Functional Environmental Genomics

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.

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.

The GEODE project aims to obtain a chromosome level reference genome for Astacus astacus. With an estimated size of 17Gb, this genome will be the largest genome available in invertebrates and will be exploited by comparative genomics and cytogenomics approaches to explore the evolution of decapod genomes, in terms of gene content, repeated elements and genome architecture, with specific focus on the sex determination system, which is still unknown in crayfish at present. In synergy, we will investigate the crayfish immune system and its evolution in decapods. First, we will identify the genes involved in the innate immune response in A. astacus by studying the differential gene expression in a controlled infection experiment across different tissues. While it has long been accepted that immune memory is absent in invertebrates, this notion has recently been challenged by the observation of immune memory responses in certain insects and crustaceans. Thus, we will attempt to demonstrate experimentally the existence of immune memory in A. astacus by an immune priming experiment, followed by single cell RNA sequencing of hemocytes. All the differentially expressed genes identified, whether they are already known or novel, will be studied in the light of their genomic and evolutionary context. Finally, we will exploit the host-pathogen model of A. astacus and Aphanomyces astaci to shed light into their coevolutionary history. We will investigate the genetic basis of host resistance and pathogen virulence by utilizing GWAS approaches between susceptible and resistant crayfish populations and between strains of varying virulence in the pathogen. The genetic variants associated with host resistance will be used to create a SNP chip that will identify resistant crayfish populations, paving the way for an advanced management strategy to conserve freshwater crayfish.

BioDive4Soil: Discovering the Hidden Universe Beneath Our Feet

Soil, the next frontier.

Dark as the deep sea, unexplored as space – 

This is the mission of BioDive4Soil.

A six-year journey:

to uncover hidden worlds beneath our feet,

to reveal the unseen life that sustains us,

to boldly study what no science has mapped before.

Soil is one of Earth’s least explored frontiers, a living world that sustains us in many subtle and invisible ways. Soil is home to about 60% of Earth’s biodiversity. It provides fertile ground for crops and filters water. It also helps to regulate the climate by storing carbon. From ancient farming to modern forestry, we have always relied on the invisible networks of soil organisms that sustain these services.

Yet despite its vital role, soil biodiversity remains poorly documented. This lack of knowledge restricts our capacity to evaluate and reduce risks, such as pollution, climate change, and the unsustainable use of land, that endanger both soil biodiversity and the essential functions it provides.

To address this knowledge gap, the German Environment Agency (UBA) launched BioDive4Soil, a six-year mission to systematically explore soil life. The project is carried out by the Fraunhofer Institute for Molecular Biology and Applied Ecology IME in cooperation with ten leading research institutions and is funded by the Federal Ministry for the Environment’s Federal Action Plan on Nature (ANK). 

Why does soil biodiversity matter?

Healthy soils are essential for our future. This principle lies at the heart of the EU’s Soil Monitoring and Resilience Law (SML), which aims to protect and restore soil health throughout Europe. The SML is fundamental to ensuring food security, clean water, and climate resilience by protecting soils. These ecosystem services are delivered by countless soil organisms ranging from archaea, bacteria, fungi, and protists to nematodes, microarthropods, potworms, and earthworms, which interact with soil, plants, and each other, thereby driving nutrient cycling, preventing erosion, and buffering extreme weather.

Healthy soils are nature’s silent superheroes, and form the basis of all life on Earth. But to protect and restore them effectively, we first need to understand their actual state.

The mission of BioDive4Soil

Our mission is to illuminate the hidden diversity of life beneath our feet in Germany, describe soil biodiversity, and pioneer innovative methods, so we can protect, restore and manage soils for a sustainable future.

Over six years (2025-2030), researchers will conduct a nationwide survey across forests, croplands, and grasslands, using standard morphological determination of soil organisms combined with state-of-the-art molecular techniques to study the trillions of organisms found in a single gram of soil. The project aims to:

• identify habitat-specific communities,
• uncover the factors shaping their distribution and resilience, and
• develop biodiversity indicators for soil health assessments.

At Senckenberg Frankfurt, we will focus on advancing molecular methods (eDNA- and comDNA metabarcoding, DNA-barcoding) for soil biodiversity assessments.

By bringing together leading institutions, including Fraunhofer IME, RWTH, iDiv, ECT, EFTAS, ahu, Mesocosm, Gaiac, and Ecossa, as well as expert soil taxonomists, BioDive4Soil bridges critical knowledge gaps and paves the way for sustainable soil management.

More than a research program

BioDive4Soil is a call to action. The diversity of life in our soils is the foundation of our existence. Protecting it isn’t just science – it’s securing our future. With BioDive4Soil, we are not just studying the ground beneath our feet. We are redefining the way we care for one of the most essential ecosystems on Earth.

Explore our project partners

It is important to educate young colleagues about obtaining molecular biodiversity data. This is probably the most efficient through hands-on experience. Our first M.Sc. course at the Faculty of Agricultural Sciences, Nutritional Sciences, and Environmental Management of the Justus-Liebig University will be Genomic tools in the evaluation of biodiversity loss (MP 227). It will be offered as a block course in the Summer Semester 2021. 

Field courses are also excellent platforms for introducing ecological data generation with molecular tools. The BiodivGenomics Field Course initiated with Markus Pfenninger and Barbara Feldmeyer was first organized between 20-30. July 2019 in the Eastern Carpathians of Romania. The COVID-19 pandemic forced us to cancel courses in 2020 and 2021, but we are planning to continue them once possible again.