Microbial Ecology

The primary focus of the department is to understand the ecology, diversity and functions of microorganisms in natural and managed ecosystems.
We are actively involved in each of the three NIOO-wide research themes: climate change, biodiversity, sustainable land & water use. More specifically, we study the role of microorganisms in
- biogeochemical cycles (carbon, nitrogen) and greenhouse gas emissions, and
- plant growth and health.
Micro-organisms studied in these two main research fields involve bacteria, fungi, viruses and archaea. For more detailed information, please visit the research and project pages of the six senior scientists in the department.
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

Wild microbiomes
Diversity & functioning of microbiomes of wild and domesticated plants.

People
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Dr. Mark Zwart
- Function
- Researcher | Tenure Track
-
Dr. Paolina Garbeva
- Function
- Senior Researcher
-
Dr. Paul Bodelier
- Function
- Senior Researcher
-
Prof. Wietse de Boer
- Function
- Senior Researcher
-
Prof. dr. ir. Eiko Kuramae PhD
- Function
- Senior Researcher
-
Prof. Jos Raaijmakers PhD
- Function
- Head of department
Peer-reviewed publications
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
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
Empirical estimates of the mutation rate for an alphabaculovirus
Fusarium diversity associated with the Sorghum-Striga interaction in Ethiopia
Deciphering belowground plant-fungal interactions to understand the effects of biodiversity on disease risk
Aromatherapy: Improving Plant health through Microbial Volatiles
Trophic interactions between predatory protists and pathogen-suppressive bacteria impact plant health
β-Glucan-Induced Immuno-Modulation
Plant neighbours can make or break the disease transmission chain of a fungal root pathogen
Population size mediates the contribution of high-rate and large-benefit mutations to parallel evolution
Does diversity matter? Soil microbial functioning and greenhouse gas fluxes in cover crop mixtures
Feasibility of early fertilization of maize with 15N application to preceding cover crop
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
Rhizosphere microbiome response to host genetic variability
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
The ubiquitous catechol moiety elicits siderophore and angucycline production in Streptomyces
Second compartment widens plasmid invasion conditions
Antimicrobial Volatiles emitted by Members of the Nest Microbiome of Social Spiders
TbasCO
Nitrogen, manganese, iron, and carbon resource acquisition are potential functions of the wild rice Oryza rufipogon core rhizomicrobiome
Rewilding plant microbiomes
epiGBS2
Eucalypt species drive rhizosphere bacterial and fungal community assembly but soil phosphorus availability rearranges the microbiome
Genetic, phenotypic and metabolic diversity of yeasts from wheat flag leaves
Air Ambulance: Antimicrobial Power of Bacterial Volatiles
Legacies at work: plant–soil–microbiome interactions underpinning agricultural sustainability
Producing organic amendments: physicochemical changes in biowaste used in anaerobic digestion, composting, and fermentation
Variations of Bacterial and Diazotrophic Community Assemblies throughout the Soil Profile in Distinct Paddy Soil Types and Their Contributions to Soil Functionality
Vinasse and straw retention decrease fungal diversity and pathogenicity in sugarcane soil
Insights into the Genomic Potential of a Methylocystis sp. from Amazonian Floodplain Sediments
Potassium phosphite enhanced the suppressive capacity of the soil microbiome against the tomato pathogen Ralstonia solanacearum
Editorial: Metabolic flexibility of microbial methane oxidation
Optimizing cover crop and fertilizer timing for high maize yield and nitrogen cycle control
Molecular detection and quantification of the Striga seedbank in agricultural soils
Long-term land use in Amazon influence the dynamic of microbial communities in soil and rhizosphere
Niche differentiation of atmospheric methane-oxidizing bacteria and their community assembly in subsurface karst caves
Exploring the Interspecific Interactions and the Metabolome of the Soil Isolate Hylemonella gracilis
Defective RNA Particles of Plant Viruses—Origin, Structure and Role in Pathogenesis
PhyloFunDB
Plant-Microbe Eco-Evolutionary Dynamics in a Changing World
Plastic mulch film residues in agriculture: impact on soil suppressiveness, plant growth and microbial communities
The biogeography of relative abundance of soil fungi versus bacteria in surface topsoil
Lessons from the Amazon biome
The nitrification inhibitor nitrapyrin has non-target effects on the soil microbial community structure, composition and functions
Ecology and functional potential of phyllosphere yeasts
Current Challenges and Pitfalls in Soil Metagenomics
Methanotrophy by a Mycobacterium species that dominates a cave microbial ecosystem
Greenhouse gas (CO2, CH4, and N2O) emissions after abandonment of agriculture, and insights on the response of the (de)nitrifier
Exploring the Volatiles Released from Roots of Wild and Domesticated Tomato Plants under Insect Attack
Insect frass and exuviae to promote plant growth and health
Fungal Planet description sheets: 1436–1477
Plant- and bacteria-derived compounds with anti-Philasterides dicentrarchi activity
Metabolic signatures of rhizobacteria-induced plant growth promotion
Methane-Derived Carbon As A Driver For Cyanobacterial Growth
Potassium phosphite enhances the antagonistic capability of Bacillus amyloliquefaciens to manage tomato bacterial wilt
Microbial volatiles as mediators of eco-evolutionary dynamics
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
Microbiome resilience of Amazonian forests:
Forage grasses steer soil nitrogen processes, microbial populations, and microbiome composition in a long-term tropical agriculture system
Back to the Roots
The Stochastic Assembly of Nitrobacter winogradskyi-Selected Microbiomes with Heterotrophs from Sewage Sludge or Grassland Soil
A combination of host ecology and habitat but not evolutionary history explains differences in the microbiomes associated with rotifers
Microbial trait-based approaches for agroecosystems
Molecular evidence for stimulation of methane oxidation in Amazonian floodplains by ammonia-oxidizing communities
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
Early nitrogen supply as an alternative management for a cover crop-maize sequence under a no-till system
The influence of soil chemistry on branched tetraether lipids in mid- and high latitude soils: implications for brGDGT- based paleothermometry
Antimicrobial Compounds in the Volatilome of Social Spider Communities
The structure of rhizosphere fungal communities of wild and domesticated rice: changes in diversity and co-occurrence patterns
Discovery of Thanafactin A, a Linear Proline-containing Octa-Lipopeptide from Pseudomonas sp. SH-C52, Motivated by Genome Mining
Designing a home for beneficial plant microbiomes
Sugarcane pre-sprouted seedlings produced with beneficial bacteria and arbuscular mycorrhizal fungi
Genome-resolved metagenomics of a photosynthetic bioreactor performing biological nutrient removal
Discrepancy in exchangeable and soluble ammonium-induced effects on aerobic methane oxidation
Optimizing biocontrol activity of Paenibacillus xylanexedens for management of hairy root disease in tomato grown in hydroponic greenhouses
Volatiles from the fungus Fusarium oxysporum affect interactions of Brassica rapa plants with root herbivores
Dissecting disease-suppressive rhizosphere microbiomes by functional amplicon sequencing and 10X metagenomics
Self-crossing leads to weak co-variation of the bacterial and fungal communities in the rice rhizosphere
Rice domestication influences the composition and function of the rhizosphere bacterial chemotaxis systems
Bringing soil fungi into action: Options for forward-looking agriculture
Somatic deficiency causes reproductive parasitism in a fungus
Extracting the GEMs: Genotype, Environment and Microbiome interactions shaping host phenotypes
Effectiveness of phosphorus control under extreme heatwaves
Metagenomic studies of viruses in weeds and wild plants
Ancestral predisposition toward a domesticated lifestyle in the termite-cultivated fungus Termitomyces