Neelus murinus, a tiny soil-dwelling springtail.

Functional Environmental Genomics

Soil invertebrate genomics and metagenomics

We are developing and adapting molecular approaches to study the structure, composition and functions of hard-to-observe organisms. We seek answers to important questions in ecology, such as the effects of the Great Acceleration on taxonomically diverse communities. 

Our main focus is on developing and testing methods to describe the structure and function of soil invertebrate communities, together with the Soil Zoology Division of Senckenberg Görlitz. The project “Metagenomic monitoring of soil communities (MetaInvert)” is part of the LOEWE Centre for Translational Biodiversity Genomics, and it is led by Miki Bálint, Ricarda Lehmitz and Peter Decker. The project is funded through the programme “LOEWE – Landes-Offensive zur Entwicklung Wissenschaftlich-ökonomischer Exzellenz” of Hesse’s Ministry of Higher Education, Research, and the Arts. We genome-sequenced over 250 species of soil invertebrates under the lead of Clem Schneider. The aim of this database is to improve species identifications through shotgun metagenomics.

Alexandra Schmidt is working on the project ‘Metagenomics of soil invertebrate mock communities’ as M.Sc. candidate. Her aim is to evaluate the identification accuracy and read-biomass relationships in mock metagenomic soil invertebrate samples. Genome information of the ‘MetaInvert’ project is used as a reference database. The mock ups cover a wide range of taxonomic groups and compositions (biomass distribution). With this research we hope to make future metagenomic field monitoring projects more efficient.

Anna Küchler is currently working on the project ‘BE-Spring as her PhD project: Discovering Collembola biodiversity on grasslands with emerging genomic and metagenomic tools’ within the Biodiversity Exploratories, funded by DFG. In this project she aims to establish a springtail (Collembola) genome reference database (SGRD) for the most abundant soil springtail species on the 150 Exploratories grassland plots distributed across Northern-, Central- and Southern Germany (in the Biosphere Reserve Schorfheide-Chorin, the National Park Hainich and the Biosphere Reserve Schwäbische Alb, respectively). Using a shotgun metagenomic approach established within ‘MetaInvert’ her goal is to then describe these springtail communities and investigate (1) how environmental drivers and the intensification of grassland-use influence springtail community composition and functioning and (2) how springtails relate to other biological components of the grassland ecosystems. Alongside Miki Bálint, also Clément Schneider (head of the Apterygota section, SGN Görlitz) and Pete Manning (head of the working group ‘Causes and Consequences of biodiversity change’, S-BikF) are involved as project PI’s, as well as Dennis Baulechner and Volkmar Wolters (Justus Liebig University, Gießen & RESOILIENCE project, Biodiversity Exploratories) as collaborative partners.

Dr. Gemma Collins is a postdoctoral fellow working on the ‘MetaInvert’ project to compare genomes from over 250 individual soil invertebrates. This includes functional analyses of the genomes as well as evaluating any factors that may influence the success of genome sequencing. One of the overarching aims of MetaInvert is to generate a representative resource of soil invertebrate species in Germany for use as a reference library for metagenomic sequencing and Dr. Gemma Collins will also be contributing towards that goal.

Funktionale Umweltgenomik
Small subsample of springtails found within one square meter of grassland soil. Springtails are a highly diverse group of microarthropods which are mostly 1-2 mm large and occur in all biomes on Earth.

Ancient environmental DNA

Another important component of the group’s work is to generate long community time series data with ancient environmental DNA preserved in lake sediments, and to interpret these. Ancient DNA can capture wide varieties of taxa which once lived in aquatic habitats, back to thousands of years. Ancient DNA time series of communities can answer questions about the ecological effects of historic climate change and human impact.

Our newest ancient eDNA project is “Predicting the future from signatures of the past: using living sediment archives and ancient DNA to understand responses of marine primary producers to environmental changes”. The project will compare the effects of Holocene and Anthropocene changes on the composition and population genomic structures of phytoplankton through the entire 8500-year history of the Baltic Sea.

The project is funded by the Leibniz Collaborative Excellence funding programme of the Leibniz Gemeinschaft. PIs are Laura Epp (Uni Konstanz), Inga Hense (Uni Hamburg), Miki Bálint, with Anke Kremp (IOW) as coordinator.

Crayfish plague transcriptomics

Dr. Kathrin Theissinger and her team are working on the project “Freshwater Crayfish and Their Invasive Disease in Europe”. The freshwater biodiversity is in severe decline. In Europe, the keystone species of these ecosystems, freshwater crayfish, are threatened by the introduction of the invasive North American crayfish species. North American crayfish species are vectors for the highly infectious disease crayfish plague, which is caused by the pathogen Aphanomyces astaci. In our research we aim to uncover the underlying molecular mechanisms of a crayfish plague induced immune response to an A. astaci infection within an original transcriptomics framework. Furthermore, we use a multi-scale approach to understand the host-parasite interactions and provide evidence for A. astaci host-jumps, shedding light on its host reservoir. We implement a wide range of novel genomic methods (WGS, RNAseq, WGBS, GWAS analysis) to answer our questions and provide high-quality reference datasets for future freshwater crayfish genomic studies. By investigating the effects of A. astaci on European freshwater ecosystems, we gain a better understanding of biological invasions, the second largest contributor to the loss of biodiversity.