News
Hunting microbes in peat bogs
Environmental Microbiology PhD students, Madison Barney and Wiebke Wilhelm, were recently featured in an ETH Globe article highlighting our research about microbial communities in peatlands! Check out the article on page 40 where we discuss land use, microbes, and climate changes in the Entlebuch Biosphere Reserve.
Team Event
D-USYS Conference
New preprint from the lab
We are delighted to present our new preprint titled: "Conserved multi-heme cytochrome machinery for extracellular electron transfer is widespread and transcriptionally active across deep peat profiles"
This study investigates how microorganisms in northern peatlands may use particulate organic matter as an extracellular electron acceptor, revealing diverse and transcriptionally active electron transfer systems in uncultured peat microbes.
These findings provide the first systematic genomic and transcriptional framework for EET-based respiration in peatlands, with implications for how we model methane emissions from one of Earth's largest carbon stores.
A great collaborative effort combining metagenomics, metatranscriptomics and environmental microbiology across Swedish bog ecosystems.
Read the full preprint external page here.
28.05.2026
New preprint released
We are pleased to share our new preprint: "Active microbial communities and their extrachromosomal elements link organic matter degradation to methane cycling in anoxic sediments"
Freshwater sediments are major methane sources. But which microorganisms and metabolisms drive this process?
We combined metagenomics with the first metatranscriptomic dataset from the anoxic sediments of meromictic Lake Cadagno to find out.
This work established a link between complex polysaccharide breakdown, fermentation, methanogenesis, and anaerobic methane oxidation within 56 cm of anoxic lake sediment.
Read the full preprint external page here.
13.04.2026
The Group welcomes Emilie Skoog as Postdoctoral Fellow
We are very happy to officially welcome our new Postdoctoral Fellow, Dr. Emilie Skoog, who has been selected as part of the 2026 cohort of NOMIS-ETH Fellows!
In our group, Emilie will explore how viruses associated with methanogens and acetogens can provide clues about the environmental conditions that supported early life.
We are excited to work with Emilie over the next four years - congratulations on this achievement and welcome to the lab!
Learn more about the NOMIS-ETH Fellows and hear more about Emilie and her research here.
01.04.2026
News article in “Mein Entlebuch 2026”
Our research was featured in a news article in the UNESCO bioshere Entlebuch magazine “mein Entlebuch 2026”, authored by our collaborator Florian Knaus.
The news article highlights Madison Barneys project on swiss peatlands.
NCCR Genesis
Our Environmental Microbiology group is proud to be part of the newly approved NCCR Genesis, which will investigate how life emerges from inanimate matter through interdisciplinary research spanning astrophysics, chemistry, and planetary sciences.
30.01.2026
Guest researcher Dr. Emilie Skoog starts in the Envrionmental Microbiology Group
We are pleased to welcome Emilie Skoog to the group.
Emilie studies microbial communities and their viruses in extreme environments, combining computational analyses and laboratory experiments to understand how microbes and viruses interact, adapt, and evolve. Her research explores how factors such as salinity, pH, and ionic stress shape viral strategies and how these processes in turn influence microbial community structure, adaptation, and evolution over time.
01.12.2025
New Publication on Borgs
A new Publication on Borgs with Marie as co-author has been published in Nature Communications. Have a read external page here.
04.12.2025
COPL seminar talk by Marie
In the COPL lunch seminar, Marie unveils how ancient microbes using the Wood–Ljungdahl pathway survive extreme energy limitation, revealing the genomic tricks that may have helped life’s earliest ancestors thrive.
Marie gave a talk in the Center for the Origin and Prevalence of Life (COPL) lunch seminar series. She discussed the ancient Wood-Ljungdahl pathway which was likely present in LUCA and is still employed by strictly anaerobic microorganisms, such as acetogenic bacteria and methanogenic archaea. She then presented how the group investigates these organisms in both natural environments and in the laboratory, highlighting their adapatations to extreme energy limitation and the genomic innovations that may help enable them to thrive.
01.12.2025
The Environmental Microbiology Group is Celebrating
All Our PhD Students Passed the Aptitude Colloquium!
We’re thrilled to share that every one of our PhD students has successfully passed their Aptitude Colloquium! Their hard work, curiosity, and dedication have truly paid off. After Donat Crippa, Sebastian Haiß and Giulia Fiorito, Madison Barney impressed with her thoughtful research ideas and confident presentation. A huge congratulations to all our PhD students. We are so proud of you and can’t wait to see where your research takes you next!
05.11.2025
Dr. Akshay Joshi joins the Environmental Microbiology Group
We are delighted to welcome Dr. Akshay Joshi to the Environmental Microbiology Group as a Postdoctoral Researcher.
Originally from Pune, India, Dr. Joshi earned his Bachelor’s and Master’s degrees in Microbiology from the University of Pune. In 2019, he moved to Switzerland to pursue a Ph.D. at the Zurich University of Applied Sciences (ZHAW), in collaboration with the University of Innsbruck (UIBK), under the supervision of Prof. Heribert Insam (UIBK) and Prof. Urs Baier (ZHAW). His doctoral research focused on “Unveiling the Potential of Anaerobic Fungi with Syntrophic Microbes for Fiber Degradation.”
In 2024, Dr. Joshi joined the University of California, Davis, as a Postdoctoral Researcher in the Department of Animal Science with Prof. Matthias Hess, where he investigated rumen microbial communities and developed CRISPR-Cas9 genome editing tools for methane mitigation.
At the Environmental Microbiology Group, Dr. Joshi will focus on the genetic engineering of methanogens to advance methane mitigation strategies.
03.11.2025
New Students joined the Environmental Microbiology Group
The group warmly welcomes Annina Kündig, Audrey Pohlman and Sibylle Vautravers
Annina Kündig is a master student in Environmental Systems Science.
For her master thesis she will be exploring how multiple climate change
perturbations will affect microbial communities and associated
biogeochemistry of peatlands in Entlebuch together with Madison Barney.
Audrey Pohlman is a master student in biochemistry. She is working on
recombinantly expressing and characterizing tandem repeat proteins in
Methanosarcina species to gain insights into their localization,
interactions, and possible functions in methanogen cell biology. For her
semester project she is working with Sebastian Haiß.
Sibylle Vautravers is a master student in Environmental Systems
Science. She works on illuminating the function of extrachromosomal DNA
elements (ecDNA) elements in isolated acetogenic bacteria in ourgGroup.
For her master thesis she is working with Donat Crippa.
27.10.2025
New group publication: Microbe of the Month - Candidatus Methanoperedens
We contributed to Trends in Microbiology's Microbe of the Month, summarizing key insights on Candidatus Methanoperedens.
Our group contributed to the 'Microbe of the Month' series of the Trends in Microbiology journal, summarizing essential information and recent findings on the anaerobic methane-oxidizing archaeon Candidatus Methanoperedens. Find the publication by Dr. Hanna Zehnle and Prof. Marie Schölmerich external page here.
04.03.2025
New Group Members
The Environmental Microbiology Group welcomes three new colleagues.
Our Group is growing. We are happy to welcome two new Postdocs, Dr. Bledina Dede and Dr. Jo Herbert, and the master student student Loïc Imsand.
Dr. Jo Herbert will be working on a number of projects but primarily bringing ONT sequencing to the group for long-read investigation of single-genome cultures and metagenomic samples and their extrachromosomal elements and methylation patterns.
Dr. Bledina Dede will explore the ecology and global distribution of mobile genetic elements, with a particular emphasis on carbon fixation and methane cycle.
Loïc Imsand is doing his master thesis in our Group. He will be working together with Giulia Fiorito on enrichments of peat microbes from northern peatlands.
24.02.2025
Marie Schölmerich receives funding from the Messerli Foundation
For researching Swiss peatlands Marie Schölmerich, group leader of the
Environmental Microbiology group, receives funding from the Messerli
Foundation.
Madison Barney PhD student in the Environmental Microbiology group
(pictured) will be leading the research project focused on illuminating
microbial communities and greenhouse gas emissions in peatlands in the
UNESCO Biosphere Entlebuch, Switzerland.
13.01.2025
2024
Visit from Dr. Astrid von Mentzer
Dr. Astrid von Mentzer from the Department of Microbiology and
Immunology at University of Gothenburg visited the Environmental
Microbiology Group.
On Monday and today Dr. Astrid von Mentzer visited Zürich. She met with members from the Environmental Microbiology Group and gave a talk on "Tracing the Evolutionary Pathways of Colonisation Factors in E. coli" at the IBP Seminar. The visit was rounded off with a delicious dinner.
03.12.2024
Marie Schölmerich receives SNSF Starting Grant
Marie Schölmerich, group leader of the Environmental Microbiology group successfully applied for a Starting Grant from the Swiss National Science Foundation.
Congratulations to Marie for being awarded the SNSF Starting Grant! The project "New Drivers of Microbial Methane Cycling" will investigate newly discovered genetic elements found in or associated with methanogenic archaea. We will investigate these in the lab and in peatlands undergoing restoration. Read more news about it here:
News from ETH
News from COPL
21.11.2024
New Students in Environmental Microbiology
We welcome Anna Beretta, Leona Tauchmann and Joaquim Barmaz.
We warmly welcome three new students to the Environmental Microbiology Group.
Anna Beretta has started her bachelor thesis. She's examining methanogenic archaea that can form aggregates, and is investigating which environmental factors trigger this aggregation.
Joaquim Barmaz is doing a three month semester project. He's working on prophages in acetogenic bacteria and wants to find out under which conditions these prophages are expressed an if they can be induced in the lab.
Leona Tauchmann started her master thesis in Environmental Microbiology. She studies the acetogen Moorella thermoacetica and wants to find out if it reduces selenite. The goal is to investigate the molecular principles and provide a foundation for developing bioremediation strategies utilizing acetogens.
30.09.2024
New Group Member in Environmental Biology Group
Welcome to the group Madison Barney!
Madison completed her master’s at the University of Oregon where she examined the anaerobic oxidation of methane in peatlands, before she worked as a lab manager at Boston University for a year.
In our group she will examine the impact of climate change on microbial communities in peatlands. We are excited to welcome Madison to the group.
01.08.2024
Fieldcourse at Lago di Cadagno
Educational week in Ticino - Biogeochemistry of Alpine Habitats
Last week some members of our group accompanied the "Biogeochemistry of Alpine Habitats" field course lead by Prof. Martin Schroth. The 1-week course takes place every year in the Lago di Cadagno area located in the beautiful Piora valley in Ticino, Switzerland. Students of different levels participated, and our group offered our own section of the course for the first time, which focused on investigating methane-cycling microorganisms in two wetland areas close to the lake. Together with the students we took soil samples and collected geochemical data from different sites within the wetlands. Afterwards, the students extracted DNA from the soil samples and ran PCRs to look for specific microbes. The week was rounded up with an alpine excursion to the Lago di Tom and a climb to a nearby mountain ridge, and a botanical excursion during which we learned about the alpine flora.
22.07.2024
New Lab Manager in Environmental Biology Group
We welcome Lukas Wanner, our new Lab Manager
Lukas will support us in the management of the
laboratory, in the execution of experiments and during field trips. He
will also be assisting in the maintenance of our digital
infrastructures. As our Biosafety Officer he will be responsible for
health and safety in the lab. Welcome to the team Lukas
01.07.2024
Field Trip to Sweden
Sample collection in peatlands
Last week some members of our group went on an exciting field trip to Swedish peatlands. PhD students Giulia Fiorito and Donat Crippa, along with Prof. Dr. Marie Schoelmerich, explored these unique ecosystems and collected many important samples for their research. They were accompanied by Prof. Dr. Martin Schroth and Prof. Dr. Michael Sander from the Environmental Chemistry group.
24.06.2024
IBP Research Fair 2024
The Environmental Microbiology Group presented their Research Projects at the IBP Research Fair. Find them among all the projects of the other groups here.
31.05.2024
Inaugural Lecture Prof. Dr. Marie Schölmerich
Microbial contributions to climate change
22.05.2024
Introduction Video Marie Schölmerich
Marie Schölmerich has been an Assistant Professor of
Environmental Microbiology (Tenure Track) at the Institute of
Biogeochemistry and Pollutant Dynamics at ETH Zurich since August 2023.
Marie deals with biochemical and bioenergetic questions relating to anaerobic bacteria that use ancient metabolic pathways. The main research focus of her group will be on anaerobic microorganisms which play a key role in the CO2 and CH4 cycle.
Marie Schölmerich was a junior group leader at Hamburg University, Germany, and later went on to become a Postdoctoral Fellow at UC Berkeley, USA. Her appointment will ideally complement interdisciplinary research within the department, as well as strengthen links with the Department of Biology and the Department of Health Sciences and Technology. Welcome, Marie!
16.01.2024
Welcome to IBP, Assistant Prof. Marie Schölmerich
We are delighted to introduce Marie Schölmerich as our new Assistant Professor of Environmental Microbiology.
Prof. Dr. Marie Schölmerich was appointed as Tenure Track Assistant Professor of Environmental Microbiology in the Department of Environmental Systems Science. Her lab at ETH will use metagenomics and biochemical approaches to investigate anaerobic microorganisms that employ ancient metabolic pathways and play a key role in the cycling of greenhouse gases. This appointment will ideally complement interdisciplinary research within the Department, as well as strengthening links with the Department of Biology, the Department of Health Sciences and Technology, and Eawag. We wish her a very pleasant start and are happy to welcome her at IBP.
IBP News from 01.08.2023