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

© UDE/Juila 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 & Biodiversität project will link artificial intelligence (AI) alghorithms 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 pathogenicty potential of the microbial community.

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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

[27-07-2023] A new study in Nature Microbiology uncovers an unexpected role of CRISPR–Cas systems in archaea, showing that these defense mechanisms can target chromosomal DNA of their own episymbionts. Using meta-omics from extreme environments, researchers found that widespread DPANN archaea use CRISPR to regulate essential genes in their symbiotic partners, suggesting a dynamic relationship that shifts between parasitism and mutualism. This discovery reshapes our understanding of host-symbiont interactions in microbial ecosystems

Esser SP et al. 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

© RESIST

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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© RESIST

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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© REASONS

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

  • 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; et al.
    MicrobioRaman : an open-access web repository for microbiological Raman spectroscopy data
    In: Nature Microbiology (2024) Nr. 9, pp. 1152 - 1156
  • 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
  • Figueroa-Gonzalez, Perla Abigail; Bornemann, Till L. V.; Hinzke, Tjorven; Maaß, Sandra; Trautwein-Schult, Anke; Starke, Joern; Moore, Carrie J.; Esser, Sarah P.; Plewka, Julia; Hesse, Tobias; Schmidt, Torsten C.; Schreiber, Ulrich; Bor, Batbileg; Becher, D et al.
    Metaproteogenomics resolution of a high-CO₂ aquifer community reveals a complex cellular adaptation of groundwater Gracilibacteria to a host-dependent lifestyle
    In: Microbiome Vol. 12 (2024) Nr. 1, 194
  • Lezcano, María Ángeles; Bornemann, Till; Sánchez-García, Laura; Carrizo, Daniel; Adam, Panagiotis; Esser, Sarah P.; Cabrol, Nathalie A.; Probst, Alexander J.; Parro, Víctor.
    Hyperexpansion of genetic diversity and metabolic capacity of extremophilic bacteria and archaea in ancient Andean lake sediments
    In: Microbiome Vol. 12 (2024) Nr. 1, 176