PhD Position in Geomicrobiology: Modern and Microbial Drivers of Biogeochemica

PhD Position in Tropical Geomicrobiology:
Modern and Ancient Microbial Drivers of Biogeochemical Cycling

We seek a highly motivated PhD student for a multidisciplinary project across two groups: (i) The Sustainable Agroecosystems (SAE) group in the Department of Environmental Systems Science at ETHZ is dedicated to bringing healthy food from fields to tables around the world for generations to come. (ii) The Surface Earth Evolution (SEE) group in the Department of Earth and Planetary Sciences at ETHZ is committed to investigating the processes that drive global climate change over human to geologic timescales.

Combined, our work intersects traditional Earth‑ and environmental‑science fields to holistically study the drivers and impacts of changing climate and land use. We effectively integrate field‑based sample collection and monitoring with lab‑based biogeochemical measurements.

This position is part of the SNSF‑funded project “Constraining tropical wetland greenhouse gas production today and through time: insights from Tumba‑Ngiri‑Maindombe, Democratic Republic of Congo (Lac Mai)”, which aims to mechanistically constrain the climatic and anthropogenic controls on greenhouse‑gas (i.e., carbon dioxide, methane, and nitrous oxide) emissions in Tumba‑Ngiri‑Maindombe, a severely understudied region that houses the world’s largest tropical wetland. To do so, we will sample greenhouse gases, peatland soils, and lake sediments, and we will analyse these using isotopes, biomarkers, and DNA‑based methods.

This PhD student will lead the microbial component of this interdisciplinary project. Using state‑of‑the‑art molecular techniques, you will identify the microbial drivers and metabolic capacity in tropical lake sediments and reconstruct how they have evolved in response to climatic shifts over the past 12,000 years (i.e., the Holocene).

• Perform fieldwork:
  Participate in sampling expeditions to DR Congo to collect high‑resolution, pristine sediment records from Lake Mai Ndombe and surrounding peatlands, ensuring appropriate preservation for molecular and biological analyses
• Contemporary microbial profiling:
  Perform DNA extraction, qPCR, and ribosomal metabarcoding on surface sediments. Quantify key functional marker genes (e.g. mcrA, pmoA, nosZ) and identify extant microbial drivers of modern carbon and nitrogen cycles
• Ancient DNA analysis:
  Execute specialized DNA extraction from deep sediment cores under rigorous contamination controls. Utilize shotgun metagenomics to reconstruct the structural and functional adaptation of microbial communities to paleo‑environmental shifts
• Integrative bioinformatics:
  Process complex sequencing datasets using advanced computational pipelines. Perform taxonomic profiling and metabolic reconstruction to link microbial drivers with shifting environmental parameters from sediment records
• Communicate findings:
  Attend international conferences and workshops and write scientific papers

This position is integral to the research team, which includes 2 PhD students, 2 senior scientists and several technicians across two research groups. You will therefore lead these tasks but will be supported by all involved researchers. This multidisciplinary team offers the opportunity to learn, develop, and apply scientific skills beyond traditional geomicrobiology!

• Education:
  
  MSc degree in (geo) microbiology, molecular ecology, or a related field
• Wet‑lab experience:
  Solid experience in molecular biology techniques (e.g. DNA extraction, PCR and qPCR, sequencing library preparation). Prior experience working in an ancient DNA facility or a similarly controlled “clean lab” is a strong asset
• Computational skills:
  Experience with analysing amplicon and metagenomic data is highly desirable
• Remote fieldwork:
  Willingness to conduct fieldwork in a remote tropical environment
• Communication:
  Proficiency in written and spoken English and ability to communicate in a cross‑cultural environment
• Knowledge of French is a plus (for fieldwork)
• Personal attributes:
  Ability to work independently with flexibility, critical thinking, and a willingness to learn new skills!

• A fully funded…