Prof. Dr. Dr. h. c. Michael Wagner

Humans are strongly impacting the global nitrogen cycle by massive use of nitrogen fertilisers. Nitrification leads to fertiliser loss, eutrophication, and greenhouse gas emission, but is essential for efficient wastewater treatment. Research in Michael Wagner‘s group focuses on the ecology, physiology, and evolution of nitrifying microorganisms. Michael Wagner’s group has discovered, cultured, and characterised important new nitrifying bacteria and archaea, including the long sought-after complete nitrifiers, describing unexpected physiological traits in the process.
Michael also has a strong interest in microbial communities driving sewage treatment and in the microbiomes of marine sponges. His group also develop innovative single cell tools to study functional properties of microbes in their natural environment. Michael is an EMBO member, has received an ERC Advanced Grant, the FWF Wittgenstein Award (highest Austrian science award), the Jim Tiedje Award of the International Society for Microbial Ecology, and the Schrödinger Prize of the Austrian Academy of Sciences. He is the director of the FWF Cluster of Excellence “Microbiomes Drive Planetary Heath”.

Since the first description of nitrifying microbes more than 100 years ago by Sergei Winogradsky nitrification was always thought to be conducted by the joint activity of two groups of microorganisms - the ammonia- and the nitrite-oxidizers. We recently discovered together with the group of Holger Daims that complete nitrifiers exist that can oxidize as single microorganisms ammonia to nitrate. These so-called Comammox (complete ammonia oxidizers) microorganisms are members of the genus Nitrospira and are widespread in terrestrial and freshwater habitats (Daims et al. 2015, Nature). In collaboration with Dr. Elena Lebedeva we obtained a pure culture from our Comammox enrichment and named it Nitrospira inopinata. Kinetic characterization of this comammox strain demonstrated that it has a higher affinity for ammonia than all studied ammonia-oxidizing bacteria (AOB) and most ammonia-oxidizing archaea (AOA). In contrast, its affinity for nitrite is rather low. Excitingly, N. inopinata has the highest biomass yield per mol of substrate oxidized among all nitrifiers analyzed. These results demonstrate that N. inopinata is very well adapted to oligotrophic conditions and that the comammox metabolism is highly efficient (Kits et al. 2017, Nature). In comparison to AOB, N. inopinata forms only very little N₂O at low oxygen conditions and can thus be considered a "green nitrifier" (Kits et al. 2019; Nature Communications). Future research on the fascinating comammox organisms in our team will focus on revealing which environmental parameters select for comammox microbes in agricultural soil and wastewater treatment plants in order to pave the way for targeted manipulation of such nitriying communities. Furthermore, we plan to perform detailed strutural and functional characterization of the very unsusual complexes I and IV in the respiratory chain of comammox microbes in order to better understand the unusual physiology of these microbes. Now working on this theme: Chris Sedlaceck, Márton Palatinszky, Man-Young Jung (previously Mario Pogoda, Julia Vierheilig, Dimitri Kits, Ping Han) Collaboration partners: Elena Lebedeva (Russian Academy of Sciences), Mads Albertsen, Per Nielsen (Aalborg University, Denmark), Nico Jehmlich, Martin van Bergen (UFZ, Leipzig, Germany), Bernd Bendinger (TU Hamburg, Germany), Lisa Stein (University of Alberta, Canada)

Ammonia oxidation is a key step in the biogeochemical nitrogen cycle and is producing nitrite for nitrite-oxidizing or nitrite-reducing microbes. This process is of major importance for nitrogen cycling in the environment and a central step in efficient wastewater treatment, but also strongly contributes to fertilizer loss and N₂O formation in agriculture. Microbial ammonia oxidation has been intensively investigated for decades, but until recently only two bacterial groups within the Proteobacteria were known to aerobically thrive on ammonia as substrate for growth. During the last decade it became apparent that members of the archaeal phylum Thaumarchaeota are also capable of ammonia-oxidation for energy generation. My lab investigates the evolution, physiology, and ecology of ammonia-oxidizing microbes. Our efforts in this field, that were also strongly supported by the ERC Advanced Grant project Nitricare, range from pure culture physiological studies to advanced single cell genomics approaches.

Recent projects:

We have obtained an enrichment of the ammonia-oxidizing thaumarchaeote Nitrososphaera gargensis and have analyzed this moderately thermophilic strain genomically (Spang et al., 2012). Interestingly, it produces F420 as a cofactor and has a more flexible central carbon metabolism than expected. In the meantime we succeeded in obtaining a pure culture of this strain. We are currently analysing the structure and function of its F420.
Now working on this theme: Chris Sedlaceck. Previously working on this theme: Roland Hatzenpichler, Alexander Galushko, Márton Palatinszky. Collaboration partner: Elena Lebedeva (Russian Academy of Sciences), Chris Greening (Monash University, Australia)

We recently demonstrated that N. gargensis is the first known organisms that can grow on cyanate as sole source of energy and reductant. While many other ammonia-oxidizers lack this capability, all genome-sequenced nitrite-oxidizers possess a cyanase for conversion of cyanate to ammonium and CO₂. Using co-culture experiments we showed that cyanase-positive nitrite-oxidizers can team up with cyanase-negative ammonia oxidizers to enable growth of both partners on cyanate. This new type of interaction between nitrifiers via reciprocal feeding also showed that the first step in nitrification can in some cases be performed by nitrite-oxidizers (Palatinszky et al. 2015, Nature). Furthermore, we demonstrated that reciprocal feeding of nitrifiers also occurs with urea as substrate (Koch et al. 2015, PNAS). Interestingly, we could recently demonstrate cyanate conversion as a source of energy and nitrogen for marine thaumarchaeotes in the Gulf of Mexico that do not encode a canonical cyanase (Kitzinger et al. 2019).

Now working on this theme: Katharina Kitzinger (previously Alexander Galushko, Márton Palatinszky, Ping Han, Mario Pogoda, Maria Mooshammer)
Collaboration partners: Marcel Kuypers (MPI Bremen, Germany), Nico Jehmlich, Martin van Bergen (UFZ, Leipzig, Germany)

In collaboration with Yujie Men and Kathrin Fenner from the EAWAG in Switzerland we investigate micropollutant degradation by ammonia-oxidizing bacteria and archaea.
Previously working on this theme: Ping Han
We have shown that close relatives of N. gargensis in an industrial wastewater treatment plant encode and express amoA, but obtain their energy from substrates other than ammonia (Mussman et al. 2011, PNAS). Using single-cell, cultivation and meta-omic techniques we are characterizing thauamarchaeotes in various municipal and industrial wastewater treatment plants to better understand (i) their contribution to nitrification in these systems and (ii) their physiological versatility.

Now working on this theme: Julia Vierheilig.
Collaboration partners: Josh Neufeld and Laura Sauder (University of Waterloo, Canada), and Ian Head (Newcastle, Uk)

We investigate the diversity of ammonia-oxidizing microbes in wastewater treatment plants by single microcolony isotope labeling, subsequent Raman sorting and single microcolony genomics. As closely attached interaction partners of the ammonia-oxidizers are also sorted, this approach does not only reveal genomic information of the active members of this guild, but also enables genomic characterization of nitrifier interaction partners in the wilderness. This project is supported by an ETOP- and a CSP-project of the JGI and is performed in collaboration with Tanja Woyke.
In order to establish an encompassing framework for comparative genomics of sorted ammonia oxidizers, we are currently sequencing the genomes of many cultures strains of this guild. This project is performed in collaboration with Andreas Pommerening-Röser (University of Hamburg, Germany) and Tanja Woyke from the JGI (Walnut Creek, USA).
Now working on this theme: Márton Palatinszky, Craig Herbold (previously Tae Kwon Lee, Esther Mader, Adrian Berger, Julius Simonis)

My group has a long-standing interest in the interaction of marine sponges with their microbial symbionts (Hentschel et al. 2002, Taylor et al. 2007, Webster et al. 2010). Using Ianthella basta from the Great Barrier Reef in Australia as model sponge we investigate by metagenomics, metaproteomics, and isotope labeling techniques the physiological interaction between this sponge and its symbionts. In contrast to many other sponges, I. basta harbors only three abundant symbionts and one of them is an ammonia-oxidizing member of the Thaumarchaeotes. This project has been supported by the Marie Curie International Training Networks Symbiomics.
Now working on this theme: Florian Moeller
Collaboration partners: Nicole Webster (AIMS, Australia), Thomas Schweder, Stephanie Markert (University of Greifswald, Germany), Mads Albertsen, Per Nielsen (Aalborg University, Denmark), Thomas Rattei, and Andreas Richter (University of Vienna, Austria)

My team has a long-standing interest in the development of methods for functional analyses of microbes within complex microbial communities (Wagner et al. 1998; Adamczyk et al. 2003). For example, we pioneered the combination of FISH and microautoradiography (Lee et al., 1999) that enabled microbial ecologists for the first time to observe substrate utilization of uncultured individual microbial cells in their natural habitat. Currently, second generation methods for single cell isotope probing mainly using ¹³C-, ¹⁵N and ²H-labeled compounds are developed and combined with single cell genomics approaches. For the detection of isotopes within microbial cells we use nanometer-scale secondary ion mass spec­trometry (NanoSIMS) and Raman microspectroscopy.

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)