Microbial Ecology

The overall aim of the ME-department is to understand the diversity and functions of microorganisms in natural and managed ecosystems. We focus on two major research areas:
- the role of microorganisms in biogeochemical cycles and greenhouse gas emission
- ecology and evolution of soil and plant-associated microorganisms
We use an interdisciplinary approach, combining microbiology, molecular biology, chemistry, modelling and computational methods to study the taxonomic and functional diversity of bacteria, archaea, fungi (including yeasts) and viruses. We closely collaborate with various national and international universities, institutes, and diverse stakeholders. Our goals are to advance the mechanistic understanding of the multipartite relationships between microorganisms and their environment, and to contribute to the development of new strategies for sustainable management of natural and man-made ecosystems.
We are actively involved in each of the three NIOO-wide research themes:
- Biodiversity: with the development of new ‘omics technologies, we have become even more aware of the vast, yet largely unknown diversity of microorganisms in natural and managed ecosystems. The ME-department studies microbial diversity and functions in national long-term ecological field sites (LTERs) as well as internationally such as the Amazon forest, the Andes Mountains and the Galapagos Islands. We use an interdisciplinary approach to illuminate the ‘microbial dark matter’ and to understand its impact on ecosystem functioning. Key questions are how soil bacteria and fungi interact in decomposition of recalcitrant organic matter and what the underlying diversity of chemical communication is within soil microbial communities and between microorganisms and plants. For soil and plant-associated viruses (including bacteriophages), we investigate the functional implications of their genome diversity and their fascinating role as guardians of plant and microbial biodiversity.
- Climate change: microorganisms are key drivers of global nutrient (carbon, nitrogen) cycles, thereby catalyzing the emission of specific greenhouse gases such as nitrous oxide and methane. We integrate(meta)genomic, isotopic and biogeochemical approaches to: a) identify key microorganisms, genes and pathways involved in these processes, and b) assess their distribution, functioning and controls in various ecosystems, including lakes, peatlands, forests and agricultural soils. The ME department adopts this knowledge to pinpoint major biogeochemical indicators of environmental disturbance and to steer microbial communities to minimize greenhouse gas emissions.
- Sustainable use of land: ME research has shown that microorganisms living on and inside plants are drivers of plant growth and health. To harness the largely unexplored functional diversity, we investigate how plants under stress recruit beneficial microorganisms for protection and how introduction or augmentation of soil microorganisms can be used as a sustainable practice to minimize fertilizer and pesticide use to enhance soil quality. We developed the concept of microbiome ‘rewilding’, which posits that plant health can be improved by reinstating key members of the diverse (ancestral) microbiota that were lost through domestication. To this end, we go back to the centers of origin of the wild relatives of our crop species to identify the ‘missing microbes’ and their beneficial traits.
Biogeochemical cycles
Functional ecology of microbial communities involved in biogeochemical cycles.
Microbial community ecology & environmental genomics
Farming soil microbial community linked to N and P (re)cycles to provide nutrients to plants, soil quality and N2O mitigation.

Chemical ecology
The chemical ecology of soil and plant-associated microbes

Virus ecology and evolution
Exploring the diversity, evolution and ecosystem impacts of plant-associated viruses.

Fungal-bacterial interactions
Interactions between fungi and bacteria play a key role in soil ecosystem functioning

Back to the Roots
Diversity & functioning of microbiomes of wild and domesticated plants.

People
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Dr. Mark Zwart
- Function
- Researcher | Tenure Track
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Dr. Paolina Garbeva
- Function
- Senior Researcher
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Dr. Paul Bodelier
- Function
- Senior Researcher
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Prof. Wietse de Boer
- Function
- Senior Researcher
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Prof. dr. ir. Eiko Kuramae PhD
- Function
- Senior Researcher
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Prof. Jos Raaijmakers PhD
- Function
- Head of department
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Dr. Viviane Cordovez
- Function
- Researcher
Peer-reviewed publications
Identification of general features in soil fungal communities modulated by phenolic acids
Soil substrate source drives the microbes involved in the degradation of gelatin used as a biostimulant
Addition of cellulose degrading bacterial agents promoting keystone fungal-mediated cellulose degradation during aerobic composting
Impact of wastewater characteristics on the removal of organic micropollutants by Chlorella sorokiniana
Enhancing phosphorus removal of photogranules by incorporating polyphosphate accumulating organisms
Effect of pre-treatment processes of organic residues on soil aggregates
Importance of Bacteroidetes in host–microbe interactions and ecosystem functioning
The Fitness of Beta-Lactamase Mutants Depends Nonlinearly on Resistance Level at Sublethal Antibiotic Concentrations
Volatile sensation: The chemical ecology of the earthy odorant geosmin
Evaluation of sequencing and PCR-based methods for the quantification of the viral genome formula
Environmental refuges from disease in host‐parasite interactions under global change
baseLess: lightweight detection of sequences in raw MinION data
Archaea and their interactions with bacteria in a karst ecosystem
MIBiG 3.0:
Radish-based cover crop mixtures mitigate leaching and increase availability of nitrogen to the cash crop
Utilizing woody materials for fungal-based management of soil nitrogen pools
Responses of soil rare and abundant microorganisms to recurring biotic disturbances
Effects of probiotic consortia on plant metabolites are associated with soil indigenous microbiota and fertilization regimes
Toward more sustainable tropical agriculture with cover crops
Disentangling the genetic basis of rhizosphere microbiome assembly in tomato
Bacillus subtilis biofilm matrix components target seed oil bodies to promote growth and anti-fungal resistance in melon
Fungal Planet description sheets: 1383-1435
Relief of phosphate limitation stimulates methane oxidation
Soil biodiversity and nature-mimicry in agriculture; the power of metaphor?
Ammonia-oxidizing bacteria and fungal denitrifier diversity are associated with N2O production in tropical soils
Comparison of methane metabolism in the rhizomicrobiomes of wild and related cultivated rice accessions reveals a strong impact of crop domestication
TbasCO
Optimizing cover crop and fertilizer timing for high maize yield and nitrogen cycle control
Rewilding plant microbiomes
Long-term land use in Amazon influence the dynamic of microbial communities in soil and rhizosphere
Molecular detection and quantification of the Striga seedbank in agricultural soils
Niche differentiation of atmospheric methane-oxidizing bacteria and their community assembly in subsurface karst caves
Vinasse and straw retention decrease fungal diversity and pathogenicity in sugarcane soil
Variations of Bacterial and Diazotrophic Community Assemblies throughout the Soil Profile in Distinct Paddy Soil Types and Their Contributions to Soil Functionality
Legacies at work: plant–soil–microbiome interactions underpinning agricultural sustainability
Producing organic amendments: physicochemical changes in biowaste used in anaerobic digestion, composting, and fermentation
Genetic, phenotypic and metabolic diversity of yeasts from wheat flag leaves
Eucalypt species drive rhizosphere bacterial and fungal community assembly but soil phosphorus availability rearranges the microbiome
Air Ambulance: Antimicrobial Power of Bacterial Volatiles
epiGBS2
Nitrogen, manganese, iron, and carbon resource acquisition are potential functions of the wild rice Oryza rufipogon core rhizomicrobiome
Insect frass and exuviae to promote plant growth and health
Exploring the Volatiles Released from Roots of Wild and Domesticated Tomato Plants under Insect Attack
Potassium phosphite enhanced the suppressive capacity of the soil microbiome against the tomato pathogen Ralstonia solanacearum
Exploring the Interspecific Interactions and the Metabolome of the Soil Isolate Hylemonella gracilis
Insights into the Genomic Potential of a Methylocystis sp. from Amazonian Floodplain Sediments
Molecular evidence for stimulation of methane oxidation in Amazonian floodplains by ammonia-oxidizing communities
A combination of host ecology and habitat but not evolutionary history explains differences in the microbiomes associated with rotifers
Defective RNA Particles of Plant Viruses—Origin, Structure and Role in Pathogenesis
The biogeography of relative abundance of soil fungi versus bacteria in surface topsoil
Plastic mulch film residues in agriculture: impact on soil suppressiveness, plant growth and microbial communities
PhyloFunDB
Microbial trait-based approaches for agroecosystems
Editorial: Metabolic flexibility of microbial methane oxidation
Plant-Microbe Eco-Evolutionary Dynamics in a Changing World
Methane-Derived Carbon As A Driver For Cyanobacterial Growth
Potassium phosphite enhances the antagonistic capability of Bacillus amyloliquefaciens to manage tomato bacterial wilt
Greenhouse gas (CO2, CH4, and N2O) emissions after abandonment of agriculture, and insights on the response of the (de)nitrifier
The Stochastic Assembly of Nitrobacter winogradskyi-Selected Microbiomes with Heterotrophs from Sewage Sludge or Grassland Soil
Forage grasses steer soil nitrogen processes, microbial populations, and microbiome composition in a long-term tropical agriculture system
Microbiome resilience of Amazonian forests:
Back to the Roots
Lessons from the Amazon biome
Zwartia hollandica gen. nov., sp. nov., Jezberella montanilacus gen. nov., sp. nov. and Sheuella amnicola gen. nov., comb. nov., representing the environmental GKS98 (betIII) cluster
Rhizosphere microbiome response to host genetic variability
Microbial volatiles as mediators of eco-evolutionary dynamics
Metabolic signatures of rhizobacteria-induced plant growth promotion
Plant- and bacteria-derived compounds with anti-Philasterides dicentrarchi activity
Fungal Planet description sheets: 1436–1477
Methanotrophy by a Mycobacterium species that dominates a cave microbial ecosystem
Current Challenges and Pitfalls in Soil Metagenomics
The nitrification inhibitor nitrapyrin has non-target effects on the soil microbial community structure, composition and functions
Ecology and functional potential of phyllosphere yeasts
Antimicrobial Volatiles emitted by Members of the Nest Microbiome of Social Spiders
Second compartment widens plasmid invasion conditions
Removal processes of individual and a mixture of organic micropollutants in the presence of Scenedesmus obliquus
Effect of strigolactones on recruitment of the rice root-associated microbiome
Does diversity matter? Soil microbial functioning and greenhouse gas fluxes in cover crop mixtures
A review on the impact of domestication of the rhizosphere of grain crops and a perspective on the potential role of the rhizosphere microbial community for sustainable rice crop production
Population size mediates the contribution of high-rate and large-benefit mutations to parallel evolution
Deciphering belowground plant-fungal interactions to understand the effects of biodiversity on disease risk
Aromatherapy: Improving Plant health through Microbial Volatiles
Fusarium diversity associated with the Sorghum-Striga interaction in Ethiopia
Trophic interactions between predatory protists and pathogen-suppressive bacteria impact plant health
Empirical estimates of the mutation rate for an alphabaculovirus
Plant neighbours can make or break the disease transmission chain of a fungal root pathogen
β-Glucan-Induced Immuno-Modulation
Feasibility of early fertilization of maize with 15N application to preceding cover crop
The ubiquitous catechol moiety elicits siderophore and angucycline production in Streptomyces
Stem traits, compartments, and tree species affect fungal communities on decaying wood
Incomplete bunyavirus particles can cooperatively support virus infection and spread
Prospects of residual streams from insect cultivation for sustainable crop management
Circular alternatives to peat in growing media
Chitin Determination in Residual Streams Derived from Insect Production by LC-ECD and LC-MS/MS methods
An automated multiplexed turbidometric and data collection system for measuring growth kinetics of anaerobes dependent on gaseous substrates
AntiSMASH 6.0
Tackling the context-dependency of microbial-induced resistance
Chitin- and Keratin-Rich Soil Amendments Suppress Rhizoctonia solani Disease via Changes to the Soil Microbial Community
Five Challenges in the Field of Viral Diversity and Evolution
Casing soil microbiome mediates suppression of bacterial blotch of mushrooms during consecutive cultivation cycles
Fusarium: more than a node or a foot-shaped basal cell
A community resource for paired genomic and metabolomic data mining
Facilitation in the soil microbiome does not necessarily lead to niche expansion
Upland rice intercropped with forage grasses in an integrated crop-livestock system
The influence of agar brands and micronutrients in the growth optimization of Granulicella sp. (Acidobacteriota)
Intraspecific variation in multiple trait responses of Alexandrium ostenfeldii towards elevated pCO2
Understanding disease suppressive soils
Linking microbial inoculants and associated changes in the soil microbiome to plant-soil performance in degraded lands
Rearranging the sugarcane holobiont via plant growth-promoting bacteria and nitrogen input
Chicken gut microbiome members limit the spread of an antimicrobial resistance plasmid in Escherichia coli
Active methane processing microbes and the disproportionate role of NC10 phylum in methane mitigation in Amazonian floodplains
Decomposing cover crops modify root-associated microbiome composition and disease tolerance of cash crop seedlings