Plant Biogeochemistry

Concept of Plant Biogeochemistry

Welcome to the Plant Biogeochemistry Lab!

Our research broadly focuses on the interplay of roots with soil minerals and microorganisms and what impact that has on the environment, food production, soil quality or the global carbon cycle. If these topics interest you, contact me!



October 2021

In October Jenin Fleischman has started her bachelor project in our group. Jenin will be investigating soil microbiome adaptation to heavy metal contamination under different farming practices. Welcome Jenin!


October 2021

Find out what are the threats to future rice production from a new ScienceNews article featuring the work of E. Marie Muehe.


October 2021

We warmly welcome Tianyu Wang as a new PhD student in our group! Tianyu will work on climate and Cd/As impacts on greenhouse gas emissions from paddy soils.


Dr. E. Marie Muehe


Dr. Carolina Vergara Cid (based at UFZ Leipzig)


Paul Richter (based at UFZ Leipzig)

Current PhD Students:

Soeren Drabesch (based at the University of Tuebingen)

Aleksandra Pienkowska (based at the UFZ Leipzig)

Natalia Sánchez (based at the UFZ Leipzig)

Tianyu Wang (based at the UFZ Leipzig)

Co-supervision of PhD Students:

Hanna Joß (co-supervision with Prof. Dr. Andreas Kappler and Prof. Dr. Christiane Zarfl)

Katrin Wunsch (co-supervision with Prof. Dr. Andreas Kappler and Dr. Prachi Joshi)

Current Master Degree Students:

Mara Breit (based at the UFZ, supervised by Marie Muehe)

Esmira Bibaj (based at the University of Tuebingen and UFZ, supervised by Soeren Drabesch)

Vicky Skudlik (based at the University of Tuebingen, supervised by Soeren Drabesch)

Current Undergraduate Students:

Jenin Fleischman (based at the UFZ, supervised by Marie Muehe and Aleksandra Pienkowska)

Current Student Interns:

Current Student Reseach Assistant:

Alexandra Glöckle (based at the University of Tuebingen)

Collaboratively advised Students:

Timm Bayer (PhD student)

Former Students:

Jenin Fleischman (Intern)

Lea Baier (BSc)

Anam Danish (Intern)

Mara Breit (Intern)

Julia Kost (BSc)

Alexandra Glöckle (BSc)

Katja Lenge (BSc and Intern)

Sebastian Müller (BSc)

Our current cultural diversity.

If you are interested in working in my team in form of a thesis or an internship, but are not interested in the following topics, contact me and let us talk. I have a lot of other ideas and am very open to yours!

From left to right: Severy of soil degradation modified from EU-JRC 2010, wheat yields in Europe modified from FAOSTAT 2017, Global Change Experimental Research Station at the UFZ.

Two of the greatest threats to future agricultural productivity and sustainability are a changing climate and increasing levels of soil contaminants such as cadmium, lead, zinc and copper. So far, our understanding of how climate affects metal mobility in rhizospheres and its direct translation to plant performance is rudimentary at best. The project will investigate how climate affects the bioavailability of multiple metals in agriculutral soils and their transport within the rhizospheres of four model plants: Arabidopsis thaliana, wheat, barley and Arabidopsis halleri; the latter being a metal-hyperaccumulating plant commonly used for phytoremediation. Metal-hyperaccumulating and non-metal-accumulating plants differ profoundly in their physiology and interaction strategies with the environment. We will elucidate how each model plant's root system interacts with soil microbial communities and minerals responding to imposed climatic and soil contamination stresses. Root physiological analysis will be combined with sophisticated soil microbiome sequencing, and further linked to shifts in soil geochemistry and mineralogy using synchrotron-based X-ray absorption spectroscopy. The overarching goal of the research group is to develop a mechanistic understanding of how climate affects contaminant transport from soil to root, in hopes of improving microscale, biogeochemical functioning within the rhizospehre that ultimately impacts macroscale plant performance, including crop productivity or phytoremediation efficiency.

This project is funded by the Young Investigator Programme of the Helmholtz Association and the Centre for Environmental Research.

Greenhouse Gas Emission from Agricultural Soils

Almost five percent of global anthropogenically derived greenhouse gas emissions originate form agricultural practices. With methane being 25 times more potent than carbon dioxide and nitrous oxide being 265 times more potent, their fate needs to be better understood. Greenhouse gases are microbially produced and consumed in the soil. The interplay and balance of these microorganisms explicitly determines whether or not greenhouse gases are released from the soil into the atmosphere. The presence, abundance, diversity and activity of the microbial community in the soil is easily altered by soil contamination including arsenic, cadmium and other heavy metals. For example for arsenic we have shown that its bioavailability and redox speciation is tightly linked to climate change. Thus, it is important to understand whether and to what extent greenhouse gas emissions from different agriculturlal fields will be altered in the future with increasing soil metal concentrations.

We have currently two ongoing projects under this theme:

  • In collaboration with the Fendorf lab at Stanford University, we investigate whether the emission of greenhouse gases from paddy soils is affected by coupled climate and soil arsenic stress. This project was funded by the Marie Sklodowska Curie Action of the European Union in form of an individual Postdoc scholarship. We are looking for a motivated Bachelor student to do a thesis in this project. Optimal expertise in geochemistry/geoecology/environmental science.

  • In collaboration with the Kappler lab at the University of Tuebingen, we elucidate how climate impacts the behaviour of cadmium in agricultural soils and how that impacts greenhouse gas emissions. This project is funded by the Elite Programme of the Baden-Württemberg Stiftung. The responsible PhD is Sören Drabesch. We are looking for MSc and BSc students interested in working on this project.

Arsenic Rice
Images taken from Muehe et al., 2019.

As rice sustains more than half of the global population, its production needs to increase to meet future demands of a growing population. Of most concern to rice production are a changing climate and increasing levels of toxic arsenic in paddy soils. In a recent study we showed that the combined threat of climate change and soil arsenic will increase arsenic bioavailability in the soil, and subsequently decrease rice productivity and increase grain arsenic levels more than currently anticipated. Soil microbial communities are responsible drivers for shifts in arsenic bioavailability in the rhizosphere and, thus, are directly influenced by soil arsenic levels, climate and the plant itself.

In collaboration with the Fendorf Lab at Stanford University, we will investigate how differences in soil arsenic, climate and plant performance cause shifts in plant communication with the rhizosphere microbiome. Using molecular tools, differences in the trancription of genes within rice's roots will be linked to soil microbial community dynamics, identifying microbial key players.

We are looking for a motivated MSc student to investigate how rice roots transcriptionally respond to the coupled threats of climate and soil arsenic and how the rhizobiome adapts to root activity. Optimal expertise in Molecular Biology and/or Microbial Ecology.

This project was funded by the German Research Foundation and the Marie Sklodowska Curie Action of the European Union in form of individual Postdoc scholarships. 

We offer expertise in:

  • Field campaigns
  • Complex plant-growth and soil incubation experiments in greenhouses and labs

Our soil lab offers the following equipment:
  • Mars6 CEM Microwave digester for plant and soil samples, 40 sample slots
  • Large scale presens imaging optodes for CO2, O2 and pH
  • MicroResp system (11 parallel set-ups)
  • Multi-gas dispenser for anoxic work
  • pH, electrical conductivity, DO, redox electrodes for field and lab
  • Shakers, scales, water baths, stir plates, vortexers, centrifuges, autoclave, microwave, fridges and freezers for soil storage

Our approaches in Plant Science include:
  • Plant material digestions for metal content quantifications
  • Biomass assessments
  • Transcriptomics of plant tissues
  • Photometric-based enzymatics
  • Synchrotron based imaging of metals and other elements across plant tissues

Our approaches in Microbial Ecology include:
  • Enrichment and isolation of microorganisms from environmental samples
  • Cultivation of microbial communities
  • Respiration assessments
  • 16S rRNA and functional gene and transcript sequencing and qPCR
  • Metabolomics

Our approaches in Soil Geochemistry and Mineralogy include:
  • Standard soil geochemical analysis (GC, DOC, HPLC, etc.)
  • Soil extractions (aqua regia, metal and nutrient bioavailability assessments)
  • Standard mineralogical tools (XRD, XRF, etc.)
  • Planar optodes (Presens)
  • Synchrotron based mineralogical analysis (XANES, EXAFS, elemental mapping) 
Bachelor Theses:
  • Julia Kost: DNA/RNA Stability in Environmental Samples. 2021
  • Alexandra Glöckle: Effect of cadmium on (a)biotic greenhouse gas emissions in agricultural soil. 2020
  • Katja Lenge: Long term effect of cadmium contamination and climatic stress on soil microorganisms and greenhouse gas emissions. 2020
  • Sebastian Müller: Cadmium stress combined with elevated temperature will increase greenhouse gas emissions more than elevated carbon dioxide combined with or without cadmium. 2020

Teaching will be offered through the Geoscience Department of the University of Tuebingen.

  • 1 week field trip Bioremediation to Saxony. Summer Semester 2022
  • Lecture and associated lab course on Rhizosphere Processes in a Changing World. Winter Semester 2022/23