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
New Publication Alert Need of the Hour: Data Reuse with Recognition
[26.09.2025] Prof. Dr. Alex Probst, together with Dr. André Soares and Dr. Cristina Moraru, has initiated the Data Reuse Core Team to update outdated guidelines on sequencing data reuse. With the rapid growth of sequencing data in recent decades, the need for modern frameworks that ensure transparency and fairness has become increasingly urgent.
To address this, the team proposes a Data Reuse Information (DRI) tag linked to ORCID accounts, highlighting the contributions of data creators. This initiative aims to provide a clear roadmap for data reusers, foster collaborations, and protect early-career researchers.
Welcome to Probst Lab Welcoming Guest Researcher: Iva Vojtkuf
[19.09.2025] We are delighted to welcome Iva Vojtkuf to our lab for a six-month research stay, funded by the Croatian Science Foundation, to advance her PhD studies on microbial biofilms in freshwater karst ecosystems.
Her PhD focuses on understanding how microbial communities influence biogeochemical cycles and extracellular enzyme activity in contrasting environments — the Plitvice Lakes National Park (continental Croatia) and the Krka National Park (Mediterranean Croatia).
Probst Lab @ Conferences Indra Represents the Probst Lab at Microscopy Conference 2025 in Karlsruhe
[01.09.2025] Indra represented the Probst Lab at the Microscopy Conference 2025 held in Karlsruhe, where she presented her recent work in collaboration with partners from Hungary.
In addition to showcasing her research, Indra took the opportunity to exchange ideas and gather inspiration for both ongoing and future microscopy collaborations. We're excited to see how these new connections and insights will shape the next steps in our projects!
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 German National Academic Foundation.
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: 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.
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 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.
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.
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
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Earth's most needed uncultivated aquatic prokaryotesIn: Water Research, Vol. 273, 2025, 122928DOI (Open Access)
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Metagenomic analysis of pristine oil sheds new light on the global distribution of microbial genetic repertoire in hydrocarbon-associated ecosystemsIn: microLife, Vol. 6, 2025, uqae027DOI, Online Full Text (Open Access)
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A roadmap for equitable reuse of public microbiome dataIn: Nature Microbiology, Vol. 10, 2025, Nr. 10, pp. 2384 – 2395
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Author Correction: A roadmap for equitable reuse of public microbiome dataIn: Nature Microbiology, 2025, in pressDOI (Open Access)
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The journey to understand previously unknown microbial genesIn: Nature, Vol. 626, 2024, Nr. 7998, pp. 267 – 269
