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Open PhD project: Biotic and abiotic control on biofilm assembly

Open PhD project: Biotic and abiotic control on biofilm assembly

Max Planck Institute for Biogeochemistry, Jena logo

Max Planck Institute for Biogeochemistry, Jena

The Max Planck Institute for Biogeochemistry is dedicated to the study of global cycles of essential elements on Earth, their interactions among the biosphere, atmosphere, geosphere and the oceans, and their interrelation with the physical climate system.

The institute was founded in 1997 by the Max Planck Society as the third Max Planck Institute in Jena. In 2003, the institute moved into its new building on the Beutenberg Campus. The Science Campus is home to several academic and for-profit research institutions and offers together with the Friedrich-Schiller University Jena excellent potential for local scientific collaborations.

Biogeochemical research is highly interdisciplinary and international. Scientists from all over the world are attracted to our institute and our research is often conducted in remote and exotic locations worldwide.


Jena, Germany


Relevant divisions
Biogeosciences (BG)
Geosciences Instrumentation and Data Systems (GI)

Full time

Student / Graduate / Internship

PhD researchers receive either a scholarship (1,200 EUR for 4 years) which is free of tax and social insurance or a support contract (about 1,600 EUR for 3 years).

Preferred education

Application deadline
27 August 2019

5 July 2019

Job description

In cooperation with the Friedrich Schiller University Jena, the Max Planck Institute for Biogeochemistry houses a unique and flexible research program that grants German and foreign students a broad selection of learning opportunities while still maintaining a research focus.
The IMPRS-gBGC offers a PhD program specializing in global biogeochemistry and related Earth system sciences. The overall research and teaching focuses on:

  • Improved understanding of biogeochemical processes with an emphasis on terrestrial ecosystems
  • Development of observational techniques to monitor and assess biogeochemical feedbacks in the Earth system
  • Theory and model development for improving the representation of biogeochemical processes in comprehensive Earth system models

Project description:
Environmental biofilms cover nearly all surfaces generating niches for synergistic and antagonistic interactions between microorganisms. The different gradients in such biofilms (nutrition, O 2, pH, etc.) form specific zones which are populated by various organisms. In such a community synergistic interactions like toleration, communication or complete cooperation but simultaneously antagonistic interaction like competition or killing can be found. Facing outside disturbances the biofilm community will be remodeled to adapt to the new conditions. [1] Such dynamic effects are not fully understood and corresponding interactions can be investigated with isotopic tracer experiments. This project will use modern analytic methods to evaluate the molecular and bacteriological changes of biofilms assemblies experiencing biotic and abiotic disturbances.
Raman spectroscopy is a phenotypic method thus analyzing all cell components without destruction. Due to the high spatial resolution Raman microscopy even can be applied to analyze single bacterial cells or monitor in vivo the development of eukaryotic cells in 2D over time. [2,3] Raman spectroscopic investigations of biofilms lead either to a sum spectrum of the entire biofilm or a 3D map of the biofilm revealing the distribution of bacteria, EPS and other components. The Raman spectroscopic analysis of planktonic and sessile bacteria already revealed distinct spectral differences due to the adaptation of the cells on the new conditions. [4] In addition, Raman spectroscopy can directly identify isotopic labeling of molecules with e.g. 2 H, 13 C, 15 N containing atoms even in organisms. [5,6]
Ultra-high resolution mass spectrometry (FT-MS) is able to identify multiple thousands individual molecules which resemble the bacteria interaction inside biofilms. [7] These molecules resemble the origin of molecules and ongoing metabolic processes. As so far the use of the isotopic information is not well established. [8] However, the use of such techniques will help to trace the flow of isotopic labels into individual molecules / organisms of the biofilm.
In this project first defined biofilms from 3 to 5 species will be created and defined by means of Raman spectroscopy and ultra-high resolution mass spectrometry (FT-MS). The combination of Raman spectroscopy and FT-MS will allow an overall picture of the molecular situation inside biofilms. According to the type of interaction of different bacteria the resulting multispecies biofilm will most probably develop completely new characteristics. These undisturbed biofilms will be analyzed by means of different chemometric methods and will then be compared to biofilms which experience abiotic or biotic events. The second step of this projects is dedicated to the carbon/nitrogen turnover of biofilms. Such experiments might use isotope labeled or unlabeled small molecules. Raman spectroscopy and FT-MS will then be used to identify the likely endpoints of these labels/molecules. In a third step specific or non-specific phages will be introduced into the system. In both experiments it is expected that not only the abundance of the single bacteria will be effected but also the EPS composition and carbon/nitrogen flow to different parts of the community.
Overall, the PhD student will mainly focus on the spectroscopic and biological realisation of this new microbial Raman spectroscopic approach of this biofilm project. Thereby, the student can rely on the unique and rich expertise of the Leibniz Institute of Photonic Technology (IPHT) and the Institute of Physical Chemistry (IPC, Friedrich-Schiller University of Jena) in Raman based microbial analysis. The ultra-high resolution mass spectrometry (FT-MS) analysis will be performed at the Max Planck Institute of Biochemistry, Molecular Biogeochemistry. The phage project will be performed in cooperation with the CRC AquaDiva and the Working Group Bioavailability, UFZ Leipzig.
The Max Planck Society seeks to increase the number of women in those areas where they are underrepresented and therefore explicitly encourages women to apply. The Max Planck Society is committed to increasing the number of individuals with disabilities in its workforce and therefore encourages applications from such qualified individuals.


  1. Flemming HC, Wingender J, Szewzyk U, Steinberg P, Rice SA, Kjelleberg S (2016) Biofilms: an emergent form of bacterial life. Nature Reviews Microbiology 14 (9):563-575. doi:10.1038/nrmicro.2016.94
  2. Hartmann K, Becker-Putsche M, Bocklitz T, Pachmann K, Niendorf A, Rösch P, Popp J (2012) A Study of Docetaxel-induced Effects in MCF-7 Cells by means of Raman Microspectroscopy. Anal Bioanal Chem 403 (3):745-753. doi:DOI: 10.1007/s00216-012-5887-9
  3. Lorenz B, Wichmann C, Stöckel S, Rösch P, Popp J (2017) Cultivation-free Raman spectroscopic investigations of bacteria. Trends Microbiol 25 (5):413-424. doi:10.1016/j.tim.2017.01.002
  4. Kusic D, Kampe B, Ramoji A, Neugebauer U, Rösch P, Popp J (2015) Raman spectroscopic differentiation of planktonic bacteria and biofilms. Anal Bioanal Chem 407 (22):6803–6813. doi:10.1007/s00216-015-8851-7
  5. Kumar B.N. V, Guo S, Bocklitz T, Rösch P, Popp J (2016) Demonstration of carbon catabolite repression in naphthalene degrading soil bacteria via Raman spectroscopy based stable isotope probing. Anal Chem 88 (15):7574-7582. doi:10.1021/acs.analchem.6b01046
  6. Taubert M, Stöckel S, Geesink P, Girnus S, Jehmlich N, von Bergen M, Rösch P, Popp J, Küsel K (2018) Tracking active groundwater microbes with D 2 O labeling to understand their ecosystem function. Environ Microbiol 20 (1):369-384. doi:10.1111/1462-2920.14010
  7. Roth V-N, Dittmar T, Gaupp R, Gleixner G (2014) Ecosystem-Specific Composition of Dissolved Organic Matter. Vadose Zone Journal 13 (7). doi:10.2136/vzj2013.09.0162
  8. Eiler J, Cesar J, Chimiak L, Dallas B, Grice K, Griep-Raming J, Juchelka D, Kitchen N, Lloyd M, Makarov A, Robins R, Schwieters J (2017) Analysis of molecular isotopic structures at high precision and accuracy by Orbitrap mass spectrometry. International Journal of Mass Spectrometry 422:126-142. doi:10.1016/j.ijms.2017.10.002

How to apply

Online applications for the program are open to well-motivated and highly-qualified candidates from all countries. A prerequisite is a diploma or master of science degree in geophysical sciences, environmental sciences, biological sciences, physics, chemistry, computer sciences or related fields, including a corresponding thesis. Proficiency in English is required since English is the official language of the program.