• Hunting for microbes since 2003

  • We seek to understand

    the role of microorganisms in Earth's nutrient cycles

    and as symbionts of other organisms

  • Cycling of carbon, nitrogen and sulfur

    affect the health of our planet

  • The human microbiome -

    Our own social network of microbial friends

  • Ancient invaders -

    Bacterial symbionts of amoebae

    and the evolution of the intracellular lifestyle

  • Marine symbioses:

    Listening in on conversations

    between animals and the microbes they can't live without

  • Single cell techniques offer new insights

    into the ecology of microbes

  • Apply for the DOME International PhD/PostDoc program

Dome News

Latest publications

Biodegradation of synthetic polymers in soils: Tracking carbon into CO2 and microbial biomass

Plastic materials are widely used in agricultural applications to achieve food security for the growing world population. The use of biodegradable instead of nonbiodegradable polymers in single-use agricultural applications, including plastic mulching, promises to reduce plastic accumulation in the environment. We present a novel approach that allows tracking of carbon from biodegradable polymers into CO2 and microbial biomass. The approach is based on 13C-labeled polymers and on isotope-specific analytical methods, including nanoscale secondary ion mass spectrometry (NanoSIMS). Our results unequivocally demonstrate the biodegradability of poly(butylene adipate-co-terephthalate) (PBAT), an important polyester used in agriculture, in soil. Carbon from each monomer unit of PBAT was used by soil microorganisms, including filamentous fungi, to gain energy and to form biomass. This work advances both our conceptual understanding of polymer biodegradation and the methodological capabilities to assess this process in natural and engineered environments.

Zumstein MT, Schintlmeister A, Nelson TF, Baumgartner R, Woebken D, Wagner M, Kohler H-PE, McNeill K, Sander M
2018 - Science Advances, 4: eaas9024

Ammonia monooxygenase-mediated cometabolic biotransformation and hydroxylamine-mediated abiotic transformation of micropollutants in an AOB/NOB co-culture

Biotransformation of various micropollutants (MPs) has been found to be positively correlated with nitrification in activated sludge communities. To further elucidate the roles played by ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB), we investigated the biotransformation capabilities of an NOB pure culture (Nitrobacter sp.), and an AOB (Nitrosomonas europaea) / NOB (Nitrobacter sp.) co-culture for fifteen MPs, whose biotransformation were reported previously to be associated with nitrification. The NOB pure culture did not biotransform any investigated MP, whereas the AOB/NOB co-culture was capable of biotransforming asulam, and five other MPs. Two transformation products (TPs) of asulam were identified and tentative structures were proposed. Inhibition studies with octyne, an ammonia monooxygenase (AMO) inhibitor, suggested that AMO was the responsible enzyme for asulam transformation that occurred co-metabolically. Interestingly, hydroxylamine, a key intermediate of all aerobic ammonia oxidizers, was found to react with several MPs at concentrations typically occurring in AOB batch cultures. All of these MPs were also biotransformed by the AOB/NOB co-culture. Moreover, the same asulam TPs were detected in both biotransformation and hydroxylamine-treated abiotic transformation experiments. Thus, in addition to cometabolism likely carried out by AMO, an abiotic transformation route indirectly mediated by AMO might also contribute to MP biotransformation by AOB. 

Yu Y, Han P, Zhou L-J, Li Z, Wagner M, Men Y
2018 - Environ Sci Technol, in press

Characterization of the first “Candidatus Nitrotoga” isolate reveals metabolic versatility and separate evolution of widespread nitrite-oxidizing bacteria

Nitrification is a key process of the biogeochemical nitrogen cycle and of biological wastewater treatment. The second step, nitrite oxidation to nitrate, is catalyzed by phylogenetically diverse, chemolithoautotrophic nitrite-oxidizing bacteria (NOB). Uncultured NOB from the genus “Candidatus Nitrotoga” are widespread in natural and engineered ecosystems. Knowledge about their biology is sparse, because no genomic information and no pure “Ca. Nitrotoga” culture was available. Here we obtained the first “Ca. Nitrotoga” isolate from activated sludge. This organism, “Candidatus Nitrotoga fabula,” prefers higher temperatures (>20°C; optimum, 24 to 28°C) than previous “Ca. Nitrotoga” enrichments, which were described as cold-adapted NOB. “Ca. Nitrotoga fabula” also showed an unusually high tolerance to nitrite (activity at 30 mM NO2) and nitrate (up to 25 mM NO3). Nitrite oxidation followed Michaelis-Menten kinetics, with an apparent Km (Km(app)) of ~89 µM nitrite and a Vmax of ~28 µmol of nitrite per mg of protein per h. Key metabolic pathways of “Ca. Nitrotoga fabula” were reconstructed from the closed genome. “Ca. Nitrotoga fabula” possesses a new type of periplasmic nitrite oxidoreductase belonging to a lineage of mostly uncharacterized proteins. This novel enzyme indicates (i) separate evolution of nitrite oxidation in “Ca. Nitrotoga” and other NOB, (ii) the possible existence of phylogenetically diverse, unrecognized NOB, and (iii) together with new metagenomic data, the potential existence of nitrite-oxidizing archaea. For carbon fixation, “Ca. Nitrotoga fabula” uses the Calvin-Benson-Bassham cycle. It also carries genes encoding complete pathways for hydrogen and sulfite oxidation, suggesting that alternative energy metabolisms enable “Ca. Nitrotoga fabula” to survive nitrite depletion and colonize new niches.

Kitzinger K, Koch H, Lücker S, Sedlacek CJ, Herbold C, Schwarz J, Daebeler A, Mueller AJ, Lukumbuzya M, Romano S, Leisch N, Karst SM, Kirkegaard R, Albertsen M, Nielsen PH, Wagner M, Daims H
2018 - mBio, 9: e01186-18

Lecture series

Eco-Evolutionary Dynamics of Microbial Populations in the Wild

Martin Polz
Massachusetts Institute of Technology
12:00 h
Hörsaal 2, UZA 1, Althanstr. 14, 1090 Wien

Modulation of the Human Gut Microbiota - An Ecological Perspective

Jens Walter
University of Alberta
12:00 h
Hörsaal 2, UZA 1, Althanstr. 14, 1090 Wien

Measurement of sulfur isotope fractionation by APS reductase and its biogeochemical implications

Shawn McGlynn
Earth-Life Science Institute Tokyo
11:00 h
Hörsaal 2, UZA 1, Althanstr. 14, 1090 Wien