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MSc Thesis Topic: Visualisation of the microbial community and associated element cycles involved in the anaerobic chlorobenzene biotransformation a model wetland system using chemical microscopy (SIMS) approaches

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Monochlorobenzene (MCB) is a frequently detected groundwater contaminant and represents the main pollutant in the anoxic aquifer of our field site in Bitterfeld. Thus far, information related to anaerobic biodegradation of MCB is very limited but we observed that degradation was enhanced in planted systems compared to unplanted columns or by the addition of e.g. Fe (III)-oxides. Therefore, to understand the biodegradation in situ, we investigated the fate of 13C labelled MCB in more detail in model wetland systems with or without plants and with or without amendment of iron oxides.
The overall aim of the project is to understand the microbial community involved in the biotransformation of MCB and connected element cycling as well as the association of with e.g. plant roots or solid material in situ. The thesis research will involve the state-of-the-art equipment of the Centre for chemical microscopy (ProVIS -
Research questions addressed include 1) is the sediment material colonised by microorganisms?; 2) can we find 13C-labeled microorganisms?; 3) how is the sediment (iron) material modified due to the incubation and microbial colonisation? Ultimately, the aim would be to determine the identity of microorganisms incorporating the MCB-derived carbon.
Scope of the study:
The tasks of the planned research include development of appropriate sample preparation approaches employing optical tweezers and laser microdissection (LMD), ultra-sonication, chemical fixation, critical point drying (CPD), high-pressure freezing, sublimation drying, freeze substitution and cryo-ultramicrotomy for subsequent analysis of available soil and plant samples using a variety of visualisation methods including epifluorescence microscopy, helium ion and electron microscopy as well as optionally nanoSIMS and TOF-SIMS optionally in combination with in situ hybridization approaches.
The sediment and plant samples from the wetland model systems will be investigated and following objectives are planned to be addressed:
  • Development and evaluation of various sample preparation methods for sediment samples and plant roots
  • Evaluation of microbial colonisation of the sediment samples and plant roots
  • Evaluation of tracer (13C) into microbial and plant biomass
  • Evaluation of the solid phase (Iron oxide) modification after colonisation
  • Identification of active microorganisms
  • Interpretation and synthesis of the data
Experience: We are looking for a motivated candidate currently enrolled in a Diploma or MSc programme of e.g. environmental sciences, (micro)biology, biotechnology or geoecology with a strong interest in microbiology, geochemistry and visualisation methods.
Conditions: The thesis can start as soon as possible and will take six to nine month. Additionally, an internship for an introduction to the topic prior to the thesis research is possible. The working place will be Leipzig. Please don’t hesitate to contact us for further information.
Please note that we are unable to provide financial support for the cost of living.


Art des Bewerbungszugangs
Please send your application including letter of motivation, CV and transcript of records of your taken courses to the e-mail address indicated above.
Kontakt für Bewerbungen
Dr. Ivonne Nijenhuis
personal web-page:

Details der Stellenanzeige

Befristete Anstellung
Diplom- & Masterarbeit
Berufserfahrung nicht vorausgesetzt
Deutschland (Sachsen)
04318 Leipzig
Geowissenschaften, Biologie & Life Sciences, Chemie, Physik