Biodiversity

Soil Biodiversity

On-site sequencing during a field-school in San Pedro de Atacama.

We study the small organisms that run soil ecosystems — nematodes, mites, and other soil invertebrates that are largely invisible but drive nutrient cycling, carbon flow, and ecosystem resilience. We want to know who is there, what they do, and how they genetically interact.

Our focus: roundworms

Nematodes are the most abundant animals on Earth — there are more of them in a handful of soil than there are humans on the planet. They drive bacterial and fungal community dynamics, move carbon and nitrogen through the soil food web, and their community composition is a sensitive indicator of soil health and ecosystem function. Despite this, the vast majority of nematode species have never been described, let alone had their genomes sequenced or their ecological roles quantified.
This gap is our quest.

Nematodes are also tractable — many species can be cultured in the lab, their genomes are small, they respond to CRISPR, and their community structure can be profiled directly from soil samples. The combination of ecological centrality and experimental accessibility makes them a uniquely powerful window into soil biodiversity — one we have barely begun to look through.

Not all nematodes are benign ecosystem engineers. A substantial fraction parasitise plants, animals, and humans. Understanding free-living nematode biology is the foundation for understanding their parasitic relatives too — we explore this on our Parasitic Nematodes & One Health page.

In the Field

Most of what we know about soil nematode communities comes from agricultural or temperate soils under relatively stable conditions. We go to the other end of the spectrum — sites where water, temperature, or both push organisms to the edge — because these are the places where the mechanisms of persistence become visible. We polarise our findings from hyper arid and arid environments through research in temperate and tropical regions, for example in Vietnam.

The Atacama

Northern Chile.
Hyper-arid.
Home of our Nature Comms. 2025 work on nematode communities and parthenogenesis along climate gradients.
The Outback

Australia. Seasonally Arid.
Comparative field programme running alongside our Atacmaa and Namib work
The Namib

Namibia. Arid.
Long-term nematode community surveys along ephemeral river systems in comparison to the older, drier Atacama desert
Northern Ghana

Semi-arid.
An incoming PhD project using eRNA sequencing to profile cryptobiotic communities and nematode-microbiome dynamics under accelerating aridification.
Vietnam

With local colleagues we have been sampling across different eco-zones in Vietnam, from tropical Islands to the rain forest. We also look at coffee plantations (see our work on parasites, where we also work with colleagues in neighboring Thailand).
Across Europe

Among many colleagues and places across Europe, we are very closely working with Dr Alex Holovachov in Stockholm, with whom we sample in Sweden.

In the lab

Biodiversity Genomics Center Cologne

The Biodiversity Genomics Center Cologne (BioC²) is a project I co-founded and now direct at the University of Cologne. Its mission is to produce reference-quality genome assemblies for organisms that are connected to the river Rhine and are ecologically important but genomically uncharted — and to develop the protocols and computational infrastructure needed to do this reliably for tiny, unculturable organisms from field samples.
We have published reference genomes for previously unstudied taxa, including the first high-quality assemblies for two microalgae species, with a further 10–20 genome assemblies in active preparation including nematodes, mites, and other soil invertebrates.
959 nematode genomes

With colleagues from the Mark Blaxter's group at the Darwin Tree of Life project we are in a long-term collaboration that aims to sequence 959 nematode genomes, equaling the number of cells in an adult hermaphrodite C. elegans. My laboratory has recently sequenced more than 80 new genomes using PacBio technology at the West German Genome Center and our own Oxford Nanopore Technologies PromethION platform. The data will be made freely available to the community.

Field training, outreach
& capacity building

We run field schools and training programmes at our field sites, combining hands-on research training with genuine knowledge exchange with local communities. In particular, we directly involve local communities in our research and learn about their traditional ecological knowledge.

Atacama field-school

In 2023 we ran our first international field school in San Pedro de Atacama, northern Chile, in collaboration with CRC 1211 and local partners. Participants learnt to sample and identify soil nematode communities in hyper-arid environments — collecting soil along elevational transects, extracting and identifying nematodes under the microscope, and collecting ecological data in the field. The programme included engagement with the local Atacameño communities who have lived alongside and shaped these landscapes for centuries. Their knowledge of seasonal change, water availability, and land use informed how we interpret the ecological data we collect. We see this kind of bi-directional exchange — scientific tools and methods going in, local ecological knowledge coming out — as central to responsible field science in regions with a colonial scientific history.
UNAM ONT workshop

In February 2026 we ran a hands-on Oxford Nanopore sequencing and bioinformatics workshop at the University of Namibia (UNAM) in Windhoek. Participants learnt to prepare ONT sequencing libraries from environmental soil samples, run real-time basecalling with Dorado, and work through community analysis pipelines for amplicon metabarcoding data. The workshop was developed together with Dr Mwangala Nalisa and colleagues at UNAM, and is part of a longer collaboration aimed at building a permanent local capacity in molecular ecology and biodiversity genomics in Namibia. A second iteration is planned for autumn 2026, and we are in discussion with the West German Genome Center and Oxford Nanopore Technologies about co-funding this ongoing programme.

BioC² - Network

For the genomics part of our biodiversity research we are working with international and national partners.

Darwin Tree of Life / Wellcome Sanger Institute We collaborate closely with Prof. Mark Blaxter, who leads the Darwin Tree of Life project. Mark is also a long-time personal collaborator; our connection goes back to my PhD. DToL data and infrastructure are directly accessible to our comparative genomics programme.

Earth BioGenome Project The EBP is the umbrella initiative aiming to sequence all eukaryotic life on Earth. BioC² contributes to the German node. In November 2024 I co-organised a national symposium at the Senckenberg Institute in Frankfurt to build the foundation for a coordinated German biodiversity genomics initiative, with Prof. Harris Lewin (EBP lead) as keynote speaker.

West German Genome Center (WGGC) Our primary sequencing infrastructure partner in Germany, providing high-throughput sequencing capacity and bioinformatics support for large-scale BioC² projects.

Bluesky: @worm-lab.bsky.social
Instagram: @worm.lab

Zülpicher Str. 47b, 50674 Köln,
Deutschland