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 us!



August 2023

We warmly welcome Natascha Kalantar as new intern and master student. She will be involved in the spatial analysis of rhizosphere processes of heavy metal hyperaccumulating plants in agricultural soils under future climatic conditions. 

Karolin Seiferth

August 2023

We warmly welcome Karolin Seiferth as a PhD student in the CLEANER TB4 PhD college. Karolin will study the Plant-microbe interplay influencing urban pollutant transformation in percolation systems.


September 2023

We warmly welcome Ayushi Parmar as an intern for 3 months in our group. Ayushi will be involved in analyzing spinach responses to coupled climate and heavy metal stress.

Head of Workgroup



Paul Richter
(based at the UFZ Leipzig)

Postdoctoral Researcher


Carolina Vergara Cid
(based at the UFZ Leipzig)

Doctoral Candidates


Sören Drabesch
(based at the Univ. of Tübingen)


Marie Mollenkopf
(based at the Univ. of Tübingen)


Aleksandra Pienkowska
(based at the UFZ Leipzig)


Natalia Sánchez
(based at the UFZ Leipzig)


Tianyu Wang
(based at the UFZ Leipzig)

Karolin Seiferth

Karolin Seiferth

(based at the UFZ Leipzig)

Master Degree and Undergraduate Students


Sarah Keldenich

supervised by: Marie Mollenkopf

(based at the University of Tuebingen)


Katja Lenge

supervised by: Marie Mollenkopf

(based at the University of Tuebingen)


Natascha Kalantar

Supervised by: Natalia Sanchez

(based at the UFZ Leipzig)

Student Research Assistant and Interns


Mara Breit
(based at the UFZ Leipzig)

  • Jannis Grafmüller (co-supervised with Prof. Dr. Daniel Kray)
  • Maria Greulich (co-supervised with Dr. Anja Worrich and Prof. Dr. Hauke Harms)
  • Hanna Grimm (co-supervised with Prof. Dr. Andreas Kappler and Prof. Dr. Christiane Zarfl)
  • Gennuo Wang (co-supervised with Dr. Ulisses Nunes da Rocha)
  • Katrin Wunsch (co-supervised with Prof. Dr. Andreas Kappler and Prachi Joshi)


Vicky Skudlik (MS)
Esmira Bibaj (MS)
Jenin Fleischmann (BS and Intern)
Lea Baier (BS)
Anam Danish (Intern)
Mara Breit (Intern)
Julia Kost (BS)
Alexandra Glöckle (BS)
Katja Lenge (BS and Intern)
Sebastian Müller (BSc)
Jennifer Horstmann (intern)
Alexandra Glöckle (MS)
Charlotte Roschke (MS)
Paula Kosel (MS)
Our current cultural diversity.

If you are interested in working in our team in form of a thesis or an internship, but are not interested in the following topics, please contact us. We have a lot of other ideas and are very open to yours!

Wheat and barley are one of the most important crops for global food security and a significant economic sector for the world's leading wheat producers, such as the European Union. Some of the biggest threats to crop production in the future will be a changing climate and increasing levels of contaminants, such as heavy metals, in agricultural soils. While there are reports on the individual effects of these two factors on the quantity and quality of crop yields, it is still largely unknown if and how their combination will affect production in the future. The main research objective of this project is to determine threats to crop production from climate change and metal pollution, and investigate which agricultural practices are most beneficial to minimize potential losses. For this purpose, we make use of UFZ’s own long-term experiments (Global Change Experimental Facility and Static Fertilization Experiment) at Bad Lauchstädt Research Station at which crops are cultivated under various climatic conditions, soil contamination regimes and farming practices and compare crop yield quantity and quality with regard to metal and nutrient accumulation. To reveal the processes responsible for final crop yield, we collect rhizosphere samples during growth and analyzed geochemically (soil properties, metal bioavailability, metal binding sites in soil) and microbiologically (abundance, diversity, taxonomy, functionality) to indicate the processes which drive metal distribution from soil to crop.

People involved:
Aleksandra Pienkowska, Alexandra Glöckle

This project is part of the Young Investigator Grant RhizoThreats: Rhizospheres under Attack from Coupled Climate and Soil Contaminant Stress, which is funded by the Helmholtz Association and the Centre for Environmental Research.

Map of European wheat production (left, data from Monfreda et al., 2008) and topsoil cadmium concentration (right, modified after Lado et al., 2008).
Soil sampling (left) and winter wheat (right) at the Global Change Experimental Facility.

Phytoremediation is an environmental sanitation tool that uses the ability of plants to accumulate contaminants, such as heavy metals, ultimately reducing the burden of harmful compounds in soils. We investigate how environmental parameters affect phytoremediation efficacy by studying the metal-hyperaccumulating model plant Arabidopsis halleri. For this purpose, we carry out greenhouse studies with different soils, metal contamination levels, climatic conditions, and plant ecotypes. We assess how this model plant's root system interacts with soil microbial communities and soil geochemistry. The combination of physiological plant responses (root architecture, metal accumulation, enzymes, chlorophyll content), a high-end soil microbial community assessment (omics, enzymatics), and key soil geochemical processes involved in metal availability and nutrient cycling (extractions, isotope pool dilution assays, synchrotron-based X-ray absorption spectroscopy) will provide novel insights into the functioning of phytoremediator rhizospheres exposed to today’s and future climatic conditions. Understanding the underlying mechanisms of phytoremediation is an important step towards a successful application of this technique, potentially even in agricultural settings.

People involved
Dr. Carolina Vergara Cid
Natalia Sánchez
Mara Breit

This project is part of the Young Investigator Grant RhizoThreats: Rhizospheres under Attack from Coupled Climate and Soil Contaminant Stress, which is funded by the Helmholtz Association and the Centre for Environmental Research.

Phytoremediation project. Arabidopsis halleri sampling (left) and pot experiment at Bad Lauchstädt (right).
Greenhouse Gas Emission from Agricultural Soils
Almost five percent of global anthropogenically derived greenhouse gas emissions originate from agricultural soils. The most relevant greenhouse gases emitted from agricultural soil are methane and nitrous oxide. 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 greenhouse gas emissions 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 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 agricultural fields will be altered in the future with a possible change in the bioavailability of heavy metals due to global warming.

We have currently three ongoing projects under this theme:
• At the UFZ, we assess how climatic change coupled to arsenic and cadmium stress affect greenhouse gas emissions from rice paddy soils under different water management regimes. This project is funded by the China Scholarship Council and the responsible PhD student is Tianyu Wang.

• In collaboration with the Kappler lab at the University of Tuebingen, we elucidate how climate impacts the behavior 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 student is Sören Drabesch.

• 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 Skłodowska-Curie Action of the European Union in form of an individual Postdoc scholarship.
Palsa fen and cotton fields from Stordalen (p.c. Eva Voggenreiter)

Northern permafrost regions experience stronger warming than other regions in the world, thus are very sensitive to environmental change. A direct consequence is the thawing of permafrost in soils which is known to unlock huge amounts of C and N to biogeochemical cycling. Thawing results in a simultaneous ecosystem and plant-community shift from elevated, dry and nutrient-poor patches (palsa) inhabited by shrubs and mosses to inundated, wet and nutrient-rich areas (fen) dominated by mosses and sedges.

Plant type and cover are important controls to greenhouse gas balances in soils and may be decisive on whether soils are a sink or a source of gases to the atmosphere. So far, the role of root-mediated greenhouse gas producing versus consuming, transporting, releasing versus retaining processes is largely unknown. Root contributions to greenhouse gas emissions may range from root architecture to root microbiome and rhizosphere biogeochemistry impacts. This project evaluates a full thawing succession at the Abisco Scientific Research Station in Northern Sweden. Field installations, complex freeze-thaw incubation experiments followed by comprehensive analyses of rhizosphere biogeochemistry as well as microbiome signatures in combination with greenhouse gas flux measurements will be used to obtain a better understanding of root-soil interactions and the implications to greenhouse gas emissions from permafrost-affected soils. Specifically, we want to unravel the following research questions:

  1. What role do root architectural variations play for both the transport versus entrapment of greenhouse gases and the presence, activity, and localization of greenhouse gas – producing versus consuming microbial communities?
  2. What role do different root exudates and plant detritus play in microbially mediated greenhouse gas emissions?

This project is funded by the German Research Foundation (DFG) and is located at the University of Tübingen.

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) 

Courses are offered through the Geoscience Department of the University of Tuebingen.

  • 20-31.03.2023: Block course (lecture, seminar and lab course) at Master degree level Rhizosphere Processes in a Changing World (M, 6 ECTS)
  • Summer Semester 2023: Geosphere-Biosphere interactions (co-teaching with Prof. Dr. Michaela Dippold)
Bachelor Theses:
  • Jenin Fleischmann: Soil microbiome adaptation to metal stress under different farming practices. 2022
  • 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
Master Theses:
  • Mara Breit: What determines intraspecific variability in heavy metal hyper-accumulation efficacy of Arabidopsis halleri? – Plant traits or soil biogeochemistry? 2022
  • Esmira Bibaj: Cadmium (Cd) and climate-impacted greenhouse gas emissions from agricultural soils. 2022
  • Viktoria Skudlik: Combined impact of elevated atmospheric CO2 and soil Cd on the nitrogen cycle in agricultural soils. 2022
  • Charlotte Roschke: Acclimating Italian paddy soil to heavy metals and to different climatic conditions for use in experiments. 2022
  • Paula Kosel: Biogeochemical adaptation of paddy soil to climate change. 2022