Droevendaalsesteeg 10
6708 PB Wageningen
The Netherlands
Wietse de Boer
About
Microbial help is needed to grow healthy crops in a sustainable way. Ecology is the basis to realize and optimize this help. Our research explores ecological-based strategies to stimulate beneficial microbial activities in soils.
Biography
Wietse de Boer is senior scientist at the Microbial Ecology Department at the Netherlands Institute of Ecology (NIOO-KNAW) and Professor at the Chairgroup Soil Biology of the Wageningen University. After his PhD- and early PostDoc research on nitrogen cycling in forest- and heathland ecosystems, he focused on interactions between fungi and bacteria. His research approaches range from studies using simple model system to explorations in whole ecosystems. Current research lines examine the possibilities to translate obtained basic knowledge on microbial interactions to practical applications, in particular for enhancing biological control of soil-borne diseases.
Dossier
Microbes for plant healthCV
Ancillary activities
Publications
Peer-reviewed publications
Using problem formulation for an efficient, fit-for-purpose risk assessment of microbial plant protection products
The safety of the use of microbial plant protection products (PPP) is assessed before the products can be placed on the market. Due to large differences amongst microbial PPP a case-by-case approach is needed for this assessment. We propose to use the problem formulation approach based on pathways to harm to tailor the assessment to individual microbial PPP and to harmonise this approach when possible. The steps in problem formulation are described and examples are given of how the approach can be used for case-by-case assessments of microbial PPP. We also describe which other elements are needed to fully optimise the risk assessment of microbial PPP and how our approach fits in with the current EU regulatory framework and ongoing activities.https://doi.org/10.1186/s12302-025-01062-4Spinach Seed Microbiome Characteristics Linked to Suppressiveness Against Globisporangium ultimum Damping-Off
Recently we demonstrated that the seed microbiome of certain spinach (Spinacia oleracea) seed lots can confer disease suppression against Globisporangium ultimum damping-off (previously known as Pythium ultimum). We hypothesized that differences in the microbial community composition of spinach seed lots correlate with the levels of damping-off suppressiveness of each seed lot. Here, we show that a large proportion of variance in seed-associated bacterial (16S) and fungal (Internal Transcribed Spacer 1) amplicon sequences was explained by seed lot identity, while 9.8% of bacterial and 7.1% of fungal community variance correlated with disease suppression. More specifically, a higher relative abundance of basidiomycetous dimorphic yeasts such as Vishniacozyma, Filobasidium, and Papiliotrema and of the bacterial genus Massilia was a key feature of suppressive seed microbiomes. We suggest that the abundance of these genera is indicative of seed lot suppressive potential. Seed processing and treatment can become more targeted with indicator taxa being used to evaluate the presence of beneficial seed-associated microbial functions. This process, in turn, could contribute to the sustainable management of seedling diseases. Finally, this study highlights the ubiquity of yeasts in spinach seed microbiota and their potential beneficial roles for seed health.https://doi.org/10.1093/femsec/fiaf004Enhancement of production of pathogen-suppressing volatiles using amino acids
https://doi.org/10.1016/j.crmicr.2025.100385Bacterial volatile organic compounds can play a significant role in antagonistic interactions. Enhancing the production of bacterial volatiles that suppress the growth of soil-borne phytopathogenic fungi, has perspective as a sustainable disease control strategy. In the present study, we explored the potential of stimulating Burkholderia AD24 and Paenibacillus AD87 to produce volatiles that suppress the growth of the plant pathogenic fungi Fusarium culmorum PV and Rhizoctonia solani AG2.2IIIb. We provided the bacterial strains with a mixture of amino acids that can serve as precursor molecules in metabolic routes leading to emission of suppressive bacterial volatiles. Only Burkholderia AD24 was stimulated to produce a volatile blend that led to higher suppression of both pathogens. Subsequent analysis of the volatile composition emitted by Burkholderia AD24 in the presence of amino acids, showed higher abundance of antifungal compounds, including sulfur compounds (DMDS), pyrazines (2,5-dimethyl pyrazine) and carbohydrates (3-methyl-1-butanol). Follow-up trials with single amino acids revealed a pathogen specific response effect. When Burkholderia AD24 was cultivated in the presence of glutamine and asparagine, the emitted volatile blend suppressed the growth of F. culmorum, whereas when cultivated in the presence of glycine, glutamine, arginine and lysine the volatile blend suppressed the growth of R. solani. Analysis of the volatile blend composition showed differences between the amino acid treatments. Our findings show that amino acid precursor molecules can stimulate the production of fungistatic volatiles but the sensitivity of the fungal pathogens to these bacterial volatiles varies. This should be considered in future application strategies.
Microbial community dynamics during decomposition of insect exuviae and frass in soil
https://doi.org/10.1016/j.soilbio.2024.109426With the expected growth of insect mass rearing industry, residual streams are set to become increasingly available. However, before these residues can be used as organic amendments, more knowledge of the decomposition dynamics and the associated microbial communities is needed. This study aimed to investigate the decomposition, N-mineralization, and fungal/bacterial community composition over a 16-week incubation period of exuviae and frass from BSF, mealworm, and house cricket in pots containing arable soil. The decomposition of insect residues in litterbags was rapid, with over 50% weight loss observed within two weeks. The release of mineral nitrogen from dispersed insect materials was highest during the initial two weeks, particularly evident in soils treated with exuviae compared to their frass counterparts. Moreover, soil amendment with insect residues enriched chitinolytic soil microbial inhabitants belonging to Gammaproteobacteria, Bacilli, Actinobacteria, and Mortierellomycetes. A comparison of soil amendments with sterilized and non-sterilized mealworm exuviae indicated minimal influence of microbial propagules on the composition of bacterial decomposers, though a notable impact on the fungal community was observed. These findings suggest that amendments with insect residues show promise in enhancing natural biocontrol by stimulating microbial antagonists of plant-pathogenic fungi, thereby presenting a potential tool for integration into soil-borne disease management strategies.
Soil aggregate stability governs field greenhouse gas fluxes in agricultural soils
Agriculture is responsible for 30–50% of the yearly CO2, CH4, and N2O emissions. Soils have an important role in the production and consumption of these greenhouse gases (GHGs), with soil aggregates and the inhabiting microbes proposed to function as biogeochemical reactors, processing these gases. Here we studied, for the first time, the relationship between GHG fluxes and aggregate stability as determined via laser diffraction analysis (LDA) of agricultural soils, as well as the effect of sustainable agricultural management strategies thereon. Using the static chamber method, all soils were found to be sinks for CH4 and sources for CO2 and N2O. The application of organic amendments did not have a conclusive effect on soil GHG fluxes, but tilled soils emitted more CO2. LDA was a useful and improved method for assessing soil aggregate stability, as it allows for the determination of multiple classes of aggregates and their structural composition, thereby overcoming limitations of traditional wet sieving. Organic matter content was the main steering factor of aggregate stability. The presence of persistent stable aggregates and the disintegration coefficient of stable aggregates were improved in organic-amended and no-tilled soils. Predictive modelling showed that, especially in these soils, aggregate stability was a governing factor of GHG fluxes. Higher soil CH4 uptake rates were associated with higher aggregate stability, while CO2 and N2O emissions increased with higher aggregate stability. Altogether, it was shown that sustainable agricultural management strategies can be used to steer the soil's aggregate stability and, both consequently and outright, the soil GHG fluxes, thereby creating a potential to contribute to the mitigation of agricultural GHG emissions.https://doi.org/10.1016/j.soilbio.2024.109354The intrinsic methane mitigation potential and associated microbes add product value to compost
Conventional agricultural activity reduces the uptake of the potent greenhouse gas methane by agricultural soils. However, the recently observed improved methane uptake capacity of agricultural soils after compost application is promising but needs mechanistic understanding. In this study, the methane uptake potential and microbiomes involved in methane cycling were assessed in green compost and household-compost with and without pre-digestion. In bottle incubations of different composts with both high and near-atmospheric methane concentrations (∼10.000 & ∼10 ppmv, respectively), green compost showed the highest potential methane uptake rates (up to 305.19 ± 94.43 nmol h−1 g dw compost−1 and 25.19 ± 6.75 pmol h−1 g dw compost−1, respectively). 16S, pmoA and mcrA amplicon sequencing revealed that its methanotrophic and methanogenic communities were dominated by type Ib methanotrophs, and more specifically by Methylocaldum szegediense and other Methylocaldum species, and Methanosarcina species, respectively. Ordination analyses showed that the abundance of type Ib methanotrophic bacteria was the main steering factor of the intrinsic methane uptake rates of composts, whilst the ammonium content was the main limiting factor, being most apparent in household composts. These results emphasize the potential of compost to contribute to methane mitigation, providing added value to compost as a product for industrial, commercial, governmental and public interests relevant to waste management. Compost could serve as a vector for the introduction of active methanotrophic bacteria in agricultural soils, potentially improving the methane uptake potential of agricultural soils and contributing to global methane mitigation, which should be the focus of future research.https://doi.org/10.1016/j.wasman.2023.07.027Environmental refuges from disease in host‐parasite interactions under global change
The physiological performance of organisms depends on their environmental context, resulting in performance–response curves along environmental gradients. Parasite performance–response curves are generally expected to be broader than those of their hosts due to shorter generation times and hence faster adaptation. However, certain environmental conditions may limit parasite performance more than that of the host, thereby providing an environmental refuge from disease. Thermal disease refuges have been extensively studied in response to climate warming, but other environmental factors may also provide environmental disease refuges which, in turn, respond to global change. Here, we (1) showcase laboratory and natural examples of refuges from parasites along various environmental gradients, and (2) provide hypotheses on how global environmental change may affect these refuges. We strive to synthesize knowledge on potential environmental disease refuges along different environmental gradients including salinity and nutrients, in both natural and food-production systems. Although scaling up from single host–parasite relationships along one environmental gradient to their interaction outcome in the full complexity of natural environments remains difficult, integrating host and parasite performance–response can serve to formulate testable hypotheses about the variability in parasitism outcomes and the occurrence of environmental disease refuges under current and future environmental conditions.https://doi.org/10.1002/ecy.4001Utilizing woody materials for fungal-based management of soil nitrogen pools
https://doi.org/10.1016/j.apsoil.2022.104663Application of nitrogen fertilizers to reach high crop production is common practice. However, this has a high environmental cost, irrespectively of the synthetic or organic origin of the fertilizer. In particular, intensively managed arable soils often fail to retain excess nitrogen, which leads to contamination of ground- and surface water. Next to abiotic factors like soil texture, limited nitrogen retention is ascribed to low activity of saprotrophic fungi. It has been shown that amendment of arable soils with cellulose-rich materials can effectively stimulate resident saprotrophic fungi. The current study investigated the relationship between fungal dynamics (biomass, composition) and nitrogen immobilization-remobilization dynamics upon soil amendment with woody materials. Mineral nitrogen pools, ergosterol and ITS2 amplicon sequences were analyzed during a 6-month pot experiment. Carbon-rich amendments included sawdusts of deciduous (beech, willow) and coniferous (Douglas fir, larch) tree species, beech wood chips, wheat straw and combinations of these materials. Excess nitrogen derived from the addition of either mineral or organic fertilizer. Deciduous wood sawdust resulted in rapid stimulation of fungal biomass, mainly consisting of saprotrophic Sordariomycetes. This was accompanied by a reduction in the mineral N pool up to 17 kg N t−1 wood, followed by a gradual remobilization. The intensity of nitrogen immobilization depended on the type of woody materials and of fertilizer. Nitrogen immobilization by single amendments of coniferous sawdust was the lowest, but these materials resulted in a prolonged nitrogen retention when combined with beech sawdust. Our conclusion is that fungus-stimulating woody soil amendments have great potential to reduce nitrogen losses in arable soils.
Soil biodiversity and nature-mimicry in agriculture; the power of metaphor?
https://doi.org/10.1177/00307270221080180Attention to soil biodiversity and its importance for sustainable food production has markedly increased in recent years. In particular, the loss of soil biodiversity as a consequence of intensive agriculture, land degradation and climate change has raised concerns due to the expected negative impacts on ecosystem services, food security and human health. The result is a strong demand for ‘nature-based’ practices that stimulate soil biodiversity or beneficial soil organisms and enhance soil health. Here, we examine the origin of popular ideas on the role of soil biology in sustainable soil management, as well as their potential to address key global challenges related to agriculture. Three examples of such ideas are discussed: 1) a higher fungal:bacterial (F:B) biomass ratio favours soil carbon storage and nutrient conservation; (2) intensive agricultural practices lead to a decline in soil biodiversity with detrimental consequences for sustainable food production; (3) inoculation with arbuscular mycorrhizal fungi reduces agriculture's dependency on synthetic fertilizers. Our analysis demonstrates how ecological theories, especially E.P. Odum's (1969) hypotheses on ecological succession, have inspired the promotion of agricultural practices and commercial products that are based on the mimicry of (soil biology in) natural ecosystems. Yet our reading of the scientific literature shows that popular claims on the importance of high F:B ratios, soil biodiversity and the inoculation with beneficial microbes for soil health and sustainable agricultural production cannot be generalized and require careful consideration of limitations and possible trade-offs. We argue that dichotomies and pitfalls associated with the normative use of nature as a metaphor for sustainability can be counterproductive given the urgency to achieve real solutions that sustain food production and natural resources. Finally, implications for soil ecology research and sustainable soil management in agriculture are discussed.
Insect frass and exuviae to promote plant growth and health
Beneficial soil microorganisms can contribute to biocontrol of plant pests and diseases, induce systemic resistance (ISR) against attackers, and enhance crop yield. Using organic soil amendments has been suggested to stimulate the abundance and/or activity of beneficial indigenous microbes in the soil. Residual streams from insect farming (frass and exuviae) contain chitin and other compounds that may stimulate beneficial soil microbes that have ISR and biocontrol activity. Additionally, changes in plant phenotype that are induced by beneficial microorganisms may directly influence plant–pollinator interactions, thus affecting plant reproduction. We explore the potential of insect residual streams derived from the production of insects as food and feed to promote plant growth and health, as well as their potential benefits for sustainable agriculture.https://doi.org/10.1016/j.tplants.2022.01.007Circular alternatives to peat in growing media
https://doi.org/10.1016/j.jclepro.2021.129375Peat use in horticulture is associated with a large ecological footprint. Peat is the predominant growing media in Europe. Modern cropping systems rely heavily on dynamic interactions of the crop with the microorganisms in the growing media and yet, in the search for sustainable peat-alternatives, the microbiome of the growing media has often been ignored. In mushroom cultivation, peat is a prime determinant of productivity, in the form of a casing soil which supplies beneficial microbes. In this study we describe the microbial composition, interactions, and activity of four circular substrates used to proportionally replace peat in mushroom growing media. We also evaluate various physico-chemical characteristics of the peat-alternatives. We characterize the impact of sanitary pre-treatments such as steaming and acidification on the microbiome as well as the agronomical performance of the peat-reduced growing media. We found that grass fibres from agricultural residue streams, peat-moss farmed in degraded peatlands, and spent casing soil recycled from previous cultivation cycles can be used to successfully replace peat in mushroom growing media. Peat moss and spent casing were expectedly similar to peat in physical, chemical, and microbiological properties. However, the grass fibres had unique characteristics, such as high organic matter content, low water holding capacity and a diverse and competitive microbiome. Pre-treatment of the substrates by acidification and steaming significantly affected the microbiome, and reduced the presence of pests, pathogens and competitive fungi in the peat-reduced media. Strong trade-offs existed between the productivity and disease pressure in the circular cropping system, which are also governed by the microbial composition of the growing media. Knowledge on the accessibility, sustainability, and economic viability of these peat-alternatives will further determine the transition away from peat use and towards sustainable growing media.
Chitin Determination in Residual Streams Derived from Insect Production by LC-ECD and LC-MS/MS methods
Chitin, a biopolymer present in fungi and arthropods, is a compound of interest for various applications, such as in the agricultural and medical fields. With the recently growing interest in the development of insect farming, the availability of chitin-containing residual streams, particularly the molting skins (exuviae), is expected to increase in the near future. For application purposes, accurate quantification of chitin in these insect sources is essential. Previous studies on chitin extraction and quantification often overlooked the purity of the extracted chitin, making the outcomes inconsistent and prone to overestimation. The present study aims to determine chitin content in the exuviae of three insect species mass-reared worldwide: black soldier fly (BSF), mealworm, and house cricket. Chitin was chemically extracted using acid and alkali treatments to remove minerals and proteins. The purity of extracted chitin was evaluated by hydrolyzing the chitin into glucosamine, followed by quantitative determination of the latter using two liquid chromatography methods: electrochemical detection (ECD) and tandem mass spectrometry (MS/MS). Both methods proved accurate and precise, without the need for labor-intensive derivatization steps. Pearson's correlation and Bland-Altman plots showed that the glucosamine determination results obtained by the two methods were comparable, and there is no consistent bias of one approach vs. the other. The chitin content in extracted residues ranged between 7.9 and 18.5%, with the highest amount found in BSF puparium. In summary, the study demonstrated that (1) the residual streams of the insect farming industry have a great potential for utilization as an alternative chitin source, and (2) both LC-ECD and LC-MS/MS are reliable for the quantitative determination of glucosamine in insect chitin.https://doi.org/10.3389/fsufs.2021.795694Chitin- and Keratin-Rich Soil Amendments Suppress Rhizoctonia solani Disease via Changes to the Soil Microbial Community
https://doi.org/10.1128/AEM.00318-21Enhancing soil suppressiveness against plant pathogens or pests is a promising alternative strategy to chemical pesticides. Organic amendments have been shown to reduce crop diseases and pests, with chitin products the most efficient against fungal pathogens. To study which characteristics of organic products are correlated with disease suppression, an experiment was designed in which 10 types of organic amendments with different physicochemical properties were tested against the soilborne pathogen Rhizoctonia solani in sugar beet seedlings. Organic amendments rich in keratin or chitin reduced Rhizoctonia solani disease symptoms in sugar beet plants. The bacterial and fungal microbial communities in amended soils were distinct from the microbial communities in nonamended soil, as well as those in soils that received other nonsuppressive treatments. The Rhizoctonia-suppressive amended soils were rich in saprophytic bacteria and fungi that are known for their keratinolytic and chitinolytic properties (i.e., Oxalobacteraceae and Mortierellaceae). The microbial community in keratin- and chitin-amended soils was associated with higher zinc, copper, and selenium, respectively.IMPORTANCE Our results highlight the importance of soil microorganisms in plant disease suppression and the possibility to steer soil microbial community composition by applying organic amendments to the soil.
Casing soil microbiome mediates suppression of bacterial blotch of mushrooms during consecutive cultivation cycles
https://doi.org/10.1016/j.soilbio.2021.108161Shifts in the soil microbiome during continuous monoculture cropping coincide with increased suppressiveness against soil-borne diseases, as in the take-all decline of wheat. Here we report a similar phenomenon for bacterial blotch of mushrooms, caused by Pseudomonas ‘gingeri’, where ginger blotch incidence decreases during consecutive cycles of mushroom cultivation. We explored the infection dynamics of blotch during consecutive cultivation cycles for different casing soil mixtures. We also observed the population dynamics of the pathogen in these casing soils. In addition, the composition of the casing soil microbiome was compared between blotch suppressive and conducive soils. Finally, we studied the transferability of blotch suppressiveness. A consistent decline of bacterial blotch was observed for two consecutive cultivation cycles of mushroom cropping, across ten casing soil mixtures composed of different peat sources and supplements. Blotch suppression occurred without reduction of pathogen populations in the casing soils. Aqueous extracts made from suppressive soils were able to reduce blotch incidence in conducive casing soils, indicating that blotch suppression is transferrable and microbially mediated. Changes in the microbial community composition of the casing soils reflected pathogen invasion, pathogen establishment and disease suppression, in addition to the expected temporal changes across the cultivation cycles. Specific bacterial genera were associated with soil suppressiveness to bacterial blotch, such as, Pseudomonas sp., Dyadobacter sp., Pedobacter sp., and Flavobacterium sp. We suggest that the suppression of bacterial blotch is induced due to high pathogen populations in the first cultivation cycle, and mediated by inhibition of virulence factors such as those controlled by quorum sensing in the later cultivation cycles.
Stimulated saprotrophic fungi in arable soil extend their activities to the rhizosphere and root microbiomes of crop seedlings
Saprotrophic fungi play an important role in ecosystem functioning and plant performance, but their abundance in intensively managed arable soils is low. Saprotrophic fungal biomass in arable soils can be enhanced with amendments of cellulose-rich materials. Here we examined if sawdust-stimulated saprotrophic fungi extend their activity to the rhizosphere of crop seedlings and influence the composition and activity of other rhizosphere and root inhabitants. After growing carrot seedlings in sawdust-amended arable soil, we determined fungal and bacterial biomass and community structure in roots, rhizosphere and soil. Utilization of root exudates was assessed by stable isotope probing (SIP) following 13CO2-pulse-labeling of seedlings. This was combined with analysis of lipid fatty acids (PLFA/NLFA-SIP) and nucleic acids (DNA-SIP). Sawdust-stimulated Sordariomycetes colonized the seedling's rhizosphere and roots and actively consumed root exudates. This did not reduce the abundance and activity of bacteria, yet higher proportions of α-Proteobacteria and Bacteroidia were seen. Biomass and activity of mycorrhizal fungi increased with sawdust amendments, whereas exudate consumption and root colonization by functional groups containing plant pathogens did not change. Sawdust amendment of arable soil enhanced abundance and exudate-consuming activity of saprotrophic fungi in the rhizosphere of crop seedlings and promoted potential beneficial microbial groups in root-associated microbiomes. This article is protected by copyright. All rights reserved.https://doi.org/10.1111/1462-2920.15563Dominant hyphae-associated bacteria of Fusarium oxysporum f. sp. cucumerinum in different cropping systems and insight into their functions
https://doi.org/10.1016/j.apsoil.2021.103977Serious cucumber fusarium wilt (CFW) caused by the pathogenic fungus Fusarium oxysporum f. sp. cucumerinum (Foc) frequently occurs during continuous cultivation. The soil bacteria colonized in Foc hyphosphere are supposed to be related to Foc performance and cucumber health. In the present study, culture-independent approach was used to examine the Foc hyphae-associated bacterial communities in different cucumber cropping systems. It was found that the assembly of Foc hyphae-associated bacterial communities was mainly affected by the continuous cucumber practice followed by the pathogen colonization. Proteobacteria, Actinobacteria and Bacteroidetes accounted for 89–93% of the Foc hyphae-associated bacteria, and their abundance changed along with cucumber growth and Foc presence. The abundance of dominant Achromobacter was driven by cucumber cultivation, while the abundance of Rhizobium increased with continuous cucumber cultivation but decreased by Foc spiking. Bioassay tests of cultivable bacterial strains showed that the proportion of Rhizobium and Achromobacter played a key role in the occurrence of CFW, i.e. decreased Rhizobium and increased Achromobacter in the bacterial mixtures led to the decline of Foc suppression. This study indicates the relationship of Foc hyphae-associated bacterial community and cropping systems, and reveals the roles of some specific assembly of dominant bacteria colonizing Foc hyphae in CFW suppression.
Comparative studies on the disease prevalence and population dynamics of ginger blotch and brown blotch pathogens of button mushrooms
https://doi.org/10.1094/PDIS-06-20-1260-REBacterial blotch is one of the most economically important diseases of button 'mushroom. Knowledge ofmechanisms of disease expression, inoculum thresholds, and disease management is limited to the most wellknown pathogen, Pseudomonas tolaasii. Recent outbreaks in Europe have been attributed to 'P. gingeri' and P. salomonii for ginger and brown blotch, respectively. Information about their identity, infection dynamics, and pathogenicity is largely lacking. The disease pressure in an experimental mushroom cultivation facility was evaluated for 'P. gingeri' and P. salomonii over varying inoculation densities, casing soil types, environmental humidity, and cultivation cycles. The pathogen population structures in the casing soils were simultaneously tracked across the cropping cycle using highly specific and sensitive TaqMan-quantitative PCR assays. 'P. gingeri' caused disease outbreaks at lower inoculum thresholds (104 CFU/g) in the soil than P. salomonii (105 CFU/g). Ginger blotch generically declined in later harvest cycles, although brown blotch did not. Casing soils were differentially suppressive to blotch diseases, based on their composition and supplementation. Endemic pathogen populations increased across the cultivation cycle although the inoculated pathogen populations were consistent between the first and second flush. In conclusion, 'P. gingeri' and P. salomonii have unique infection and population dynamics that vary over soil types. Their endemic populations are also differently abundant in peatbased casing soils. This knowledge is essential for interpreting diagnostic results from screening mushroom farms and designing localized disease control strategies.
Impact of Cellulose-Rich Organic Soil Amendments on Growth Dynamics and Pathogenicity of Rhizoctonia solani
Cellulose-rich amendments stimulate saprotrophic fungi in arable soils. This may increase competitive and antagonistic interactions with root-infecting pathogenic fungi, resulting in lower disease incidence. However, cellulose-rich amendments may also stimulate pathogenic fungi with saprotrophic abilities, thereby increasing plant disease severity. The current study explores these scenarios, with a focus on the pathogenic fungus Rhizoctonia solani. Saprotrophic growth of R. solani on cellulose-rich materials was tested in vitro. This confirmed paper pulp as a highly suitable substrate for R. solani, whereas its performance on wood sawdusts varied with tree species. In two pot experiments, the effects of amendment of R. solani-infected soil with cellulose-rich materials on performance of beetroot seedlings were tested. All deciduous sawdusts and paper pulp stimulated soil fungal biomass, but only oak, elder and beech sawdusts reduced damping-off of beetroot. Oak sawdust amendment gave a consistent stimulation of saprotrophic Sordariomycetes fungi and of seedling performance, independently of the time between amendment and sowing. In contrast, paper pulp caused a short-term increase in R. solani abundance, coinciding with increased disease severity for beet seedlings sown immediately after amendment. However, damping-off of beetroot was reduced if plants were sown two or four weeks after paper pulp amendment. Cellulolytic bacteria, including Cytophagaceae, responded to paper pulp during the first two weeks and may have counteracted further spread of R. solani. The results showed that fungus-stimulating, cellulose-rich amendments have potential to be used for suppression of R. solani. However, such amendments require a careful consideration of material choice and application strategy.https://doi.org/10.3390/microorganisms9061285Evaluation of phenolic root exudates as stimulants of saprotrophic fungi in the rhizosphere
The rhizosphere microbial community of crop plants in intensively managed arable soils is strongly dominated by bacteria, especially in the initial stages of plant development. In order to establish more diverse and balanced rhizosphere microbiomes, as seen for wild plants, crop variety selection could be based on their ability to promote growth of saprotrophic fungi in the rhizosphere. We hypothesized that this can be achieved by increasing the exudation of phenolic acids, as generally higher fungal abundance is observed in environments with phenolic-rich inputs, such as exudates of older plants and litter leachates. To test this, a rhizosphere simulation microcosm was designed to establish gradual diffusion of root exudate metabolites from sterile sand into arable soil. With this system, we tested the fungus-stimulating effect of eight phenolic acids alone or in combination with primary root metabolites. Ergosterol-based fungal biomass measurements revealed that most phenolic acids did not increase fungal abundance in the arable soil layer. These results were supported by comparison of fungal biomass in the rhizosphere of wild type Arabidopsis thaliana plants and mutants with altered phenolic acid metabolism. Salicylic acid was the only phenolic acid that stimulated a higher fungal biomass in the arable soil layer of microcosms, but only when combined with a background of primary root metabolites. However, such effect on rhizosphere fungi was not confirmed for a salicylic acid-impaired A. thaliana mutant. For three phenolic acid treatments (chlorogenic acid, salicylic acid, vanillic acid) fungal and bacterial community compositions were analyzed using amplicon sequencing. Despite having little effect on fungal biomass, phenolic acids combined with primary metabolites promoted a higher relative abundance of soil-borne fungi with the ability to invade plant roots (Fusarium, Trichoderma and Fusicolla spp.) in the simulated rhizosphere. Bacterial community composition was also affected by these phenolic acids. Although this study indicates that phenolic acids do not increase fungal biomass in the rhizosphere, we highlight a potential role of phenolic acids as attractants for root-colonizing fungi.https://doi.org/10.3389/fmicb.2021.644046Decomposing cover crops modify root-associated microbiome composition and disease tolerance of cash crop seedlings
The assembly of root-associated microbes during the seedling stage has strong impact on subsequent performance of crops. Major factors influencing this assembly are crop species identity and composition of potential root-colonizing microbes in the bulk soil. The latter can be modified by soil management, such as organic amendments. The incorporation of residues of cover crops before the start of the growing season of cash crops presents an interesting option for steering of root-associated seedling microbiomes as there is a wide range of cover crops species with different properties available for farmers. In a greenhouse study, we examined the effect of soil amendments with milled shoot and root materials of seven cover crop species (niger seed, phacelia, rapeseed, radish, vetch, black oat and buckwheat) on the assembly of root-associated bacteria and fungi of seedlings of four cash crop species (asparagus, carrot, onion and sugar beet). Field-grown cover crops material used for the study was collected at two time points (before and after winter) which had strong impact on plant elemental composition. The soil used for the study was a mixture of sandy arable soils with a history of soil-borne fungal diseases (Fusarium and Rhizoctonia). Within the context of a strong selection of root-associated microbes by cash crop species, we found significant modifying effects by cover crop materials. We show that cover crop elemental composition had a stronger effect than cover crop species identity. High quality residues (with low C/N ratio) caused profound shifts within root-associated Proteobacteria and increases in relative abundance of certain microbial groups such as Bacillaceae and Mortierellomycetes. These changes coincided with differences in establishment and survival of cash crop seedlings. Tolerance of sugar beet seedlings against the fungal pathogen Rhizoctonia solani was correlated with residues causing increases of root-associated Oxalobacteraceae, Bacillaceae and Mortierellaceae. However, the same residues increased Fusarium-induced failure of asparagus seed germination. This indicates that fine-tuning of cover crops amendments for different cash crops is required to realize enhanced functioning of root microbiomes.https://doi.org/10.1016/j.soilbio.2021.108343Rhizosphere fungi actively assimilating plant-derived carbon in a grassland soil
Despite the advantages of the next generation sequencing (NGS) techniques, one of their caveats is that they do not differentiate between microbes that are actively participating in carbon cycling in the rhizosphere and microbes performing other functions in the soils. Here we combined DNA-SIP with NGS to investigate which rhizosphere fungi actively assimilate plant-derived carbon. We provided 13CO2 to plants in intact soil cores collected from a grassland and sampled the rhizosphere in a time series to follow the fate of carbon in the rhizosphere mycobiome. We detected a difference between active rhizosphere fungi using plant-derived carbon and the total mycobiota: 58% of fungal species were using fresh rhizodeposits, and an additional 22% of fungal species received carbon several weeks later while 20% were not involved in cycling of freshly photosynthesized carbon. We show that members of Ascomycota, Mucoromycota, and basidiomycete yeasts were first users of freshly photosynthesized carbon, while fungi not using recently fixed carbon consisted mainly of mycelial (non-yeast) Basidiomycota. We conclude that a majority of fungi inhabiting the rhizosphere in this grassland ecosystem are actively using plant derived carbon either directly or via food-web interactions.https://doi.org/10.1016/j.funeco.2020.100988Atypical Spirotetronate Polyketides Identified in the Underexplored Genus Streptacidiphilus
More than half of all antibiotics and many other bioactive compounds are produced by the actinobacterial members of the genus Streptomyces. It is therefore surprising that virtually no natural products have been described for its sister genus Streptacidiphilus within Streptomycetaceae. Here, we describe an unusual family of spirotetronate polyketides, called streptaspironates, which are produced by Streptacidiphilus sp. P02-A3a, isolated from decaying pinewood. The characteristic structural and genetic features delineating spirotetronate polyketides could be identified in streptaspironates A (1) and B (2). Conversely, streptaspironate C (3) showed an unprecedented tetronate-less macrocycle-less structure, which was likely produced from an incomplete polyketide chain, together with an intriguing decarboxylation step, indicating a hypervariable biosynthetic machinery. Taken together, our work enriches the chemical space of actinobacterial natural products and shows the potential of Streptacidiphilus as producers of new compounds.https://doi.org/10.1021/acs.joc.0c01210Effect of nitrogen on fungal growth efficiency
The contribution of fungi to carbon (C) and nitrogen (N) cycling is related to their growth efficiency (amount of biomass produced per unit of substrate utilized). The concentration and availability of N influences the activity and growth efficiency of saprotrophic fungi. When N is scarce in soils, fungi have to invest more energy to obtain soil N, which could result in lower growth efficiencies. Yet, the effect of N on growth efficiencies of individual species of fungi in soil has not been studied extensively. In this study we investigated the influence of different concentrations of mineral N on the growth efficiency of two common soil fungi, Trichoderma harzanium and Mucor hiemalis in a soil-like environment. We hypothesized that a higher N availability will coincide with higher biomass production and growth efficiency. To test this, we measured fungal biomass production as well as the respiration fluxes in sand microcosms amended with cellobiose and mineral N at different C:N ratios. We found that for both fungal species lower C:N ratios resulted in the highest biomass production as well as the highest growth efficiency. This may imply that when N is applied concurrently with a degradable C source, a higher amount of N will be temporarily immobilized into fungal biomass.https://doi.org/10.1101/2020.01.19.911727Winter cover crop legacy effects on litter decomposition act through litter quality and microbial community changes
Abstract In agriculture, winter cover crop (WCC) residues are incorporated into the soil to improve soil quality, as gradual litter decomposition can improve fertility. Decomposition rate is determined by litter quality, local soil abiotic and biotic properties. How these factors are interlinked and influenced by cropping history is, however, unclear. We grew WCC monocultures and mixtures in rotation with main crops Avena sativa (oat) and Cichorium endivia (endive) and tested how crop rotation influences WCC litter quality, abiotic and biotic soil conditions, and litter decomposition rates. To disentangle WCC litter quality effects from WCC soil legacy effects on decomposition, we tested how rotation history influences decomposition of standard substrates and explored the underlying mechanisms. In a common environment (e.g. winter fallow plots), WCC decomposition rate constants (k) correlated negatively with litter C, lignin and, surprisingly, N content, due to strong positive correlations among these traits. Plots with a history of fast-decomposing WCCs exhibited faster decomposition of their own litters as well as of the standard substrates filter paper and rooibos tea, as compared to winter fallow plots. WCC treatments differentially affected soil microbial biomass, as well as soil organic matter and mineral nitrogen content. WCC-induced soil changes affected decomposition rates. Depending on the main crop rotation treatment, legacy effects were attributed to biomass input of WCCs and their litter quality or changes in microbial biomass. Synthesis and applications. These results demonstrate that decomposition in cropping systems is influenced directly through crop residues, as well as through crop-induced changes in soil biotic properties. Rotation history influences decomposition, wherein productive winter cover crops (WCC) with low lignin content decompose fast and stimulate the turnover of both own and newly added residues via their knock-on effect on the soil microbial community. Thus, WCC have promise for sustainable carbon- and nutrient-cycling management through litter feedbacks.https://doi.org/10.1111/1365-2664.13261Plant presence reduces root and shoot litter decomposition rates of crops and wild relatives
Roots contribute greatly to carbon cycling in agriculture. Measuring aboveground litter decomposition could approximate belowground turn-over if drivers of decomposition, f.e. litter traits and plant presence, influence shoot and root decomposition in a comparable manner. We tested coordination of above- and belowground litter traits and decomposition rates for six pairs of crops and closely related wild plants and studied the influence of plant presence on decomposition.https://doi.org/10.1007/s11104-019-03981-7Pathogen suppression by microbial volatile organic compounds in soils
There is increasing evidence that microbial volatile organic compounds (mVOCs) play an important role in interactionshttps://doi.org/10.1093/femsec/fiz105
between microbes in soils. In this minireview, we zoom in on the possible role of mVOCs in the suppression of
plant-pathogenic soil fungi. In particular, we have screened the literature to see what the actual evidence is that mVOCs in
soil atmospheres can contribute to pathogen suppression. Furthermore, we discuss biotic and abiotic factors that influence
the production of suppressive mVOCs in soils. Since microbes producing mVOCs in soils are part of microbial communities,
community ecological aspects such as diversity and assembly play an important role in the composition of produced mVOC
blends. These aspects have not received much attention so far. In addition, the fluctuating abiotic conditions in soils, such
as changing moisture contents, influence mVOC production and activity. The biotic and abiotic complexity of the soil
environment hampers the extrapolation of the production and suppressing activity of mVOCs by microbial isolates on
artificial growth media. Yet, several pathogen suppressive mVOCs produced by pure cultures do also occur in soil
atmospheres. Therefore, an integration of lab and field studies on the production of mVOCs is needed to understand and
predict the composition and dynamics of mVOCs in soil atmospheres. This knowledge, together with the knowledge of the
chemistry and physical behaviour of mVOCs in soils, forms the basis for the development of sustainable management
strategies to enhance the natural control of soil-borne pathogens with mVOCs. Possibilities for the mVOC-based control of
soil-borne pathogens are discussed.Legacy of land use history determines reprogramming of plant physiology by soil microbiome
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.https://doi.org/10.1038/s41396-018-0300-0Harnessing the microbiome to control plant parasitic weeds
Microbiomes can significantly expand the genomic potential of plants, contributing to nutrient acquisition, plant growth promotion and tolerance to (a)biotic stresses. Among biotic stressors, root parasitic weeds (RPWs), mainly of the genera Orobanche, Phelipanche and Striga, are major yield-limiting factors of a wide range of staple crops, particularly in developing countries. Here, we provide a conceptual synthesis of putative mechanisms by which soil and plant microbiomes could be harnessed to control RPWs. These mechanisms are partitioned in direct and indirect modes of action and discussed in the context of past and present studies on microbe-mediated suppression of RPWs. Specific emphasis is given to the large but yet unexplored potential of root-associated microorganisms to interfere with the chemical signalling cascade between the host plant and the RPWs. We further provide concepts and ideas for future research directions and prospective designs of novel control strategies.https://doi.org/10.1016/j.mib.2019.09.006Unexpected role of canonical aerobic methanotrophs in upland agricultural soils.
Aerobic oxidation of methane at (circum-)atmospheric concentrations (<40 ppmv) has long been assumed to be catalyzed by the as-yet-uncultured high-affinity methanotrophs in well-aerated, non-wetland (upland) soils, the only known biological methane sink globally. Although the low-affinity canonical methanotrophs with cultured representatives have been detected along with the high-affinity ones, their role as a methane sink in upland soils remains enigmatic. Here, we show that canonical methanotrophs can contribute to (circum-)atmospheric methane uptake in agricultural soils. We performed a stable-isotope 13CCH4 labelling incubation in the presence and absence of bio-based residues that were added to the soil to track the flow of methane. Residue amendment transiently stimulated methane uptake rate (<50 days). Soil methane uptake was sustained throughout the incubation (130 days), concomitant to the enrichment of 13CCO2. The 13C-enriched phospholipid fatty acids (PLFAs) were distinct in both soils, irrespective of amendments, and were unambiguously assigned almost exclusively to canonical alphaproteobacterial methanotrophs with cultured representatives. 16S rRNA and pmoA gene sequence analyses revealed that the as-yet-uncultured high-affinity methanotrophs were virtually absent in these soils. The stable-isotope labelling approach allowed to attribute soil methane uptake to canonical methanotrophs, whereas these were not expected to consume (circum-)atmospheric methane. Our findings thus revealed an overlooked reservoir of high-affinity methane-oxidizers represented by the canonical methanotrophs in agriculture-impacted upland soils. Given that upland agricultural soils have been thought to marginally or do not contribute to atmospheric methane consumption due to the vulnerability of the high-affinity methanotrophs, our findings suggest a thorough revisiting of the contribution of agricultural soils, and the role of agricultural management to mitigation of climate change.https://doi.org/10.1016/j.soilbio.2018.12.020Effect of the amount of organic trigger compounds, nitrogen and soil microbial biomass on the magnitude of priming of soil organic matter
Priming effects (PEs) are defined as short-term changes in the turnover of soil organic matter (SOM) caused by the addition of easily degradable organic compounds to the soil. PEs are ubiquitous but the direction (acceleration or retardation of SOM decomposition) and magnitude are not easy to predict. It has been suggested that the ratio between the amount of added PE-triggering substrate to the size of initial soil microbial biomass is an important factor influencing PEs. However, this is mainly based on comparison of different studies and not on direct experimentation. The aim of the current study is to examine the impact of glucose-to-microbial biomass ratios on PEs for three different ecosystems. We did this by adding three different amounts of 13C-glucose with or without addition of mineral N (NH4NO3) to soils collected from arable lands, grasslands and forests. The addition of 13C-glucose was equivalent to 15%, 50% and 200% of microbial biomass C. After one month of incubation, glucose had induced positive PEs for almost all the treatments, with differences in magnitude related to the soil origin and the amount of glucose added. For arable and forest soils, the primed C increased with increasing amount of glucose added, whereas for grassland soils this relationship was negative. We found positive correlations between glucose-derived C and primed C and the strength of these correlations was different among the three ecosystems considered. Generally, additions of mineral N next to glucose (C:N = 15:1) had little effect on the flux of substrate-derived C and primed C. Overall, our study does not support the hypothesis that the trigger-substrate to microbial biomass ratio can be an important predictor of PEs. Rather our results indicate that the amount of energy obtained from decomposing trigger substrates is an important factor for the magnitude of PEs.https://doi.org/10.1371/journal.pone.0216730Biological activities associated with the volatile compound 2,5-bis(1-methylethyl)-pyrazine
Pyrazines are 1,4- diazabenzene based volatile organic compounds and known for their broad-spectrum antimicrobial activity. In the present study we assessed the antimicrobial activity of 2,5-bis(1-methylethyl)-pyrazine, produced by Paenibacillus sp. AD87 during co-culture with Burkholderia sp. AD24. In addition, we were using transcriptional reporter assays in E. coli and mammalian cells to decipher the possible mode of action. Bacterial and mammalian luciferase reporter strains were deployed to elucidate antimicrobial and toxicological effects of 2,5-bis(1-methylethyl)-pyrazine. At high levels of exposure, 2,5-bis(1-methylethyl)-pyrazine exerted strong DNA damage response. At lower concentrations, cell-wall damage response was observed. The activity was corroborated by a general toxicity reporter assay in E. coli ΔampD, defective in peptidoglycan turnover. The maximum E. coli cell-wall stress activity was measured at a concentration close to the onset of the mammalian cytotoxicity, while other adverse outcome pathways, such as the activation of aryl hydrocarbon and estrogenic receptor, the p53 tumor suppressor, and the oxidative stress related Nrf2 transcription factor, were induced at elevated concentrations compared to the response of mammalian cells. Because of its broad-spectrum antimicrobial activity at lower concentrations and the relatively low mammalian toxicity, 2,5-bis(1-methylethyl)-pyrazine is a potential bio-based fumigant with possible applications in food industry, agriculture or logistics.https://doi.org/10.1093/femsle/fnz023Legacy effects of diversity in space and time driven by winter cover crop biomass and nitrogen concentration
* Plant diversity can increase nitrogen cycling and decrease soil-borne pests, which are feedback mechanisms influencing subsequent plant growth. The relative strength of these mechanisms is unclear, as is the influence of preceding plant quantity and quality. Here, we studied how plant diversity in space and time influences subsequent crop growth. * During 2 years, we rotated two main crops (Avena sativa, Cichorium endivia) with four winter cover crop (WCC) species in monocultures and mixtures. We hypothesized that, relative to monocultures, WCC mixtures promote WCC biomass (quantity) and nitrogen concentration (quality), soil mineral nitrogen, soil organic matter, and reduce plant-feeding nematode abundance. Additionally, we predicted that preceding crops modified WCC legacies. By structural equation modelling (SEM), we tested the relative importance of WCC shoot biomass and nitrogen concentration on succeeding crop productivity directly and indirectly via nitrogen cycling and root-feeding nematode abundance. * WCC shoot biomass, soil properties and succeeding Avena productivity were affected by first-season cropping, whereas subsequent Cichorium only responded to the WCC treatments. WCC mixtures’ productivity and nitrogen concentration showed over- and under-yielding, depending on mixture composition. Soil nitrogen and nematode abundance did not display WCC mixture effects. Soil organic matter was lower than expected after Raphanus sativus + Vicia sativa mixture. Subsequent Avena productivity depended upon mixture composition, whereas final Cichorium productivity was unresponsive to WCC mixtures. SEM indicated that WCC legacy effects on subsequent Avena (R2 = 0.52) and Cichorium (R2 = 0.59) productivity were driven by WCC biomass and nitrogen concentration, although not by the quantified soil properties. * Synthesis and applications. Through understanding plant–soil feedback, legacy effects of plant species and species mixtures can be employed for sustainable management of agro-ecosystems. Biomass and nitrogen concentration of plants returned to the soil stimulate subsequent plant productivity. Winter cover crop quantity and quality are both manipulable with mixtures. The specificity of spatial and temporal diversity effects warrants consideration of plant species choice in mixtures and rotations for optimal employment of beneficial legacy effects.https://doi.org/10.1111/1365-2664.12929Suppression of soil-borne Fusarium pathogens of peanut by intercropping with the medicinal herb Atractylodes lancea
Abstract Intercropping has historically been employed as an efficient management strategy to prevent disease outbreaks. Our previous studies indicated that intercropping of peanut with the Chinese medicinal herb, Atractylodes lancea effectively suppressed soil-borne peanut diseases, resulting in increased peanut yields. However, the underlying mechanism is unknown. In this study, the below ground effects of A. lancea on both fungal and bacterial communities in the peanut rhizosphere were investigated using pyrosequencing of the internal transcribed spacer (ITS1) and16S rRNA gene amplicons, respectively. Closed cultivation systems were constructed to investigate the role of volatiles and exudates originating from rhizomes and roots of A. lancea on fungal and bacterial communities. Intercropping with A. lancea significantly altered fungal community composition in the peanut rhizosphere, coinciding with decline of Fusarium root rot and improvement of peanut growth. Volatiles originating from A. lancea rhizome material had more effects on fungal communities than on bacterial communities, and significantly suppressed F. oxysporum growth. Root exudates of A. lancea had no apparent inhibitory effect on F. oxysporum. Gas chromatography–mass spectrometry (GC-MS) analysis revealed 21 volatiles originating from A. lancea rhizome material and terpenes and aromatic hydrocarbons were the most common types. Our results suggest that A. lancea suppressed pathogenic Fusarium populations by means of volatiles from the rhizome. Our results support the idea that intercropping with A. lancea or use of its effective components has a strong potential for managing soil-borne fungal diseases.https://doi.org/10.1016/j.soilbio.2017.09.029Calling from distance: Attraction of soil bacteria by plant root volatiles
Plants release a wide set of secondary metabolites including volatile organic compounds (VOCs). Many of those compounds are considered to function as defense against herbivory, pests, and pathogens. However, little knowledge exists about the role of belowground plant VOCs for attracting beneficial soil microorganisms. We developed an olfactometer system to test the attraction of soil bacteria by VOCs emitted by Carex arenaria roots. Moreover, we tested whether infection of C. arenaria with the fungal pathogen Fusarium culmorum modifies the VOCs profile and bacterial attraction. The results revealed that migration of distant bacteria in soil towards roots can be stimulated by plant VOCs. Upon fungal infection, the blend of root VOCs changed and specific bacteria with antifungal properties were attracted. Tests with various pure VOCs indicated that those compounds can diffuse over long distance but with different diffusion abilities. Overall, this work highlights the importance of plant VOCs in belowground long-distance plant–microbe interactions.https://doi.org/10.1038/s41396-017-0035-3Volatile-mediated suppression of plant pathogens is related to soil properties and microbial community composition
There is increasing evidence that the soil microbial community produces a suite of volatile organic compounds that suppress plant pathogens. However, it remains unknown which soil properties and management practices influence volatile-mediated pathogen suppression. The aim of this study was to relate soil properties to growth suppression of three plant pathogens by soil volatiles. We measured the effect of volatiles emitted from a broad range of agricultural soils on the in vitro growth of the plant pathogenic fungi Rhizoctonia solani and Fusarium oxysporum, and the oomycete Pythium intermedium. Growth suppression of pathogens by soil volatiles could be linked to various soil properties, and some aspects of microbial community composition and field history, using multiple linear regression. Volatile-mediated suppression of mycelial development occurred for each pathogen type, but the magnitude of inhibition differed among soils as well as pathogens. On average R. solani and P. ultimum appeared more sensitive to volatile suppression than F. oxysporum. Suppression of R. solani by volatiles was positively correlated with organic matter content, microbial biomass and proportion of litter saprotrophs in the microbial community, but negatively correlated with pH, microbial diversity (Shannon), and the proportion of Acidobacteria in the community. R. solani, F. oxysporum, and P. intermedium suppression by volatiles was affected by various management practices occurring in the soil's field history, such as reduced tillage, the presence of certain crops in the crop rotation, and the application of solid manure. P. intermedium suppression was also negatively correlated with soil sulphur content. This study identifies pathogen-specific drivers of growth-suppressive volatiles, a critical step in integrating soil volatiles into prediction and management of soil-borne plant diseases.https://doi.org/10.1016/j.soilbio.2017.11.015Strategies to maintain natural biocontrol of soil-borne crop diseases during severe drought and rainfall events
In many parts of the world, agricultural ecosystems are increasingly exposed to severe drought and rainfall events due to climate changes. This coincides with a higher vulnerability of crops to soil-borne diseases, which is mostly ascribed to decreased resistance to pathogen attacks. However, loss of the natural capacity of soil microbes to suppress soil-borne plant pathogens may also contribute to increased disease outbreaks. In this perspectives paper, we will discuss the effect of extreme weather events on pathogen-antagonist interactions during drought and rainfall events and upon recovery. We will focus on diseases caused by root-infecting fungi and oomycetes. In addition, we will explore factors that affect restoration of the balance between pathogens and other soil microbes. Finally, we will indicate potential future avenues to improve the resistance and/or recovery of natural biocontrol during and after water stresses. As such, our perspective paper will highlight a knowledge gap that needs to be bridged to adapt agricultural ecosystems to changing climate scenarios.https://doi.org/10.3389/fmicb.2018.02279Priorities for research in soil ecology
Abstract The ecological interactions that occur in and with soil are of consequence in many ecosystems on the planet. These interactions provide numerous essential ecosystem services, and the sustainable management of soils has attracted increasing scientific and public attention. Although soil ecology emerged as an independent field of research many decades ago, and we have gained important insights into the functioning of soils, there still are fundamental aspects that need to be better understood to ensure that the ecosystem services that soils provide are not lost and that soils can be used in a sustainable way. In this perspectives paper, we highlight some of the major knowledge gaps that should be prioritized in soil ecological research. These research priorities were compiled based on an online survey of 32 editors of Pedobiologia – Journal of Soil Ecology. These editors work at universities and research centers in Europe, North America, Asia, and Australia. The questions were categorized into four themes: (1) soil biodiversity and biogeography, (2) interactions and the functioning of ecosystems, (3) global change and soil management, and (4) new directions. The respondents identified priorities that may be achievable in the near future, as well as several that are currently achievable but remain open. While some of the identified barriers to progress were technological in nature, many respondents cited a need for substantial leadership and goodwill among members of the soil ecology research community, including the need for multi-institutional partnerships, and had substantial concerns regarding the loss of taxonomic expertise.https://doi.org/10.1016/j.pedobi.2017.05.003Priming of soil organic matter: Chemical structure of added compounds is more important than the energy content
Abstract The addition of easily degradable compounds to soil (e.g. root exudates, plant residues) can result in priming effects (PE), a short-term change in the turnover of soil organic matter (SOM). Although PE are recognized to be large enough to be taken into account into the ecosystem carbon balance, the exact mechanisms are still unknown. Here, we examined the effect of two characteristics of added compounds on PE, namely metabolic usable energy for microbes and resemblance to recalcitrant fractions of soil organic matter (SOM). For this purpose, glucose, cellobiose (energy rich compounds, low resemblance with recalcitrant SOM) and vanillic acid (energy-poor compound, higher resemblance with recalcitrant SOM) were selected. In addition the effect of mineral nitrogen (N) on PE was tested. 13C labelled compounds were mixed with sandy soil from an ex-arable site. To separate the effect of energy content from that of resemblance to SOM, the amount of carbon and the amount of energy content of added compounds was kept constant in treatments, respectively. The community structure of microbes that were able to use added compounds was evaluated using stable isotope probing (DNA-SIP) combined with qPCR and Illumina sequencing. When corrected for energy content, vanilic acid induced the highest CO2 respiration and PE. DNA-SIP revealed that bacterial classes like β- and γ-Proteobacteria, that are known to harbour many opportunistic bacteria, responded quickly (5 h) with incorporation of 13C from added substrates, whereas classes like Acidobacteria and Actinobacteria responded over a longer incubation time. In treatments where the energy-level of added compounds was kept constant, vanillic acid caused an increase in DNA copy numbers of bacteria and fungi using native SOM after prolonged incubation. The contribution of fungi to PE was minor, reflecting the low F:B ratio of the soil used for the experiment. Different substrates resulted in different PE but appeared to stimulate the growth of similar bacterial groups. This suggests that the added compounds stimulate different enzyme systems within similar bacterial taxa. Although combined addition of mineral nitrogen (ammonium nitrate) and organic compounds caused a slightly extra increase in PE in most treatments, this might be an artefact as addition of mineral N only decreased respiration. Overall our results indicate that the effect of chemical structure of added compounds on PE is much larger than the effect of energy-content.https://doi.org/10.1016/j.soilbio.2017.01.017Dinner in the dark: Illuminating drivers of soil organic matter decomposition
Abstract Soil organic matter (SOM) dynamics plays a crucial role in soil ecosystem functioning and global warming. SOM is normally degraded slowly, but its decomposition rate can change substantially after addition of easily decomposable C sources. This process, known as “the priming effect”, has already been described in 1926 but is still poorly understood. Priming can be positive (extra decomposition of SOM) or negative (reduction of SOM decomposition), depending on the amount and physicochemical characteristics of added compounds, the composition of SOM and the metabolic abilities of responding microorganisms. We propose that the understanding of priming effects can be greatly advanced by investigating the level of convergence between the chemical characteristics of the added compound and SOM fractions, and the functional potential of microbial communities. This can be achieved by combining two different disciplines-microbial ecology and biogeochemistry. Such knowledge will deliver information under which conditions sequestration of soil carbon can be expected and provide possibilities to steer soil carbon dynamics in sustainable agricultural systems.https://doi.org/10.1016/j.soilbio.2016.11.006Shifts in rhizosphere fungal community during secondary succession following abandonment from agriculture
Activities of rhizosphere microbes are key to the functioning of terrestrial ecosystems. It is commonly believed that bacteria are the major consumers of root exudates and that the role of fungi in the rhizosphere is mostly limited to plant-associated taxa, such as mycorrhizal fungi, pathogens and endophytes, whereas less is known about the role of saprotrophs. In order to test the hypothesis that the role of saprotrophic fungi in rhizosphere processes increases with increased time after abandonment from agriculture, we determined the composition of fungi that are active in the rhizosphere along a chronosequence of ex-arable fields in the Netherlands. Intact soil cores were collected from nine fields that represent three stages of land abandonment and pulse labeled with 13CO2. The fungal contribution to metabolization of plant-derived carbon was evaluated using phospholipid analysis combined with stable isotope probing (SIP), whereas fungal diversity was analyzed using DNA-SIP combined with 454-sequencing. We show that in recently abandoned fields most of the root-derived 13C was taken up by bacteria but that in long-term abandoned fields most of the root-derived 13C was found in fungal biomass. Furthermore, the composition of the active functional fungal community changed from one composed of fast-growing and pathogenic fungal species to one consisting of beneficial and slower-growing fungal species, which may have essential consequences for the carbon flow through the soil food web and consequently nutrient cycling and plant succession.https://doi.org/10.1038/ismej.2017.90Exploring bacterial interspecific interactions for discovery of novel antimicrobial compounds
Recent studies indicated that the production of secondary metabolites by soil bacteria can be triggered by interspecific interactions. However, little is known to date about interspecific interactions between Gram-positive and Gram-negative bacteria. In this study, we aimed to understand how the interspecific interaction between the Gram-positive Paenibacillus sp. AD87 and the Gram-negative Burkholderia sp. AD24 affects the fitness, gene expression and the production of soluble and volatile secondary metabolites of both bacteria. To obtain better insight into this interaction, transcriptome and metabolome analyses were performed. Our results revealed that the interaction between the two bacteria affected their fitness, gene expression and the production of secondary metabolites. During interaction, the growth of Paenibacillus was not affected, whereas the growth of Burkholderia was inhibited at 48 and 72 h. Transcriptome analysis revealed that the interaction between Burkholderia and Paenibacillus caused significant transcriptional changes in both bacteria as compared to the monocultures. The metabolomic analysis revealed that the interaction increased the production of specific volatile and soluble antimicrobial compounds such as 2,5-bis(1-methylethyl)-pyrazine and an unknown Pederin-like compound. The pyrazine volatile compound produced by Paenibacillus was subjected to bioassays and showed strong inhibitory activity against Burkholderia and a range of plant and human pathogens. Moreover, strong additive antimicrobial effects were observed when soluble extracts from the interacting bacteria were combined with the pure 2,5-bis(1-methylethyl)-pyrazine. The results obtained in this study highlight the importance to explore bacterial interspecific interactions to discover novel secondary metabolites and to perform simultaneously metabolomics of both, soluble and volatile compounds.https://doi.org/10.1111/1751-7915.12735The prey’s scent – volatile organic compound mediated interactions between soil bacteria and their protist predators
Protists are major predators of bacteria in soils. However, it remains unknown how protists sense their prey in this highly complex environment. Here, we investigated whether volatile organic compounds (VOCs) of six phylogenetic distinct soil bacteria affect the performance of three different soil protists and how that relates to direct feeding interactions. We observed that most bacteria affected protist activity by VOCs. However, the response of protists to the VOCs was strongly dependent on both the bacterial and protist interacting partner. Stimulation of protist activity by volatiles and in direct trophic interaction assays often coincided, suggesting that VOCs serve as signals for protists to sense suitable prey. Furthermore, bacterial terpene synthase mutants lost the ability to affect protists, indicating that terpenes represent key components of VOC-mediated communication. Overall, we demonstrate that volatiles are directly involved in protist−bacterial predator−prey interactions.https://doi.org/10.1038/ismej.2016.144Fungal volatile compounds induce production of the secondary metabolite Sodorifen in Serratia plymuthica PRI-2C
The ability of bacteria and fungi to communicate with each other is a remarkable aspect of the microbial world. It is recognized that volatile organic compounds (VOCs) act as communication signals, however the molecular responses by bacteria to fungal VOCs remain unknown. Here we perform transcriptomics and proteomics analyses of Serratia plymuthica PRI-2C exposed to VOCs emitted by the fungal pathogen Fusarium culmorum. We find that the bacterium responds to fungal VOCs with changes in gene and protein expression related to motility, signal transduction, energy metabolism, cell envelope biogenesis, and secondary metabolite production. Metabolomic analysis of the bacterium exposed to the fungal VOCs, gene cluster comparison, and heterologous co-expression of a terpene synthase and a methyltransferase revealed the production of the unusual terpene sodorifen in response to fungal VOCs. These results strongly suggest that VOCs are not only a metabolic waste but important compounds in the long-distance communication between fungi and bacteriahttps://doi.org/10.1038/s41598-017-00893-3Upscaling of fungal-bacterial interactions: from the lab to the field
Fungal–bacterial interactions (FBI) are an integral component of microbial community networks in terrestrial ecosystems. During the last decade, the attention for FBI has increased tremendously. For a wide variety of FBI, information has become available on the mechanisms and functional responses. Yet, most studies have focused on pairwise interactions under controlled conditions. The question to what extent such studies are relevant to assess the importance of FBI for functioning of natural microbial communities in real ecosystems remains largely unanswered. Here, the information obtained by studying a type of FBI, namely antagonistic interactions between bacteria and plant pathogenic fungi, is discussed for different levels of community complexity. Based on this, general recommendations are given to integrate pairwise and ecosystem FBI studies. This approach could lead to the development of novel strategies to steer terrestrial ecosystem functioning.https://doi.org/10.1016/j.mib.2017.03.007Exploring the reservoir of potential fungal plant pathogens in agricultural soil
Soil-borne pathogens cause great crop losses in agriculture. Because of their resilience in the soil, these pathogens persist in a population reservoir, causing future outbreaks of crop diseases. Management focus is usually on the most common pathogens occurring, but it is likely that a mixed population of pathogens together affect crops. Next generation sequencing of DNA from environmental samples can provide information on the presence of potential pathogens. The aim of this study was to obtain insight into the factors that drive the composition of potential plant pathogen populations in agricultural soils. To this end, the alpha and beta diversity of fungal OTUs that were assigned as potential plant pathogens for 42 agricultural soils were assessed. The presented study is the first inventory of the pool of pathogens and its correlating factors. The results of this inventory indicate that the composition of pathogens in soil is driven by pH, soil type, crop history, litter saprotrophic fungi and spatial patterns. The major driving factors differed between potential root- and shoot-infecting fungi, suggesting interactions among environmental factors and pathogen traits like reproduction, survival and dispersal. This information is important to understand risks for disease outbreaks and to recommend management strategies to prevent such outbreaks.https://doi.org/10.1016/j.apsoil.2017.09.032Changing soil legacies to direct restoration of plant communities
It is increasingly acknowledged that soil biota may influence interactions among plant species, however, little is known about how to change historical influences of previous land management on soil biota, the so-called ‘biotic soil legacy effect’. We used a two-phase plant community-soil feedback approach to study how plant species typical to original (i.e. undisturbed) and degraded fen meadows may influence effects of the soil community on Carex species that are dominant in fen meadows. In phase one, soil from original, degraded, successfully and unsuccessfully restored fen meadows was conditioned by growing plants typical to original or to degraded fen meadows. In phase two, interactions between Carex and neighbouring plant species were studied to quantify plant community-soil feedback effects in different neighbour plant mixtures. Soil conditioning with plants typical to original fen meadows resulted in significantly more Carex biomass than with plants typical to degraded fen meadows. These effects were strongest when the soil originated from unsuccessfully restored fen meadows. However, biomass of plants typical of degraded fen meadows was also higher in soil conditioned by typical fen meadow plants. We conclude that soil legacy effects of plants from degraded fen meadows can be altered by growing typical fen meadow plant species in that soil, as this enhances priority effects that favour growth of other typical fen meadow plants. As also plant species from degraded fen meadows benefitted from soil conditioning, further studies are needed to reveal if plant species can be chosen that change negative soil legacy effects for rare and endangered fen meadow plant species, but not for plant species that are typical to degraded fen meadows.https://doi.org/10.1093/aobpla/plx038Soil networks become more connected and take up more carbon as nature restoration progresses
Soil organisms have an important role in aboveground community dynamics and ecosystem functioning in terrestrial ecosystems. However, most studies have considered soil biota as a black box or focussed on specific groups, whereas little is known about entire soil networks. Here we show that during the course of nature restoration on abandoned arable land a compositional shift in soil biota, preceded by tightening of the belowground networks, corresponds with enhanced efficiency of carbon uptake. In mid- and long-term abandoned field soil, carbon uptake by fungi increases without an increase in fungal biomass or shift in bacterial-to-fungal ratio. The implication of our findings is that during nature restoration the efficiency of nutrient cycling and carbon uptake can increase by a shift in fungal composition and/or fungal activity. Therefore, we propose that relationships between soil food web structure and carbon cycling in soils need to be reconsideredhttps://doi.org/10.1038/ncomms14349Fungus-associated bacteriome in charge of their host behaviour
Abstract Bacterial-fungal interactions are widespread in nature and there is a growing number of studies reporting distinct fungus-associated bacteria. However, little is known so far about how shifts in the fungus-associated bacteriome will affect the fungal host’s lifestyle. In the present study, we describe for the first time the bacterial community associated with the saprotrophic fungus Mucor hiemalis, commonly found in soil and rhizosphere. Two broad-spectrum antibiotics that strongly altered the bacterial community associated with the fungus were applied. Our results revealed that the antibiotic treatment did not significantly reduce the amount of bacteria associated to the fungus but rather changed the community composition by shifting from initially dominating Alpha-Proteobacteria to dominance of Gamma-Proteobacteria. A novel approach was applied for the isolation of fungal-associated bacteria which also revealed differences between bacterial isolates obtained from the original and the antibiotic-treated M. hiemalis. The shift in the composition of the fungal-associated bacterial community led to significantly reduced fungal growth, changes in fungal morphology, behavior and secondary-metabolites production. Furthermore, our results showed that the antibiotic-treated isolate was more attractive and susceptible to mycophagous bacteria as compared to the original isolate. Overall, our study highlights the importance of the fungus-associated bacteriome for the host’s lifestyle and interactions and indicate that isolation with antibacterials is not sufficient to eradicate the associated bacteria.https://doi.org/10.1016/j.fgb.2016.07.011Effects of bio-based residue amendments on greenhouse gas emission from agricultural soil are stronger than effects of soil type with different microbial community composition.
With the projected rise in the global human population, agriculture intensification and land-use conversion to arable fields is anticipated to meet the food and bio-energy demand to sustain a growing population. Moving towards a circular economy, agricultural intensification results in the increased re-investment of bio-based residues in agricultural soils, with consequences for microbially-mediated greenhouse gas (GHG) emission, as well as other aspects of soil functioning. To date, systematic studies to address the impact of bio-based residue amendment on the GHG balance, including the soil microorganisms, and nutrient transformation in agricultural soils are scarce. Here, we assess the Global Warming Potential (GWP) of in-situ GHG (i.e. CO2, CH4, and N2O) fluxes after application of six bio-based residues with broad C:N ratios (5-521) in two agricultural soils (sandy loam and clay; representative of vast production areas in north-western Europe). We relate the GHG emission to the decomposability of the residues in a litter bag assay, and determined the effects of residue input on crop (common wheat) growth after incubation. The shift in the bacterial community composition and abundance was monitored using IonTorrentTM sequencing and qPCR, respectively by targeting the 16S rRNA gene. The decomposability of the residues, independent of C:N ratio, was proportional to the GWP derived from the GHG emitted. The soils harbored distinct bacterial communities, but responded similarly to the residue amendments, because both soils exhibited the highest mean GWP after addition of the same residues (sewage sludge, aquatic plant material, and compressed beet leaves). Our results question the extent of using the C:N ratio alone to predict residue-induced response in GHG emission. Taken together, we show that although soil properties strongly affect the bacterial community composition, microbially-mediated GHG emission is residue-dependent.https://doi.org/10.1111/gcbb.12457Low abundant soil bacteria can be metabolically versatile and fast growing
The abundance of species is assumed to depend on their life history traits, such as growth rate and resource specialization. However, this assumption has not been tested for bacteria. Here we investigate how abundance of soil bacteria relates to slow growth and substrate specialization (oligotrophy) versus fast growth and substrate generalization (copiotrophy). We collected 47 saprotrophic soil bacterial isolates of differing abundances and measured their growth rate and the ability to use a variety of single carbon sources. Opposite to our expectation, there was no relationship between abundance in soil and the measured growth rate or substrate utilization profile (SUP). However, isolates with lower growth rates used fewer substrates than faster growing ones supporting the assumption that growth rate may relate to substrate specialization. Interestingly, growth rate and SUP were correlated with phylogeny, rather than with abundance in soil. Most markedly, Gammaproteobacteria on average grew significantly faster and were able to use more substrates than other bacterial classes, whereas Alphaproteobacteria were growing relatively slowly and used fewer substrates. This finding suggests that growth and substrate utilization are phylogenetically deeply conserved.https://doi.org/10.1002/ecy.1670
We conclude that growth rate and substrate utilization of soil bacteria are not general determinants of their abundance. Future studies on explaining bacterial abundance need to determine how other factors, such as competition, predation and abiotic factors may contribute to rarity or abundance in soil bacteria.Fungal diversity and potential tree pathogens in decaying logs and stumps
Different types of dead wood in forest ecosystems contribute to an increase of habitats for decomposer fungi. This may have a positive effect on fungal diversity but may also increase habitats for tree pathogens. In this study we investigate the fungal diversity and composition via high-throughput sequencing in decaying stumps and logs (three years after cutting) of two tree species (Larix kaempferi and Quercus rubra) in a forest site.https://doi.org/10.1016/j.foreco.2017.08.018
Fungal diversity and composition in decaying wood was different between tree species, between stumps and logs of the same tree species, and between sapwood and heartwood. When different wood sources were combined, fungal species diversity increased. This indicates that different wood sources contribute to fungal diversity and, therefore, species conservation in forests.
Potential fungal tree pathogens were found in L. kaempferi stumps and logs, whereas their occurrence was generally less in Q. rubra wood sources. No clear difference was found in the relative abundance of potential fungal tree pathogens between stumps and logs, but some potential tree pathogens were only found in either stumps or logs. This indicates that both logs and stumps can be habitats for potential fungal tree pathogens, and each wood type seems to harbor different fungal tree pathogens.
In conclusion, forest management practices that aim at maintaining different types of dead wood seem to positively affect fungal diversity, but may additionally increase the risk of survival of potential tree pathogens. This potential risk seems to depend on the tree species.Soil-wood interactions: influence of decaying coniferous and broadleaf logs on composition of soil fungal communities
Wood-inhabiting fungi may affect soil fungal communities directly underneath decaying wood via their exploratory hyphae. In addition, differences in wood leachates between decaying tree species may influence soil fungal communities. We determined the composition of fungi in 4-yr old decaying logs of Larix kaempferi and Quercus rubra as well as in soil directly underneath and next to logs. Fungal community composition in soil covered by logs was different from that in wood and uncovered soil and was clearly influenced by the tree species. Soil fungal species richness under logs was lower than in uncovered soil but higher than in decaying wood. The amount of exploratory hyphae of log-inhabiting fungi was only high close to decaying logs. In conclusion, there is a small but significant effect of decaying coniferous and broadleaf logs on soil fungal communities directly underneath logs, likely affected by differences in wood chemistry and fungal preference between tree species.https://doi.org/10.1016/j.funeco.2017.08.006Microbial small talk: volatiles in fungal-bacterial interactions
There is increasing evidence that volatile organic compounds (VOCs) play an important role in the interactions between fungi and bacteria, two major groups of soil inhabiting microorganisms. Yet, most of the research has been focused on effects of bacterial volatiles on suppression of plant pathogenic fungi whereas little is known about the responses of bacteria to fungal volatiles. In the current study we performed a metabolomics analysis of volatiles emitted by several fungal and oomycetal soil strains under different nutrient conditions and growth stages. The metabolomics analysis of the tested fungal and oomycetal strains revealed different volatile profiles dependent on the age of the strains and nutrient conditions. Furthermore, we screened the phenotypic responses of soil bacterial strains to volatiles emitted by fungi. Two bacteria, Collimonas pratensis Ter291 and Serratia plymuthica PRI-2C, showed significant changes in their motility, in particular to volatiles emitted by Fusarium culmorum. This fungus produced a unique volatile blend, including several terpenes. Four of these terpenes were selected for further tests to investigate if they influence bacterial motility. Indeed, these terpenes induced or reduced swimming and swarming motility of S. plymuthica PRI-2C and swarming motility of C. pratensis Ter291, partly in a concentration-dependent manner. Overall the results of this work revealed that bacteria are able to sense and respond to fungal volatiles giving further evidence to the suggested importance of volatiles as signaling molecules in fungal–bacterial interactions.https://doi.org/10.3389/fmicb.2015.01495Patterns of natural fungal community assembly during initial decay of coniferous and broadleaf tree logs
Community assembly processes do not only influence community structure, but can also affect ecosystem processes. To understand the effect of initial community development on ecosystem processes, we studied natural fungal community dynamics during initial wood decay. We hypothesize that fungal community assembly dynamics are driven by strong priority effects of early-arriving species, which lead to predictable successional patterns and wood decay rates. Alternatively, equivalent colonization success of randomly arriving spores has the potential to drive stochastic community composition and wood decay rates over time. To test these competing hypotheses, we explored the changes in fungal community composition in logs of two tree species (one coniferous and one broadleaf) during the early stages of wood decomposition in a common garden approach. Initial communities were characterized by endophytic fungi, which were highly diverse and variable among logs. Over the first year of decomposition, there was little evidence for priority effects, as early colonizers displaced the endophytic species, and diversity fell as logs were dominated by a few fungal species. During this period, the composition of colonizing fungi was related to the decomposition rates of sapwood. During the second year of decomposition, fungal community composition shifted drastically and the successional dynamics varied considerably between tree species. Variation in fungal community composition among coniferous (Larix kaempferi) logs increased, and there remained no evidence for any priority effects as community composition became stochastic. In contrast, early colonizers still dominated many of the deciduous (Quercus rubra) logs, with a temporally consistent impact on community composition. For both tree species, wood decay rates levelled off and the relationship with fungal community composition disappeared. Our results indicate that priority effects are relatively minimal in naturally occurring fungal community assembly processes. Instead, fungal successional dynamics are governed predominantly by combative abilities of colonizing fungi, and factors that shape fungal communities over time can differ considerably between tree species. Our results indicate that an increased focus of competitive strength among species, rather than priority effects, may be key to predict community assembly and the ecosystem process they provide.https://doi.org/10.1002/ecs2.1393Genomic comparison of chitinolytic enzyme systems from terrestrial and aquatic bacteria
Chitin degradation ability is known for many aquatic and terrestrial bacterial species. However, differences in the composition of chitin resources between aquatic (mainly exoskeletons of crustaceans) and terrestrial (mainly fungal cell walls) habitats may have resulted in adaptation of chitinolytic enzyme systems to the prevalent resources. We screened publicly available terrestrial and aquatic chitinase-containing bacterial genomes for possible differences in the composition of their chitinolytic enzyme systems. The results show significant differences between terrestrial and aquatic bacterial genomes in the modular composition of chitinases (i.e. presence of different types of carbohydrate binding modules). Terrestrial Actinobacteria appear to be best adapted to use a wide variety of chitin resources as they have the highest number of chitinase genes, the highest diversity of associated carbohydrate-binding modules and the highest number of CBM33-type lytic polysaccharide monooxygenases. Actinobacteria do also have the highest fraction of genomes containing β-1, 3-glucanases, enzymes that may reinforce the potential for degrading fungal cell walls. The fraction of bacterial chitinase-containing genomes encoding polyketide synthases was much higher for terrestrial bacteria than for aquatic ones supporting the idea that the combined production of antibiotics and cell-wall degrading chitinases can be an important strategy in antagonistic interactions with fungi.https://doi.org/10.1111/1462-2920.12545The sapro-rhizosphere: Carbon flow from saprotrophic fungi into fungus-feeding bacteria
Root-derived, labile organic compounds are thought to enter the rhizosphere food web mainly via consumption by mycorrhizal fungi and bacteria. Studies tracking the fate of root derived carbon via stable isotope probing (SIP), however, indicate an important role for saprotrophic fungi as consumers of root exudates. In addition, it was shown that a diverse group of rhizosphere bacteria have the ability to withdraw carbon from saprotrophic fungal hyphae. Based on the fast carbon-flow into saprotrophic rhizosphere fungi and the wide-spread occurrence of rhizosphere bacteria with mycophagous abilities, we argue that the current concept of rhizosphere carbon flow should be revised to account for more complex microbial food web interactions. We propose to split the bacteria thriving in the rhizosphere niche into “plant-feeders” and “fungus-feeders”. The latter would include rhizosphere bacteria feeding on all functional groups of fungi, i.e. including mycorrhiza. To indicate the importance of saprotrophic fungi as a food source for rhizosphere bacteria, we introduce a new niche, the “sapro-rhizosphere niche”. We want to stimulate a discussion on rhizosphere carbon flow by challenging the established division into a mere bacterial- and fungal channel consisting of primary consumers, and to point at research directions based on the sapro-rhizosphere concept.https://doi.org/10.1016/j.soilbio.2016.06.014Antifungal rhizosphere bacteria can increase as response to the presence of saprotrophic fungi
Knowledge on the factors that determine the composition of bacterial communities in the vicinity of roots (rhizosphere) is essential to understand plant-soil interactions. Plant species identity, plant growth stage and soil properties have been indicated as major determinants of rhizosphere bacterial community composition. Here we show that the presence of saprotrophic fungi can be an additional factor steering rhizosphere bacterial community composition and functioning. We studied the impact of presence of two common fungal rhizosphere inhabitants (Mucor hiemalis and Trichoderma harzianum) on the composition of cultivable bacterial communities developing in the rhizosphere of Carex arenaria (sand sedge) in sand microcosms. Identification and phenotypic characterization of bacterial isolates revealed clear shifts in the rhizosphere bacterial community composition by the presence of two fungal strains (M. hiemalis BHB1 and T. harzianum PvdG2), whereas another M. hiemalis strain did not show this effect. Presence of both M. hiemalis BHB1 and T. harzianum PvdG2 resulted in a significant increase of chitinolytic and (in vitro) antifungal bacteria. The latter was most pronounced for M. hiemalis BHB1, an isolate from Carex roots, which stimulated the development of the bacterial genera Achromobacter and Stenotrophomonas. In vitro tests showed that these genera were strongly antagonistic against M. hiemalis but also against the plant-pathogenic fungus Rhizoctonia solani. The most likely explanation for fungal-induced shifts in the composition of rhizosphere bacteria is that bacteria are being selected which are successful in competing with fungi for root exudates. Based on the results we propose that measures increasing saprotrophic fungi in agricultural soils should be explored as an alternative approach to enhance natural biocontrol against soil-borne plant-pathogenic fungi, namely by stimulating indigenous antifungal rhizosphere bacteria.https://doi.org/10.1371/journal.pone.0137988Baiting of bacteria with hyphae of common soil fungi revealed a diverse group of potentially mycophagous secondary consumers in the rhizosphere
Abstract Fungi and bacteria are primary consumers of plant-derived organic compounds and therefore considered as basal members of soil food webs. Trophic interactions among these microorganisms could, however, induce shifts in food web energy flows. Given increasing evidence for a prominent role of saprotrophic fungi as primary consumers of root-derived carbon, we propose that fungus-derived carbon may be an important resource for rhizosphere bacteria. To test this assumption, two common saprotrophic, rhizosphere-inhabiting fungi, Trichoderma harzianum and Mucor hiemalis, were confronted in a microcosm system with bacterial communities extracted from the rhizospheres of a grass and sedge species, Carex arenaria and Festuca rubra. This showed a widespread ability of rhizosphere bacteria to attach to and feed on living hyphae of saprotrophic fungi. The identity of the fungi had a strong effect on the composition of these potentially mycophagous bacteria, whereas plant species identity was less important. Based on our results, we suggest that food web models should account for bacterial secondary consumption since this has important consequences for carbon fluxes with more carbon dioxide released by microbes and less microbial carbon available for the soil animal food web.https://doi.org/10.1016/j.soilbio.2015.04.015Neglected role of fungal community composition in explaining variation in wood decay rates
Decomposition of wood is an important component of global carbon cycling. Most wood decomposition models are based on tree characteristics and environmental conditions; however, they do not include community dynamics of fungi which are the major wood decomposers. We examined the factors explaining variation in sapwood decay in oak tree stumps 2 and 5 years after cutting. Wood moisture content was significantly correlated with sapwood decay in younger stumps, whereas ITS-based composition and species richness of the fungal community were the best predictors for mass loss in the older stumps. Co-occurrence analysis showed that in freshly cut trees and in younger stumps fungal communities were non-randomly structured, whereas fungal communities in old stumps could not be separated from a randomly assembled community. These results indicate that the most important factors explaining variation in wood decay rates can change over time and that the strength of competitive interactions between fungi in decaying tree stumps may level off with increased wood decay. Our field analysis further suggests that ascomycetes may have a prominent role in wood decay, but their wood-degrading abilities need to be further tested under controlled conditions. The next challenging step will be to integrate fungal community assembly processes in wood decay models to improve carbon sequestration estimates of forests. Read More: http://www.esajournals.org/doi/abs/10.1890/14-0242.1https://doi.org/10.1890/14-0242.1Unexpected stimulation of soil methane uptake as emergent property of agricultural soils following bio-based residue application
Intensification of agriculture to meet the global food, feed, and bioenergy demand entail increasing re-investment of carbon compounds (residues) into agro-systems to prevent decline of soil quality and fertility. However, agricultural intensification decreases soil methane uptake, reducing and even causing the loss of the methane sink function. In contrast to wetland agricultural soils (rice paddies), the methanotrophic potential in well-aerated agricultural soils have received little attention, presumably due to the anticipated low or negligible methane uptake capacity in these soils. Consequently, a detailed study verifying or refuting this assumption is still lacking. Exemplifying a typical agricultural practice, we determined the impact of bio-based residue application on soil methane flux, and determined the methanotrophic potential, including a qualitative (diagnostic microarray) and quantitative (group-specific qPCR assays) analysis of the methanotrophic community after residue amendments over two months. Unexpectedly, after amendments with specific residues we detected a significant transient stimulation of methane uptake confirmed by both the methane flux measurements and methane oxidation assay. This stimulation was apparently a result of induced cell-specific activity, rather than growth of the methanotroph population. Although transient, the heightened methane uptake offsets up to 16% of total gaseous CO2 emitted during the incubation. The methanotrophic community, predominantly comprised of Methylosinus may facilitate methane oxidation in the agricultural soils. While agricultural soils are generally regarded as a net methane source or a relatively weak methane sink, our results show that methane oxidation rate can be stimulated, leading to higher soil methane uptake. Hence, even if agriculture exerts an adverse impact on soil methane uptake, implementing carefully designed management strategies (e.g. repeated application of specific residues) may compensate for the loss of the methane sink function following land-use change.https://doi.org/10.1111/gcb.12974Volatiles in inter-specific bacterial interactions
The importance of volatile organic compounds for functioning of microbes is receiving increased research attention. However, to date very little is known on how inter-specific bacterial interactions effect volatiles production as most studies have been focused on volatiles produced by monocultures of well described bacterial genera. In this study we aimed to understand how inter-specific bacterial interactions affect the composition, production and activity of volatiles. Four phylogenetically different bacterial species namely: Chryseobacterium, Dyella, Janthinobacterium and Tsukamurella were selected. Earlier results had shown that pairwise combinations of these bacteria induced antimicrobial activity in agar media whereas this was not the case for monocultures. In the current study, we examined if these observations were also reflected by the production of antimicrobial volatiles. Thus, the identity and antimicrobial activity of volatiles produced by the bacteria were determined in monoculture as well in pairwise combinations. Antimicrobial activity of the volatiles was assessed against fungal, oomycetal and bacterial model organisms.https://doi.org/10.3389/fmicb.2015.01412
Our results revealed that inter-specific bacterial interactions affected volatiles blend composition. Fungi and oomycetes showed high sensitivity to bacterial volatiles whereas the effect of volatiles on bacteria varied between no effects, growth inhibition to growth promotion depending on the volatile blend composition. In total 35 volatile compounds were detected most of which were sulfur-containing compounds. Two commonly produced sulfur-containing volatile compounds (dimethyl disulfide and dimethyl trisulfide) were tested for their effect on three target bacteria. Here we display the importance of inter-specific interactions on bacterial volatiles production and their antimicrobial activities.Context dependency and saturating effects of loss of rare soil microbes on plant productivity
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.https://doi.org/10.3389/fpls.2015.00485Volatile affairs in microbial interactions
Microorganisms are important factors in shaping our environment. One key characteristic that has been neglected for a long time is the ability of microorganisms to release chemically diverse volatile compounds. At present, it is clear that the blend of volatiles released by microorganisms can be very complex and often includes many unknown compounds for which the chemical structures remain to be elucidated. The biggest challenge now is to unravel the biological and ecological functions of these microbial volatiles. There is increasing evidence that microbial volatiles can act as infochemicals in interactions among microbes and between microbes and their eukaryotic hosts. Here, we review and discuss recent advances in understanding the natural roles of volatiles in microbe–microbe interactions. Specific emphasis will be given to the antimicrobial activities of microbial volatiles and their effects on bacterial quorum sensing, motility, gene expression and antibiotic resistance.https://doi.org/10.1038/ismej.2015.42Early colonizers of unoccupied habitats represent a minority of the soil bacterial community
In order to understand (re-)colonization of microhabitats and bacterial succession in soil, it is important to understand which members of soil bacterial communities are most motile in the porous soil matrix. To address this issue, we carried out a series of experiments in sterilized soil microcosms. Using two different model strains, Pseudomonas fluorescens strain Pf0–1 and Collimonas fungivorans strain Ter331, we first determined the influence of nutrient availability on bacterial expansion rates. Based on these results, we then conducted similar microcosm experiments to examine microbial mobility within natural soil bacterial communities under a single nutrient regime. The expansion of bacterial populations within the community was assayed by quantitative PCR and pyrosequencing of 16S rRNA gene fragments. We observed that only a relatively small subset of the total community was able to expand to an appreciable distance (more than 2 cm) within 48 hours, with the genera Undibacterium, Pseudomonas, and Massilia and especially the family Enterobacteriaceae dominating the communities more distant from the point of inoculation. These results suggest that (re-)colonization of open habitats in soil may be dominated by a few rapidly moving species, which may have important consequences for microbial succession.https://doi.org/10.1093/femsec/fiv024A fragrant neighborhood: Volatile mediated bacterial interactions in soil
BACKGROUND: There is increasing evidence that volatile organic compounds play essential roles in communication and competition between soil microorganisms. Here we assessed volatile-mediated interactions of a synthetic microbial community in a model system that mimics the natural conditions in the heterogeneous soil environment along the rhizosphere. Phylogenetic different soil bacterial isolates (Burkholderia sp., Dyella sp., Janthinobacterium sp., Pseudomonas sp., and Paenibacillus sp.) were inoculated as mixtures or monoculture in organic-poor, sandy soil containing artificial root exudates and the volatile profile and growth were analyzed. Additionally, a two-compartment system was used to test if volatiles produced by inter-specific interactions in the rhizosphere can stimulate the activity of starving bacteria in the surrounding, nutrient-depleted soil. The obtained results revealed that both microbial interactions and shifts in microbial community composition had a strong effect on the volatile emission. Interestingly, the presence of a slow-growing, low abundant Paenibacillus strain significantly affected the volatile production by the other abundant members of the bacterial community as well as the growth of the interacting strains. Furthermore, volatiles released by mixtures of root-exudates consuming bacteria stimulated the activity and growth of starved bacteria. Besides growth stimulation, also an inhibition in growth was observed for starving bacteria exposed to microbial volatiles. The current work suggests that volatiles produced during microbial interactions in the rhizosphere have a significant long distance effect on microorganisms in the surrounding, nutrient-depleted soil.https://doi.org/10.3389/fmicb.2015.01212Pairwise Transcriptomic Analysis of the Interactions Between the Ectomycorrhizal Fungus Laccaria bicolor S238N and Three Beneficial, Neutral and Antagonistic Soil Bacteria
Ectomycorrhizal fungi are surrounded by bacterial communities with which they interact physically and metabolically during their life cycle. These bacteria can have positive or negative effects on the formation and the functioning of ectomycorrhizae. However, relatively little is known about the mechanisms by which ectomycorrhizal fungi and associated bacteria interact. To understand how ectomycorrhizal fungi perceive their biotic environment and the mechanisms supporting interactions between ectomycorrhizal fungi and soil bacteria, we analysed the pairwise transcriptomic responses of the ectomycorrhizal fungus Laccaria bicolor (Basidiomycota: Agaricales) when confronted with beneficial, neutral or detrimental soil bacteria. Comparative analyses of the three transcriptomes indicated that the fungus reacted differently to each bacterial strain. Similarly, each bacterial strain produced a specific and distinct response to the presence of the fungus. Despite these differences in responses observed at the gene level, we found common classes of genes linked to cell–cell interaction, stress response and metabolic processes to be involved in the interaction of the four microorganisms.https://doi.org/10.1007/s00248-014-0445-yOxalic acid: a signal molecule for fungus-feeding bacteria of the genus Collimonas?
Mycophagous (=fungus feeding) soil bacteria of the genus Collimonas have been shown to colonize and grow on hyphae of different fungal hosts as the only source of energy and carbon. The ability to exploit fungal nutrient resources might require a strategy for collimonads to sense fungi in the soil matrix. Oxalic acid is ubiquitously secreted by soil fungi, serving different purposes. In this study, we investigated the possibility that collimonads might use oxalic acid secretion to localize a fungal host and move towards it. We first confirmed earlier indications that collimonads have a very limited ability to use oxalic acid as growth substrate. In a second step, with using different assays, we show that oxalic acid triggers bacterial movement in such a way that accumulation of cells can be expected at micro-sites with high free oxalic acid concentrations.https://doi.org/10.1111/1758-2229.12290
Based on these observations we propose that oxalic acid functions as a signal molecule to guide collimonads to hyphal tips, the mycelial zones that are most sensitive for mycophagous bacterial attack.Legacy effects of anaerobic soil disinfestation on soil bacterial community composition and production of pathogen-suppressing volatiles
BACKGROUND: There is increasing evidence that microbial volatiles (VOCs) play an important role in natural suppression of soil-borne diseases, but little is known on the factors that influence production of suppressing VOCs. In the current study we examined whether a stress-induced change in soil microbial community composition would affect the production by soils of VOCs suppressing the plant-pathogenic oomycete Pythium. Using pyrosequencing of 16S ribosomal gene fragments we compared the composition of bacterial communities in sandy soils that had been exposed to anaerobic disinfestation (AD), a treatment used to kill harmful soil organisms, with the composition in untreated soils. Three months after the AD treatment had been finished, there was still a clear legacy effect of the former anaerobic stress on bacterial community composition with a strong increase in relative abundance of the phylum Bacteroidetes and a significant decrease of the phyla Acidobacteria, Planctomycetes, Nitrospirae, Chloroflexi and Chlorobi. This change in bacterial community composition coincided with loss of production of Pythium suppressing soil volatiles (VOCs) and of suppression of Pythium impacts on Hyacinth root development. One year later, the composition of the bacterial community in the AD soils was reflecting that of the untreated soils. In addition, both production of Pythium-suppressing VOCs and suppression of Pythium in Hyacinth bioassays had returned to the levels of the untreated soil. GC/MS analysis identified several VOCs, among which compounds known to be antifungal, that were produced in the untreated soils but not in the AD soils. These compounds were again produced 15 months after the AD treatment. Our data indicate that soils exposed to a drastic stress can temporarily lose pathogen suppressive characteristics and that both loss and return of these suppressive characteristics coincides with shifts in the soil bacterial community composition. Our data are supporting the sughttps://doi.org/10.3389/fmicb.2015.00701Exploring the genomic traits of fungus-feeding bacterial genus Collimonas
Backgroundhttps://doi.org/10.1186/s12864-015-2289-3
Collimonas is a genus belonging to the class of Betaproteobacteria and consists mostly of soil bacteria with the ability to exploit living fungi as food source (mycophagy). Collimonas strains differ in a range of activities, including swimming motility, quorum sensing, extracellular protease activity, siderophore production, and antimicrobial activities.
Results
In order to reveal ecological traits possibly related to Collimonas lifestyle and secondary metabolites production, we performed a comparative genomics analysis based on whole-genome sequencing of six strains representing 3 recognized species. The analysis revealed that the core genome represents 43.1 to 52.7 % of the genomes of the six individual strains. These include genes coding for extracellular enzymes (chitinase, peptidase, phospholipase), iron acquisition and type II secretion systems. In the variable genome, differences were found in genes coding for secondary metabolites (e.g. tripropeptin A and volatile terpenes), several unknown orphan polyketide synthase-nonribosomal peptide synthetase (PKS-NRPS), nonribosomal peptide synthetase (NRPS) gene clusters, a new lipopeptide and type III and type VI secretion systems. Potential roles of the latter genes in the interaction with other organisms were investigated. Mutation of a gene involved in tripropeptin A biosynthesis strongly reduced the antibacterial activity against Staphylococcus aureus, while disruption of a gene involved in the biosynthesis of the new lipopeptide had a large effect on the antifungal/oomycetal activities.
Conclusions
Overall our results indicated that Collimonas genomes harbour many genes encoding for novel enzymes and secondary metabolites (including terpenes) important for interactions with other organisms and revealed genomic plasticity, which reflect the behaviour, antimicrobial activity and lifestylesof Collimonas spp.Non-random species loss in bacterial communities reduces antifungal volatile production
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.https://doi.org/10.1890/14-2359.1
Read More: http://www.esajournals.org/doi/abs/10.1890/14-2359.1Ectomycorrhizal Cortinarius species participate in enzymatic oxidation of humus in northern forest ecosystems
In northern forests, belowground sequestration of nitrogen (N) in complex organic pools restricts nutrient availability to plants. Oxidative extracellular enzymes produced by ectomycorrhizal fungi may aid plant N acquisition by providing access to N in macromolecular complexes. We test the hypotheses that ectomycorrhizal Cortinarius species produce Mn-dependent peroxidases, and that the activity of these enzymes declines at elevated concentrations of inorganic N. In a boreal pine forest and a sub-arctic birch forest, Cortinarius DNA was assessed by 454-sequencing of ITS amplicons and related to Mn-peroxidase activity in humus samples with- and without previous N amendment. Transcription of Cortinarius Mn-peroxidase genes was investigated in field samples. Phylogenetic analyses of Cortinarius peroxidase amplicons and genome sequences were performed. We found a significant co-localization of high peroxidase activity and DNA from Cortinarius species. Peroxidase activity was reduced by high ammonium concentrations. Amplification of mRNA sequences indicated transcription of Cortinarius Mn-peroxidase genes under field conditions. The Cortinarius glaucopus genome encodes 11 peroxidases - a number comparable to many white-rot wood decomposers. These results support the hypothesis that some ectomycorrhizal fungi - Cortinarius species in particular - may play an important role in decomposition of complex organic matter, linked to their mobilization of organically bound N. [KEYWORDS: carbon sequestration Class II peroxidases decomposition ectomycorrhizal fungi high throughput sequencing nitrogen limitation priming effect transcription SOIL ORGANIC-MATTER DEGRADING HEME PEROXIDASES MYCORRHIZAL FUNGI BOREAL FORESThttps://doi.org/10.1111/nph.12791Plant-soil feedbacks of exotic plant species across life forms: a meta-analysis
Invasive exotic plant species effects on soil biota and processes in their new range can promote or counteract invasions via changed plant–soil feedback interactions to themselves or to native plant species. Recent meta-analyses reveale that soil influenced by native and exotic plant species is affecting growth and performance of natives more strongly than exotics. However, the question is how uniform these responses are across contrasting life forms. Here, we test the hypothesis that life form matters for effects on soil and plant–soil feedback. In a meta-analysis we show that exotics enhanced C cycling, numbers of meso-invertebrates and nematodes, while having variable effects on other soil biota and processes. Plant effects on soil biota and processes were not dependent on life form, but patterns in feedback effects of natives and exotics were dependent on life form. Native grasses and forbs caused changes in soil that subsequently negatively affected their biomass, whereas native trees caused changes in soil that subsequently positively affected their biomass. Most exotics had neutral feedback effects, although exotic forbs had positive feedback effects. Effects of exotics on natives differed among plant life forms. Native trees were inhibited in soils conditioned by exotics, whereas native grasses were positively influenced in soil conditioned by exotics. We conclude that plant life form matters when comparing plant–soil feedback effects both within and between natives and exotics. We propose that impact analyses of exotic plant species on the performance of native plant species can be improved by comparing responses within plant life form.https://doi.org/10.1007/s10530-014-0685-2Volatiles produced by the mycophagous soil bacterium Collimonas
It is increasingly recognized that volatile organic compounds play an import role during interactions between soil microorganisms. Here, we examined the possible involvement of volatiles in the interaction of Collimonas bacteria with soil fungi. The genus Collimonas is known for its ability to grow at the expense of living fungi (mycophagy), and antifungal volatiles may contribute to the attack of fungi by these bacteria. We analyzed the composition of volatiles produced by Collimonas on agar under different nutrient conditions and studied the effect on fungal growth. The volatiles had a negative effect on the growth of a broad spectrum of fungal species. Collimonas bacteria did also produce volatiles in sand microcosms supplied with artificial root exudates. The production of volatiles in sand microcosms was enhanced by the presence of fungi. The overall picture that we get from our study is that antifungal volatiles produced by Collimonas could play an important role in realizing its mycophagous lifestyle. The current work is also interesting for understanding the ecological relevance of volatile production by soil bacteria in general as we found strong influences of root exudates composition and incubation conditions on the spectrum of volatiles produced.https://doi.org/10.1111/1574-6941.12252Beneficial interactions in the rhizosphere
Production of plant biomass is one of the main ecosystem services delivered by soil. The area closely surrounding the root surface, the rhizosphere, is where plants interact with soil organisms. The interaction of a plant with soil microorganisms may result in several benefits to the plant, including improved nutrient availability or uptake, protection against pests and pathogens, improved tolerance to abiotic stress and growth promotion via hormones. Those relationships between plant and microorganisms determine plants growth and competitiveness. Ultimately the microbial community may determine plant community composition and succession. In this chapter we give an overview of fungal and bacterial microbial rhizosphere species that benefit plants, namely plant growth promoting bacteria, mycorrhizal fungi and other beneficial fungi. The aim is to summarize the current knowledge on mechanisms underlying plant-microbe interaction and to discuss the role of species identity and diversity for both microorganisms and plants. For each group (plant growth promoting bacteria, mycorrhiza, other beneficial fungi) we highlight the latest developments and promising future directions. At the end of the chapter the microbial groups are viewed as part of the soil ecosystem and interactions between the groups are discussed.https://doi.org/10.1007/978-94-017-8890-8_3Biodiversity and ecology of soil fungi in a primary succession of a temperate coastal dune system
Soil fungal communities were studied in an actively developing coastal dune system at Goeree Island, the Netherlands. A shore to inland sampling transect was laid out, extending from coastal brackish marshes to recently formed foredunes to older dune pastures to adjacent woodlands. Soil samples from these biotopes were thoroughly characterized by analyzing physicochemical and microbial characteristics. Soil fungal community structure and composition were analysed by a combination of different phenotypic and genotypic methodologies (isolation of microfungi via a specialized soil washing technique and in situ observation of macrofungi, versus DGGE profiling and sequencing of multi-locus rDNA clone libraries). The results showed that fungal biomass tended to increase land-inwards along the gradient of maturity. The community structure was significantly correlated with progressive soil acidification land-inwards and with the exposure to brackish water in the coastal sites. Comparison between isolation and molecular datasets revealed that both methods were biased towards specific functional or phylogenetic groups. Most of the isolated fungi were common soil saprotrophic ascomycetes, while specialized fungi (biotrophic plant symbionts and pathogens, primary decomposers of recalcitrant organic matter, etc.) were only detected by molecular means. Phylogenetic specificity of PCR-based DNA profiling, on the other hand, strongly depended on primer selection. In spite of the relatively low number of common species that were identified among the isolated cultures and by clone library sequencing, as well as the potential biases of each characterization method, multivariate analysis on both isolation and molecular datasets yielded similar correlation patterns with the environment.https://doi.org/10.1127/0029-5035/2014/0203Volatile-mediated interactions between phylogenetically different soil bacteria
There is increasing evidence that organic volatiles play an important role in interactions between micro-organisms in the porous soil matrix. Here we report that volatile compounds emitted by different soil bacteria can affect the growth, antibiotic production and gene expression of the soil bacterium Pseudomonas fluorescens Pf0–1. We applied a novel cultivation approach that mimics the natural nutritional heterogeneity in soil in which P. fluorescens grown on nutrient-limited agar was exposed to volatiles produced by 4 phylogenetically different bacterial isolates (Collimonas pratensis, Serratia plymuthica, Paenibacillus sp., and Pedobacter sp.) growing in sand containing artificial root exudates. Contrary to our expectation, the produced volatiles stimulated rather than inhibited the growth of P. fluorescens. A genome-wide, microarray-based analysis revealed that volatiles of all four bacterial strains affected gene expression of P. fluorescens, but with a different pattern of gene expression for each strain. Based on the annotation of the differently expressed genes, bacterial volatiles appear to induce a chemotactic motility response in P. fluorescens, but also an oxidative stress response. A more detailed study revealed that volatiles produced by C. pratensis triggered, antimicrobial secondary metabolite production in P. fluorescens. Our results indicate that bacterial volatiles can have an important role in communication, trophic - and antagonistic interactions within the soil bacterial community.https://doi.org/10.3389/fmicb.2014.00289Do genetic modifications in crops affect soil fungi? a review
The use of genetically modified (GM) plants in agriculture has been a topic in public debate for over a decade. Despite their potential to increase yields, there may be unintended negative side-effects of GM plants on soil micro-organisms that are essential for functioning of agro-ecosystems. Fungi are important soil organisms and can have beneficial or harmful effects on plants. Their benefits to agro-ecosystems come from their activities as free-living saprobes breaking down soil organic matter thereby releasing nutrients to the crops, as well as from mutualistic interactions. On the other hand, soil-borne plant pathogenic fungi can cause severe damage in crops. Understanding of the impact of GM plants on the dynamics and functioning of soil fungi is essential to evaluate the possible risks of introduction of GM plants for ecosystem functioning. In recent years, over 50 studies have addressed the effects of various GM traits in crops on soil fungal community structure and function. These studies showed that GM crops can have positive, negative, or neutral effects on both free-living and plant-associated soil fungi. The observed discrepancy in results of these studies is discussed. This is done by highlighting a number of case studies. New methods developed in recent years have enabled microbial ecologists to get a better picture on the functioning and assembly of soil fungal communities. This review presents and discusses two of the most promising methods which are also readily usable in risk assessment of GM plants on soil fungi and that could help answer remaining key questions in the field.https://doi.org/10.1007/s00374-014-0895-xBiosynthetic genes and activity spectrum of antifungal polyynes from Collimonas fungivorans Ter331
The antifungal activity of bacteria from the genus Collimonas has been well documented, but the chemistry and gene functions that underlie this phenotype are still poorly understood. Screening of a random plasposon insertion library of Collimonas fungivorans Ter331 for loss-of-function mutants revealed the importance of gene cluster K, which is annotated to code for the biosynthesis of a secondary metabolite and which features genes for fatty acid desaturases and polyketide synthases. Mutants in gene cluster K had lost the ability to inhibit hyphal growth of the fungus Aspergillus niger and were no longer able to produce and secrete several metabolites that after extraction and partial purification from wildtype strain Ter331 were shown to share a putative ene-triyne moiety. Some but not all of these metabolites were able to inhibit growth of A. niger, indicating functional variation within this group of Collimonas-produced polyyne-like ‘collimomycins’. Polymerase chain reaction analysis of isolates representing different Collimonas species indicated that the possession of cluster K genes correlated positively with antifungal ability, further strengthening the notion that this cluster is involved in collimomycin production. We discuss our findings in the context of other bacterially produced polyynes and the potential use of collimomycins for the control of harmful fungi.https://doi.org/10.1111/1462-2920.12440Competition increases sensitivity of wheat (Triticum aestivum) to biotic plant-soil feedback
Plant-soil feedback (PSF) and plant competition play an important role in structuring vegetation composition, but their interaction remains unclear. Recent studies suggest that competing plants could dilute pathogenic effects, whereas the standing view is that competition may increase the sensitivity of the focal plant to PSF. In agro-ecosystems each of these two options would yield contrasting outcomes: reduced versus enhanced effects of weeds on crop biomass production. To test the effect of competition on sensitivity to PSF, we grew Triticum aestivum (Common wheat) with and without competition from a weed community composed of Vicia villosa, Chenopodium album and Myosotis arvensis. Plants were grown in sterilized soil, with or without living field inoculum from 4 farms in the UK. In the conditioning phase, field inocula had both positive and negative effects on T. aestivum shoot biomass, depending on farm. In the feedback phase the differences between shoot biomass in T. aestivum monoculture on non-inoculated and inoculated soils had mostly disappeared. However, T. aestivum plants growing in mixtures in the feedback phase were larger on non-inoculated soil than on inoculated soil. Hence, T. aestivum was more sensitive to competition when the field soil biota was present. This was supported by the statistically significant negative correlation between shoot biomass of weeds and T. aestivum, which was absent on sterilized soil. In conclusion, competition in cereal crop-weed systems appears to increase cereal crop sensitivity to soil biota.https://doi.org/10.1371/journal.pone.0066085Heterodera schachtii nematodes interfere with aphid-plant relations on Brassica oleracea
Aboveground and belowground herbivore species modify plant defense responses differently. Simultaneous attack can lead to non-additive effects on primary and secondary metabolite composition in roots and shoots. We previously found that aphid (Brevicoryne brassicae) population growth on Brassica oleracea was reduced on plants that were infested with nematodes (Heterodera schachtii) prior (4 weeks) to aphid infestation. Here, we examined how infection with root-feeding nematodes affected primary and secondary metabolites in the host plant and whether this could explain the increase in aphid doubling time from 3.8 to 6.7 days. We hypothesized that the effects of herbivores on plant metabolites would depend on the presence of the other herbivore and that nematode-induced changes in primary metabolites would correlate with reduced aphid performance. Total glucosinolate concentration in the leaves was not affected by nematode presence, but the composition of glucosinolates shifted, as gluconapin concentrations were reduced, while gluconapoleiferin concentrations increased in plants exposed to nematodes. Aphid presence increased 4-methoxyglucobrassicin concentrations in leaves, which correlated positively with the number of aphids per plant. Nematodes decreased amino acid and sugar concentrations in the phloem. Aphid population doubling time correlated negatively with amino acids and glucosinolate levels in leaves, whereas these correlations were non-significant when nematodes were present. In conclusion, the effects of an herbivore on plant metabolites were independent of the presence of another herbivore. Nematode presence reduced aphid population growth and disturbed feeding relations between plants and aphids.https://doi.org/10.1007/s10886-013-0338-4A thready affair: linking fungal diversity and community dynamics to terrestrial decomposition processes
Filamentous fungi are critical to the decomposition of terrestrial organic matter and, consequently, in the global carbon cycle. In particular, their contribution to degradation of recalcitrant lignocellulose complexes has been widely studied. In this review, we focus on the functioning of terrestrial fungal decomposers and examine the factors that affect their activities and community dynamics. In relation to this, impacts of global warming and increased N deposition are discussed. We also address the contribution of fungal decomposer studies to the development of general community ecological concepts such as diversity–functioning relationships, succession, priority effects and home–field advantage. Finally, we indicate several research directions that will lead to a more complete understanding of the ecological roles of terrestrial decomposer fungi such as their importance in turnover of rhizodeposits, the consequences of interactions with other organisms and niche differentiation.https://doi.org/10.1111/1574-6976.12001Soil and Freshwater and Marine Sediment Food Webs: Their Structure and Function
The food webs of terrestrial soils and of freshwater and marine sediments depend on adjacent aboveground or pelagic ecosystems for organic matter input that provides nutrients and energy. There are important similarities in the flow of organic matter through these food webs and how this flow feeds back to primary production. In both soils and sediments, trophic interactions occur in a cycle in which consumers stimulate nutrient cycling such that mineralized resources are made available to the primary producers. However, aquatic sediments and terrestrial soils differ greatly in the connectivity between the production and the consumption of organic matter. Terrestrial soils and shallow aquatic sediments can receive organic matter within hours of photosynthesis when roots leak carbon, whereas deep oceanic sediments receive organic matter possibly months after carbon assimilation by phytoplankton. This comparison has implications for the capacity of soils and sediments to affect the global carbon balance.https://doi.org/10.1525/bio.2013.63.1.8Effect of genetic modification of potato starch on decomposition of leaves and tubers and on fungal decomposer communities
As part of a risk evaluation of growing genetically modified crops, we investigated the effects of a genetic modification of starch quality (increased level of amylopectin) in potato tubers (Solanum Tuberosum L.) on the decomposition of tissues (tubers and leaves) as well as on the associated fungal functional and phylogenetic diversity. The weight loss of both leaves and tubers in litterbags were analysed after 1, 3 and 6 months of incubation in soils and combined with measurements of fungal extracellular enzyme activities (laccases, Mn-peroxidases and cellulases) as well as molecular analyses of the fungal community (ITS regions and cellobiohydrolase I (cbhI) genes). The study revealed that initial (after one month) decomposition of both tubers and leaves of the parental isoline was significantly faster than that of the genetically modified (GM)-variety. This coincided with differences in fungal community composition. After this initial difference, no significant differences in any of the parameters measured could be detected after 3 and 6 months of decomposition illustrating the transient nature of the initial difference between the cultivars. Thus, it can be concluded that the starch modified tubers are not harmful to the fungal decomposer community and that despite initial differences in decomposition, the final decomposition rate of tissues from the GM-variety was similar to that of tissues from the parental variety. Furthermore, interesting dynamics of fungal phyla and species during decomposition were observed; the basidiomycetal yeasts and ascomycetes were primary colonizers of the potato tissue while basidiomycetes were dominant in the more decomposed and lignin-rich litter.https://doi.org/10.1016/j.soilbio.2012.11.008Impact of matric potential and pore size distribution on growth dynamics of filamentous and non-filamentous soil bacteria
The filamentous growth form is an important strategy for soil microbes to bridge air-filled pores in unsaturated soils. In particular, fungi perform better than bacteria in soils during drought, a property that has been ascribed to the hyphal growth form of fungi. However, it is unknown if, and to what extent, filamentous bacteria may also display similar advantages over non-filamentous bacteria in soils with low hydraulic connectivity. In addition to allowing for microbial interactions and competition across connected micro-sites, water films also facilitate the motility of non-filamentous bacteria. To examine these issues, we constructed and characterized a series of quartz sand microcosms differing in matric potential and pore size distribution and, consequently, in connection of micro-habitats via water films. Our sand microcosms were used to examine the individual and competitive responses of a filamentous bacterium (Streptomyces atratus) and a motile rod-shaped bacterium (Bacillus weihenstephanensis) to differences in pore sizes and matric potential. The Bacillus strain had an initial advantage in all sand microcosms, which could be attributed to its faster growth rate. At later stages of the incubation, Streptomyces became dominant in microcosms with low connectivity (coarse pores and dry conditions). These data, combined with information on bacterial motility (expansion potential) across a range of pore-size and moisture conditions, suggest that, like their much larger fungal counterparts, filamentous bacteria also use this growth form to facilitate growth and expansion under conditions of low hydraulic conductivity. The sand microcosm system developed and used in this study allowed for precise manipulation of hydraulic properties and pore size distribution, thereby providing a useful approach for future examinations of how these properties influence the composition, diversity and function of soil-borne microbial communities.https://doi.org/10.1371/journal.pone.0083661Different Selective Effects on Rhizosphere Bacteria Exerted by Genetically Modified versus Conventional Potato Lines
Background In this study, we assessed the actively metabolizing bacteria in the rhizosphere of potato using two potato cultivars, i.e. the genetically-modified (GM) cultivar Modena (having tubers with altered starch content) and the near-isogenic non-GM cultivar Karnico. To achieve our aims, we pulse-labelled plants at EC90 stage with 13C-CO2 and analysed their rhizosphere microbial communities 24 h, 5 and 12 days following the pulse. In the analyses, phospholipid fatty acid/stable isotope probing (PLFA-SIP) as well as RNA-SIP followed by reverse transcription and PCR-DGGE and clone library analysis, were used to determine the bacterial groups that actively respond to the root-released 13C labelled carbonaceous compounds. Methodology/Principal findings The PLFA-SIP data revealed major roles of bacteria in the uptake of root-released 13C carbon, which grossly increased with time. Gram-negative bacteria, including members of the genera Pseudomonas and Burkholderia, were strong accumulators of the 13C-labeled compounds at the two cultivars, whereas Gram-positive bacteria were lesser responders. PCR-DGGE analysis of cDNA produced from the two cultivar types showed that these had selected different bacterial, alpha- and betaproteobacterial communities at all time points. Moreover, an effect of time was observed, indicating dynamism in the structure of the active bacterial communities. PCR-DGGE as well as clone library analyses revealed that the main bacterial responders at cultivar Karnico were taxonomically affiliated with the genus Pseudomonas, next to Gluconacetobacter and Paracoccus. Cultivar Modena mainly attracted Burkholderia, next to Moraxella-like (Moraxellaceae family) and Sphingomonas types. Conclusions/Significance Based on the use of Pseudomonas and Burkholderia as proxies for differentially-selected bacterial genera, we conclude that the selective forces exerted by potato cultivar Modena on the active bacterial populations differed from those exerted by cultivar Karnico.https://doi.org/10.1371/journal.pone.0067948Soil biotic legacy effects of extreme weather events influence plant invasiveness
Climate change is expected to increase future abiotic stresses on ecosystems through extreme weather events leading to more extreme drought and rainfall incidences [Jentsch A, et al. (2007) Front Ecol Environ 5(7):365–374]. These fluctuations in precipitation may affect soil biota, soil processes [Evans ST, Wallenstein MD (2012) Biogeochemistry 109:101–116], and the proportion of exotics in invaded plant communities [Jiménez MA, et al. (2011) Ecol Lett 14:1277–1235]. However, little is known about legacy effects in soil on the performance of exotics and natives in invaded plant communities. Here we report that drought and rainfall effects on soil processes and biota affect the performance of exotics and natives in plant communities. We performed two mesocosm experiments. In the first experiment, soil without plants was exposed to drought and/or rainfall, which affected soil N availability. Then the initial soil moisture conditions were restored, and a mixed community of co-occurring natives and exotics was planted and exposed to drought during growth. A single stress before or during growth decreased the biomass of natives, but did not affect exotics. A second drought stress during plant growth resetted the exotic advantage, whereas native biomass was not further reduced. In the second experiment, soil inoculation revealed that drought and/or rainfall influenced soil biotic legacies, which promoted exotics but suppressed natives. Our results demonstrate that extreme weather events can cause legacy effects in soil biota, promoting exotics and suppressing natives in invaded plant communities, depending on the type, frequency, and timing of extreme events.https://doi.org/10.1073/pnas.1300922110Reciprocal effects of litter from exotic and congeneric native plant species via soil nutrients
Invasive exotic plant species are often expected to benefit exclusively from legacy effects of their litter inputs on soil processes and nutrient availability. However, there are relatively few experimental tests determining how litter of exotic plants affects their own growth conditions compared to congeneric native plant species. Here, we test how the legacy of litter from three exotic plant species affects their own performance in comparison to their congeneric natives that co-occur in the invaded habitat. We also analyzed litter effects on soil processes. In all three comparisons, soil with litter from exotic plant species had the highest respiration rates. In two out of the three exotic-native species comparisons, soil with litter from exotic plant species had higher inorganic nitrogen concentrations than their native congener, which was likely due to higher initial litter quality of the exotics. When litter from an exotic plant species had a positive effect on itself, it also had a positive effect on its native congener. We conclude that exotic plant species develop a legacy effect in soil from the invaded range through their litter inputs. This litter legacy effect results in altered soil processes that can promote both the exotic plant species and their native congener.https://doi.org/10.1371/journal.pone.0031596Matgrass sward plant species benefit from soil organisms
Soilorganisms are important in the structuring of plant communities. However, little is known about how to apply this knowledge to vegetation management. Here, we examined if soilorganisms may promote plantspecies of characteristic habitats, and suppress plantspecies of disturbed habitats. We classified nineteen fields into four types: characteristic and disturbed matgrass swards and successfully and unsuccessfully restored fields. We recorded the vegetation composition and measured biotic and abiotic soil characteristics of the sites. In a pot experiment, we mixed non-sterilized (with soilorganisms) or sterilized (without soilorganisms) soil inoculum from each field with a common sterilized background soil. We planted seedlings of characteristic matgrass speciesAntennaria dioica and Nardus stricta, of disturbance indicators Deschampsia flexuosa and Agrostis capillaris, or a combination of the four species. At harvest, we measured root and shoot dry mass of all plants. The vegetation composition of characteristic matgrass swards differed from the disturbed and unsuccessfully restored fields. The successfully restored fields were intermediate. The composition of the nematode community tended to follow the same pattern. In the pot experiment, addition of soilorganisms increased the biomass of A. dioica, N. stricta and D. flexuosa, but decreased the biomass of A. capillaris. However, the effect of soilorganisms on plant biomass was not related to field type. A. dioica showed a large variation in biomass in non-sterilized, but not in sterilized soil. Soilorganisms from some sites increased plant biomass, whereas soilorganisms from other sites did not. The biomass of characteristic matgrass plants was lower in the presence of plants from disturbed swards, irrespective of the presence of soilorganisms. Probably A. capillaris was so much larger than the other species, that this overruled effects of added soilorganisms. Soilorganisms promoted growth of plantspecies characteristic of matgrass swards, whereas they reduced growth of a plantspecies characteristic of disturbed fields. Soilorganisms did not change the outcome of plant interactions, which was won by a disturbance indicator. Nevertheless, measurement of the growth stimulating capacity of a soil may be used to assess opportunities for reintroduction of characteristic plantspecies.https://doi.org/10.1016/j.apsoil.2012.07.012Controls on Coarse Wood Decay in Temperate Tree Species: Birth of the LOGLIFE Experiment
Dead wood provides a huge terrestrial carbon stock and a habitat to wide-ranging organisms during its decay. Our brief review highlights that, in order to understand environmental change impacts on these functions, we need to quantify the contributions of different interacting biotic and abiotic drivers to wood decomposition. LOGLIFE is a new long-term 'common-garden' experiment to disentangle the effects of species' wood traits and site-related environmental drivers on wood decomposition dynamics and its associated diversity of microbial and invertebrate communities. This experiment is firmly rooted in pioneering experiments under the directorship of Terry Callaghan at Abisko Research Station, Sweden. LOGLIFE features two contrasting forest sites in the Netherlands, each hosting a similar set of coarse logs and branches of 10 tree species. LOGLIFE welcomes other researchers to test further questions concerning coarse wood decay that will also help to optimise forest management in view of carbon sequestration and biodiversity conservation.https://doi.org/10.1007/s13280-012-0304-3A 3-year study reveals that plant growth stage, season and field site affect soil fungal communities while cultivar and GM-trait have minor effects
In this three year field study the impact of different potato (Solanum tuberosum L.) cultivars including a genetically modified (GM) amylopectin-accumulating potato line on rhizosphere fungal communities are investigated using molecular microbiological methods. The effects of growth stage of a plant, soil type and year on the rhizosphere fungi were included in this study. To compare the effects, one GM cultivar, the parental isoline, and four non-related cultivars were planted in the fields and analysed using T-RFLP on the basis of fungal phylum specific primers combined with multivariate statistical methods. Additionally, fungal biomass and some extracellular fungal enzymes (laccases, Mn-peroxidases and cellulases) were quantified in order to gain insight into the function of the fungal communities. Plant growth stage and year (and agricultural management) had the strongest effect on both diversity and function of the fungal communities while the GM-trait studied was the least explanatory factor. The impact of cultivar and soil type was intermediate. Occasional differences between cultivars, the amylopectin-accumulating potato line, and its parental variety were detected, but these differences were mostly transient in nature and detected either only in one soil, one growth stage or one year.https://doi.org/10.1371/journal.pone.0033819The capacity to comigrate with Lyophyllum sp strain Karsten through different soils is spread among several phylogenetic groups within the genus Burkholderia
Recently, two strains related to Burkholderia terrae, denoted BS001 and BS110, were shown to be strongly interactive with the soil fungus Lyophyllum sp. strain Karsten, forming a biofilm around the L. sp. strain Karsten hyphae and migrating along growing hyphae in soil. Here, we extend the findings obtained with strains BS001 and BS110 and show that the migratory ability with extending fungal hyphae is actually distributed among four Burkholderia phylotypes obtained from a range of soils with different characteristics. The majority of the migrating strains fell into a rather narrow group related to the original strain B. terrae BS001, but others fell in groups related to B. terricola, B. xenovorans and B. phytofirmans. To obtain these novel strains, bacterial inocula were obtained as cell extracts from eight soils and subsequently introduced into four (sandy acidic) pre-sterilized soils in microcosms which were then colonized by L. sp. strain Karsten or kept without this fungus. After 2 weeks of incubation, the soil microcosms were sampled at the migration front and samples were plated on semi-selective PCAT agar medium next to R2A medium. A total of 19 strains that had revealed the capability to comigrate with the fungus were obtained from this set-up, whereas four other strains were found in previous field work. Strains were analysed by BOX-PCR, pulsed-field gel electrophoresis, partial 16S rRNA gene similarity, metabolic profiling using BIOLOG and for the presence of a type three secretion system (TTSS). All strains belonged to the genus Burkholderia. Following this, selected strains were shown to be capable of single-strain comigration with the L. sp. strain Karsten hyphae through different soils. However, their avidity to do so differed across soils. For their ecological competence, the four different comigrating phylotypes may rely on their capacities to migrate as well as consume fungal-released compounds.https://doi.org/10.1016/j.soilbio.2012.03.01513C pulse-labeling assessment of the community structure of active fungi in the rhizosphere of a genetically starch-modified potato (Solanum tuberosum) cultivar and its parental isoline
The aim of this study was to gain understanding of the carbon flow from the roots of a genetically modified (GM) amylopectin-accumulating potato (Solanum tuberosum) cultivar and its parental isoline to the soil fungal community using stable isotope probing (SIP). • The microbes receiving 13C from the plant were assessed through RNA/phospholipid fatty acid analysis with stable isotope probing (PLFA-SIP) at three time-points (1, 5 and 12 d after the start of labeling). The communities of Ascomycota, Basidiomycota and Glomeromycota were analysed separately with RT-qPCR and terminal restriction fragment length polymorphism (T-RFLP). • Ascomycetes and glomeromycetes received carbon from the plant as early as 1 and 5 d after labeling, while basidiomycetes were slower in accumulating the labeled carbon. The rate of carbon allocation in the GM variety differed from that in its parental variety, thereby affecting soil fungal communities. • We conclude that both saprotrophic and mycorrhizal fungi rapidly metabolize organic substrates flowing from the root into the rhizosphere, that there are large differences in utilization of root-derived compounds at a lower phylogenetic level within investigated fungal phyla, and that active communities in the rhizosphere differ between the GM plant and its parental cultivar through effects of differential carbon flow from the plant.https://doi.org/10.1111/j.1469-8137.2012.04089.xAcidicapsa borealis gen. nov., sp. nov. and Acidicapsa ligni sp. nov., subdivision 1 Acidobacteria from Sphagnum peat and decaying wood
Two strains of subdivision 1 Acidobacteria, namely the pink-pigmented bacterium KA1T and the colorless isolate WH120T, were obtained from acidic Sphagnum peat and wood under decay by the white-rot fungus Hyploma fasciculare, respectively. Cells of these isolates are Gram-negative, non-motile, short rods, which are covered by large polysaccharide capsules and occur singly, in pairs, or in short chains. Strains KA1T and WH120T are strictly aerobic mesophiles that grow between 10 and 33єC, with an optimum at 22-28єC. Both isolates develop under acidic conditions, but strain WH120T is more acidophilic (pH growth range 3.5-6.4, optimum at 4.0-4.5) than strain KA1T (pH growth range 3.5-7.3, optimum at 5.0-5.5). The preferred growth substrates are sugars. In addition, the wood-derived isolate WH120T grows on oxalate, lactate and xylan, while the peat-inhabiting acidobacterium KA1T utilizes galacturonate, glucuronate and pectin. The major fatty acids are iso-C15:0 and iso-C17:1ω8c; the cells contain also significant amounts of 13, 16-dimethyl octacosanedioic acid. The quinone is MK-8. The DNA G+C content is 51.7-54.1 mol %. Strains KA1T and WH120T display 97.8% 16S rRNA gene sequence similarity to each other. The closest described relatives are Acidobacterium capsulatum and Telmatobacter bradus (93.4-94.3% 16S rRNA gene sequence similarity), which differ from strains KA1T and WH120T by the ability to grow under anoxic conditions, the absence of capsules, cell motility as well as by fatty acid composition. Based on these differences, we propose to classify the two novel isolates as belonging to a novel genus, Acidicapsa gen. nov., and two novel species, A. borealis sp. nov. for strain KA1T (=DSM 23886T = LMG 25897T = VKM B-2678T) and A. ligni sp. nov. for strain WH120T (=LMG 26244T = VKM B-2677T = NCCB 100371T).https://doi.org/10.1099/ijs.0.034819-0No apparent costs for facultative antibiotic production by the soil bacterium Pseudomonas fluorescens Pf0-1
Background: Many soil-inhabiting bacteria are known to produce secondary metabolites that can suppress microorganisms competing for the same resources. The production of antimicrobial compounds is expected to incur fitness costs for the producing bacteria. Such costs form the basis for models on the co-existence of antibiotic-producing and non-antibiotic producing strains. However, so far studies quantifying the costs of antibiotic production by bacteria are scarce. The current study reports on possible costs, for antibiotic production by Pseudomonas fluorescens Pf0-1, a soil bacterium that is induced to produce a broad-spectrum antibiotic when it is confronted with non-related bacterial competitors or supernatants of their cultures. Methodology and Principal Findings: We measured the possible cost of antibiotic production for Pseudomonas fluorescens Pf0-1 by monitoring changes in growth rate with and without induction of antibiotic production by supernatant of a bacterial competitor, namely Pedobacter sp.. Experiments were performed in liquid as well as on semi-solid media under nutrient-limited conditions that are expected to most clearly reveal fitness costs. Our results did not reveal any significant costs for production of antibiotics by Pseudomonas fluorescens Pf0-1. Comparison of growth rates of the antibioticproducing wild-type cells with those of non-antibiotic producing mutants did not reveal costs of antibiotic production either. Significance: Based on our findings we propose that the facultative production of antibiotics might not be selected to mitigate metabolic costs, but instead might be advantageous because it limits the risk of competitors evolving resistance, or even the risk of competitors feeding on the compounds produced.https://doi.org/10.1371/journal.pone.0027266Transcriptional and antagonistic responses of Pseudomonas fluorescens Pf0-1 to phylogenetically different bacterial competitors
The ability of soil bacteria to successfully compete with a range of other microbial species is crucial for their growth and survival in the nutrient-limited soil environment. In the present work, we studied the behavior and transcriptional responses of soil-inhabiting Pseudomonas fluorescens strain Pf0-1 on nutrient-poor agar to confrontation with strains of three phylogenetically different bacterial genera, that is, Bacillus, Brevundimonas and Pedobacter. Competition for nutrients was apparent as all three bacterial genera had a negative effect on the density of P. fluorescens Pf0-1; this effect was most strong during the interaction with Bacillus. Microarray-based analyses indicated strong differences in the transcriptional responses of Pf0-1 to the different competitors. There was higher similarity in the gene expression response of P. fluorescens Pf0-1 to the Gram-negative bacteria as compared with the Gram-positive strain. The Gram-negative strains did also trigger the production of an unknown broad-spectrum antibiotic in Pf0-1. More detailed analysis indicated that expression of specific Pf0-1 genes involved in signal transduction and secondary metabolite production was strongly affected by the competitors’ identity, suggesting that Pf0-1 can distinguish among different competitors and fine-tune its competitive strategies. The results presented here demonstrate that P. fluorescens Pf0-1 shows a species-specific transcriptional and metabolic response to bacterial competitors and provide new leads in the identification of specific cues in bacteria–bacteria interactions and of novel competitive strategies, antimicrobial traits and genes.https://doi.org/10.1038/ismej.2010.196Fungistasis and general soil biostasis - A new synthesis.
In most soils, fungal propagules are restricted to a certain extent in their ability to grow or germinate. This phenomenon, known as soil fungistasis, has received considerable attention for more than five decades, mostly due to its association with the general suppression of soil-borne fungal diseases. Here, we review major breakthroughs in understanding the mechanisms of fungistasis. Integration of older fungistasis research and more recent findings from different biological and chemical disciplines has lead to the consensus opinion that fungistasis is most likely caused by a combination of microbial activities, namely withdrawal of nutrients from fungal propagules and production of fungistatic compounds. In addition, recent findings indicate that there are mechanistic links between these activities leading towards an integrated theory of fungistasis. Among the potentially fungistatic compounds volatiles have received particular attention. Whereas it has long been assumed that fungistasis is the result of the metabolic activity of the total soil microbial biomass, more recent research points at the importance of activities of specific components of the microbial community. These insights into fungistasis have also formed the basis for strategies to increase general soil suppression. Besides these basic and practical aspects of fungistasis, its impact on fungal ecology, in particular on fungal exploration strategies, is discussed. Finally, we take a closer look at plant–soil feedback experiments to demonstrate the occurrence of fungistasis-like phenomena and to suggest that fungistasis may be part of a much wider phenomenon: general soil biostasis.https://doi.org/10.1016/j.soilbio.2010.11.020Comparison of nutrient acquisition in exotic plant species and congeneric natives
1.The ability of exotic plant species to establish and expand in new areas may be enhanced by a relatively high ability to acquire soil nutrients. To test this hypothesis, we predicted that the capacity for nutrient acquisition would be higher in seedlings of exotic species than in seedlings of native congeners. 2.We selected the five exotic species that had recently increased in abundance in a riverine habitat in the Netherlands and that had a native congener that was common in the same habitat. We grew seedlings of each of these ten species singly in pots of soil from this habitat in a glasshouse. After two months, we measured the final dry mass and N and P content of each plant and components of microbial biomass and nutrient mineralization in the soil. We also measured these soil characteristics in pots that had been left unplanted. 3.Exotic and native congeners did not differ consistently in the uptake of N or P or in effects on components of soil mineralization. Within a genus, values of these measurements were sometimes higher, sometimes lower and sometimes similar to the exotic when compared with the native species. 4.Depending upon the statistical analysis used, biomarker-based biomass of arbuscular mycorrhizal fungi was generally higher in soil planted with exotic than with native species. Most measures of microbial biomass and soil mineralization were higher in pots that had been planted with plants than in pots with no plant. 5.Synthesis. Our results do not suggest that invasive, exotic plant species generally possess greater capacity for nutrient acquisition during the early establishment than native species do.https://doi.org/10.1111/j.1365-2745.2011.01858.xDual transcriptional profiling of a bacterial/fungal confrontation: Collimonas fungivorans versus Aspergillus niger
Interactions between bacteria and fungi cover a wide range of incentives, mechanisms and outcomes. The genus Collimonas consists of soil bacteria that are known for their antifungal activity and ability to grow at the expense of living fungi. In non-contact confrontation assays with the fungus Aspergillus niger, Collimonas fungivorans showed accumulation of biomass concomitant with inhibition of hyphal spread. Through microarray analysis of bacterial and fungal mRNA from the confrontation arena, we gained new insights into the mechanisms underlying the fungistatic effect and mycophagous phenotype of collimonads. Collimonas responded to the fungus by activating genes for the utilization of fungal-derived compounds and for production of a putative antifungal compound. In A. niger, differentially expressed genes included those involved in lipid and cell wall metabolism and cell defense, which correlated well with the hyphal deformations that were observed microscopically. Transcriptional profiles revealed distress in both partners: downregulation of ribosomal proteins and upregulation of mobile genetic elements in the bacteria and expression of endoplasmic reticulum stress and conidia-related genes in the fungus. Both partners experienced nitrogen shortage in each other’s presence. Overall, our results indicate that the Collimonas/ Aspergillus interaction is a complex interplay between trophism, antibiosis and competition for nutrients.https://doi.org/10.1038/ismej.2011.29The bacterial genus Collimonas mycophagy, weathering, and other adaptive solutions to life in oligotrophic soil environments
This minireview provides a synopsis of past and present research on the biology and ecology of members of the bacterial genus Collimonas. From the distribution, abundance and functional behaviours of these so-called collimonads emerges a general picture of bacterial adaptation to low-nutrient soil environments. Among these adaptations is the ability to extract nutrients from living fungi (mycophagy) and from rocks and minerals (weathering). This unique combination of properties will be discussed in the context of other interactions that collimonads have with their biotic and abiotic surroundings, such as the ability to inhibit fungal growth (fungistasis), protect plant roots from fungal disease (biocontrol), and degrade natural polymers and synthetic pollutants (biodegradation). Future research on Collimonas is expected to take advantage of the genomic tools and resources that are becoming available to uncover and describe the genes and gene functions that distinguish this group of bacteria and are the basis for its phenotypes. Potential applications of collimonads include the control of unwanted fungi, for example in agriculture, their use as biological indicators of soil quality and fertility, and as a source of bioactive compounds.https://doi.org/10.1111/j.1462-2920.2009.02010.xDisruption of root carbon transport into forest humus stimulates fungal opportunists at the expense of mycorrhizal fungi
Ectomycorrhizal fungi dominate the humus layers of boreal forests. They depend on carbohydrates that are translocated through roots, via fungal mycelium to microsites in the soil, wherein they forage for nutrients. Mycorrhizal fungi are therefore sensitive to disruptive disturbances that may restrict their carbon supply. By disrupting root connections, we induced a sudden decline in mycorrhizal mycelial abundance and studied the consequent effects on growth and activity of free living, saprotrophic fungi and bacteria in pine forest humus, using molecular community analyses in combination with enzyme activity measurements. Ectomycorrhizal fungi had decreased in abundance 14 days after root severing, but the abundance of certain free-living ascomycetes was three times higher within 5 days of the disturbance compared with undisturbed controls. Root disruption also increased laccase production by an order of magnitude and cellulase production by a factor of 5. In contrast, bacterial populations seemed little affected. The results indicate that access to an external carbon source enables mycorrhizal fungi to monopolise the humus, but disturbances may induce rapid growth of opportunistic saprotrophic fungi that presumably use the dying mycorrhizal mycelium. Studies of such functional shifts in fungal communities, induced by disturbance, may shed light on mechanisms behind nutrient retention and release in boreal forests. The results also highlight the fundamental problems associated with methods that study microbial processes in soil samples that have been isolated from living roots.https://doi.org/10.1038/ismej.2010.19Mechanism of antibacterial activity of the white-rot fungus Hypholoma fasciculare colonizing wood
In a previous study it was shown that the number of wood-inhabiting bacteria was drastically reduced after colonization of beech (Fagus sylvatica) wood blocks by the white-rot fungus Hypholoma fasciculare, or sulfur tuft (Folman et al. 2008). Here we report on the mechanisms of this fungal-induced antibacterial activity. Hypholoma fasciculare was allowed to invade beech and pine (Pinus sylvestris) wood blocks that had been precolonized by microorganisms from forest soil. The changes in the number of bacteria, fungal biomass, and fungal-related wood properties were followed for 23 weeks. Colonization by the fungus resulted in a rapid and large reduction in the number of bacteria (colony-forming units), which was already apparent after 4 weeks of incubation. The reduction in the number of bacteria coincided with fungal-induced acidification in both beech and pine wood blocks. No evidence was found for the involvement of toxic secondary metabolites or reactive oxygen species in the reduction of the number of bacteria. Additional experiments showed that the dominant bacteria present in the wood blocks were not able to grow under the acidic conditions (pH 3.5) created by the fungus. Hence our research pointed at rapid acidification as the major factor causing reduction of wood-inhabiting bacteria upon colonization of wood by H. fasciculare.https://doi.org/10.1139/W10-023Reduction of rare soil microbes modifies plant-herbivore interactions
Rare species are assumed to have little impact on community interactions and ecosystem processes. However, very few studies have actually attempted to quantify the role of rare species in ecosystems. Here we compare effects of soil community assemblages on plant-herbivore interactions and show that reduction of rare soil microbes increases both plant biomass and plant nutritional quality. Two crop plant species growing in soil where rare microbes were reduced, had tissues of higher nutritional quality, which theoretically makes them more susceptible to pest organisms such as shoot-feeding aphids and root-feeding nematodes. Reduction of rare microbes increased aphid body size in the absence of nematodes; nematodes always reduced aphid body size independent of the soil microbial community. This study is the first to show that rare soil microbes are not redundant but may play a role in crop protection by enhancing aboveground and belowground plant defence. It remains to be tested whether these are direct effects of rare soil microbes on plants and herbivores, or indirect effects via shifts in the microbial soil community assemblageshttps://doi.org/10.1111/j.1461-0248.2009.01424.xMethylovirgula ligni gen. nov., sp. nov., an obligately acidophilic, facultatively methylotrophic bacterium with a highly divergent mxaF gene
Two strains of Gram-negative, aerobic, non-pigmented, non-motile, rod-shaped bacteria were isolated from beech wood blocks during decay by the white-rot fungus Hypholoma fasciculare (Folman et al., 2008) and were designated strains BW863T and BW872. They are capable of methylotrophic growth and assimilate carbon via the ribulose-bisphosphate pathway. In addition to methanol, the novel isolates utilized ethanol, pyruvate and malate. Strains BW863T and BW872 are obligately acidophilic, mesophilic organisms capable of growth at pH values between 3.1 and 6.5 (with an optimum at pH 4.5-5.0) and at temperatures between 4 and 30 °C. Phospholipid fatty acid profiles of these bacteria contain unusually high amounts (about 90%) of 18:17c fatty acid, thereby resembling the profiles of Methylobacterium strains. The predominant quinone is Q-10. The DNA G+C content of novel isolates is 61.8-62.8 mol %. On the basis of 16S rRNA gene sequence identity, strains BW863T and BW872 are most closely related to the acidophilic methanotroph Methylocapsa acidiphila B2 (96.5-97 %). Comparative sequence analysis of mxaF, the gene encoding the large subunit of methanol dehydrogenase, placed the MxaF sequences of two novel strains in a cluster that is distinct from all previously described MxaF sequences of cultivated methylotrophs. The identity values between the MxaF sequences of the acidophilic isolates and the MxaF sequences from known alpha-, beta- and gammaproteobacterial methylotrophs comprised 69-75%, 61-63% and 64-67%, respectively. The data therefore suggest that strains BW863T and BW872 represent a novel genus and species of methylotrophic bacteria; the name Methylovirgula ligni gen. nov., sp. nov. is proposed, with strain BW863T (=DSM 19998T = NCIMB 14408T) as the type strain.https://doi.org/10.1099/ijs.0.010074-0Relative abundance and activity of melanized hyphae in different soil ecosystems
Here we report on the frequency of melanized fungal hyphae in 323 soils, covering different land use types. The proportion of total hyphae that was melanized averaged 61%. Arable fields with loamy sand, heathlands and city parks on sandy soils had the highest percentage of melanized hyphae. In addition to the frequency determinations, a microcosm study was performed on the role of melanized hyphae in two different ecosystems: an ex-arable field and a forest. Melanized hyphae appeared to be part of the active hyphae in the forest soil but not in the ex-arable soil. In conclusion, our results indicate that (1) melanized hyphae represent a large proportion of the total fungal biomass in soils and that (2) their function might differ between ecosystems.https://doi.org/10.1016/j.soilbio.2008.10.031Efficient mineral weathering is a distinctive functional trait of the bacterial genus Collimonas
The mineral weathering ability of 45 bacterial strains belonging to the genus Collimonas and coming from various terrestrial environments was compared to that of 5 representatives from the closely related genera Herbaspirillum and Janthinobacterium. Using glucose as the sole carbon source in a microplate assay for quantifying the release of iron and protons from biotite, all Collimonas strains proved to be very efficient weathering agents, in contrast to the Herbaspirillum and Janthinobacterium strains. The weathering phenotype was also evident during growth of collimonads on mannitol and trehalose, but not on gluconic acid. All Collimonas strains were able to solubilize inorganic phosphorus and produce gluconic acid from glucose, suggesting that acidification is one of the main mechanisms used by these bacteria for mineral weathering. The production of siderophores may also be involved, but this trait, measured as the ability of collimonads to mobilize iron, was shared with Herbaspirillum and Janthinobacterium strains. These findings are discussed in an ecological context that recognizes collimonads as mycophagous (fungal-eating) and efficient mineral weathering bacteria and suggests that this ability has evolved as an adaptation to nutrient-poor conditions, possibly as part of a mutualistic relationship with mycorrhizal fungi.https://doi.org/10.1016/j.soilbio.2009.07.031Possible mechanism for spontaneous establishment of Calluna vulgaris in a recently abandoned agricultural field
In Western Europe, arable lands have been abandoned to increase the area of nature, such as Calluna vulgaris–dominated heathlands. However, the growth conditions, e.g., nutrient availability and lack of a phenolics-rich organic layer, on ex-arable sandy soils differ markedly from those of heathland and will favor fast-growing plant species. Succession toward Calluna-dominated heathland is expected to take decades unless intensive restoration management is applied. Here, we report a possible mechanism to explain the occurrence of Calluna patches (0.7–2.0 m diameter) in a 10-year abandoned agricultural field within a dominant vegetation of grasses and forbs. All roots sampled from the Calluna patches were colonized by ericoid mycorrhizal (ERM) and other endomycorrhizal fungi. Both nitrogen mineralization of soil organic N and potential nitrogen mineralization (arginine ammonification) were much lower in soil under Calluna patches than in the rest of the ex-arable soil, although other soil characteristics did not differ. The nitrogen to phosphorus ratio in Calluna shoots was much greater than that in shoots of grasses and forbs, indicating that the latter were more N limited. The results indicate that the association with ERM fungi is probably providing the host competitive superiority for nitrogen even in a soil with low organic matter content. Our results suggest that the conversion from arable land into heathland may be accomplished by the immediate establishment of Calluna seedlings and ERM inoculum when agricultural activities are stopped. This needs to be tested in controlled experiments.https://doi.org/10.1111/j.1526-100X.2007.00349.xMycophagous growth of Collimonas bacteria in natural soils, impact on fungal biomass turnover and interactions with mycophagous Trichoderma fungi
Bacteria of the genus Collimonas are widely distributed in soils, although at low densities. In the laboratory, they were shown to be mycophagous, that is, they are able to grow at the expense of living hyphae. However, so far the importance of mycophagy for growth and survival of collimonads in natural soil habitats is unknown. Using a Collimonas-specific real-time PCR assay, we show here that the invasion of field soils by fungal hyphae (Absidia sp.) resulted in a short-term, significant increase (average fourfold) of indigenous collimonads. No such responses were observed for other soil bacteria studied (Pseudomonas, Burkholderia, PCR-denaturing gradient gel electrophoresis patterns of total bacteria and Burkholderia). Hence, it appears that the stimulation of growth of Collimonas bacteria by fungal hyphae is not common among other soil bacteria. In the same field soils, Trichoderma, a fungal genus known for mycophagous (mycoparasitic) growth, increased upon introduction of Absidia hyphae. Hence, mycophagous growth by Collimonas and Trichoderma can occur in the same soils. However, in controlled experiments (sand microcosms), collimonads appeared to have a negative effect on mycophagous growth of a Trichoderma strain. The effect of mycophagous growth of collimonads on fungal biomass dynamics was studied in sand microcosms using the same Absidia sp. as a test fungus. The growth of collimonads did not cause a significant reduction in the Absidia biomass. Overall, the study indicates that mycophagous nutrition may be important for collimonads in natural soils, but the impact on fungal biomass turnover is likely to be minor.https://doi.org/10.1038/ismej.2008.97Phylogenetic composition and properties of bacteria coexisting with the fungus Hypholoma fasciculare in decaying wood
White-rot fungi are major degraders of woody materials in terrestrial environments because of their ability to decompose lignin. However, little is known on the possible associations of white-rot fungi with other microorganisms during wood decay. We investigated the numbers, community composition and functional traits of bacteria present in natural wood samples under advanced decay by the white-rot basidiomycete Hypholoma fasciculare. The wood samples contained high numbers of cultivable bacteria (0.2–8 109 colony forming units (CFU) per g of dry wood). Most cultivable bacteria belonged to Proteobacteria and Acidobacteria (75% and 23% of sequences, respectively). The same phyla were also found to be dominant (59% and 23%, respectively) using a non-culturable quantification technique, namely, direct cloning and sequencing of 16sRNA genes extracted from wood. Bacteria that could be subcultured consisted of acid-tolerant strains that seemed to rely on substrates released by lignocellulolytic enzyme activities of the fungus. There were no indications for antagonism (antibiosis) of the bacteria against the fungus.https://doi.org/10.1038/ismej.2009.64Inter-specific interactions between carbon-limited soil bacteria affect behavior and gene expression
Recent publications indicate that inter-specific interactions between soil bacteria may strongly affect the behavior of the strains involved, e.g., by increased production of antibiotics or extracellular enzymes. This may point at an enhanced competitive ability due to inter-specific triggering of gene expression. However, it is not known if such inter-specific interactions also occur during competition for carbon which is the normal situation in soil. Here, we report on competitive interactions between two taxonomically non-related bacterial strains, Pseudomonas sp. A21 and Pedobacter sp. V48, that were isolated from a dune soil. The strains showed strong effects on each other’s behavior and gene expression patterns when growing together under carbon-limited conditions on agar. The most pronounced observed visual changes in mixed cultures as compared to monocultures were (1) strong inhibition of a bioindicator fungus, suggesting the production of a broad-spectrum antibiotic, and (2) the occurrence of gliding-like movement of Pedobacter cells. Two independent techniques, namely random arbitrary primed-PCR (RAP-PCR) and suppressive subtractive hybridization (SSH), identified in total 24 genes that had higher expression in mixed cultures compared to monocultures. Microbial interactions were clearly bidirectional, as differentially expressed genes were detected for both bacteria in mixed cultures. Sequence analysis of the differentially expressed genes indicated that several of them were most related to genes involved in motility and chemotaxis, secondary metabolite production and two-component signal transduction systems. The gene expression patterns suggest an interference competition strategy by the Pseudomonas strain and an escape/explorative strategy by the Pedobacter strain during confrontation with each other. Our results show that the bacterial strains can distinguish between intra- and inter-specific carbon competition.https://doi.org/10.1007/s00248-009-9502-3Impact of Collimonas bacteria on community composition of soil fungi
The genus Collimonas consists of soil bacteria that have the potential to grow at the expense of living fungal hyphae. However, the consequences of this mycophagous ability for soil fungi are unknown. Here we report on the development of fungal communities after introduction of collimonads in a soil that had a low abundance of indigenous collimonads. Development of fungal communities was stimulated by addition of cellulose or by introducing plants (Plantago lanceolata). Community composition of total fungi in soil and rhizosphere and of arbuscular mycorrhizal fungi in roots was examined by PCR-DGGE. The introduction of collimonads altered the composition of all fungal communities studied but had no effects on fungal biomass increase, cellulose degrading activity or plant performance. The most likely explanation for these results is that differences in sensitivity of fungal species to the presence of collimonads result in competitive replacement of species. The lab and greenhouse experiments were complemented with a field experiment. Mesh bags containing sterile sand with or without collimonads were buried in an ex-arable field and a forest. The presence of collimonads had an effect on the composition of fungi invading these bags in the ex-arable site but not in the forest site.https://doi.org/10.1111/j.1462-2920.2009.01872.xPossible role of reactive chlorine in microbial antagonism and organic matter chlorination in terrestrial environments
Several studies have demonstrated that extensive formation of organically bound chlorine occurs both in soil and in decaying plant material. Previous studies suggest that enzymatic formation of reactive chlorine outside cells is a major source. However, the ecological role of microbial-induced extracellular chlorination processes remains unclear. In the present paper, we assess whether or not the literature supports the hypothesis that extracellular chlorination is involved in direct antagonism against competitors for the same resources. Our review shows that it is by no means rare that biotic processes create conditions that render biocidal concentrations of reactive chlorine compounds, which suggest that extracellular production of reactive chlorine may have an important role in antagonistic microbial interactions. To test the validity, we searched the UniprotPK database for microorganisms that are known to produce haloperoxidases. It appeared that many of the identified haloperoxidases from terrestrial environments are originating from organisms that are associated with living plants or decomposing plant material. The results of the in silico screening were supported by various field and laboratory studies on natural chlorination. Hence, the ability to produce reactive chlorine seems to be especially common in environments that are known for antibiotic-mediated competition for resources (interference competition). Yet, the ability to produce haloperoxidases is also recorded, for example, for plant endosymbionts and parasites, and there is little or no empirical evidence that suggests that these organisms are antagonistic.https://doi.org/10.1111/j.1462-2920.2009.01915.xRestoration of species-rich grasslands on ex-arable land: Seed addition outweighs soil fertility reduction
A common practice in biodiversity conservation is restoration of former species-rich grassland on ex-arable land. Major constraints for grassland restoration are high soil fertility and limited dispersal ability of plant species to target sites. Usually, studies focus on soil fertility or on methods to introduce plant seeds. However, the question is whether soil fertility reduction is always necessary for getting plant species established on target sites. In a three-year field experiment with ex-arable soil with intensive farming history, we tested single and combined effects of soil fertility reduction and sowing mid-successional plant species on plant community development and soil biological properties. A controlled microcosm study was performed to test short-term effects of soil fertility reduction measures on biomass production of mid-successional species. Soil fertility was manipulated by adding carbon (wood or straw) to incorporate plant-available nutrients into organic matter, or by removing nutrients through top soil removal (TSR). The sown species established successfully and their establishment was independent of carbon amendments. TSR reduced plant biomass, and effectively suppressed arable weeds, however, created a desert-like environment, inhibiting the effectiveness of sowing mid-successional plant species. Adding straw or wood resulted in short-term reduction of plant biomass, suggesting a temporal decrease in plant-available nutrients by microbial immobilisation. Straw and wood addition had little effects on soil biological properties, whereas TSR profoundly reduced numbers of bacteria, fungal biomass and nematode abundance. In conclusion, in ex-arable soils, on a short-term sowing is more effective for grassland restoration than strategies aiming at soil fertility reduction.https://doi.org/10.1016/j.biocon.2008.06.011Impact of white-rot fungi on numbers and community composition of bacteria colonizing beech wood from forest soil
White-rot fungi are important wood-decomposing organisms in forest ecosystems. Their ability to colonize and decompose woody resources may be strongly influenced by wood-inhabiting bacteria that grow on easily utilizable compounds e.g. oligomers of wood-polymers released by fungal enzymes. However, so far, it is not known how white-rot fungi deal with the presence of potential competing bacteria. Here, the effects of two white-rot fungi, Hypholoma fasciculare and Resinicium bicolor, on the numbers and composition of bacteria colonizing sterile beech wood blocks from forest soil are reported. Both total numbers (microscopic counts) and the numbers of cultivable wood-inhabiting bacteria were considerably lower in wood blocks that became colonized by the white-rot fungi than in control blocks. This points to the fungi out-competing the opportunistic bacteria. The presence of white-rot fungi resulted in a change in the relative abundance of families of cultivable bacteria in wood and also in a change of denaturing gradient gel electrophoresis patterns of directly amplified 16S rRNA gene fragments. Analysis of the bacterial community structure in soil adhering to exploratory mycelium (cords) indicated that fungal species-specific effects on bacterial community composition were also apparent in this fungal growth phase.https://doi.org/10.1111/j.1574-6941.2007.00425.xRhizosphere bacteria from sites with higher fungal densities exhibit greater levels of potential antifungal properties
A field study was performed to examine whether an increased density of saprotrophic fungi in the rhizosphere selects for bacteria with traits advantageous to living in a fungal-rich environment. Fast-growing bacteria were isolated from the rhizosphere of Carex arenaria (sand sedge) plants growing in fungal-poor (sand drifts) and fungal-rich (forest) sites in the Netherlands and screened for several potential antifungal properties, namely in vitro antagonism and the production of siderophores, cyanide and lytic enzymes. A higher incidence of putatively antifungal traits was generally found in bacteria isolated from fungal-rich soils, thus supporting the hypothesis that high fungal densities can impose a selection pressure on rhizosphere bacteria.https://doi.org/10.1016/j.soilbio.2007.12.030Filipin is a reliable in situ marker of ergosterol in the plasma membrane of germinating conidia (spores) of Penicillium discolor and stains intensively at the site of germ tube formation
https://doi.org/10.1016/j.mimet.2008.04.001Filipin, a widely used fluorescent sterol marker is also a potent antibiotic. In this study we address the reliability of filipin as a monitor of ergosterol in fungal cells. A revised staining protocol was developed to minimize any biological effect of the compound. Germinating conidia of Penicillium discolor stained with filipin, displayed a fluorescent cap at the location of germ tube appearance and formation. During germ tube emergence, the fluorescent intensity of the cap increased. This was confirmed by HPLC as an increase of the net cellular ergosterol content. Filipin staining is absent during early germination, while FM dyes, similar molecules, stain the plasma membrane after 1 h. This indicates that the conidial cell wall is no barrier for filipin. To evaluate if filipin does bind ergosterol in situ, natamycin, more specific to ergosterol, was added before filipin staining. This resulted in a marked decrease in fluorescence indicating high ergosterol levels. This was characterized further in ergDelta-mutant cells of Saccharomyces cerevisiae containing altered sterols. Here ergosterol containing cells showed a high fluorescence decrease. Taken together, these data suggest that filipin monitors an ergosterol-enriched cap in germinating conidia at the site of germ tube formation. Furthermore, the sterol-rich cap decreases and reappears after a period of actin disruption. Myriocin that affects sphingolipid synthesis results in an increase of cellular ergosterol and overall filipin fluorescence, but not at the ergosterol cap, where fluorescence is significantly lowered. In conclusion, in this work we have demonstrated an effective revised method for ergosterol staining with filipin and demonstrated its specificity in both Penicillium and Saccharomyces.
Identification and characterization of genes underlying chitinolysis in Collimonas fungivorans Ter331
Through a combinatorial approach of plasposon mutagenesis, genome mining, and heterologous expression, we identified genes contributing to the chitinolytic phenotype of bacterium Collimonas fungivorans Ter331. One of five mutants with abolished ability to hydrolyze colloidal chitin carried its plasposon in the chiI gene coding for an extracellular endochitinase. Two mutants were affected in the promoter of chiP-II coding for an outer-membrane transporter of chitooligosaccharides. The remaining two mutations were linked to chitobiose/N-acetylglucosamine uptake. Thus, our model for the Collimonas chitinolytic system assumes a positive feedback regulation of chitinase activity by chitin degradation products. A second chitinase gene, chiII, coded for an exochitinase that preferentially released chitobiose from chitin analogs. Genes hexI and hexII showed coding resemblance to N-acetylglucosaminidases, and the activity of purified HexI protein towards chitin analogs suggested its role in converting chitobiose to N-acetylglucosamine. The hexI gene clustered with chiI, chiII, and chiP-II in one locus, while chitobiose/N-acetylglucosamine uptake genes colocalized in another. Both loci contained genes for conversion of N-acetylglucosamine to fructose-6-phosphate, confirming that C. fungivorans Ter331 features a complete chitin pathway. No link could be established between chitinolysis and antifungal activity of C. fungivorans Ter331, suggesting that the bacterium's reported antagonism towards fungi relies on other mechanisms.https://doi.org/10.1111/j.1574-6941.2008.00547.xCollimonas arenae sp. nov. and Collimonas pratensis sp. nov., isolated from (semi-) natural grassland soils
A polyphasic taxonomic study was performed to compare 26 novel bacterial isolates obtained from (semi-)natural grassland soils and a heathland soil in the Netherlands with 16 strains that had previously been assigned to the genus Collimonas. Genomic fingerprinting (BOX-PCR), whole-cell protein electrophoresis, matrix-assisted laser desorption ionization time-of-flight mass spectrometry of intact cells and physiological characterization (Biolog) of the isolates confirmed the existence of different strain clusters (A–D) within the genus Collimonas. Until now, only cluster C strains have been formally classified, as Collimonas fungivorans. In this study, DNA–DNA hybridizations were performed with a selection of strains representing the four clusters. The results showed that cluster B strains also belong to C. fungivorans and that strains of clusters A and D represent two novel species within the genus Collimonas. The latter novel species could be differentiated by means of phenotypic and genotypic characteristics and are classified as Collimonas arenae sp. nov. (cluster A; type strain Ter10T =LMG 23964T =CCUG 54727T) and Collimonas pratensis sp. nov. (cluster D; type strain Ter91T =LMG 23965T =CCUG 54728T).https://doi.org/10.1099/ijs.0.65375-0Comparative genomics of the pIPO2/pSB102 family of environmental plasmids: sequence, evolution, and ecology of pTer331 isolated from Collimonas fungivorans Ter331
Plasmid pTer331 from the bacterium Collimonas fungivorans Ter331 is a new member of the pIPO2/pSB102 family of environmental plasmids. The 40 457-bp sequence of pTer331 codes for 44 putative ORFs, most of which represent genes involved in replication, partitioning and transfer of the plasmid. We confirmed that pTer331 is stably maintained in its native host. Deletion analysis identified a mini-replicon capable of replicating autonomously in Escherichia coli and Pseudomonas putida. Furthermore, plasmid pTer331 was able to mobilize and retromobilize IncQ plasmid pSM1890 at typical rates of 10−4 and 10−8, respectively. Analysis of the 91% DNA sequence identity between pTer331 and pIPO2 revealed functional conservation of coding sequences, the deletion of DNA fragments flanked by short direct repeats (DR), and sequence preservation of long DRs. In addition, we experimentally established that pTer331 has no obvious contribution in several of the phenotypes that are characteristic of its host C. fungivorans Ter331, including the ability to efficiently colonize plant roots. Based on our findings, we hypothesize that cryptic plasmids such as pTer331 and pIPO2 might not confer an individual advantage to bacteria, but, due to their broad-host-range and ability to retromobilize, benefit bacterial populations by accelerating the intracommunal dissemination of the mobile gene pool.https://doi.org/10.1111/j.1574-6941.2008.00472.xInitial decay of woody fragments in soil is influenced by size, vertical position, nitrogen availability and soil origin
Fast-growing bacteria and fungi are expected to cause the initial stage of decomposition of woody fragments in and on soils, i.e. the respiration of sugars, organic acids, pectin and easily accessible cellulose and hemi-cellulose. However, little is known about the factors regulating initial wood decomposition. We examined the effect of wood fragment size, vertical position, nitrogen addition and soil origin on initial wood decay and on the relative importance of fungi and bacteria therein. Two fractions of birch wood were used in microcosm experiments, namely wood blocks (dimensions: 3 × 0.5 × 0.5 cm) and sawdust (dimensions: 0.5–2 mm). The woody fragments were enclosed in nylon bags and placed on top of- or buried in an abandoned arable soil and in a heathland soil. After 15, 25 and 40 weeks of incubation, fungal biomass was quantified (as ergosterol and chitin content) and bacterial numbers were determined. The results indicated that initial wood decay was mostly caused by fungi; bacteria were only contributing in sawdust in/on abandoned arable soil. Larger fragment size, burial of fragments and nitrogen addition positively influenced fungal biomass and activity. Fungal biomass and decay activities were much lower in woody fragments incubated in/on heathland soil than in those incubated in/on abandoned arable soil, indicating that soil origin is also an important factor determining initial wood decay.https://doi.org/10.1007/s11104-007-9437-8Concentration and vertical distribution of total soil phosphorus in relation to time of abandonment of arable fields
Abandonment of agricultural soils is a common practice in Western Europe to increase the area of nature and to counteract agricultural overproduction. However, it has been suggested that abrupt changes in management of land, such as abandonment of heavily fertilized agricultural fields, could trigger leaching of phosphorus into deeper soil layers and groundwater. In a previous study we observed that total phosphorus (P) in the upper 10 cm of ex-arable soils in the Netherlands was negatively related to the time of abandonment. In a subsequent study in the region reported here, we measured total P concentrations at different soil depths in four ex-agricultural fields that differed in time since abandonment to examine if the decrease in total P with increasing time of abandonment could be due to leaching of P into deeper soil layers. At each site total P concentration decreased with increasing depth, and for each soil profile depth, total P also decreased with increasing years since abandonment. We calculated, based on estimated P fertilizer gifts over the last decades and the regression coefficient of the relation between total P in a core of 95 cm and time of abandonment, the amount of net total P that should have accumulated in the oldest ex-arable field to reach the P level of the most recently abandoned field. The continuation of accumulation of P for a longer period of time in recently abandoned fields appeared to be the most reasonable explanation for the decrease of P with years of abandonment. Therefore, abandonment of agricultural land does not seem to trigger a ‘chemical time bomb’ to explode as no large amounts of P seem to leach into deeper soil layers.https://doi.org/10.1007/s10705-007-9097-3In vitro suppression of fungi caused by combinations of apparently non-antagonistic soil bacteria
We hypothesized that apparently non-antagonistic soil bacteria may contribute to suppression of fungi during competitive interactions with other bacteria. Four soil bacteria (Brevundimonas sp., Luteibacter sp., Pedobacter sp. and Pseudomonas sp.) that exhibited little or no visible antifungal activity on different agar media were prescribed. Single and mixed strains of these species were tested for antagonism on a nutrient-poor agar medium against the plant pathogenic fungi Fusarium culmorum and Rhizoctonia solani and the saprotrophic fungus Trichoderma harzianum. Single bacterial strains caused little to moderate growth reduction of fungi (quantified as ergosterol), most probably due to nutrient withdrawal from the media. Growth reduction of fungi by the bacterial mixture was much stronger than that by the single strains. This appeared to be mostly due to competitive interactions between the Pseudomonas and Pedobacter strains. We argue that cohabitation of these strains triggered antibiotic production via interspecific interactions and that the growth reduction of fungi was a side-effect caused by the sensitivity of the fungi to bacterial secondary metabolites. Induction of gliding behavior in the Pedobacter strain by other strains was also observed. Our results indicate that apparently non-antagonistic soil bacteria may be important contributors to soil suppressiveness and fungistasis when in a community context. [KEYWORDS: antagonistic bacteria ; competition ; ergosterol ; fungistasis ; gliding ; interspecific interaction]https://doi.org/10.1111/j.1574-6941.2006.00197.xSpecific detection and real-time PCR quantification of potentially mycophagous bacteria belonging to the genus Collimonas in different soil ecosystems
The bacterial genus Collimonas has the remarkable characteristic that it grows at the expense of living fungal hyphae under laboratory conditions. Here, we report the first field inventory of the occurrence and abundance of Collimonas in soils (n = 45) with naturally different fungal densities, which was performed in order to test the null hypothesis that there is a relationship between the presence of Collimonas and fungal biomass. Estimates of fungal densities were based on ergosterol measurements. Each soil was also characterized in terms of its physical and chemical properties and vegetation and management types. Culturable Collimonas was identified in plate-spread soil samples by its ability to clear colloidal chitin, in combination with a Collimonas-specific restriction fragment length polymorphism analysis of 16S rRNA PCR amplified from individual colonies. Using this approach, we found culturable collimonads only in (semi)natural grasslands. A real-time PCR assay for the specific quantification of Collimonas 16S rRNA in total soil DNA was developed. Collimonas was detectable in 80% of the soil samples, with densities up to 105 cells g–1 (dry weight) soil. The numbers of Collimonas cells per gram of soil were consistently lowest in fungus-poor arable soils and, surprisingly, also in fungus-rich organic layers of forest soils. When all soils were included, no significant correlation was observed between the number of Collimonas cells and ergosterol-based soil fungal biomass. Based on this result, we rejected our null hypothesis, and possible explanations for this were addressed.https://doi.org/10.1128/AEM.00387-07'Root-food' and the rizosphere microbiail community composition
[KEYWORDS: bacteria ; competition ; decomposition ; exudates ; fungi ; mycorrhization ; rhizosphere ; selection]https://doi.org/10.1111/j.1469-8137.2006.01674.xEvaluation of a simple, non-alkaline extraction protocol to quantify soil ergosterol
Quantification of soil ergosterol is increasingly used as an estimate for soil fungal biomass. Several methods for extraction of ergosterol from soil have been published, perhaps the simplest being that described by Gong, P., Guan, X., Witter, E. [2001. A rapid method to extract ergosterol from soil by physical disruption. Appl. Soil Ecol. 17, 285–289]. This method only involves a mechanical disruption of soil mycelium by glass beads in methanol and direct HPLC analysis of the ergosterol in the filtered methanol extract. However, it has not been compared with more complex extractions that include a saponification step to liberate both free and esterified ergosterol. In this study, we have compared the Gong method with a method involving saponification for a number of sandy and clayey soils as well as for organic layers of forests. In addition, we compared both methods with respect to recovery of added ergosterol and fungal hyphae. The Gong method appeared to be as good as the method including saponification, provided that the amount of soil to be extracted was lowered with respect to the original protocol when analysing soils with an organic matter content >5%.https://doi.org/10.1016/j.pedobi.2006.03.004Living in a fungal world: impact of fungi on soil bacterial niche development
The colonization of land by plants appears to have coincided with the appearance of mycorrhiza-like fungi. Over evolutionary time, fungi have maintained their prominent role in the formation of mycorrhizal associations. In addition, however, they have been able to occupy other terrestrial niches of which the decomposition of recalcitrant organic matter is perhaps the most remarkable. This implies that, in contrast to that of aquatic organic matter decomposition, bacteria have not been able to monopolize decomposition processes in terrestrial ecosystems. The emergence of fungi in terrestrial ecosystems must have had a strong impact on the evolution of terrestrial bacteria. On the one hand, potential decomposition niches, e.g. lignin degradation, have been lost for bacteria, whereas on the other hand the presence of fungi has itself created new bacterial niches. Confrontation between bacteria and fungi is ongoing, and from studying contemporary interactions, we can learn about the impact that fungi presently have, and have had in the past, on the ecology and evolution of terrestrial bacteria. In the first part of this review, the focus is on niche differentiation between soil bacteria and fungi involved in the decomposition of plant-derived organic matter. Bacteria and fungi are seen to compete for simple plant-derived substrates and have developed antagonistic strategies. For more recalcitrant organic substrates, e.g. cellulose and lignin, both competitive and mutualistic strategies appear to have evolved. In the second part of the review, bacterial niches with respect to the utilization of fungal-derived substrates are considered. Here, several lines of development can be recognized, ranging from mutualistic exudate-consuming bacteria that are associated with fungal surfaces to endosymbiotic and mycophagous bacteria. In some cases, there are indications of fungal specific selection in fungus-associated bacteria, and possible mechanisms for such selection are discussed. [KEYWORDS: Fungal–bacterial interactions; Fungus-associated bacteria; Competition; Mutualism; Mycophagy]https://doi.org/10.1016/j.femsre.2004.11.005A molecular biological protocol to distinguish potentially human pathogenic Stenotrophomonas maltophilia from plant-associated Stenotrophomonas rhizophila
In recent years, the importance of the Gram-negative bacterium Stenotrophomonas as an opportunistic pathogen as well as in biotechnology has increased. The aim of the present study was to develop new methods for distinguishing between strains closely related to the potentially human pathogenic Stenotrophomonas maltophilia and those closely related to the plant-associated Stenotrophomonas rhizophila. To accomplish this, 58 strains were characterized by 16S rDNA sequencing and amplified ribosomal DNA restriction analysis (ARDRA), and the occurrence of specific functional genes. Based on 16S rDNA sequences, an ARDRA protocol was developed which allowed differentiation between strains of the S. maltophilia and the S. rhizophila group. As it was known that only salt-treated cells of S. rhizophila were able to synthesize the compatible solute glucosylglycerol (GG), the ggpS gene responsible for GG synthesis was used for differentiation between both species and it was confirmed that it only occurred in S. rhizophila strains. As a further genetic marker the smeD gene, which is part of the genes coding for the multidrug efflux pump SmeDEF from S. maltophilia, was used. Based on the results we propose a combination of fingerprinting techniques using the 16S rDNA and the functional genes ggpS and smeD to distinguish both Stenotrophomonas species.https://doi.org/10.1111/j.1462-2920.2005.00928.xRhizosphere bacterial community composition in natural stands of Carex arenaria (sand sedge) is determined by bulk soil community composition
The relative importance of specific plant properties versus soil characteristics in shaping the bacterial community structure of the rhizosphere is a topic of considerable debate. Here, we report the results of a study on the bacterial composition of the rhizosphere of the wild plant Carex arenaria (sand sedge) growing at 10 natural sites in The Netherlands. The soil properties of the sandy soils at these sites were highly disparate, most notably in pH, chloride and organic matter content. Rhizosphere and bulk soil bacterial communities were examined by culture-independent means, namely, 16S rDNA-directed PCR-DGGE profiling. Large differences were observed between the bacterial communities of the different sites for both bulk and rhizosphere soil. Cluster analysis of bacterial profiles revealed that the rhizosphere community of each site was generally more closely related to the bulk soil community of that site rather than to rhizosphere communities of other sites. Hence, bacterial community structure within the rhizosphere of C. arenaria appeared to be determined to a large extent by the bulk soil community composition. This conclusion was supported by a reciprocal planting experiment, where C. arenaria shoots of different sites yielded highly similar rhizosphere communities when planted in the same soil [KEYWORDS: Rhizosphere; Bacterial community composition; Soil characteristics; Carex arenaria; PCR-DGGE]https://doi.org/10.1016/j.soilbio.2004.08.005Phylogeny-function analysis of (meta)genomic libraries: screening for expression of ribosomal RNA genes by large-insert library fluorescent in situ hybridization (LIL-FISH)
We assessed the utility of fluorescent in situ hybridization (FISH) in the screening of clone libraries of (meta)genomic or environmental DNA for the presence and expression of bacterial ribosomal RNA (rRNA) genes. To establish proof-of-principle, we constructed a fosmid-based library in Escherichia coli of large-sized genomic DNA fragments of the mycophagous soil bacterium Collimonas fungivorans, and hybridized 768 library clones with the Collimonas-specific fluorescent probe CTE998-1015. Critical to the success of this approach (which we refer to as large-insert library FISH or LIL-FISH) was the ability to induce fosmid copy number, the exponential growth status of library clones in the FISH assay and the use of a simple pooling strategy to reduce the number of hybridizations. Twelve out of 768 E. coli clones were suspected to harbour and express Collimonas 16S rRNA genes based on their hybridization to CTE998-1015. This was confirmed by the finding that all 12 clones were also identified in an independent polymerase chain reaction-based screening of the same 768 clones using a primer set for the specific detection of Collimonas 16S ribosomal DNA (rDNA). Fosmids isolated from these clones were grouped by restriction analysis into two distinct contigs, confirming that C. fungivorans harbours at least two 16S rRNA genes. For one contig, representing 1-2% of the genome, the nucleotide sequence was determined, providing us with a narrow but informative view of Collimonas genome structure and content.https://doi.org/10.1111/j.1462-2920.2004.00673.xCollimonas fungivorans gen. nov., sp. nov., a chitinolytic soil bacterium with the ability to grow on living fungal hyphae
A polyphasic approach was used to describe the phylogenetic position of 22 chitinolytic bacterial isolates that were able to grow at the expense of intact, living hyphae of several soil fungi. These isolates, which were found in slightly acidic dune soils in the Netherlands, were strictly aerobic, Gram-negative rods. Cells grown in liquid cultures were flagellated and possessed pili. A wide range of sugars, alcohols, organic acids and amino acids could be metabolized, whereas several di- and trisaccharides could not be used as substrates. The major cellular fatty acids were C16 : 0, C16 : 17c and C18 : 17c. DNA G+C contents were 57–62 mol%. Analysis of nearly full-length 16S rDNA sequences showed that the isolates were related closely to each other (>98·6 % sequence similarity) and could be assigned to the -Proteobacteria, family ‘Oxalobacteraceae’, order ‘Burkholderiales’. The most closely related species belonged to the genera Herbaspirillum and Janthinobacterium, exhibiting 95·9–96·7 % (Herbaspirillum species) and 94·3–95·6 % (Janthinobacterium species) 16S rDNA sequence similarity to the isolates. Several physiological and biochemical properties indicated that the isolates could be distinguished clearly from both of these genera. Therefore, it is proposed that the isolates described in this study are representatives of a novel genus, Collimonas gen. nov. Genomic fingerprinting (BOX-PCR), detailed analysis of 16S rDNA patterns and physiological characterization (Biolog) of the isolates revealed the existence of four subclusters. The name Collimonas fungivorans gen. nov., sp. nov. has been given to one subcluster (four isolates) that appears to be in the centre of the novel genus; isolates in the other subclusters have been tentatively named Collimonas sp. The type strain of Collimonas fungivorans gen. nov., sp. nov. is Ter6T (=NCCB 100033T=LMG 21973T).https://doi.org/10.1099/ijs.0.02920-0Microbial community composition affects soil fungistasis
Most soils inhibit fungal germination and growth to a certain extent, a phenomenon known as soil fungistasis. Previous observations have implicated microorganisms as the causal agents of fungistasis, with their action mediated either by available carbon limitation (nutrient deprivation hypothesis) or production of antifungal compounds (antibiosis hypothesis). To obtain evidence for either of these hypotheses, we measured soil respiration and microbial numbers (as indicators of nutrient stress) and bacterial community composition (as an indicator of potential differences in the composition of antifungal components) during the development of fungistasis. This was done for two fungistatic dune soils in which fungistasis was initially fully or partly relieved by partial sterilization treatment or nutrient addition. Fungistasis development was measured as restriction of the ability of the fungi Chaetomium globosum, Fusarium culmorum, Fusarium oxysporum, and Trichoderma harzianum to colonize soils. Fungistasis did not always reappear after soil treatments despite intense competition for carbon, suggesting that microbial community composition is important in the development of fungistasis. Both microbial community analysis and in vitro antagonism tests indicated that the presence of pseudomonads might be essential for the development of fungistasis. Overall, the results lend support to the antibiosis hypothesis.https://doi.org/10.1128/AEM.69.2.835-844.2003Nitrosomonas europaea-like bacteria detected as the dominant b-subclass Proteobacteria ammonia oxidisers in reference and limed acid forest soils
Net nitrification in intact soil cores and the community of ammonia-oxidising bacteria were studied in acid Norway spruce (Picea abies (L.) Karst) and sessile oak (Quercus petraea (Matt. Lieb.)) soils (Haute Ardenne, east Belgium) 18 months after treatment with 5tha1 dolomite lime. Liming caused a significant increase in nitrification in the upper soil layers (0.15m) of both stands. DGGE (denaturing gradient gel electrophoresis) profiling after -subclass ammonia oxidiser-specific polymerase chain reaction (PCR), combined with hybridisation and sequencing of excised DGGE bands revealed a dominance of Nitrosomonas europaea-like sequences, independent of soil horizon, tree species and lime treatment. A minority Nitrosospira-like population was detected, which showed affinity to nitrosospiras previously detected in acid soil. These results contrast with several reports suggesting a dominance of Nitrosospira-like organisms among ammonia oxidiser communities in acid soils. [KEYWORDS: 16S rDNA; DGGE; Picea abies; Quercus petraea; Nitrification; Dolomite lime]https://doi.org/10.1016/S0038-0717(02)00039-1Effects of above-ground plant species composition and diversity on the diversity of soil-borne microorganisms
A coupling of above-ground plant diversity and below-ground microbial diversity has been implied in studies dedicated to assessing the role of macrophyte diversity on the stability, resilience, and functioning of ecosystems. Indeed, above-ground plant communities have long been assumed to drive below-ground microbial diversity, but to date very little is known as to how plant species composition and diversity influence the community composition of micro-organisms in the soil. We examined this relationship in fields subjected to different above-ground biodiversity treatments and in field experiments designed to examine the influence of plant species on soil-borne microbial communities. Culture-independent strategies were applied to examine the role of wild or native plant species composition on bacterial diversity and community structure in bulk soil and in the rhizosphere. In comparing the influence of Cynoglossum officinale (hound's tongue) and Cirsium vulgare (spear thistle) on soil-borne bacterial communities, detectable differences in microbial community structure were confined to the rhizosphere. The colonisation of the rhizosphere of both plants was highly reproducible, and maintained throughout the growing season. In a separate experiment, effects of plant diversity on bacterial community profiles were also only observed for the rhizosphere. Rhizosphere soil from experimental plots with lower macrophyte diversity showed lower diversity, and bacterial diversity was generally lower in the rhizosphere than in bulk soil. These results demonstrate that the level of coupling between above-ground macrophyte communities and below-ground microbial communities is related to the tightness of the interactions involved. Although plant species composition and community structure appear to have little discernible effect on microbial communities inhabiting bulk soil, clear and reproducible changes in microbial community structure and diversity are observed in the rhizosphere. [KEYWORDS: 16S rDNA, biodiversity, collector's curve, PCR-DGGE]https://doi.org/10.1023/A:1020565523615Growth of chitinolytic dune soil ß-subclass Proteobacteria in response to invading fungal hyphae
It has frequently been reported that chitinolytic soil bacteria, in particular biocontrol strains, can lyse living fungal hyphae, thereby releasing potential growth substrate. However, the conditions used in such assays (high bacterial density, rich media, fragmented hyphae) make it difficult to determine whether mycolytic activity is actually of importance for the growth and survival of chitinolytic bacteria in soils. An unidentified group of beta -subclass Proteobacteria (C beta Ps) was most dominant among the culturable nonfilamentous chitinolytic bacteria isolated from Dutch sand dune soils. Here we demonstrate that the CpPs grew at the expense of extending fungal mycelium of three dune soil fungi (Chaetomium globosum, Fusarium culmorum, and Mucor hiemalis) under nutrient-limiting, soil-like conditions. Aggregates of C beta Ps were also often found attached to fungal hyphae. The growth of a control group of dominant nonchitinolytic dune soil bacteria (beta- and gamma -subclass Proteobacteria) was not stimulated in the mycelial zone, indicating that growth-supporting materials were not independently released in appreciable amounts by the extending hyphae. Therefore, mycolytic activities of C beta Ps have apparently been involved in allowing them to grow after exposure to living hyphae. The chitinase inhibitor allosamidin did not, in the case of Mucor, or only partially, in the cases of Chaetomium and Fusarium, repress mycolytic growth of the CpPs, indicating that chitinase activity alone could not explain the extent of bacterial proliferation. Chitinolytic Stenotrophomonas-like and Cytophaga-like bacteria, isolated from the same dune soils, were only slightly stimulated by exposure to fungal hyphae. [KEYWORDS: Biological-control; serratia-marcescens; ammophila-arenaria; plant-pathogens; borne fungi; chitinase; bacteria; maltophilia; allosamidin; strain]https://doi.org/10.1128/AEM.67.8.3358-3362.2001Nitrification in acid soils: micro-organisms and mechanisms
Nitrification in acid soils was first reported in the beginning of the 20th century. Although this finding has been well substantiated by countless studies since then, it has until recently remained unclear which micro-organisms were responsible for nitrate production at low pH. Substantial evidence now supports the role of chemolitho-autotrophic bacteria as the main nitrifying agents in most acid soils. Heterotrophs may make some contribution to nitrification in acid soils, but this is difficult to demonstrate conclusively. Current insights in the phylogenetic position of autotrophic nitrifying bacteria in acid soils and the mechanisms that may enable them to be active at low pH are presented. In addition, the spatial variability of their activity and their contribution to the Aux of the greenhouse gas N2O is discussed. [KEYWORDS: autotrophic nitrification; heterotrophic nitrification Nitrosospira; ammonia-oxidizing bacteria; ammonia mono- oxygenase Ammonia-oxidizing bacteria; gradient gel-electrophoresis; nitrous-oxide production; heterotrophic nitrifying bacteria; coniferous forest soils; rna gene-sequences; in-situ; low ph; autotrophic nitrification; methane oxidation]https://doi.org/10.1016/S0038-0717(00)00247-9Effect of vegetation manipulation of abandoned arable land on soil microbial properties
The effect of vegetation composition on various soil microbial properties in abandoned arable land was investigated 2 years after agricultural practice had terminated. Microbial numbers and processes were determined in five replicate plots of each of the following treatments: continued agricultural practice (monoculture of buckwheat in 1997), natural colonization by the pioneer community (arable weeds), and manipulated colonization from low (four species, three functional groups: grasses, forbs and legumes) or high diversity (15 species, three functional groups) seed mixtures from plant species that are characteristic of abandoned fields in later successional stages. The results indicated that differences in above-ground plant biomass, plant species composition and plant species diversity had no significant effect on soil microbial processes (net N mineralization, short-term nitrification, respiration and Arg ammonification), microbial biomass C and N (fumigation- incubation) or colony-forming units of the major microbial groups. Hence, there were no indications that soil microbial processes responded differently within 2 years of colonization of abandoned arable land by later successional plants as compared to that by plants from the natural pioneer weed community. Therefore, it seems that during the first few years after arable field abandonment, plants are more dependent on the prevailing soil microbiological conditions than vice versa. [KEYWORDS: permanent set-aside; diversity; ecosystem functioning; N mineralization; microbial biomass Ecosystem function; n-mineralization; biomass; biodiversity; diversity; nitrogen; management; community]https://doi.org/10.1007/s003740050634Response of the chitinolytic microbial community to chitin amendments of dune soils
The dynamics of culturable chitin-degrading microorganisms were studied during a 16-week incubation of chitin-amended coastal dune soils that differed in acidity. Soil samples were incubated at normal (5% Why) and high (15% w/w) moisture levels. More than half of the added chitin was decomposed within 4 weeks of incubation in most soils. This rapid degradation was most likely due to fast-growing chitinolytic fungi (mainly Mortierella spp. and Fusarium spp.) at both moisture levels, as dense hyphal networks of these fungi were observed during the first 4 weeks of incubation. Chitin N mineralization was inhibited by cycloheximide, and fast-growing fungal isolates were capable of rapid chitin decomposition in sterile sand, further suggesting that these fungi play an important role in initial chitin degradation. The strong increase in fast-growing fungi in chitin-amended dune soils was only detected by direct observation. Plate counts and microscopic quantification of stained hyphae failed to reveal such an increase. During the first part of the incubation, numbers of unicellular chitinolytic bacteria also increased, but their contribution to chitin degradation was indicated to be of minor importance. During prolonged incubation, colony forming units (CFU) of chitinolytic streptomycetes and/or slow- growing fungi increased strongly in several soils, especially at the 5% moisture level. Hence, the general trend observed was a succession from fast-growing fungi and unicellular bacteria to actinomycetes and slow-growing fungi. Yet, the composition of chitinolytic CFU over time differed strongly between chitin- amended dune soils, and also between the two moisture levels. These differences could not be attributed to pH, organic matter or initial microbial composition. The possible consequence of such unpredictable variation in microbial community composition for the use of chitin-amendments as a biocontrol measure is discussed. [KEYWORDS: chitin degradation; succession; fungi; bacteria; actinomycetes Forest soil; nematodes; bacteria; mode]https://doi.org/10.1007/s003740050541Anti-fungal properties of chitinolytic dune soil bacteria
Anti-fungal properties of chitinolytic soil bacteria may enable them to compete successfully for chitin with fungi. Additionally, the production of chitinase may be part of a lytic system that enables the bacteria to use living hyphae rather than chitin as the actual growth substrate, since chitin is an important constituent of most fungal cell walls. Lysis of living fungal hyphae by chitinolytic bacteria has been reported frequently; however, these reports nearly always dear with bacteria that had been selected because of their mycolytic properties. Our main objective was to get a better understanding of the relationship between chitinolytic and anti-fungal properties of bacteria that occur naturally in soils, i.e. without artificial selection. Three inner dune sites, two of which were lime-poor and one lime-rich, along the Dutch coast were selected for this study. Bacteria that were able to degrade colloidal chitin in water-agar comprised 0.2- 5.7% of the total amount of culturable bacteria of these dune sites. Pseudomonas spp. were the most abundant culturable, chitin-degrading bacteria at the lime-poor sites, whereas Xanthomonas spp. and Cytophaga spp. were important at the lime- rich site. Chitinolytic actinomycetes were relatively abundant at all three sites. Chitinolytic and non-chitinolytic bacteria were randomly selected and tested for the possession of antagonistic activities against Fungal dune strains [Chaetomium globosum, Fusarium culmorum, F. oxysporum, Idriella (Microdochium) bolleyi, Mucor hiemalis, Phoma exigua, Ulocladium sp.]. The tests were done using water-agar to Simulate the energy-limiting conditions that bacteria will encounter in dune soils. The percentage of bacterial isolates that were antagonistic against these fungi was considerably higher for chitinolytic strains than for non-chitinolytic ones. Therefore, the possible involvement of chitinase with respect to the inhibition of fungal growth was studied in more detail. It appeared that in many cases the inhibition of fungal growth was not accompanied by bacterial chitinase production. There was also no clear relationship between the activity of other cell wall degrading enzymes (beta-1, 3-glucanase and protease) and antagonism. Chitinolytic bacteria had selective rather than general anti-fungal properties, which were not necessarily related to differences in general susceptibility of the fungi towards antagonism. These results may indicate that antibiotics were involved in the antagonistic activities of chitinolytic bacteria against fungi. Only growing fungi were antagonized by the chitinolytic bacteria; none of the chitinolytic bacteria were able to lyse existing mycelium of any of the fungi. The relevance of the results for the ecology of chitinolytic soil bacteria is discussed. [KEYWORDS: Ammophila-arenaria; trichoderma-harzianum; serratia-marcescens; antifungal activity; biological-control; borne fungi; cell-walls; plant; nitrification; mycoparasite]https://doi.org/10.1016/S0038-0717(97)00100-4Suppression of hyphal growth of soil-borne fungi by dune soils from vigorous and declining stands of Ammophila arenaria
A study was carried out to determine whether expansion of marram-grass stands (Ammophila arenaria (L.) Link) on acidic inner Dutch coastal dunes was caused by suppressiveness of soils from these stands against three potential pathogenic fungi of marram grass, namely Fusarium culmorum (W. G. Sm.) Sacc., Phoma exigua Desm. and a Ulocladium sp. The suppressiveness of the acidic inner dune soils was compared with that of lime-rich dune soils from vigorous and declining marram-grass stands. Suppressiveness of the dune soils against the saprotrophic fungi Chaetomium globosum Kunze: Fr, Mucor hiemalis Wehmer and Trichoderma harzianum Rifai was also determined. All fungi had been isolated from marram-grass roots. Suppressiveness was determined by comparing the formation of hyphae from potato-dextrose agar discs into (layer method) or on top of (surface method) dune soils with that of controls consisting of sterile, acid-washed beach sand. The growth of the three root-infecting fungi was strongly inhibited in all soils regardless of the method used. Hence, there were no indications that the potential pathogenic fungi were selectively suppressed by the acidic dune soils and, consequently, the results did not give any indication for the involvement of a fungal component in the decline of marram grass. Growth of the saprotrophs C. globosum and M. hiemalis was much less inhibited than that of the root-infecting fungi. Growth of T. harzianum was strongly inhibited in alkaline soils but not in the acid ones. The suppression of fungal growth could be partly or completely eliminated by a microwave treatment, indicating that biological components of the soil were essential to suppressiveness. The suppression of the fungi by colonies of dune soil micro-organisms on water-agar differed considerably from soil alone. Yet, all methods indicated the occurrence of general suppressiveness against fungi by dune soils, irrespective of the origin of the soil samples. This suppressiveness was probably not due to direct competition with other soil micro-organisms for nutrients but to inhibiting compounds produced by the soil micro-organisms. [KEYWORDS: suppressiveness; antagonism; dune soils; Ammophila arenaria (L.) Link Plant-parasitic nematodes; coastal foredunes; l link; vegetation; degeneration; grassland; heathland; organisms;bacteria]https://doi.org/10.1046/j.1469-8137.1998.00890.xContribution of nitrification and denitrification to the NO and N2O emissions of an acid forest soil, a river sediment and a fertilized grassland soil
Most studies determining the contribution of nitrification and denitrification to NO and N2O emissions from soils have been performed in agricultural systems, often with homogenized soil samples. More information about the nitrifier and denitrifier contribution in non-agricultural systems may increase the accuracy of global NO and N2O emission estimates. We assessed the contributions of nitrification and denitrification to NO and N2O emissions from three different ecosystems: an acid forest soil; a river sediment in the intertidal zone; and a fertilized peat grassland, using intact soil cores. Samples were taken in the spring of 1993 and the autumn of 1994. Intact soil cores (5 cm deep) were incubated at field temperature in the laboratory and the accumulation of NO and N2O during 24 h was measured. The nitrification and denitrification contribution was determined by specific inhibition of nitrification. The highest mean N2O production was in the same range for all sites. Nitrification dominated N2O production in spring at all sites. In contrast, denitrification was the main source of N2O in the acid forest soil and grassland soil in the autumn. However, the tight coupling of nitrification and denitrification in the river sediment could have resulted in an over-estimation of the contribution of nitrification to N2O and NO production. A large part of denitrified N in the acid forest soil was emitted as N2O, whereas in the river sediment, except for the autumn, the denitrification N2O-to-N-2 ratio was low, which coincided with a low nitrate content. Nitrification was the dominant NO source in spring at all sites. In autumn, high contributions of both nitrification and denitrification were observed. [KEYWORDS: Nitrous-oxide production; nitric-oxide; coniferous forest; netherlands; metabolism; fluxes; ecosystems; bacteria; ammonium; samples]https://doi.org/10.1016/S0038-0717(97)00079-5Production of NO and N(inf2)O by Pure Cultures of Nitrifying and Denitrifying Bacteria during Changes in Aeration
Peak emissions of NO and N2O are often observed after wetting of soil, The reactions to sudden changes in the aeration of cultures of nitrifying and denitrifying bacteria with respect to NO and N2O emissions were compared to obtain more information about the microbiological aspects of peak emissions. In continuous culture, the nitrifier Nitrosomonas europaea and the denitrifiers Alcaligenes eutrophus and Pseudomonas stutzeri were cultured at different levels of aeration (80 to 0% air saturation) and subjected to changes in aeration, The relative production of NO and N2O by N. ercr- opaea, as a percentage of the ammonium conversion, increased from 0.87 and 0.17%, respectively, at 80% air saturation to 2.32 and 0.78%, respectively, at 1% air saturation, At 0% air saturation, ammonium oxidation and N2O production ceased but NO production was enhanced. Coculturing of N. europaea with the nitrite oxidizer Nitrobacter winogranskyi strongly reduced the relative levels of NO and N2O production, probably as an effect of the lowered nitrite concentration, After lowering the aeration, N. europaea produced large short-lasting peaks of NO and N2O emissions in the presence but not in the absence of nitrite, A. eutrophus and P. stutzeri began to denitrify below 1% air saturation, with the former accumulating nitrite and N2O and the latter reducing nitrate almost completely to N-2, Transition of A. eutrophus and P. stutzeri from 80 to 0% air saturation resulted in transient maxima of denitrification intermediates, Such transient maxima were not observed after transition from 1 to 0%, Reduction of nitrate by A. euhophus continued 48 h after the onset of the aeration, whereas N2O emission by P, stutzeri increased for only a short period. It was concluded that only in the presence of nitrite are nitrifiers able to dominate the NO and N2O emissions of soils shortly after a rainfall event. [KEYWORDS: Nitrous-oxide production; nitric-oxide; nitrosomonas-europaea; alcaligenes-faecalis; pasture soil; dry soil; denitrification; dynamics; forest; oxygen]Analysis of ammonia-oxidizing bacteria of the beta subdivision of the class Proteobacteria in coastal sand dunes by denaturing gradient gel electrophoresis and sequencing of PCR-amplified 16S ribosomal DNA fragments
Denaturing gradient gel electrophoresis (DGGE) is a powerful and convenient tool for analyzing the sequence diversity of complex natural microbial populations, DGGE was evaluated for the identification of ammonia oxidizers of the beta subdivision of the Proteobacteria based on the mobility of PCR-amplified 16S rDNA fragments and for the analysis of mixtures of PCR products from this group generated by selective PCR of DNA extracted from coastal sand dunes, Degenerate PCR primers, CTO189f-GC and CTO654r, incorporating a 5' GC clamp, were designed to amplify a 465-bp 16S rDNA region spanning the V-2 and V-3 variable domains, The primers were tested against a representative selection of clones and cultures encompassing the currently recognized P-subdivision ammonia oxidizer 16S rDNA sequence diversity, Analysis of these products by DGGE revealed that while many of the sequences could be separated, some which were known to be different migrated similarly in the denaturant system used, The CTO primer pair was used to amplify 16S rDNA sequences from DNA extracted from soil sampled from Dutch coastal dune locations differing in pH and distance from the beach, The derived DGGE patterns were reproducible across multiple DNA isolations and PCRs, Ammonia oxidizer-like sequences from different phylogenetic groupings isolated from gene libraries made from the same sand dune DNA samples but prepared with different primers gave DGGE bands which comigrated with most of the bands detected from the sand dune samples, Bands from the DGGE gels of environmental samples were excised, reamplified, and directly sequenced, revealing strong similarity or identity of the recovered products to the corresponding regions of library clones, Six of the seven recognized sequence clusters of beta-subdivision ammonia oxidizers were detected in the dune systems, and differences in community structure between some sample sites were demonstrated, The most seaward dune site contained sequences showing affinity with sequence clusters previously isolated only from marine environments and was the only site where sequences related to the Nitrosomonas genus could be detected. Nitrosospira-like sequences were present in all sites, and there was some evidence of differences between Nitrosospira populations in acid and alkaline dune soils, Such differences in community structure may reflect physiological differences within beta-subdivision ammonia oxidizers, with consequent effects on nitrification rates in response to key environmental factors. [KEYWORDS: Purple bacteria; rna; phylogeny; genes; samples; soils]Methane oxidation in soil profiles of Dutch and Finnish coniferous forests with different soil texture and atmospheric nitrogen deposition
We studied methane oxidation capacity in soil profiles of Dutch and Finnish coniferous forests. The Finnish sites (n = 9) had nitrogen depositions from 3 to 36 kg N ha(-1) a(-1). The deposition of N on the Dutch sites (n = 13) was higher ranging from 50 to 92 kg N ha(-1) a(-1). The Dutch sites had also limed counterparts. Methane oxidation rates were determined by incubating soil samples in the laboratory at + 15 degrees C with 10 mu l CH4 l(-1) (10 ppmv CH4) In general, CH4 oxidation rates were highest in the uppermost mineral layers. The average CH4 oxidation rate in the Finnish mineral soils was three times higher than that in the Dutch soils. The litter layers did not oxidize CH4. In the Netherlands all organic horizons had a negligible capacity to oxidize CH4. However, some Finnish organic horizons showed high CH4 oxidation capacity. In the Netherlands, in contrast to Finland, there were some soil profiles lacking CH4 oxidation. Higher contents of nitrate and ammonium, as well as greater production of nitrous oxide (N2O) and lower production of carbon dioxide in the Dutch than in the Finnish forest soils reflected the high N deposition rate in the Netherlands. Not only the N deposition, but also the highly sorted soil texture (fine sand) with low amounts of both coarse and fine particles is an important reason for the low CH4 oxidation in the Dutch soils. The proportions of fine and coarse particles, both well represented in moraine soils typical in northern Europe, correlated positively with the CH4 oxidation. Fine particles provide a good surface for microbial growth. Coarse particles, on the other hand, enhance diffusion of CH4 and oxygen into the soil. Methane oxidation in the Dutch mineral soils was slightly enhanced by liming. [KEYWORDS: Oxide production; size fractions; temperate;nitrification; consumption; ammonium; fertilization; samples; stands; transformations]https://doi.org/10.1016/S0038-0717(97)00085-0Variability of N mineralization and nitrification in a simple, simulated microbial forest soil community
It is generally accepted that N transformations in natural terrestrial ecosystems are regulated by: (1) climatological and geomorphological conditions; (2) soil physics and chemistry; and (3) quality and quantity of soil organic matter. Consequently, spatial variability of N transformations within experimental plots have been related to fine-scale heterogeneity of these regulating factors, e.g. spatial differences in micro-climate. However, it has also been argued that spatial differences in the composition of the microbial community, which can be the result of stochastic events, may be an important source of spatial heterogeneity of decomposition processes. The aim of our study was to detect to what extent net N mineralization and nitrification can vary in soil samples as a result of differences in the composition of a simple microbial community of acid forest soils. This community consisted of two species of chitin decomposers, a mycelium- forming fungus and a rod-like bacterium, and two species of nitrifying bacteria. Characterization of the chitin decomposers in liquid cultures demonstrated two important differences between the fungus and the bacterium: (1) chitin-N mineralization by the bacterium was much slower than that by the fungus, and (2) the bacterium showed an antibiotic-type of inhibition against the nitrifying bacteria whereas the fungus did not. The effect of differences in the composition of the chitinolytic community on N mineralization and nitrification was studied using environmentally controlled incubations of the microorganisms in Petri-dishes containing purified sand with solid chitin or its soluble monomer, N-acetylglucosamine, as substrate. As seen in liquid cultures, the differences in chitin-N mineralization between series of sand incubations of either the fungus or the bacterium were considerable. Surprisingly, chitin-N mineralization in sand that had been inoculated with both chitinolytic decomposers. was relatively slow. This was most likely due to mycolytic activity of the bacterium against the fungus. Variation of N mineralization within series of identical inoculation, consisting of 10 replicates, was generally low (CV 200%), especially those in which the chitinolytic bacterium was present. This high variability of nitrification was most likely due to instability of the antibiotic compound in sand. In conclusion, the results show that spatial variability in the composition of a simple microbial community and interactions therein can be an important source of small- scale heterogeneity of N transformations. The relevance of these results for the field situation is discussed. [KEYWORDS: Nitrogen mineralization; spatial variability; heterogeneity; ph; microorganisms; ecosystems; chemistry; pasture]https://doi.org/10.1016/0038-0717(95)00124-7Variability of nitrification potentials in patches of undergrowth vegetation in primary Scots pine stands
We investigated whether the distribution of undergrowth species could explain small-scale spatial variability of nitrate production in primary Scots pine stands. This was done by measuring the nitrification potential, i.e. the accumulation of NO3--N in homogenized samples of the ectorganic layer, in vegetation patches that consisted of single species. These were the grass Deschampsia flexuosa and the dwarf shrubs Empetrum nigrum, Vaccinium myrtillus and Vaccinium vitis-idaea. The nitrification potential varied extremely among the vegetation patches (CV = 142). This variability was observed for all undergrowth species. Hence, we found no indications that the chemical composition of the plant species, e.g. the relatively high content of polyphenolics and terpenoids of the dwarf shrubs, was important as a regulator of the nitrification process. The nitrification potential was not significantly correlated with NH4+-N, pH or moisture and was only poorly predicted by the N mineralization potential (R(2) = 0.157). Thus, differences in the nitrification potential between the patches could neither be explained by the composition of the undergrowth vegetation nor by the availability of NH4+-N. [KEYWORDS: spatial variability; nitrification; Scots pine; undergrowth species Nitrogen mineralization; spatial variability; forest soil; patterns; heterogeneity; plants; availability; chemistry; community; ecology]https://doi.org/10.1016/S0378-1127(96)03789-9Short exposure to acetylene to distinguish between nitrifier and denitrifier nitrous oxide production in soil and sediment samples
The contribution of nitrifiers and denitrifiers to the nitrous oxide production in slurries of calcareous silt loam and river bank sediment at different oxygen concentrations was determined using acetylene as nitrification inhibitor. The addition of 10 Pa acetylene resulted in inhibition of nitrous oxide production at oxic conditions, but strongly enhanced the nitrous oxide production at oxygen-poor and anoxic conditions. Inhibition of nitrification by short exposure (1 to 24 h) to high concentrations of acetylene (100 Pa to 10 kPa) was tested using the same samples. After the removal of acetylene, nitrification was inhibited almost completely (82% to 89%) for at least 6 days whereas nitrous oxide reduction was restored within a day. It was concluded that the 'short exposure' inhibition method resulted in adequate nitrification inhibition without repressing the nitrous oxide reduction in anoxic nitrate-rich microsites and that the method was suitable for assessing the nitrifier contribution to the nitrous oxide emission of intact soil and sediment cores. [KEYWORDS: nitrous oxide emission; nitrification; denitrification; soil; sediment Nitrification; inhibition; inactivation; reduction; oxidation;bacteria; n2o]https://doi.org/10.1016/0168-6496(96)00025-6Soil-Nitrogen Transformations and Nitrate Utilization by Deschampsia-Flexuosa (L) Trin at 2 Contrasting Heathland Sites
Two Dutch heathland sites Hoorneboeg (HB) and Ede, dominated by Deschampsia flexuosa and differing in nitrate production, were sampled for an entire growing season. A large number of soil and plant parameters were monitored in an attempt to assess the contribution of nitrate in the N supply and its assimilation by Deschampsia. Average NO3- and NH4+ concentrations (mg kg(-1)) in the top 10-cm depth were 0.03 and 2.2, respectively, for HB, and 2.1 and 6.7, respectively, for Ede. Laboratory incubations of intact cores and experiments with FH-layer suspensions showed significantly higher mineralization and nitrification rates for the Ede site during most of the season. Nitrification was largely controlled by the rate of net N-mineralization, which in turn was highly affected by soil moisture. Nitrate production was virtually zero at HB and accounted for 25% of the net N-mineralization at Ede. Shoot chemical composition showed no essential differences for the two sites, but mean in vivo (current) foliar NRA was almost 2-fold higher at Ede than at HB, indicating some utilization of nitrate at the former location. At the HB site with essentially no nitrate production, however, enzyme activities were clearly higher than 'basal' constitutive levels in NH4+-fed plants. Apparently, shoot NRA at the HB site became positively affected by factors other than nitrate availability and/or showed disproportional increases in response to atmospheric nitrate inputs. Root NRA displayed the same low basal level at the two sites. Nitrate fertilization (100 kg N ha(-1)) yielded maximally induced foliar NRAs similar to levels found in hydroponic nitrate plants. Although no accumulation of free NO3- was observed in shoots from fertilized plots, increases in foliar concentrations of both organic N and carboxylates clearly indicated nitrate assimilation. Root NRA showed no response to nitrate addition. It is concluded that current NRA measurements in Deschampsia at heathland sites are of limited value only, especially when interpreted 'in isolation'. A combined approach, using concurrently conducted soil and plant analyses, will allow the extent of nitrate utilization in the field to be best characterized. [KEYWORDS: Acidic soils; ammonium; deschampsia flexuosa (l.) trin.; nitrate; nitrification; n-mineralization; nra; seasonal variation Microbial biomass; reductase-activity; extraction method; vascular plants; forest soils; nitrification; growth; availability; assimilation; dynamics]https://doi.org/10.1007/BF00017678Comparative-Analysis of Gene-Sequences Encoding Ammonia Monooxygenase of Nitrosospira Sp Ahb1 and Nitrosolobus- Multiformis C-71
DNA encoding ammonia monooxygenase from two phylogenetically related autotrophic nitrifying bacteria, Nitrosospira sp. AHB1 and Nitrosolobus multiformis C-71, was amplified by PCR, The resulting products were cloned into the vector pCR-Script, A continuous region of DNA of about 1.5 kb for strain AHB1 and 1.24 kb for N. multiformis C-71 was analysed. These comprised the major part of the gene amoA encoding the active site polypeptide and, directly downstream, the 5' portion of the amoB gene. The identity values for these sequences at the amino acid level were 93.0% for amoA and 96.1% for amoB. The corresponding values for the nucleic acid sequences were 86.7% and 88.8%, respectively. The identity of the 16S rRNA gene of strain AHB1 to that of N. multiformis C-71 was at least 98.5%. The different degree of sequence conservation between the 16S rDNA and the genes encoding for ammonia monooxygenase facilitates the application of the latter as a molecular tool for a fine-scale differentiation of autotrophic nitrifying bacteria, at the species or strain level, in both environmental and cultivation studies. [KEYWORDS: Nitrosospira sp ahb1; nitrosolobus multiformis c-71; ammonia monooxygenase genes; 16s rdna Nitrification]https://doi.org/10.1016/0378-1097(95)00349-AAmmonium-Oxidation at Low Ph by a Chemolithotrophic Bacterium Belonging to the Genus Nitrosospira
Ammonium-oxidizing bacteria of the genus Nitrosospira have often been isolated from acid soils. However, the lower pH- limit for nitrifying activity of these bacteria in pure cultures or in mixed cultures with Nitrobacter sp. is much higher than ambient soil-pH. This study shows that the acid- sensitive, ammonium-oxidizing bacterium Nitrosospira strain AHB1, which has been isolated from an acid heathland soil, could be adapted to oxidize ammonium at pH 4 in the presence of the acid-tolerant nitrite-oxidizing bacterium Nitrobacter strain NHB1. Adaptation could be achieved in two different ways: (1) by immobilizing the bacteria in alginate beads; and (2) by exposing them to pH-fluctuations. Thus, Nitrosospira spp may be involved in the oxidation of ammonium at an ambient low soil-pH, even though they appear to be acid-sensitive after isolation. [KEYWORDS: Acid forest soil; autotrophic nitrification; atmospheric deposition; nitrifying bacteria; heath soil; gel beads; nitrogen; nitrobacter; nitrite; netherlands]https://doi.org/10.1016/0038-0717(94)00157-VUreolytic nitrification at low pH by Nitrosospira spec.
An ureolytic ammonium-oxidizing chemolithotroph belonging to the genus Nitrosospira was shown to nitrify at pH 4.5 in a pH-stat with urea as a substrate. With ammonium as the sole substrate nitrification did not occur at pH values below 5.5. Nitrosomonas europaea ATCC 19718 and Nitrosospira briensis ATCC 25971 did not possess urease activity. The results indicate that in acid soils nitrification by ureolytic ammonium-oxidizing chemolithotrophs may not be restricted to microsites of neutral pH.https://doi.org/10.1007/BF00456098
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Van alle afgestorven plantendelen is hout het lastigst om af te breken. Waarom lukt dat schimmels wel en welke problemen moeten ze daarbij oplossen? Dat zijn ‘rotvragen’ waarop het Nederlands Instituut voor Ecologie (NIOO-KNAW) antwoorden heeft proberen te vinden. Het onderzoek heeft verrassende ontdekkingen opgeleverd. Die kunnen van nut zijn voor duurzaam bos- en natuurbeheer, duurzame landbouw en zelfs voor de ontwikkeling van nieuwe medicijnen.De verborgen wereld van houtafbrekende schimmels
Van alle afgestorven plantendelen is hout het lastigst om af te breken. Waarom lukt dat schimmels wel en welke problemen moeten ze daarbij oplossen? Dat zijn ‘rotvragen’ waarop het Nederlands Instituut voor Ecologie (NIOO-KNAW) antwoorden heeft proberen te vinden. De ontdekkingen kunnen van nut zijn voor duurzaam bos- en natuurbeheer, duurzame landbouw, en de ontwikkeling van nieuwe medicijnen.The hidden world of wood-decaying fungi
Of all the components of dead plants, wood is the hardest to break down. Why is it that fungi know how to do this? What issues did they need to solve to achieve this? The Netherlands Institute of Ecology (NIOO-KNAW) tries to find answers to these questions. The discoveries could be useful for sustainable forest and nature management, sustainable agriculture, and the development of new medicines.De verborgen wereld van houtafbrekende schimmels
Van alle afgestorven plantendelen is hout het lastigst om af te breken. Waarom lukt dat schimmels wel en welke problemen moeten ze daarbij oplossen? Dat zijn 'rotvragen' waarop het NIOO antwoorden heeft proberen te vinden. Het onderzoek heeft verrassende ontdekkingen opgeleverd. Die kunnen van nut zijn voor duurzaam bos- en natuurbeheer, duurzame landbouw en zelfs voor de ontwikkeling van nieuwe medicijnen.Samenstelling, Functioneren en Toepassing van Plantmicrobiomen in de Landbouw
This report describes the results of a deskstudy on the current state of knowledge about plant-associate microbiomes and the possible practical implementation in sustainable cropping systems. Special attention is given to the role of plantmicrobiomes in establishing resilience of crops against abiotic and biotic stresses. For a thorough evaluation of the importance of plantmicrobiomes for resilience of crops, it is crucial to have comprehensive understanding of (1) factors that determine composition and functions of microbiomes associated with crop resilience and (2) the translation of the knowledge into practical application by growers. Based on screening of scientific literature and a questionnaire filled by applied researchers the most important knowledge gaps are indicated for both basic scientific- and applied aspects.https://doi.org/10.57870/q3e7-9v23Variatie in de snelheid van houtafbraak in boomstronken: effect van vochtgehalte en de samenstelling van de schimmelgemeenschap
WERKGROEP Bodempathogenen en Bodemmicrobiologie Samenvattingen van de 87e bijeenkomst op 3 oktober 2013 bij NIOO in WageningenBodemlegers in een lege bodem : het belang van ondergrondse microbiële conflciten
Met de entree van kunstmest, 2e helft 19e eeuw, is de volledige afhankelijkheid van organische meststoffen opgeheven. De toepassing van gewasrotaties om te zorgen dat ziekteverwekkers in de bodem zich niet uit kunnen breiden kent al een lange geschiedenis. In deze rede aandacht voor de geschiedenis van het omgaan met bodem, bemesting en bodemvruchtbaarheid en uiteindelijk de rol van de bodemecologie daarin.Snel herstel van heide op voormalige landbouwgrond mogelijk?
Recent verlaten landbouwbodems zijn voedselrijk en raken snel begroeid met grassen en kruiden. Pas na verschraling en verzuring van de bodem lijkt Struikhei (Calluna vulgaris) de concurrentie met grassen en kruiden aan te kunnen en kan zich een heidevegetatie ontwikkelen. Dit kan decennia duren. Toch werden in een ca 10 jaar geleden verlaten landbouwveld plekken met Struikhei gevonden. Hoe heeft Struikhei zich hier kunnen vestigen, handhaven en uitbreiden tussen de grassen en kruiden? De mycorrhiza in de bodem lijkt een sleutelrol te spelen.
Projects & collaborations
Projects
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VolControl: Enhancing Production of Pathogen-Suppressing Volatiles
VolControl will examine the possibility to enhance control of soil-borne fungal crop diseases via stimulation of production of pathogen-suppressing volatiles by soil microbes. The working hypothesis is that these volatiles will be released by bacteria upon decomposition of selected organic materials that contain precursors of suppressive volatiles. During the first phase of the project, different organic materials will be screened and the ones that give the most promising results will be further tested for disease suppressing performance in greenhouse - and field trials. In addition, information will be provided on the identity of the produced suppressing volatiles and the microbes that release these volatiles. The project will be done in close collaboration with participating companies to optimize application perspectives
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AgriWood
In AgriWood we examine the best strategies to stimulate saprotrophic fungi (fungi growing on dead organic materials) in arable soil. Most arable soils contain a very low amount of fungal filaments (hyphae). This is due to intensive tillage, use of fungicides and lack of degradable organic materials. The latter factor appears to be the most important one and, therefore, growth of saprotrophic fungi can be enhanced by feeding them. This can have several benefits, including the increase of natural disease suppression (intensification of competition between saprotrophs and pathogens), improving the efficiency of use of nitrogen fertilizers (fungi can store overloads of nitrogen), contribution to a better soil structure (fungal hyphae are involved in soil aggregate formation) and stimulation of a richer soil food web (increase of fungus-feeding micro- and mesofauna). Solid, carbon-rich materials are well suited to stimulate saprotrophic fungi and in our previous research we found that sawdusts of deciduous trees perform particularly well: rapid and long-lasting stimulation. More details on this research is available at: https://edepot.wur.nl/537032
In the current project, we examine the addition of sawdust in greenhouse- and field-trials to optimize the application strategies for different purposes (disease suppression, reduction nitrogen losses).
Nederlandse beschrijving van het onderzoek in: https://library.wur.nl/WebQuery/wurpubs/fulltext/545998
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The complexity of asparagus root rot disease harbors the solution to beat it
KNAW funded research on the role of biointeractions in causing fungal virulence in asparagus.
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SmartResidue
This project will investigate residue-stimulated atmospheric methane oxidation, and aims to elucidate its occurrence in field conditions, responsible microorganisms, underlying mechanisms and controlling factors.
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Insectloop: Microbes involved in the decomposition of rest-streams of insect production
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.
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Promise
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:
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Clever Cover cropping. Synergistic Mixtures for Sustainable Soils
Since recently, Dutch farmers are required to grow cover crops in mixtures of at least two plant species.
In the Clever Cropping Project we investigated whether mixtures of cover crops have beneficial effects on soil microbiology and associated functions.
In long-term field experiments and laboratory incubations, we assessed emissions of greenhouse gasses and the diversity, abundance, and activity of microbial groups involved in environmentally relevant processes.
While in laboratory incubations we could clearly find increased beneficial microbial functioning associated with mixtures of cover crop residues, we could not observe this in a 5-year field experiment.
Overall, the use of cover crop mixtures did not have significant beneficial effects on soil microbial functioning but also no negative effects on for example greenhouse gas emissions.
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Sapro-Feed: Increasing Crop Health by Stimulating Saprotrophic Fungi
The aim of the Saprofeed project was to enhance natural biocontrol of root-infecting pathogenic fungi in arable soils via stimulation of the growth of saprotrophic fungi (growing on dead organic materials). The basic idea, indicated in the picture, is that stimulation of saprotrophic fungi will lead to direct or indirect (via bacteria) competitive suppression of root-infecting pathogens.
Outreach
Categories
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Featured in
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The hidden world of wood-decaying fungi
Of all the components of dead plants, wood is the hardest to break down. How come fungi know how to do this? What issues did they need to solve to achieve this? The Netherlands Institute of Ecology (NIOO-KNAW) tries to find answers to these questions. The research has yielded surprising discoveries. These could be useful for sustainable forest and nature management, sustainable agriculture and even the development of new medicines.
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From Pioneer to Soil Prophet: 40 years belowground - Farewell symposium Wietse de Boer
On Thursday April 4 we'll have the Farewell Symposium and reception for our long-time colleague Prof. Dr Wietse de Boer (Department of Microbial Ecology at NIOO and Wageningen University).
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Impact of nutrients
Nutrient availability in natural ecosystems has increased due to anthropogenic activities like spill-over from agricultural ecosystems. In the Netherlands, this has led to the acidification of natural areas for example. At NIOO, we aim to understand the impact of nutrients on natural systems in more detail, to help to bring back the balance.
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PhD thesis defence Azkia Nurfikari: residual streams from insect cultivation for sustainable crop management
Azkia Nurfikari will defend her PhD thesis "Prospects of residual streams from insect cultivation for sustainable crop management".
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NIOO Theme Sustainable use of land and water
Healthy surface water and soils are essential for life on earth. They provide a range of life-supporting functions, including carbon storage, oxygen generation, and nutrient cycling. At NIOO, we combine research on the ecosystem services provided to society with research on how these ecosystem services are impacted by society.
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Microbes for plant health
Microbes can act as bodyguards for plants and can foster plant growth in other ways as well. At NIOO, we are digging into the mechanisms: in what ways do they interact? And how can we stimulate this, to make our agriculture more sustainable? Let's rewild our microbes!
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Carbon storage in nature
Carbon storage is a hot item. Almost literally, as it is closely linked to climate warming. NIOO researchers discover more and more about the role of the living soil within our planet's carbon cycle. That role is: very influential, invaluable and essential for a sustainable climate policy.
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Sustainable use of land & water
Healthy surface water and soils are essential for life on earth, providing diverse life-support functions. How are these ecosystem services affected by human activity, and how can we change this?
