P5 Pollutant Transformations at the Water-Rock Interface

People Involved

Principal Investigators

Jun.-Prof. Dr. Sara Kleindienst

University of Tübingen, Microbial Ecology

Prof. Dr. Andreas Kappler

University of Tübingen, Geomicrobiology

Prof. Dr. Peter Grathwohl

University of Tübingen, Hydrogeochemistry


Dr. Sergey Abramov

University of Tübingen, Microbial Ecology (since 01/2020)

Dr. Karsten Osenbrück

University of Tübingen, Hydrogeochemistry

Ana-Neva Visser, MSc

University of Tübingen, Geomicrobiology (until 2018)

Dr. Nia Blackwell

University of Tübingen, Microbial Ecology (until 09/2019)

Natalia Jakus, MSc

University of Tübingen, Geomicrobiology

Elena Petrova, MSc

(associated researcher)
University of Tübingen, RTG Hydrosystem Modelling

Research Questions and General Approach

Research Questions

Groundwater in limestone-fractured aquifers is often polluted by nitrate and pesticides, including legacy compounds such as atrazine. Due to long groundwater residence-times in these aquifers, microbial activities associated with pollutant turnover may substantially influence the fate of pollutants. A particular example is denitrification, which depends on the availability of electron donors such as organic carbon or Fe(II) minerals within the rock matrix. Further, storage of pollutants (e.g. atrazine) in immobile water of the rock matrix may become relevant and impact contaminant loads in these systems. A multidisciplinary approach is used to:

  • Determine the locations of pollutant (nitrate, atrazine) turnover in fractured rock aquifers
  • Identify microbial key players mediating these processes and study their physiology
  • Quantify rates of microbial pollutant turnover
  • Examine factors that limit microbial activities and associated pollutant transformations

General Approach of P5

A combination of field studies and laboratory experiments is employed to address the above mentioned research objectives:

  • To examine microbial key players of pollutant turnover and their metabolic capabilities in situ, molecular tools (e.g. 16S rRNA amplicon sequencing and omics) are applied to fractured aquifer samples.
  • To quantify pollutant turnover, examine the factors limiting pollutant turnover, identify the involved microorganisms, and determine sorption as well as diffusion of pollutants, laboratory experiments using aquifer limestone material are conducted.


Denitrification Coupled to Oxidation of Fe(II)-Minerals
Microbial Key Players and Genomic Potential
Aquifer Drilling Campaign at Baisingen



Glodowska, M., Stopelli, E., Schneider, M., Rathi, B., Straub, D., Lightfoot, A., Kipfer, R., Berg, M., AdvectAs team members, Jetten, M., Kleindienst, S., Kappler, A., (submitted): Arsenic mobilization in groundwater driven by microbial iron-dependent anaerobic oxidation of methane.

Jakus, N., Blackwell, N., Osenbrueck, K., Straub, D., Byrne, J.M., Wang, Z., Lueders, T., Grathwohl, P., Kleindienst, S., Kappler, A. (submitted): Nitrate removal by a novel autotrophic nitrate-reducing iron(II)-oxidizing culture isolated from a pyrite-rich limestone aquifer.

Petrova, E., Kortunov, E., Finkel, M., Mayer, U.K., Grathwohl, P. (submitted): Travel time based modelling of nitrate reduction in a pyrite and iron carbonates bearing fractured limestone aquifer.

Yang, Z., Sun, T., Kleindienst, S., Straub, D., Kretztschmar, R., Angenent, L.T., Kappler, A. (submitted): Coupled function of biochar as geobattery and geoconductor alters microbial community composition and electron transfer pathways in a paddy soil.

Visser, A.-N., Lehmann, M.F., Rügner, H., D'Affonseca, F.M., Grathwohl, P., Blackwell, N., Kappler, A., Osenbrück, K. (submitted): Fate of nitrate during groundwater recharge in a fractured karst aquifer.

in press

Abramov, S., Tejada, J., Grimm, L., Schaedler, F., Bulaev, A.G., Tomaszewski, E., Byrne, J., Straub, D., Thorwarth, H., Amils, R., Kleindienst, S., Kappler, A. (2020): Role of biogenic Fe(III) minerals as a sink and carrier of heavy metals in the Rio Tinto river, Spain. Sci Total Environ (in press)

Blackwell, N., Bryce, C., Straub, D., Kappler, A., Kleindienst, S. (2020): Genomic insights into two novel Zetaproteobacteria Fe(II)-oxidizing isolates reveal lifestyle adaption to coastal marine sediments. Appl Environ Microbiol (in press)

Glodowska, M., Stopelli, E., Schneider, M., Lightfoot, A., Rathi, B., Straub, D., Patzner, M., Berg, M., Vu, D., Kleindienst, S., Kappler, A. (2020): Role of in-situ natural organic matter in mobilizing As during microbial reduction of FeIII-mineral-bearing aquifer sediments from Hanoi (Vietnam). Environ Sci Technol (in press)


Straub, D., Blackwell, N., Langarica Fuentes, A., Peltzer, A., Nahnsen, S., Kleindienst, S. (2019): Interpretations of microbial community studies are biased by the selected 16S rRNA gene amplicon sequencing pipeline. bioRxiv 2019.12.17.880468; doi: https://doi.org/10.1101/2019.12.17.880468


Schaedler, F., Kappler, A., Schmidt, C. (2018): A revised iron extraction protocol for environmental samples enriched in nitrate, nitrite and carbonate. Geomicrobiology Journal, 35: 23-30

BSc and MSc Theses

BSc Theses

Jonah Schooss (ongoing): Nitrate reduction rates in heterotrophic, mixotrophic and autotrophic cultures enriched from a pyrite-bearing limestone aquifer. Supervisor: Prof. Dr. Andreas Kappler

Freya Fünfgeld (2020): Tritium-Helium Dating of Groundwater in the Fractured and Karstified Muschelkalk Aquifer of the Ammer Catchment (Baden-Württemberg, Germany). Supervisors: Prof. Dr. Peter Grathwohl, Dr. Karsten Osenbrück

Moritz Lyska (2019): Hydrochemische und hydrogeologische Charakterisierung von Lettenkeuperquellen westlich von Tübingen. Supervisors: Prof. Dr. Peter Grathwohl, Dr. Karsten Osenbrück

Barbara Kurz (2018): Development of a headspace vial method for identifying active microaerophilic iron oxidizers in environmental samples. Supervisors: Prof. Dr. Andreas Kappler, Dr. Nia Blackwell

Raphael König (2018): Atrazine and nitrate degradation in selected wells in the Ammer catchment. Supervisors: Jun.-Prof. Dr. Sara Kleindienst, Dr. Nia Blackwell

MSc Theses

Yelin Tang (ongoing): Isolation of glyphosate-degrading bacteria from soils in the Ammer catchment and metagenomic insights into pesticide and xenobiotic degradation in the Artesian Well, Altingen. Supervisors: Jun.-Prof. Dr. Sara Kleindienst, Dr. Nia Blackwell

Ines Sanchez (ongoing): Isolation of atrazine-degrading bacteria from soils in the Ammer catchment and metagenomic insights into atrazine and hydrocarbon degradation in the Artesian Well, Altingen. Supervisors: Jun.-Prof. Dr. Sara Kleindienst, Dr. Nia Blackwell

Rebecca Debo (2019): Enrichment and characterization of pesticide degraders in the Ammer catchment area. Supervisors: Jun.-Prof. Dr. Sara Kleindienst, Dr. Nia Blackwell, Dr. Adrian Langarica-Fuentes