Environmental Metagenomics

Environmental Metagenomics
Prof. Dr. Alexander Probst

Welcome to ...

... the research unit
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.


© UDE/Bettina Engel-Albustin

The new section "Environmental Metagenomics" of the Research Center One Health Ruhr is launched First One Health Ruhr Professorship

[04.11.2022] "A healthy person needs a healthy environment," says UDE Professor Alexander Probst, summarizing the concept of the One Health Ruhr Research Center of the University Alliance Ruhr (UA Ruhr). The biologist is now also the first research professor at One Health Ruhr. He is working on the environmental metagenomics of organisms.

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© Archean Park

"Environmental Metagenomics" receives the ERC Synergy Award 11.5 million euros for research into the microbial carbon cycle

[26.10.2023] A research team from the Universities of Münster, Bremen, Duisburg-Essen and the German Research Centre for Geosciences (GFZ) in Potsdam has been awarded prestigious funding from the European Research Council (ERC): an "ERC Synergy Grant" worth a total of 11.5 million euros. In the six-year "Archean Park" project, the scientists want to gain insights into life under primitive conditions and find previously unknown metabolic pathways that made life possible for microorganisms on the primordial Earth 4,000 to 2,500 million years ago. 2.56 million euros of the funding will go to the UDE.

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© Nature

Pubication in Nature Microbiology A predicted CRISPR-mediated symbiosis between uncultivated archaea

Esser SP, Rahlff J, Zhao W, Predl M, Plewka J, Sures K, Wimmer F, Lee J, Adam PS, McGonigle J, Turzynski V, Banas I, Schwank K, Krupovic M, Bornemann TLV, Figueroa-Gonzalez PA, Jarett J, Rattei T, Amano Y, Blaby IK, Cheng JF, Brazelton WJ, Beisel CL, Woyke T, Zhang Y, Probst AJ.

Nat Microbiol. 2023 Sep;8(9):1619-1633. doi: 10.1038/s41564-023-01439-2. Epub 2023 Jul 27. PMID: 37500801.

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Research Projects


CRC 1439 Multilevel response to stressor increase and release in stream ecosystems

Project A01

Direct and indirect effects of multiple stressors in freshwater ecosystems on microbial parasites and scavengers

Freshwater ecosystems can be exposed to multiple stressors over time, some of them being imposed due to natural (e.g. seasonal) fluctuations, others due to human activity. While the effects of stressors on microbial community composition has been investigated for several freshwater ecosystems, the resulting impacts on microbial interactions including virus-host dynamics remains unexplored. Here, we propose to investigate the dynamics and interactions of microbial parasites, including viruses and microbial scavengers, and their potential hosts when exposed to multiple stressors in freshwater systems.

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Project Z-INF

Data management and integration

The Z-INF project represents the backbone for data management and data integration to facilitate collaboration inside RESIST. Data storage and data exchange between RESIST’s individual projects and with external institutions will be coordinated by Z-INF, for which a respective infrastructure will be established. Central data storage facilities will ensure archiving and accessibility of raw and processed data of RESIST. Management of research data for exchange between projects, for publications and future internal and external use will be provided and maintained.

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Proposed Cluster of Excellence REASONS: River ecosystems in the Anthropocene

Rising temperatures, antibiotic residues, droughts and flooding: worldwide, rivers are increasingly under pressure. To prepare them for the challenges of the future, researchers from the proposed Cluster of Excellence REASONS are developing a new, sustainable concept for the management of freshwater ecosystems.

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Selected Publications

  • Valentin-Alvarado, Luis E.; Fakra, Sirine C.; Probst, Alexander J.; Giska, Jonathan R.; Jaffe, Alexander L.; Oltrogge, Luke M.; West-Roberts, Jacob; Rowland, Joel; Manga, Michael; Savage, David F.; Greening, Chris; Baker, Brett J.; Banfield, Jillian F.
    Autotrophic biofilms sustained by deeply sourced groundwater host diverse bacteria implicated in sulfur and hydrogen metabolism
    In: Microbiome Vol. 12 (2024) Nr. 1, 15
  • 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
  • Lee, Kang Soo; Landry, Zachary; Athar, Awais; Alcolombri, Uria; Pramoj Na Ayutthaya, Pratchaya; Berry, David; de Bettignies, Philippe; Cheng, Ji-Xin; Csucs, Gabor; Cui, Li; Deckert, Volker; Dieing, Thomas; Dionne, Jennifer; Doskocil, Ondrej; D’Souza, Glen; García-Timermans, Cristina; Gierlinger, Notburga; Goda, Keisuke; Hatzenpichler, Roland; Henshaw, Richard J.; Huang, Wei E.; Iermak, Ievgeniia; Ivleva, Natalia P.; Kneipp, Janina; Kubryk, Patrick; Küsel, Kirsten; Lee, Tae Kwon; Lee, Sung Sik; Ma, Bo; Martínez-Pérez, Clara; Matousek, Pavel; Meckenstock, Rainer; Min, Wei; Mojzeš, Peter; Müller, Oliver; Kumar, Naresh; Nielsen, Per Halkjær; Notingher, Ioan; Palatinszky, Márton; Pereira, Fátima C.; Pezzotti, Giuseppe; Pilat, Zdenek; Plesinger, Filip; Popp, Jürgen; Probst, Alexander J.; Riva, Alessandra; Saleh, Amr. A. E.; Samek, Ota; Sapers, Haley M.; Schubert, Olga T.; Stubbusch, Astrid K. M.; Tadesse, Loza F.; Taylor, Gordon T.; Wagner, Michael; Wang, Jing; Yin, Huabing; Yue, Yang; Zenobi, Renato; Zini, Jacopo; Sarkans, Ugis; Stocker, Roman
    MicrobioRaman : an open-access web repository for microbiological Raman spectroscopy data
    In: Nature Microbiology (2024) Nr. 9, pp. 1152 - 1156
  • Turzynski, Victoria; Griesdorn, Lea; Moraru, Cristina; Soares, André; Simon, Sophie A.; Stach, Tom L.; Rahlff, Janina; Esser, Sarah P.; Probst, Alexander J.
    Virus-Host Dynamics in Archaeal Groundwater Biofilms and the Associated Bacterial Community Composition
    In: Viruses Vol. 15 (2023) Nr. 4, 910
  • Esser, Sarah P.; Rahlff, Janina; Zhao, Weishu; Predl, Michael; Plewka, Julia; Sures, Katharina; Wimmer, Franziska; Lee, Janey; Adam, Panagiotis; McGonigle, Julia; Turzynski, Victoria; Banas, Indra; Schwank, Katrin; Krupovic, Mart; Bornemann, Till L. V.; Figueroa-Gonzalez, Perla Abigail; Jarett, Jessica; Rattei, Thomas; Amano, Yuki; Blaby, Ian K.; Cheng, Jan-Fang; Brazelton, William J.; Beisel, Chase L.; Woyke, Tanja; Zhang, Ying; Probst, Alexander J.
    A predicted CRISPR-mediated symbiosis between uncultivated archaea
    In: Nature Microbiology Vol. 8 (2023) Nr. 9, pp. 1619 - 1633