Doctoral Position in Groundwater Microbial and Viral Ecology and Environmental Bioinformatics

100%, Zurich, fixed-term

The Geomitigation of Greenhouse Gases group at ETH Zürich is actively recruiting a highly motivated and curious Doctoral candidate with a strong interest in environmental microbiology, biogeochemical cycling, and bioinformatics. The position is part of a newly funded SNSF interdisciplinary project investigating how microbial and viral communities influence carbon cycling in groundwater systems. The project brings together microbial and viral ecology, environmental genomics, and hydrogeochemistry to better understand how biological processes influence the fate of carbon in the subsurface.

Groundwater represents an important but poorly understood component of the global carbon cycle. While water-rock interactions strongly influence groundwater chemistry, microbial communities actively transform carbon through diverse metabolic pathways, and viruses may further regulate these processes through infection and metabolic reprogramming. However, how microbial and viral communities respond to changes in groundwater age and geochemistry, and how these interactions influence carbon cycling, remains largely unknown.

• Analyze large-scale environmental metagenomic, metatranscriptomic, and viral sequencing datasets to investigate microbial and viral diversity, activity, and function in groundwater systems
• Characterize microbial metabolic potential and activity, with a particular focus on pathways involved in carbon cycling and their responses to environmental conditions
• Investigate microbial and viral community dynamics, virus-host interactions, and evolutionary adaptation across groundwater age and geochemical gradients
• Integrate environmental multi-omics datasets with hydrogeochemical measurements to better understand the biological processes influencing subsurface carbon cycling
• Perform DNA and RNA extractions from environmental samples and contribute to complementary laboratory analyses, including microbial cell abundance and activity measurements using flow cytometry and microscopy
• Synthesize research findings into scientific manuscripts and present results at international conferences and workshops
• Collaborate closely with the Principal Investigator, project partner, another Doctoral student working on groundwater hydrogeochemistry, and other group members while contributing to a supportive and communicative research environment

We are looking for a candidate who is curious, independent, and motivated by questions at the intersection of microbial ecology, evolution, and environmental biogeochemistry. You enjoy working with large biological datasets and are excited about using computational approaches to understand how microorganisms and viruses interact with their environments.

• An MSc degree in microbiology, microbial ecology, bioinformatics, computational biology, geobiology, or a closely related discipline
• Previous hands‑on experience with metagenomic data analysis or closely related environmental bioinformatics approaches
• Experience working in Linux/Unix command-line environments and familiarity with computational biology workflows
• Experience with at least one programming or scripting language, such as Python, R or Bash
• A strong understanding of microbial ecology, physiology, and/or metabolism
• Excellent analytical and problem‑solving skills, including the ability to work with complex biological datasets
• Creativity, curiosity, and motivation to explore new research questions and computational approaches
• Ability to work both independently and as part of a collaborative interdisciplinary team
• Excellent spoken and written English
• Experience with…