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.

Medewerkers
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Dr. Mark Zwart
- Functie
- Researcher | Tenure Track
-
Dr. Paolina Garbeva
- Functie
- Senior Researcher
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Dr. Paul Bodelier
- Functie
- Senior Researcher
-
Prof. Wietse de Boer
- Functie
- Senior Researcher
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Prof. dr. ir. Eiko Kuramae PhD
- Functie
- Senior Researcher
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Prof. Jos Raaijmakers PhD
- Functie
- Afdelingshoofd
Evenementen
Peer-reviewed publicaties
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
Relief of phosphate limitation stimulates methane oxidation
Ammonia-oxidizing bacteria and fungal denitrifier diversity are associated with N2O production in tropical soils
Long-term land use in Amazon influence the dynamic of microbial communities in soil and rhizosphere
Comparison of methane metabolism in the rhizomicrobiomes of wild and related cultivated rice accessions reveals a strong impact of crop domestication
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
β-Glucan-Induced Immuno-Modulation
Plant neighbours can make or break the disease transmission chain of a fungal root pathogen
Feasibility of early fertilization of maize with 15N application to preceding cover crop
Trophic interactions between predatory protists and pathogen-suppressive bacteria impact plant health
Molecular detection and quantification of the Striga seedbank in agricultural soils
Biosynthesis, Evolution and Ecology of Microbial Terpenoids
epiGBS2
Air Ambulance: The Antimicrobial Power of Bacterial Volatiles
Variations of Bacterial and Diazotrophic Community Assemblies throughout the Soil Profile in Distinct Paddy Soil Types and Their Contributions to Soil Functionality
Eucalypt species drive rhizosphere bacterial and fungal community assembly but soil phosphorus availability rearranges the microbiome
Plastic mulch film residues in agriculture: impact on soil suppressiveness, plant growth and microbial communities
Potassium phosphite enhanced the suppressive capacity of the soil microbiome against the tomato pathogen Ralstonia solanacearum
Vinasse and straw retention decrease fungal diversity and pathogenicity in sugarcane soil
Stem traits, compartments, and tree species affect fungal communities on decaying wood
Rhizosphere microbiome response to host genetic variability
Metabolic signatures of rhizobacteria-induced plant growth promotion
Plant- and bacteria-derived compounds with anti-Philasterides dicentrarchi activity
The ubiquitous catechol moiety elicits siderophore and angucycline production in Streptomyces
Potassium phosphite enhances the antagonistic capability of Bacillus amyloliquefaciens to manage tomato bacterial wilt
Second compartment widens plasmid invasion conditions
Greenhouse gas (CO2, CH4, and N2O) emissions after abandonment of agriculture, and insights on the response of the (de)nitrifier
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
The nitrification inhibitor nitrapyrin has non-target effects on the soil microbial community structure, composition and functions
Forage grasses steer soil nitrogen processes, microbial populations, and microbiome composition in a long-term tropical agriculture system
Lessons from the Amazon biome
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
Dominant hyphae-associated bacteria of Fusarium oxysporum f. sp. cucumerinum in different cropping systems and insight into their functions
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
Modulation of the soil microbiome by long-term Ca-based soil amendments boosts soil organic carbon and physicochemical quality in a tropical no-till crop rotation system
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
Discovery of Thanafactin A, a Linear Proline-containing Octa-Lipopeptide from Pseudomonas sp. SH-C52, Motivated by Genome Mining
Genome-resolved metagenomics of a photosynthetic bioreactor performing biological nutrient removal
Discrepancy in exchangeable and soluble ammonium-induced effects on aerobic methane oxidation
Designing a home for beneficial plant microbiomes
The structure of rhizosphere fungal communities of wild and domesticated rice: changes in diversity and co-occurrence patterns
Antimicrobial Compounds in the Volatilome of Social Spider Communities
Sugarcane pre-sprouted seedlings produced with beneficial bacteria and arbuscular mycorrhizal fungi
Optimizing biocontrol activity of Paenibacillus xylanexedens for management of hairy root disease in tomato grown in hydroponic greenhouses
Ancestral predisposition toward a domesticated lifestyle in the termite-cultivated fungus Termitomyces
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
Effectiveness of phosphorus control under extreme heatwaves
Volatiles from the fungus Fusarium oxysporum affect interactions of Brassica rapa plants with root herbivores
Self-crossing leads to weak co-variation of the bacterial and fungal communities in the rice rhizosphere
Dissecting disease-suppressive rhizosphere microbiomes by functional amplicon sequencing and 10X metagenomics
Plant functional group drives the community structure of saprophytic fungi in a grassland biodiversity experiment
Competition sensing changes antibiotic production in streptomyces
Stimulated saprotrophic fungi in arable soil extend their activities to the rhizosphere and root microbiomes of crop seedlings
Unresolved advantages of multipartitism in spatially structured environments
Impact of Cellulose-Rich Organic Soil Amendments on Growth Dynamics and Pathogenicity of Rhizoctonia solani
Microbial volatile organic compounds in intra-kingdom and inter-kingdom interactions
Complete and Draft Genome Sequences of Aerobic Methanotrophs Isolated from a Riparian Wetland
Soil microbial legacies differ following drying-rewetting and freezing-thawing cycles
Metabolic differentiation of co-occurring accumulibacter clades revealed through genome-resolved metatranscriptomics
Plant-Growth Endophytic Bacteria Improve Nutrient Use Efficiency and Modulate Foliar N-Metabolites in Sugarcane Seedling
USCγ Dominated Community Composition and Cooccurrence Network of Methanotrophs and Bacteria in Subterranean Karst Caves
Resolving broad patterns of prokaryotic community structure in New Zealand pasture soils
Beneficial microbial species and metabolites alleviate soybean oxidative damage and increase grain yield during short dry spells
Linking microbial inoculants and associated changes in the soil microbiome to plant-soil performance in degraded lands
Understanding disease suppressive soils
Modulation of the soil microbiome by long-term Ca-based soil amendments boosts soil organic carbon and physicochemical quality in a tropical no-till crop rotation system
Trophic and non-trophic effects of fish and macroinvertebrates on carbon emissions
Soybean in Crop Rotation with Maize and Palisade Grass Intercropping Enhances the Long-term Effects of Surface Liming in No-till System
Microbial inoculants modulate growth traits, nutrients acquisition and bioactive compounds accumulation of Cyclocarya paliurus
Steering microbiomes by organic amendments towards climate-smart agricultural soils
Rearranging the sugarcane holobiont via plant growth-promoting bacteria and nitrogen input
Fungal proteases
On-site blackwater treatment fosters microbial groups and functions to efficiently and robustly recover carbon and nutrients
Plant-Microbe Eco-Evolutionary Dynamics in a Changing World
Chicken gut microbiome members limit the spread of an antimicrobial resistance plasmid in Escherichia coli
Combined use of vinasse and nitrogen as fertilizers affects nitrification, ammonification and denitrification by prokaryotes
Comparative studies on the disease prevalence and population dynamics of ginger blotch and brown blotch pathogens of button mushrooms
Successive plant growth amplifies genotype-specific assembly of the tomato rhizosphere microbiome
Towards meaningful scales in ecosystem microbiome research
Extension of Plant Phenotypes by the Foliar Microbiome
The Chemistry of Stress: Understanding the ‘Cry for Help’ of Plant Roots
Decomposing cover crops modify root-associated microbiome composition and disease tolerance of cash crop seedlings
Active methane processing microbes and the disproportionate role of NC10 phylum in methane mitigation in Amazonian floodplains
Optimizing cover crop and fertilizer timing for high maize yield and nitrogen cycle control
Evaluation of phenolic root exudates as stimulants of saprotrophic fungi in the rhizosphere
Bringing soil fungi into action: Options for forward-looking agriculture
Rice domestication influences the composition and function of the rhizosphere bacterial chemotaxis systems
Effects of Sulfur Assimilation in Pseudomonas fluorescens SS101 on Growth, Defense, and Metabolome of Different Brassicaceae
Somatic deficiency causes reproductive parasitism in a fungus
Succession of the Resident Soil Microbial Community in Response to Periodic Inoculations
Impact of root-associated strains of three Paraburkholderia species on primary and secondary metabolism of Brassica oleracea
Metagenomic studies of viruses in weeds and wild plants
Disentangling soil microbiome functions by perturbation
Extracting the GEMs: Genotype, Environment and Microbiome interactions shaping host phenotypes
Biocontrol traits correlate with resistance to predation by protists in soil pseudomonads
Bacterial consortium and microbial metabolites increase grain quality and soybean yield
Nitrogen-Fertilized Systems of Maize Intercropped With Tropical Grasses for Enhanced Yields and Estimated Land Use and Meat Production
Biological nitrification inhibition in the rhizosphere