• CUBE - Computational Systems Biology

  • DOME - Microbial Ecology

  • TER - Terrestrial Ecosystem Research


  • 5th International Symposium on Microbial Sulfur Metabolism in Vienna


    Jillian Petersen, Marc Mussmann, and Alexander Loy are organizing together with Monika Bright the 5th International Symposium on Microbial Sulfur Metabolism (ISMSM-5) that takes place in Vienna, 16-18 April 2018. 

  • International FISH course - Impressions 2017


    13 participants from all over the world learned the essentials of fluorescence in situ hybridization (FISH) in several seminars and by applying diverse FISH techniques to pure cultures and their own environmental and clinical samples in the lab.

  • CAMI paper published in Nature Methods


    The paper about the first round of the "Critical Assessment of Metagenome Interpretation" (CAMI) challenge was published in Nature Methods. The challenge was organized and run by an international team, including Dmitrij Turaev and Thomas Rattei from CUBE.

    That's not the ...

  • Alexander Loy and Holger Daims appointed Full Professors


    After a competitive international review process in the context of the tenure track system at the University of Vienna, Alex and Holger have been appointed Full Professors today. Their new positions are Professor of Microbial Communities (Alex) and Professor of ...

Latest publications

Abiotic conversion of extracellular NH2OH contributes to N2O emission during ammonia oxidation

In contrast to the commonly accepted view of solely biological (enzymatic) production of N2O during nitrification, recent data indicate the contribution of coupled biotic–abiotic processes involving the reactive ammonia-oxidation intermediates nitric oxide (NO) or hydroxylamine (NH2OH). The latter process would require the availability of substantial amounts of free NH2OH for chemical reactions during ammonia (NH3) oxidation, but little is known about extracellular NH2OH formation by the different clades of ammonia-oxidizing microbes. Here we determined extracellular NH2OH concentrations in culture media of several ammonia-oxidizing bacteria (AOB) and archaea (AOA), as well as one complete ammonia oxidizer (comammox) enrichment (Ca. Nitrospira inopinata) during incubation at two NH4+ concentrations (0.5 and 2 mM) under standard cultivation conditions. NH2OH was measurable in the incubation media of Nitrosomonas europaea, Nitrosospira multiformis, Nitrososphaera gargensis, and Ca. Nitrosotenuis uzonensis, but not in media of the other tested AOB and AOA. NH2OH was also formed by the comammox enrichment during NH3 oxidation. This enrichment exhibited the largest NH2OH:final product ratio (1.92%), followed by N. multiformis (0.56%) and N. gargensis (0.46%) in medium with 2 mM NH4+. The maximum proportions of NH4+ converted to N2O via extracellular NH2OH during incubation, estimated on the basis of NH2OH abiotic conversion rates, were 0.12%, 0.08% and 0.14% for AOB, AOA and N. inopinata, respectively.


Liu S, Han P, Hink L, Prosser J, Wagner M, Brüggemann N
2017 - Environ Sci Technol, in press

Application of stable-isotope labelling techniques for the detection of active diazotrophs

Investigating active participants in the fixation of dinitrogen gas is vital as N is often a limiting factor for primary production. Biological nitrogen fixation (BNF) is performed by a diverse guild of bacteria and archaea (diazotrophs), which can be free-living or symbionts. Free-living diazotrophs are widely distributed in the environment, yet our knowledge about their identity and ecophysiology is still limited. A major challenge in investigating this guild is inferring activity from genetic data as this process is highly regulated. To address this challenge, we evaluated and improved several 15N-based methods for detecting N2 fixation activity (with a focus on soil samples) and studying active diazotrophs. We compared the acetylene reduction assay and the 15N2 tracer method and demonstrated that the latter is more sensitive in samples with low activity. Additionally, tracing 15N into microbial RNA provides much higher sensitivity compared to bulk soil analysis. Active soil diazotrophs were identified with a 15N-RNA-SIP approach optimized for environmental samples and benchmarked to 15N-DNA-SIP. Lastly, we investigated the feasibility of using SIP-Raman microspectroscopy for detecting 15N-labelled cells. Taken together, these tools allow identifying and investigating active free-living diazotrophs in a highly sensitive manner in diverse environments, from bulk to the single-cell level.

Angel R, Panhölzl C, Gabriel R, Herbold C, Wanek W, Richter A, Eichorst SA, Woebken D
2017 - Environmental microbiology, in press

NanoSIMS and tissue autoradiography reveal symbiont carbon fixation and organic carbon transfer to giant ciliate host

The giant colonial ciliate Zoothamnium niveum harbors a monolayer of the gammaproteobacteria Cand. Thiobios zoothamnicoli on its outer surface. Cultivation experiments revealed maximal growth and survival under steady flow of high oxygen and low sulfide concentrations. We aimed at directly demonstrating the sulfur-oxidizing, chemoautotrophic nature of the symbionts and at investigating putative carbon transfer from the symbiont to the ciliate host. We performed pulse-chase incubations with 14C- and 13C-labeled bicarbonate under varying environmental conditions. A combination of tissue autoradiography and nanoscale secondary ion mass spectrometry coupled with transmission electron microscopy was used to follow the fate of the radioactive and stable isotopes of carbon, respectively. We show that symbiont cells fix substantial amounts of inorganic carbon in the presence of sulfide, but also (to a lesser degree) in the absence of sulfide by utilizing internally stored sulfur. Isotope labeling patterns point to translocation of organic carbon to the host through both release of these compounds and digestion of symbiont cells. The latter mechanism is also supported by ultracytochemical detection of acid phosphatase in lysosomes and in food vacuoles of ciliate cells. Fluorescence in situ hybridization of freshly collected ciliates revealed that the vast majority of ingested microbial cells were ectosymbionts.

Volland J-M, Schintlmeister A, Zambalos H, Reipert S; Mozetič P, Espada-Hinojosa S; Turk V, Wagner M, Bright M
2017 - ISME J., in press