Members & Current Projects

Microbial Ecology Group Members

Head of the Group - Jun.-Prof. Dr. Sara Kleindienst

We are highly interested in topics related to Microbial Ecology of pelagic and benthic marine as well as freshwater aquifer communities. Our research employs cutting-edge techniques (e.g. stable-isotope probing, Omics, Nanometer-scale Secondary Ion Mass Spectrometry) to identify microbial key-players within diverse microbial communities, to determine microbial activities and its limiting and stimulating factors, to unravel metabolic pathways, and to shed light on the fate of pollutants in the environment.

Postdoc - Dr. Sergey Abramov

The limestone-fractured aquifer is an important source of drinking water. However, extensive application of fertilizers and pesticides in agricultural area led to infiltration of pollutants into groundwater. Due to long groundwater residence-time, the fate of these pollutants depends on microbial activity. An example is denitrification, which contributes to nitrate turnover. However, in the subsurface, determination of spatial hot spots and key microbial players of denitrification remained extremely challenging due to reduced cell number and difficult access. In order to reveal the hot spots of subsurface microbial activity I retrieved limestone cores from the saturated zone at the depth of up to 70 meters during drilling campaign in the catchment of River Ammer, a tributary of River Neckar in SW-Germany (DFG funded CRC 1253 CAMPOS). Collected rock samples are currently used for identification microbial key players and their metabolic capabilities by applying molecular tools (e.g. 16S rRNA amplicon sequencing, omics techniques) and culture-based methods.

Postdoc - Dr. Adrian Langarica Fuentes

Human activity in urban and rural areas has resulted in diffuse pollution of anthropogenic contaminants across the environment. Despite decades of research, serious knowledge gaps exist concerning the fate of these compounds on the landscape scale and their impact on water quality, ecology, and human health. My research will focus on the assessment of microbial pathways of pollutant turnover (e.g. nitrate, pesticides) in contrasting landscape elements (rivers, sub-catchments, floodplains, aquifers and soils) in the catchment area of River Ammer in Germany. A variety of molecular-biological tools will be used to achieve this goal, such as qPCR, amplicon sequencing, and cutting edge meta-omics techniques.

Postdoc - Dr. Kate Thompson

Ongoing research into the detrimental effects of anthropogenic activities, specifically the use of herbicides in agricultural practices, have delineated the persistence and ubiquity of both herbicides and their degradation by-products in nature. Further work is needed to elucidate the impact of these herbicides, for example widely used glyphosate, and their degradation on the micro- and macro-communities. My research will utilize a multi-facetted approach with both molecular-biological tools, such as ‘omics’, and geochemistry to investigate the factors that control or limit glyphosate degradation under laboratory conditions designed to better reflect those of the environment. These data will subsequently be used to better inform and untangle the complexity of microbial community interactions in environmental studies of herbicide biodegradation and thus pollutant turnover.

Technician - Franziska Schädler

As technician my main duty is the organization of lab structure including the instruction of new students and postdocs, maintenance of instruments, monitoring and updating of SOPs and preparation of standardized buffers and solutions. In addition I supervise Bachelor and Master Students and support PhD students and Postdocs e.g. in the optimization of DNA extraction methods, the development of qPCR assays or in the preparation and completion of field sampling campaigns.

PhD Student - Constantin B. App

Small-scale oil pollution events, i.e. diffuse inputs, contribute to greater extends to global anthropogenic oil contamination than large-scale pollution events. To elucidate this major environmental thread on marine ecosystems, the response of marine microbiomes to small-scale pollution scenarios will be studied. For this, I will evaluate a molecular-biological method to characterize microbial seawater communities by their potential and actual hydrocarbon degrading properties. Subsequently, pure cultures, microcosms, and field samples will be studied to quantify hydrocarbon degradation rates, determine rate-influencing factors, identify microbial key players, and elucidate metabolic pathways.

PhD Student - Yu-Ming Huang

Nitrate-dependent iron(II)-oxidizing bacteria (NDFOB) are widespread in the environment. NDFOB can perform nitrate removal and carbon fixation, which leads to the fate of greenhouse gases, i.e. nitrous oxide and carbon dioxide. Additionally, microbial iron(II) oxidation plays and important role for the fate of many contaminants (e.g. arsenic and cadmium) and nutrients in the environment. The autotrophic growth of NDFOB is rarely investigated. The most prominent model system for NDFOB are enrichment cultures, i.e. it is not performed by an individual strain but a cooperation among the bacterial community. We used several cultivation and molecular biological techniques, including metagenomics, metatranscriptomics, and metaproteomics to gain insights in the metabolic survival strategies of NDFOB from freshwater ecosystems. Thus, it could serve as the foundation for the development of NDFOB for the decontamination of polluted environments.

PhD Student - Anjela L. Vogel

Despite the fact that diffuse oil sources are the main anthropogenic input of oil into the marine environment, the knowledge on microbial hydrocarbon degradation at low oil concentrations is still insufficient. Thus, during my PhD, pure cultures and environmental water microcosms will be investigated using molecular biology, GC-MS analysis and 14C-based hydrocarbon degradation assays. Furthermore, a model will be developed to predict hydrocarbon degradation, taking into account different environmental parameters. The overall aim is to gain a comprehensive understanding on the impact of small-scale pollution on different microbial communities and their hydrocarbon degradation performances by applying a combination of experimental and modelling approaches.

MSc student - Paola Hernandez

Among the different processes to remediate glyphosate from contaminated ecosystems, microbial degradation is an effective and environmentally friendly method. Scientists have begun to enrich and isolate microorganisms capable of degrading glyphosate at different rates. The influence of specific conditions, such as available carbon, could alter the ability of these microorganisms to degrade glyphosate. Therefore, my thesis explores the optimization of microbial degradation of glyphosate by isolated bacteria when provided with a set of conditions that mirror those found in the environment.

Associated Group Members

PhD Student - Natalia Jakus

The fate of critical pollutants in aquifers, obtaining recharge from agricultural landscapes, frequently depends on microorganisms that have the ability to metabolize these pollutants, such as pesticides. In my research, I will quantify the metabolic rates of pollutant turnover and determine the factors limiting these rates using biomass obtained from groundwater monitoring wells. I will also examine the potential key players responsible for pollutant turnover using microcosm experiments including stable-isotope probing in combination with gene sequencing.



  • Dr. Nia Blackwell, postdoctoral project: "In situ microbial community and metabolic functions contributing to pollutant turnover in a fractured aquifer" (2016 - 2020)
    Associated postdoctoral project: "Identification of microbial key players of Fe(II) oxidation under nitrate-reducing conditions" (2014 - 2016)
  • Dr. Daniel Straub, postdoctoral project: "Management and integrative bioinformatics analyses of omics data sets of environmental samples" (2017 - 2020)
  • Dr. Sergey Abramov, postdoctoral project: "Microbial Fe(II) oxidation and heavy metal co-precipitation in the Rio Tinto region, Spain" (2017 - 2019)
  • Dr. Lu Lu, postdoctoral project: "Dispersant impacts on the activity of dispersant- and/or oil-degrading microorganisms as well as phytoplankton in pristine habitats of the North Sea" (2016 - 2018)

PhD Students

  • Saskia Rughöft, PhD thesis: "Impacts of chemical dispersants on oil-degrading microorganisms" (2016-2020)
  • Martyna Glodowska, PhD thesis: "Role of microbial processes in arsenic cycling" (2017 - 2020)
  • Julia M. Otte, PhD thesis: "The distribution of active iron-cycling microorganisms in marine and freshwater sediments and their implications for greenhouse gas emission" (2014 - 2018)

Master Students

  • Nicole Smith, MSc thesis: "Metagenome Study of a Novel, Autotrophic, Nitrate-Reducing Fe(II)-Oxidizing Enrichment Culture from a Freshwater Ecosystem" (2021)
  • Inés Sanchez, MSc thesis: "Isolation of atrazine-degrading bacteria from sediments in the Ammer catchment area and metagenomic insights into atrazine and hydrocarbon degradation at the Artesian Well, Altingen " (2020)
  • Yelin Tang, MSc thesis: "Isolation of Glyphosate-degrading Bacteria from Soils in the Ammer Catchment Area and Metagenomic Insights into Pesticide and Xenobiotic Degradation at the Artesian Well, Altingen" (2020)
  • Hannah McNeil, MSc thesis: "Analysis of hydrocarbon degradation by marine microbial communities in response to simulated pollution scenarios" (2020)
  • Rebecca Debo, MSc thesis: "Enrichment and characterisation of pesticide degraders in the Ammer catchment area" (2019)
  • Katrin Wunsch, MSc thesis: "Effects of crude oil versus water-accommodated fraction (WAF) addition on marine microbial communities and hydrocarbon degrading bacteria" (2018)
  • Joseph Donald Martin, MSc thesis: "Assessing the efficiency of a novel isolation technique: Microbial Trapping Devices and their influence on the bacterial community of a karst aquifer" (2018)
  • Anjela L. Thon, MSc thesis: "Effects of surfactants on marine hydrocarbon degrading microorganisms" (2017)

Bachelor Students

  • Raphael König, BSc thesis: "Atrazine and nitrate degradation in selected wells in the Ammer catchment area" (2018)
  • Nelly Wang, BSc thesis: "Identification of potential crude oil or chemical dispersant degrading marine bacteria" (2017)
  • Katharina Meyer, BSc thesis: "Identification of acetate-assimilating bacteria in the nitrate-reducing iron-oxidizing Culture KS using stable-isotope probing" (2016)