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.