What are they doing there? New single cell tools for functional analyses of microbes in their ecosystems

NanoSIMS. NanoSIMS imaging is perfectly suited to measure and visualize the distribution of virtually any elements and their stable isotopes of interest in microbial cells. We run in our team since 2010 a CAMECA NanoSIMS 50L (the only NanoSIMS instrument in Austria) that offers a spatial resolution for element/ isotope mapping down to 50 nm and thus even allows highly sen­sitive analyses at the sub-cellular level. The NanoSIMS 50L is equipped with Cs+ and O- primary ion sources, an electron gun for analysis of insulating samples, a secondary electron detector, and a magnetic sector mass analyser with a large version of the magnet and a multi-collection system of 7 detectors all equipped with Faraday cups and electron multiplier detectors. In microbial ecology we combine NanoSIMS with stable isotope prob­ing and cell identification techniques such as fluo­rescence in situ hybridization to obtain previously inaccessible information about the functional role of microorganisms in their environment. Using this approach, previously unrecognized physio­logical properties of bacteria and archaea thriving in soils, microbial mats, deep groundwater sam­ples and within corals as well as mice guts could be deciphered.

Now working on this theme: Arno Schintlmeister

Raman microspectroscopy. In my lab we develop new confocal Raman microspectrocopy-based methods for functional analyses of microbes in complex ecosystems. Raman microspectroscopy has single cell resolution and is nondestructive. It enables us to record within seconds a chemical fingerprint of a microbial cell that reveals the presence of defined storage compounds (Milucka et al., 2012), cytochromes and pigments. Raman microspectroscopy can be directly combined with FISH (Huang et al. 2007) for simultaneous identification of the analyzed microbes.  Furthermore, Raman microspectroscopy can be applied to detect and quantify the incorporation of stable isotopes in individual microbial cells and is the most straightforward technique to perform single cell stable isotope probing experiments with complex microbial communities. In addition to detection of 13C-labeled cells (Huang et al. 2007), we recently applied Raman microspectroscopy for tracking the incorporation of deuterium from heavy water in microbial cells in order to measure their activity (Berry et al. 2015). Excitingly, Raman spectra of microbial cells can also be recorded while holding them with an optical tweezer. Subsequently, cells can then be sorted according to their Raman spectrum for single cell genomics or cultivation (Berry et al. 2015). In collaboration with Roman Stocker (ETH, Switzerland) we have developed a microfluidics chamber for high-throughput sorting of microbial cells according to their Raman spectra for directly combining single cell stable isotope probing and single cell genomics or cultivation (Lee et al. 2019).

At DOME two cutting edge confocal Raman microspectrometer are available. A LabRAM HR800 and an HR Evolution (both from Horiba Jobin-Yvon). Availabe lasers are a 532-nm neodymium-yttrium aluminium garnet laser,  a pulsed 532-nm laser, a 785 nm laser, and a 1,064-nm laser for optical trapping.

Now working on this theme: Márton Palatinszky, Markus Schmid, (previously Tae Kwon Lee, Christoph Böhm, Esther Mader)