ProVIS Center for Chemical Microscopy

Research Themes

Key activities:

We aim to visualize and quantify microbial mediated biochemical processes in natural an polluted environments using innovative high-resolution chemical and surface imaging techniques i.e. nanoSIMS, AFM, HIM, SEM, confocal RAMAN microspectroscopy and LMD. Using these techniques in combination with stable isotope tracer experiments and fluorescence in situ hybridization we will obtain a direct correlation of phylogenetic/morphologic identity of microorganisms with their metabolic activity. The final aim is to determine the contribution/role of specific populations to certain biochemical process e.g. metal cycling and therefore microorganisms role in ecosystem functioning.

Current topics:

  • Study of microbe-metal/mineral interactions e.g. biofilms on metal surfaces, intracellular and extracellular sequestration of metals on terrestrial pristine and polluted environments
  • Development of novel methods using isotope-containing nano-markers for cell identification, imaging of molecules (proteins, mRNA) and activity tracing.

Methods and instruments:

  • Tracer experiments in oxic/anoxic conditions, aerobic/anaerobic cultivation methods
  • Sample preparation

            - high pressure freezing
            - freeze substitution/sublimation
            - ultramicrotome with cryogenic sample environment
            - critical point drying
            - thin metal layer deposition

  • Microscopy

            - Epifluorescence microscope, steromicroscope
            - Laser microdissection system (LMD) combined with optical tweezers
            - Confocal Raman microscope with atomic force microscope (AFM) option

  • High resolution surface imaging and treatment

            - Helium ion microscope (ORION NanoFab)

  • Elemental analysis

            - Nano-scale secondary ion mass spectrometry (nanoSIMS),
            - Time of flight secondary ion mass spectrometer (ToF-SIMS),
            - Scanning electron microscope (SEM) with option of energy dispersive X-ray
               analysis using wavelength dispersive spectrometer (WDS) and energy
               dispersive X-ray detector (EDX)
            - Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS)

  • Molecular biology techniques including PCR, clone libraries, DNA sequencing, and DNA/RNA-stable isotope probing


Dr. Helle Ploug, Professor Marine Ecology, Department for Biology and Environmental Sciences, University of Gothenburg, Sweden.

Dr. Stefan Sievert, Associate Scientist, Biology Department, Laboratory for Biogeochemistry, Woods Hole Oceanographic Institution, USA.

Dr. Alexander Zaichenko, Department of Organic Chemistry, Lviv Polytechnical National University, Ukraine.

Dr. Sanna Leppänen and  Dr. Marja Tiirola, Biological and Environmental Science, University of Jyväskylä, Finland.

Dr. Amelia-Elena Rotaru, Postdoctoral Researcher, Nordic Center for Earth Evolution, Department of Biology, University of Southern Denmark.

Dr. Jean-Nicolas Audinot, Public Research Centre Gabriel Lippmann (CRP-Gabriel Lippmann), Belvaux, Luxembourg

Dr. Michael Wiedenbeck, SIMS Laboratory, Helmholtz-Zentrum Potsdam, Deutsches GeoForschungsZentrum

Dr. Silke Merchel & Dr. Axel Renno, Helmholtz-Institut Freiberg für Ressourcentechnologie, Helmholtz-Zentrum Dresden-Rossendorf