AG Bonkowski

Our group investigates how microbial interactions—especially involving soil protists—regulate the functioning and stability of terrestrial ecosystems. While soils are among the most biologically diverse habitats on Earth, the ecological roles of microbial eukaryotes remain underexplored. We aim to close this gap by studying how protists structure microbial communities, drive nutrient cycling, and ultimately shape ecosystem functioning and ecosystem services.

A key focus lies in the trophic networks of the soil microbiome, where protists act as bacterial grazers, fungal consumers, or plant parasites. Their predatory behavior affects microbial turnover and nutrient release, with cascading effects on plant productivity and carbon dynamics. Early work from our group demonstrated how protist activity can enhance plant nutrient uptake by stimulating bacterial mineralization—a central mechanism in soil-plant feedbacks.

Our research now expands these insights across land-use gradients and under changing environmental conditions. In collaborative frameworks such as the Jena Experiment, we investigate how management intensity, biodiversity loss, and climate extremes (particularly drought) alter microbial food webs. We are especially interested in soil legacy effects—how past land use or environmental stress leaves persistent microbial imprints that influence future community assembly, nutrient cycling, and plant-soil interactions.

Within the CRC AquaDiva and DFG Priority Program SPP 2089 "Rhizosphere Spatiotemporal Organisation", we explore how biotic interactions in the rhizosphere are shaped over time and space, and how microbial traits influence belowground community dynamics. These studies seek to understand how root-associated protists interact with bacteria and fungi across developmental stages, under fluctuating moisture regimes, and across plant species.

We are also involved in the SOB4ES project, which is a project co-funded by the EU, aiming to disentangle the link between biodiversity, ecosystem functions and services. Our part focuses on investigating how soil health is affected by soil pathogens and which ecological indicators are involved.

A growing body of our work is dedicated to extreme or understudied terrestrial habitats, such as cryptogamic covers polar environments. These systems offer unique opportunities to study the resilience and metabolic capacity of microbial communities under environmental stress, and their contribution to soil development and primary productivity in the absence of vascular plants.

We also address fundamental questions in microbial biogeography and evolutionary ecology, linking protist phylogeny with ecological function. Through molecular approaches, trait-based frameworks, and high-throughput sequencing, we aim to move from species descriptions to predictive models of microbial ecosystem function.

Ultimately, our goal is to place microbial eukaryotes—especially protists—at the center of terrestrial ecological theory. Understanding their roles in soil processes is critical for managing ecosystem services, restoring degraded soils, and predicting how ecosystems respond to global change.