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. Nia Blackwell

Around 30 % of freshwater on Earth occurs as groundwater stored in aquifers, which are valuable sources of drinking water. However, anthropogenic activities such as fertilizer and pesticide application to agricultural land can have deleterious effects on the quality of the groundwater resulting in elevated concentrations of harmful pollutants. My research uses in-situ microcosms deployed in groundwater wells to characterize the microbial community and identify active microbes involved with pollutant turnover. The genomic potential and capabilities of these crucial microbes will also be investigated by applying omics techniques such as metagenomics, metatranscriptomics and metaproteomics.

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. Daniel Straub

Diffuse pollution of soils, surface waters, and ground-water by a multitude of anthropogenic organic and inorganic compounds is a growing global concern. To shed light on the fate and behavior of these pollutants on the landscape scale microbial pollutant turnover will be examined by applying 16S amplicon sequencing, metagenomics, metatranscriptomics, and metaproteomics to field samples. I will focus on the management and integrative bioinformatics analyses of omics data sets of environmental samples. The aim is to identify major microbial players in pollutant degradation and the underlying molecular processes.

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

Microbial iron(II) oxidation plays an important role for the fate of many contaminants (e.g., arsenic) and nutrients in the environment, however, the metabolic mechanisms of iron(II) oxidation still remain unclear. In my PhD project, I will investigate metabolic survival strategies of iron(II)-oxidizing bacteria from freshwater ecosystems via several cultivation and molecular biological techniques, including metagenomics, metatranscriptomics, and metaproteomics. In particular, I will enrich, identify, and examine nitrate-reducing iron(II)-oxidizing bacteria to shed light on so far unresolved mechanisms of microbial iron(II) oxidation.

PhD Student - Saskia Rughöft

In my PhD project, I am investigating the impacts of dispersant and/or oil addition on hydrocarbon-degrading microbial populations in different aquatic environments. Recently, it was shown that chemical dispersants can suppress the activity of hydrocarbon degraders but the underlying mechanisms still remain unclear. Using molecular biological methods, my goal is to identify and examine hydrocarbon- and dispersant-degrading microorganisms in environmental samples and to further characterize their activity under different conditions. Podcast with Saskia Rughöft from the Microbiology Society Annual Conference:

PhD Student - Anjela Thon

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 - Hannah McNeil

Anthropogenic input and natural seeps result in hydrocarbon pollution throughout the marine environment. Different pollution scenarios cause varying concentrations within the environment, comprised of complex hydrocarbon mixtures. The aim of my research is to analyze hydrocarbon degradation by marine microbial communities and determine the impact of the pollutant concentration.

MSc Student - Inés Sanchez

Atrazine is an herbicide that is extensively used worldwide for the control of weeds in agricultural fields. Although it has been banned in Germany since 1991 due to its toxicity, its residues still persist in soil, surface water and groundwater, in concentrations often exceeding the stipulated EU threshold. Microbial degradation is considered to be the most effective pathway for atrazine breakdown. The aim of my research is to characterize and identify microbes involved in atrazine degradation and then study their activity under different conditions.

MSc Student - Yelin Tang

Glyphosate is one of the most widely used herbicides worldwide. Although its usage is under strict supervision of the European Union, residues in the ambient and food may still cause harm to the environment and organisms. My research is dedicated to investigating the whole process of biodegradation of glyphosate by potential degraders isolated from agricultural field samples. To achieve this, the concentration variation of glyphosate and its secondary products, as well as microbial cell numbers, will be discovered.

Associated Group Members

Postdoc - Dr. E. Marie Muehe

I am currently a Marie Skłodowska Curie Fellow at the University of Tübingen, Germany and Stanford University, USA. My research focuses on biogeochemical processes in the rhizospheres of crops and phytoremediating plants when stressed with metallic soil contaminants and a shifting climate. I investigate biogeochemical changes that occur at the micrometer scale in the rhizosphere to explain macrosopic outcomes of plant productivity and quality. My goal is to contribute to advancing sustainable agriculture, which is key to the global challenge of food security.

PhD Student - Martyna Glodowska

High level of arsenic (As) in groundwater of the densely populated Red River delta is a serious health threat for millions of people. The rural population of Hanoi region mainly depend on shallow wells which provides drinking water from Holocene aquifer. However, As concentration in these waters frequently exceeds WHO drinking water limit of 10 µg/L, in some cases reaching over 300 µg/L. Microbially mediated processes are important for As mobilization, yet these processes are still not fully understood. The main goal of my PhD project is to investigate the role of bacteria controlling As dynamics in the Fe-dominated redox transition zones, which might be crucial in As transport and retention.

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. 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

  • 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

  • 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 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)