Doctoral Position in Groundwater Microbial and Viral Ecology and Environmental Bioinformatics

ETH Zurich; Zürich; On-site; CHF 60,000 - 75,000; Full time

Benefits offered by this job

Fully funded PhD position

Job summary

ETH Zurich's Geomitigation of Greenhouse Gases group invites applications for a fully funded 4-year Doctoral position combining groundwater microbial and viral ecology with environmental bioinformatics. You will analyze omics datasets and integrate them with hydrogeochemistry to understand carbon cycling in groundwater.

We seek a curious, independent researcher with MSc in a relevant field, experience in metagenomics, Linux, and programming (Python/R/Bash), and excellent English.

Qualifications

• MSc in microbiology, microbial ecology, bioinformatics, computational biology, geobiology, or closely related discipline.
• Experience with metagenomic data analysis or related environmental bioinformatics approaches.
• Experience with Linux/Unix command-line environments and computational biology workflows.
• Experience with Python, R or Bash.
• Strong understanding of microbial ecology, physiology, and/or metabolism.
• Excellent analytical and problem-solving skills with complex datasets.
• Creativity and motivation to explore new questions and computational approaches.
• Ability to work independently and in a collaborative team.
• Excellent spoken and written English.

Responsibilities

• Analyze large-scale environmental metagenomic, metatranscriptomic, and viral sequencing datasets to investigate microbial and viral diversity, activity, and function.
• Characterize microbial metabolic potential and activity, focusing on carbon cycling pathways and environmental responses.
• 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 understand biological processes influencing subsurface carbon cycling.
• Perform DNA and RNA extractions from environmental samples and contribute to lab analyses, including 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, and other group members in a supportive research environment.

Skills

Linux/Unix

Python

R

Bash

Analytical skills

Independent work

English

Education

MSc in microbiology

Job description

Doctoral Position in Groundwater Microbial and Viral Ecology and Environmental Bioinformatics

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.

Project background

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.

In this project, you will investigate microbial and viral diversity, metabolic activity, and evolutionary adaptation across groundwater age gradients. By combining metagenomics, metatranscriptomics, and viral metagenomics with hydrogeochemical measurements, you will explore how microbial metabolism and virus-host interactions influence carbon cycling in the subsurface.

• 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

Profile

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 genome‑resolved metagenomics, metatranscriptomics, comparative genomics, or high‑performance computing is particularly advantageous. Previous experience with DNA and/or RNA extraction from environmental samples is also desirable. A background in groundwater microbiology, environmental geochemistry, or biogeochemical cycling is beneficial but not required.

Workplace

We offer

• A collaborative research environment: You will join an enthusiastic, inclusive, and highly collaborative research group where high quality research, open discussion, and creative scientific thinking are strongly valued. You will benefit from a dynamic departmental setting with broad expertise, excellent research infrastructure, and opportunities for interdisciplinary exchange
• Mentorship and career development: You will receive direct mentorship from the PI and specialized guidance in environmental bioinformatics, microbial ecology, and viral ecology from the project's scientific partner,
• Mentorship and career development: You will participate in the broader academic community through publications and presentations at scientific conferences
• Mentorship and career development:Additional development opportunities are available through teaching assistantships, ETH doctoral courses, and transferable‑skills training
• Access to extensive multi‑omics datasets and computational resources: You will work with large-scale groundwater metagenomic, metatranscriptomic, and viral sequencing datasets and you will have access to ETH Zürich's computational infrastructure and resources for environmental bioinformatics, providing opportunities to develop and apply advanced computational approaches to important questions in microbial ecology and biogeochemistry
• A supportive and inclusive workspace: We are committed to creating a respectful, inclusive, and constructive working environment
• A supportive and inclusive workspace:Flexible working arrangements can be discussed where compatible with laboratory and project responsibilities
• Employment conditions and benefits: We offer a fully funded 48-month Doctoral Position, with that, you can expect numerous benefits, such as public transport season tickets and car sharing, a wide range of sports offered by the ASVZ, childcare, and attractive pension benefits

In line with our values , ETH Zurich encourages an inclusive culture. We promote equality of opportunity, value diversity and nurture a working and learning environment in which the rights and dignity of all our staff and students are respected. Visit our Equal Opportunities and Diversity website to find out how we ensure a fair and open environment that allows everyone to grow and flourish. Sustainability is a core value for us – we are consistently working towards a climate‑neutral future .

Further information about the Geological Institute can be found on our Website . Questions regarding the position should be directed to Prof. Nicole Fernandez-Franzan, [e-mail] (no applications).

We will get in touch with you after 2 - 3 weeks following the submission deadline.

The position is fully funded for 4 years, with an expected start date of 1 March 2027.

ETH Zurich is one of the world’s leading universities specialising inscience and technology. We are renowned for our excellent education,cutting‑edge fundamental research and direct transfer of new knowledge into society. Over 30,000 people from more than 120 countries find ouruniversity to be a place that promotes independent thinking and anenvironment that inspires excellence. Located in the heart of Europe,yet forging connections all over the world, we work together todevelop solutions for the global challenges of today and tomorrow.