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/Julian Künkel

Probst Lab Goes International (USA) UDE Team Visits LBNL for Genial Project

[02-06-2025] As part of the Genial project, our team members Indra and Julian from UDE arrived at the Lawrence Berkeley National Laboratory to begin work using their advanced light source facilities. The visit focuses on conducting SR-FTIR on the first batch of algal samples obtained from the Central Collection of Algal Cultures (CCAC) at UDE.

We're excited to kick off this phase of the project and look forward to the insights this collaboration will bring!

© UDE/Alex Probst

Probst Lab Goes International (Japan) Strengthening International Collaboration: UDE Delegation Visits Japan

[05.06.2025] A delegation from the University of Duisburg-Essen, including representatives from ACTIVE SITES, the UA Ruhr Research Center One Health, and ZWU, spent the past week in Japan to renew and establish new research collaborations. Alex represented our group as a member of all three consortia, alongside colleagues from the CENIDE consortium.

The visit featured a joint symposium with the University of Tsukuba, a collaborative workshop at RIKEN, and a visit to the National Institute of Advanced Industrial Science and Technology (AIST). This productive trip has opened up exciting new avenues for future collaboration, and we are now moving forward with planning the next steps.

Regional Research Promotion WAFL Project Presented at DBU Conference in Osnabrück

[11-06-2025] Linda, the DBU fellow in our lab, presented a poster on her research as part of the WAFL project at the recent DBU conference held in Osnabrück on Wednesday.

The WAFL project is a collaborative effort involving R. Schmitthausen (University Hospital Essen) and M. Savin-Hoffmeyer (University Hospital Bonn). We're proud to see Linda representing the project and contributing to the ongoing dialogue on sustainability-focused research!

© UKE/Deep

A new Dr. rer. nat. emerges Lennard Successfully Defends his PhD Thesis

[16.07.2025] We warmly congratulate Lennard on the successful defense of his PhD thesis titled:
"Structural and Functional Response of Stream Microbiomes to Multiple Anthropogenic Stressors."

His work was conducted as part of the first phase of CRC-RESIST and supported by a prestigious fellowship from the Studienstiftung des deutschen Volkes.

We will miss having Lennard in the lab and wish him all the very best for the next chapter of his career!

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.

Read more

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
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

  • 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
  • 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
  • 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
  • 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
  • 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