionally, the statistical methods and scripts used for analyzing large datasets are outlined. The aim is to assist researchers by addressing common challenges in large-scale field experiments, offering practical recommendations to avoid common pitfalls, and proposing potential analyses, thereby encouraging collaboration among diverse research groups. • Interdisciplinary methods and scientific questions allow for exploring broader interconnected environmental problems. • The proposed method can serve as a model and protocol for evaluating the impact of soil amendments on soil microbiome, GHG emissions, and plant productivity, promoting more sustainable management practices. • Time-series data can offer detailed insights into specific ecosystems, particularly concerning soil microbiota (taxonomy and functions).
Cultivar governs plant response to inoculation with single isolates and the microbiome associated with arbuscular mycorrhizal fungi
https://doi.org/10.1016/j.apsoil.2024.105347Plant 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.
A Comparison of Different Protocols for the Extraction of Microbial DNA Inhabiting Synthetic Mars Simulant Soil
Compared with typical Earth soil, Martian soil and Mars simulant soils have distinct properties, including pH > 8.0 and high contents of silicates, iron-rich minerals, sulfates, and metal oxides. This unique soil matrix poses a major challenge for extracting microbial DNA. In particular, mineral adsorption and the generation of destructive hydroxyl radicals through cationic redox cycling may interfere with DNA extraction. This study evaluated different protocols for extracting microbial DNA from Mars Global Simulant (MGS-1), a Mars simulant soil. Two commercial kits were tested: the FastDNA SPIN Kit for soil (“MP kit”) and the DNeasy PowerSoil Pro Kit (“PowerSoil kit”). MGS-1 was incubated with living soil for five weeks, and DNA was extracted from aliquots using the kits. After extraction, the DNA was quantified with a NanoDrop spectrophotometer and used as the template for 16S rRNA gene amplicon sequencing and qPCR. The MP kit was the most efficient, yielding approximately four times more DNA than the PowerSoil kit. DNA extracted using the MP kit with 0.5 g soil resulted in 28,642–37,805 16S rRNA gene sequence reads and 30,380–42,070 16S rRNA gene copies, whereas the 16S rRNA gene could not be amplified from DNA extracted using the PowerSoil kit. We suggest that the FastDNA SPIN Kit is the best option for studying microbial communities in Mars simulant soils.https://doi.org/10.3390/microorganisms12040760Soil substrate source drives the microbes involved in the degradation of gelatin used as a biostimulant
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.https://doi.org/10.1016/j.apsoil.2023.104906Transcriptional regulation underlying the temperature response of embryonic development rate in the winter moth
https://doi.org/10.1111/mec.16705Climate change will strongly affect the developmental timing of insects, as their development rate depends largely on ambient temperature. However, we know little about the genetic mechanisms underlying the temperature sensitivity of embryonic development in insects. We investigated embryonic development rate in the winter moth (Operophtera brumata), a species with egg dormancy which has been under selection due to climate change. We used RNA sequencing to investigate which genes are involved in the regulation of winter moth embryonic development rate in response to temperature. Over the course of development, we sampled eggs before and after an experimental change in ambient temperature, including two early development weeks when the temperature sensitivity of eggs is low and two late development weeks when temperature sensitivity is high. We found temperature-responsive genes that responded in a similar way across development, as well as genes with a temperature response specific to a particular development week. Moreover, we identified genes whose temperature effect size changed around the switch in temperature sensitivity of development rate. Interesting candidate genes for regulating the temperature sensitivity of egg development rate included genes involved in histone modification, hormonal signalling, nervous system development and circadian clock genes. The diverse sets of temperature-responsive genes we found here indicate that there are many potential targets of selection to change the temperature sensitivity of embryonic development rate. Identifying for which of these genes there is genetic variation in wild insect populations will give insight into their adaptive potential in the face of climate change.
Rhizosphere microbiome response to host genetic variability
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.https://doi.org/10.1093/femsec/fiac061Responses of Acidobacteria Granulicella sp. WH15 to high carbon revealed by integrated omics analyses
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.https://doi.org/10.3390/microorganisms8020244Cultivation-independent and cultivation-dependent metagenomes reveal genetic and enzymatic potential of microbial community involved in the degradation of a complex microbial polymer
Backgroundhttps://doi.org/10.1186/s40168-020-00836-7
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.
Results
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.
Conclusions
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.Exploration of tissue-specific gene expression patterns underlying timing of breeding in contrasting temperature environments in a song bird
Seasonal timing of breeding is a life history trait with major fitness consequences but the genetic basis of the physiological mechanism underlying it, and how gene expression is affected by date and temperature, is not well known. In order to study this, we measured patterns of gene expression over different time points in three different tissues of the hypothalamic-pituitary-gonadal-liver axis, and investigated specifically how temperature affects this axis during breeding. We studied female great tits (Parus major) from lines artificially selected for early and late timing of breeding that were housed in two contrasting temperature environments in climate-controlled aviaries. We collected hypothalamus, liver and ovary samples at three different time points (before and after onset of egg-laying). For each tissue, we sequenced whole transcriptomes of 12 pools (n = 3 females) to analyse gene expression.https://doi.org/10.1186/s12864-019-6043-0Nitrification inhibitors effectively target N2O-producing Nitrosospira spp. in tropical soil
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.https://doi.org/10.1111/1462-2920.14557Fine-tuning of seasonal timing of breeding is regulated downstream in the underlying neuro-endocrine system in a small songbird
Timing of breeding is under selection in wild populations due to climate change, and understanding the underlying physiological processes mediating timing provides insight in the potential rate of adaptation. Current knowledge on this variation in physiology is, however, mostly limited to males. We assessed whether individual differences in timing of breeding in females are reflected in differences in candidate gene expression and if so, whether these differences occur in the upstream (hypothalamus), or downstream (ovary and liver) parts of the neuroendocrine system. We used 72 female great tits from two generations of lines artificially selected for early and late egg-laying, which were housed in climate controlled aviaries and went through two breeding cycles within one year. In the first breeding season we obtained individual egg-laying dates, while in the second breeding season, using the same individuals, we sampled several tissues at three time points based on timing of the first breeding attempt. For each tissue, mRNA expression levels were measured using qPCR for a set of candidate genes associated with timing of reproduction and subsequently analysed for differences between generations, time points and individual timing of breeding. We found differences in gene expression between generations in all tissues with most pronounced differences in the hypothalamus. Differences between time points, and early and late laying females, were found exclusively in ovary and liver. Altogether, we show that fine-tuning of seasonal timing of breeding, and thereby the opportunity for adaptation in the neuroendocrine system, is regulated mostly downstream in the neuro-endocrine system.https://doi.org/10.1242/jeb.202481Correction to
https://doi.org/10.1007/s00442-017-4001-6Unfortunately, Table 1 was incorrectly published in the original article and the same is corrected by this Erratum. The original article was corrected.
Resilience of the resident soil microbiome to organic and inorganic amendment disturbances and to temporary bacterial invasion
Backgroundhttps://doi.org/10.1186/s40168-018-0525-1
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.
Results
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.
Conclusion
Our analysis showed that the resident soil microbial community was not resistant to vinasse and inorganic N application but was highly resilient.Nitrosospira sp. govern nitrous oxide emissions in a tropical soil amended with residues of bioenergy crop
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.https://doi.org/10.3389/fmicb.2018.00674Insights on dispersal and recruitment paradigms: sex- and age-dependent variations in a nomadic breeder
Sex- and age-dependence in recruitment and dispersal are often explained by costs arising from competition for holding a breeding territory over the years—a typical feature of species living in stable habitats. For instance, long-lived birds with male territoriality often exhibit large variation in recruitment age and higher dispersal in females and young individuals. As a corollary, we expected that species with ephemeral habitat suitability, and hence nomadic breeding, would show weak age- and sex-dependence in dispersal and low variation in recruitment age, because territory ownership is not maintained over the years. In addition, the higher cost of reproduction in females might not be (over)compensated for by costs of territoriality in males. Accordingly, females would recruit later than males. We explored these variations using multievent capture–recapture models over 13 years, 3479 (2392 sexed) slender-billed gulls (Chroicocephalus genei) and 45 colony sites along the French Mediterranean coast. As expected, variability in recruitment age was low with males recruiting earlier than females. Nonetheless, dispersal in and out of the study area decreased with age and was slightly higher in males than in females. Decreased dispersal with age might result from foraging benefits associated with increased spatial familiarity. Higher dispersal in males might be explained by a male-biased sex ratio or higher philopatry benefits in females (arising from their higher cost of reproduction). Sex- and age-dependent dispersal and recruitment may thus occur in the absence of year-to-year breeding territory ownership, which stresses the importance of considering other processes in shaping recruitment and dispersal patterns.https://doi.org/10.1007/s00442-017-3972-7Dominance of bacterial ammonium oxidizers and fungal denitrifiers in the complex nitrogen cycle pathways related to nitrous oxide emission
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.https://doi.org/10.1111/gcbb.12519
Citing LiteratureRecycling organic residues in agriculture impacts soil-borne microbial community structure, function and N2O emissions.
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.https://doi.org/10.1016/j.scitotenv.2018.03.116Nitrous oxide emission related to ammonia-oxidizing bacteria and mitigation options from N fertilization in a tropical soil
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.https://doi.org/10.1038/srep30349The genome of the winter moth (Operophtera brumata) provides a genomic perspective on sexual dimorphism and phenology
The winter moth (Operophtera brumata) belongs to one of the most species-rich families in Lepidoptera, the Geometridae (approx. 23,000 species). This family is of great economic importance as most species are herbivorous and capable of defoliating trees. Genome assembly of the winter moth allows the study of genes and gene families, such as the cytochrome P450 gene family, which is known to be vital in plant secondary metabolite detoxification and host plant selection. It also enables exploration of the genomic basis for female brachyptery (wing reduction), a feature of sexual dimorphism in winter moth, and for seasonal timing, a trait extensively studied in this species. Here we present a reference genome for the winter moth, the first geometrid and largest sequenced Lepidopteran genome to date (638 Mb) including a set of 16,912 predicted protein-coding genes. This allowed us to assess the dynamics of evolution on a genome wide scale using the P450 gene family. We also identified an expanded gene family potentially linked to female brachyptery, and annotated the genes involved in the circadian clock mechanism as main candidates for involvement in seasonal timing. The genome will contribute to Lepidopteran genomic resources and comparative genomics. In addition, the genome enhances our ability to understand the genetic and molecular basis of insect seasonal timing and thereby provides a reference for future evolutionary and population studies on the winter moth.https://doi.org/10.1093/gbe/evv145Acidobacterial community responses to agricultural management of soybean in Amazon forest soils
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.https://doi.org/10.1111/1574-6941.12018Impacts of 3 years of elevated atmospheric CO2 on rhizosphere carbon flow and microbial community dynamics
Carbon (C) uptake by terrestrial ecosystems represents an important option for partially mitigating anthropogenic CO2 emissions. Short-term atmospheric elevated CO2 exposure has been shown to create major shifts in C flow routes and diversity of the active soil-borne microbial community. Long-term increases in CO2 have been hypothesized to have subtle effects due to the potential adaptation of soil microorganism to the increased flow of organic C. Here, we studied the effects of prolonged elevated atmospheric CO2 exposure on microbial C flow and microbial communities in the rhizosphere. Carex arenaria (a nonmycorrhizal plant species) and Festuca rubra (a mycorrhizal plant species) were grown at defined atmospheric conditions differing in CO2 concentration (350 and 700 ppm) for 3 years. During this period, C flow was assessed repeatedly (after 6 months, 1, 2, and 3 years) by C-13 pulse-chase experiments, and label was tracked through the rhizosphere bacterial, general fungal, and arbuscular mycorrhizal fungal (AMF) communities. Fatty acid biomarker analyses and RNA-stable isotope probing (RNA-SIP), in combination with real-time PCR and PCR-DGGE, were used to examine microbial community dynamics and abundance. Throughout the experiment the influence of elevated CO2 was highly plant dependent, with the mycorrhizal plant exerting a greater influence on both bacterial and fungal communities. Biomarker data confirmed that rhizodeposited C was first processed by AMF and subsequently transferred to bacterial and fungal communities in the rhizosphere soil. Over the course of 3 years, elevated CO2 caused a continuous increase in the C-13 enrichment retained in AMF and an increasing delay in the transfer of C to the bacterial community. These results show that, not only do elevated atmospheric CO2 conditions induce changes in rhizosphere C flow and dynamics but also continue to develop over multiple seasons, thereby affecting terrestrial ecosystems C utilization processes. [KEYWORDS: C-13 arbuscular mycorrhizal fungi bacterial communities Carex arenaria elevated CO2 Festuca rubra fungal communities N/PLFA rhizosphere RNA-SIP mycorrhizal fungi climate-change fatty-acids arbuscular mycorrhizae environmental-change soil nitrogen plant microorganisms enrichment]https://doi.org/10.1111/gcb.12045A comparison of rpoB and 16S rRNA as markers in pyrosequencing studies of bacterial diversity
Background The 16S rRNA gene is the gold standard in molecular surveys of bacterial and archaeal diversity, but it has the disadvantages that it is often multiple-copy, has little resolution below the species level and cannot be readily interpreted in an evolutionary framework. We compared the 16S rRNA marker with the single-copy, protein-coding rpoB marker by amplifying and sequencing both from a single soil sample. Because the higher genetic resolution of the rpoB gene prohibits its use as a universal marker, we employed consensus-degenerate primers targeting the Proteobacteria. Methodology/Principal Findings Pyrosequencing can be problematic because of the poor resolution of homopolymer runs. As these erroneous runs disrupt the reading frame of protein-coding sequences, removal of sequences containing nonsense mutations was found to be a valuable filter in addition to flowgram-based denoising. Although both markers gave similar estimates of total diversity, the rpoB marker revealed more species, requiring an order of magnitude fewer reads to obtain 90% of the true diversity. The application of population genetic methods was demonstrated on a particularly abundant sequence cluster. Conclusions/Significance The rpoB marker can be a complement to the 16S rRNA marker for high throughput microbial diversity studies focusing on specific taxonomic groups. Additional error filtering is possible and tests for recombination or selection can be employed.https://doi.org/10.1371/journal.pone.0030600Soil characteristics more strongly influence soil bacterial communities than land-use type
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.https://doi.org/10.1111/j.1574-6941.2011.01192.xShifting carbon flow from roots into associated microbial communities in response to elevated atmospheric CO2
Rising atmospheric CO2 levels are predicted to have major consequences on carbon cycling and the functioning of terrestrial ecosystems. Increased photosynthetic activity is expected, especially for C-3 plants, thereby influencing vegetation dynamics; however, little is known about the path of fixed carbon into soil-borne communities and resulting feedbacks on ecosystem function. Here, we examine how arbuscular mycorrhizal fungi (AMF) act as a major conduit in the transfer of carbon between plants and soil and how elevated atmospheric CO2 modulates the belowground translocation pathway of plant-fixed carbon. Shifts in active AMF species under elevated atmospheric CO2 conditions are coupled to changes within active rhizosphere bacterial and fungal communities. Thus, as opposed to simply increasing the activity of soil-borne microbes through enhanced rhizodeposition, elevated atmospheric CO2 clearly evokes the emergence of distinct opportunistic plant-associated microbial communities. Analyses involving RNA-based stable isotope probing, neutral/phosphate lipid fatty acids stable isotope probing, community fingerprinting, and real-time PCR allowed us to trace plant-fixed carbon to the affected soil-borne microorganisms. Based on our data, we present a conceptual model in which plant-assimilated carbon is rapidly transferred to AMF, followed by a slower release from AMF to the bacterial and fungal populations well-adapted to the prevailing (myco-)rhizosphere conditions. This model provides a general framework for reappraising carbon-flow paths in soils, facilitating predictions of future interactions between rising atmospheric CO2 concentrations and terrestrial ecosystems.https://doi.org/10.1073/pnas.0912421107
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Video Byte: Forest floor microbes produce tough biofilm breaker
Background
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.
Results
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.
Conclusions
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.
Projecten & samenwerkingen
Projecten
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Deciphering the role of fungal denitrifiers in N2O production from soils
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.
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The role of beneficial microbe in soil aggregation
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.
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Microbial Farming to increase plant productivity
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.
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Harnessing the rhizosphere microbiome to enhance plant productivity
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
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REPHORM - REcycled PHOsphorus Resolved by Microbes
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.
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Farming microbial community for plant probiotic - MicroProFarm
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.
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Unravelling the mechanisms underlying health and productivity promoting agricultural practices by fine-mapping rhizosphere communities
Plant species shape their own rhizosphere community, and on its turn selected soil biota shape the growth and development of plants.
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Microbial Networks controlling soil greenhouse gases emissions
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.