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.
Facilities
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
- Senior Researcher
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Prof. dr. Paolina Garbeva
- Function
- Senior Researcher
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Dr. Paul Bodelier
- Function
- Senior Researcher
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Prof. dr. 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
Metabolic coupling between soil aerobic methanotrophs and denitrifiers in rice paddy fields
Cover crop mixtures do not assemble markedly distinct soil microbiotas as compared to monocultures in a multilocation field experiment
Mode of application of sulfonated graphene modulated bioavailable heavy metal contents and microbial community composition in long-term heavy metal contaminated soil
Evaluating Mechanisms of Soil Microbiome Suppression of Striga Infection in Sorghum
Intentional summer flooding of an Avicennia germinans mangrove forest has a more direct effect on ammonia-oxidizing Betaproteobacteria than on Thaumarchaea
Exploring modes of microbial interactions with implications for methane cycling
The use of living labs to advance agro-ecological theory in the transition towards sustainable land use
Dairy effluent applications to a pasture enhance soil fertility and microbial activity without impacting soil bacterial and fungal community composition
Exploring microbial diversity and interactions for asbestos modifying properties
The role of strigolactone structural diversity in the host specificity and control of Striga, a major constraint to sub-Saharan agriculture
Enhancing cucumber plantlet growth and rhizosphere microbial communities with chitin and gelatin biostimulants
Darwin’s expedition revisited to reveal the evolution of plant–microbe interactions on Galápagos
Exploring the temporal dynamics of a disease suppressive rhizo-microbiome in eggplants
Diverse bacterial consortia
Methane-cycling microbial communities from Amazon floodplains and upland forests respond differently to simulated climate change scenarios
Biological Characterization of Physostegia Chlorotic Mottle Virus, an Emergent Virus Infecting Vegetables in Diversified Production Systems
Microbial community dynamics during decomposition of insect exuviae and frass in soil
Effect of microplastic pollution on the gut microbiome of anecic and endogeic earthworms
Bacterial genomes recovered from litter’s metagenomes in Amazonian Dark Earths
What are the 100 most cited fungal genera?
Fungal Planet description sheets: 1614-1696
Mix-method toolbox for monitoring greenhouse gas production and microbiome responses to soil amendments
Why change a winning formula?
Enhanced surface colonisation and competition during bacterial adaptation to a fungus
C4 cereal and biofuel crop microbiomes
Redefining Ellisembia sensu stricto with a reassessment of related taxa in Sordariomycetes
Arbuscular mycorrhizal fungi originated from soils with a fertility gradient highlight a strong intraspecies functional variability
Cultivar governs plant response to inoculation with single isolates and the microbiome associated with arbuscular mycorrhizal fungi
Comparison of distinctive diversities, co-occurrence patterns and potential ecological functions of microbial communities in heterogeneous soil areas in typical subtropical forests, southeast China
Discovery and Derivatization of Tridecaptin Antibiotics with Altered Host Specificity and Enhanced Bioactivity
A Comparison of Different Protocols for the Extraction of Microbial DNA Inhabiting Synthetic Mars Simulant Soil
Harnessing regulatory networks in Actinobacteria for natural product discovery
Soil aggregate stability governs field greenhouse gas fluxes in agricultural soils
Unraveling the impact of protein hydrolysates on rhizosphere microbial communities
Impact of insect herbivory and microbial inoculants on the rhizosphere microbiome and volatilome
The soil microbiome modulates the sorghum root metabolome and cellular traits with a concomitant reduction of Striga infection
Stem decomposition of temperate tree species is determined by stem traits and fungal community composition during early stem decay
bacLIFE: a user-friendly computational workflow for genome analysis and prediction of lifestyle-associated genes in bacteria
Enhancing phosphate-solubilising microbial communities through artificial selection
Robust Approaches to the Quantitative Analysis of Genome Formula Variation in Multipartite and Segmented Viruses
Impact of bacterial and fungal inoculants on the resident rhizosphere microbiome and the volatilome of tomato plants under leaf herbivory stress
Impact of mixed microalgal and bacterial species on organic micropollutants removal in photobioreactors under natural light
Taxonomic and metabolic diversity of Actinomycetota isolated from faeces of a 28,000‐year‐old mammoth
Editorial: Synthetic microbial communities
The effect of intentional summer flooding for mosquito control on the nitrogen dynamics of impounded Avicennia germinans mangrove forests
Stable isotope probing reveals compositional and functional shifts in active denitrifying communities along the soil profile in an intensive agricultural area
Threats to the soil microbiome from nanomaterials
Fungal Planet description sheets: 1550-1613
The Tomato’s Tale: Exploring taxonomy, biogeography, domestication and microbiome for enhanced resilience
Crop rotation and native microbiome inoculation restore soil capacity to suppress a root disease
Plant grafting
Repeated exposure of wheat to the fungal root pathogen Bipolaris sorokiniana modulates rhizosphere microbiome assembly and disease suppressiveness
Shotgun Metagenomics-Guided Prediction Reveals the Metal Tolerance and Antibiotic Resistance of Microbes in Poly-Extreme Environments in the Danakil Depression, Afar Region
Carbon and Nutrients from Organic Residues Modulate the Dynamics of Prokaryotic and Fungal Communities
Unravelling key enzymatic steps in C-ring cleavage during angucycline biosynthesis
Fungal planet description sheets
Interactions between Cyanobacteria and Methane Processing Microbes Mitigate Methane Emissions from Rice Soils
Unraveling the prevalence of soil-borne fungal pathogens in the North China Plain
Widespread and largely unknown prophage activity, diversity, and function in two genera of wheat phyllosphere bacteria
Stability of ammonia oxidizer communities upon nitrogen fertilizer pulse disturbances is dependent on diversity
Variability of earthworm's functional traits in eastern Amazon is more species-dependent than environment-dependent
The plant stress hormone jasmonic acid evokes defensive responses in streptomycetes
The ecology of multipartite plant viruses
Uncovering the biodiversity of root endophytic fungi in Europe
Fungal Community Succession of Populus grandidentata (Bigtooth Aspen) during Wood Decomposition
Microbial volatiles mediate bacterial evolutionary dynamics
Deciphering the effects of crop rotation on tobacco bacterial wilt through general and specific disease suppression
Experimental erosion of microbial diversity decreases soil CH4 consumption rates
The intrinsic methane mitigation potential and associated microbes add product value to compost
Diversity of viruses and viroids in the rhizosphere of common bean cultivars differing in resistance to the fungal root pathogen Fusarium oxysporum
Do temporal and spatial heterogeneity modulate biodiversity–functioning relationships in com-munities of methanotrophic bacteria?
Tomato growth stage modulates bacterial communities across different soil aggregate sizes and disease levels
Methanotrophs dominate methanogens and act as a methane sink in a subterranean karst cave
Editorial: Microbial volatiles and communication
Artificial intelligence for natural product drug discovery
Mixed viral infection constrains the genome formula of multipartite cucumber mosaic virus
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
Phosphorus-mediated succession of microbial nitrogen, carbon, and sulfur functions in rice-driven saline-alkali soil remediation
Chemotaxis mediates nitrogen acquisition of maize under long-term nitrogen input
Long term co-application of lime and phosphogypsum increases 15 N recovery and reduces 15 N losses by modulating soil nutrient availability, crop growth and N cycle genes
Steering crop yields, soil nitrogen processes and the microbiome in tropical agriculture system
Acidification suppresses the natural capacity of soil microbiome to fight pathogenic Fusarium infections
Impact of the fungal pathogen Fusarium oxysporum on the taxonomic and functional diversity of the common bean root microbiome
A widely distributed gene cluster compensates for uricase loss in hominids
Addition of cellulose degrading bacterial agents promoting keystone fungal-mediated cellulose degradation during aerobic composting
Cross-cultural adaptation and validation of the family needs assessment scale for Brazilian families of children and adolescents with disabilities
Dynamic effects of probiotic formula ecologic®825 on human small intestinal ileostoma microbiota
Carbohydrate metabolism bacteria positive effect determines the increasing soil organic carbon during long-term straw fertilization returning
Impact of wastewater characteristics on the removal of organic micropollutants by Chlorella sorokiniana
Fungal Planet description sheets: 1478-1549
Editorial: Predicting virus evolution
Enhancing phosphorus removal of photogranules by incorporating polyphosphate accumulating organisms
Nitrogen input on organic amendments alters the pattern of soil–microbe-plant co-dependence
Importance of Bacteroidetes in host–microbe interactions and ecosystem functioning
Effect of pre-treatment processes of organic residues on soil aggregates
The Fitness of Beta-Lactamase Mutants Depends Nonlinearly on Resistance Level at Sublethal Antibiotic Concentrations
Breaking the witches' spell: towards steering the soil microbiome for volatile-mediated control of the root parasitic weed Striga
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
Utilizing woody materials for fungal-based management of soil nitrogen pools
Pro- and eukaryotic keystone taxa as potential bio-indicators for the water quality of subtropical Lake Dongqian
Composition, function and succession of bacterial communities in the tomato rhizosphere during continuous cropping
Responses of soil rare and abundant microorganisms to recurring biotic disturbances
MIBiG 3.0:
Radish-based cover crop mixtures mitigate leaching and increase availability of nitrogen to the cash crop
Prospects of residual streams from insect cultivation for sustainable crop management
Effects of probiotic consortia on plant metabolites are associated with soil indigenous microbiota and fertilization regimes
Toward more sustainable tropical agriculture with cover crops
Nutrient Availability Does Not Affect Community Assembly in Root-Associated Fungi but Determines Fungal Effects on Plant Growth