Environmental Metagenomics

Environmental Metagenomics
Prof. Dr. Alexander Probst

Welcome to ...

... the department
Environmental Metagenomics
as part of the Research Center One Health Ruhr of the Research Alliance Ruhr.

The Research Alliance Ruhr was founded by the University of Duisburg-Essen, the Ruhr University Bochum, and the Technical University of Dortmund to address pressing scientific issues of the future.

NEWS

+1 for Good Scientific Practices New drone in Probstlab, Upgrade for Science

[01.03.2026] We have a new drone to help with documentaiton of sampling sites, making a big difference for how our lab does science.

Subsurface drilling has begun Successfull Domestic Drilling Mission

[05–20.03.2026] The 2026 drilling season is still underway with the Archean Park (and DeepH) campaign at Mendig, where numerous high-quality cores were successfully recovered. Led by Jens Kallmeyer, the expedition was joined by six members of our lab and delivered an excellent start to the season.

The freshly recovered cores are now being processed for DNA extraction, bringing us one step closer to uncovering the hidden microbial stories preserved deep underground.

Subsurface comes up in the USA Successfull Sampling at Crystal Gyser

[06–14.04.2026] A team of three senior scientists from our lab (Alex, Till, and André) successfully headed into the Utah desert to sample Crystal Geyser and several surrounding high-CO₂ geysers. Equipped with field gear and scientific curiosity, they returned with a valuable collection of preserved samples.

The material will now support further research within the Archean Park and DeepH projects, helping us explore extreme environments and the microbial life they host.

Research Projects

© Archean Park

Archean Park Archean Park: Relics of Ancient Cellular Biochemistry in High-CO2 Subsurface Ecosystems

The Archean Park project aims to investigate how microbial life functioned under early Earth conditions, particularly in high-CO₂ and oxygen-free environments. The goal is to uncover ancient metabolic pathways that support carbon cycling in these extreme settings. By integrating deep drilling, genomics, biochemistry, and geochemistry, the project seeks to reconstruct early microbial ecosystems. Insights from this work may inform modern biotechnology and enhance our understanding of Earth's early climate and life.

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DFG Funded CRC RESIST: Collaborative Research Centre on multiple stressors affecting streams and rivers

RESIST aims to unravel the interactions of multiple stressors in rivers. With manipulative lab and field experiments, field studies and models we will test why, when and how stressors interact – and develop options for mitigation and restoration.

Project A01
Direct and indirect effects of multiple stressors in freshwater ecosystems on microbial parasites and scavengers
More Info

Project A22
Viral (and host) microdiversity response to multiple stressors in freshwater ecosystems. See project description for information on open Bsc/Msc theses/internship topics for this sub-project
More Info

Project Z-INF
Data management and integration
More Info

IQ-Wasser/Julia Nuy

IQ-Wasser funded by Federal Ministry of Education and Research (BMBF) Exploring the use of AI in water monitoring

[28-01-2025] Biodiversity and water quality are strongly interconnected. The newly funded IQ-Wasser: KI & Biodiversity project will link artificial intelligence (AI) algorithms to predict biodiversity changes in riverdam-mediated drinking water reservoirs in Germany to evaluate the effects on drinking water quality. As leader of the subproject Microbial diversity and ecology, Julia Nuy from our lab is contributing to this groundbreaking initiative disclosing ecosystem functions and pathogenicity potential of the microbial community.

© UDE/Bank Beszteri

GENIAL funded by US Department of Energy Genomics of Algae and their Interactions in Aquatic Life

Algae are important organisms on planet Earth as they transform carbon dioxide into organic matter fueling the food chain in freshwater ecosystems. With the help of JGI's ( Department of Energy, USA) Community Science Project (CSP), project Gen omics of Algae and their Interactions in Aquatic Life (GENIAL) will aim at unraveling the evolution of carbon turnover modes of algae and their interaction with other organisms like bacteria or viruses for acquiring cellular nitrogen. The basis for our work will be deciphering the DNA and RNA sequences of more than one hundred algae (and their partners) which will be used for predicting their capabilities and their evolution from their genomes. To do this, we will work with the Central Collection of Algal Cultures (CCAC) at the University of Duisburg-Essen (UDE), one of the world's largest freshwater algae collections, along with a large network of collaborators at UDE, Germany and around the world.

© UDE/Manan Shah

BMBF BIOSTABIL for Water Security

The BIOSTABIL project aims to implement the concept of biologically stable drinking water along the entire distribution path from the water treatment plant to the consumer. The project seeks to create the foundation for a sustainable and resilient water supply under the changing conditions introduced by climate change. As part of this, we contribute microbiome analyzes that support and enhance biological stability. Our mission in this project aims to investigate microbiomes that play a key role in ensuring biological stability.

Selected Publications

  • Hug, Laura A.; Hatzenpichler, Roland; Moraru, Cristina; Soares, André R.; Meyer, Folker; Heyder, Anke; Probst, Alexander J.; The Data Reuse Consortium
    Author Correction: A roadmap for equitable reuse of public microbiome data
    In: Nature Microbiology, Vol. 11, 2026, Nr. 1, pp. 335
  • Simon, Sophie A.; Aschmann, Vera; Behrendt, Annika; Hügler, Michael; Engl, Lisa M.; Pohlner, Marion; Rolfes, Sönke; Brinkhoff, Thorsten; Engelen, Bert; Könneke, Martin; Rodriguez-R, Luis M.; Bornemann, Till; Nuy, Julia K.; Rothe, Louisa; Stach, Tom L.; Beblo-Vranesevic, Kristina; Leuko, Stefan; Runzheimer, Katharina; Möller, Ralf; Conrady, Marius; Huth, Markus; Trabold, Thomas; Herkendell, Katharina; Probst, Alexander J.
    Earth's most needed uncultivated aquatic prokaryotes
    In: Water Research, Vol. 273, 2025, 122928
  • Hug, Laura A.; Hatzenpichler, Roland; Moraru, Liliana Cristina; Soares, André R.; Meyer, Folker; Heyder, Anke; Probst, Alexander J.; The Data Reuse Consortium
    A roadmap for equitable reuse of public microbiome data
    In: Nature Microbiology, Vol. 10, 2025, Nr. 10, pp. 2384 – 2395
  • Plewka, Julia; Alibrandi, Armando; Bornemann, Till; Esser, Sarah P; Stach, Tom L; Sures, Katharina; Becker, Jannis; Moraru, Liliana Cristina; Soares, André; di Primio, Rolando; Kallmeyer, Jens; Probst, Alexander J.
    Metagenomic analysis of pristine oil sheds new light on the global distribution of microbial genetic repertoire in hydrocarbon-associated ecosystems
    In: microLife, Vol. 6, 2025, uqae027
  • Wirbel, Jakob; Bhatt, Ami S.; Probst, Alexander J.
    The journey to understand previously unknown microbial genes
    In: Nature, Vol. 626, 2024, Nr. 7998, pp. 267 – 269
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