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    Bacterial symbionts of amoebae

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Latest publications


L. n. nitrum, native soda, natron, nitrate; L. fem. n. lancea. a lance; N.L. fem. n. Nitrolancea, a nitrate (‐forming) lance‐shaped bacterium.

Chloroflexi / Thermomicrobia / Sphaerobacterales / Sphaerobacteraceae / Nitrolancea

The genus Nitrolancea, classified within the family Sphaerobacteriaceae, order Sphaerobacteriales, class Thermomicrobia, phylum Chloroflexi, consists of aerobic bacteria that grow chemolithoautotrophically by oxidation of nitrite to nitrate and can also oxidize formate to CO2 as an additional energy source. The electron acceptor is O2. Nitrolancea represents the first example of nitrite‐oxidizing bacteria (NOB) in the phylum Chloroflexi. The only known species of the genus is the type species, Nitrolancea hollandica. The only strain (N. hollandica LbT) has been isolated from a lab‐scale nitrifying bioreactor with a high loading rate of ammonium bicarbonate.

DNA G + C content (mol%): 62.6 (genome).

Type species: Nitrolancea hollandica Sorokin, Vejmelkova, Lücker, Streshinskaya, Rijpstra, Sinninghe‐Damsté, Kleerbezem, van Loosdrecht, Muyzer and Daims 2014, 1864VP.

Sorokin DY, Lücker S, Daims H
2018 - in Bergey’s Manual of Systematics of Archaea and Bacteria. John Wiley & Sons

Surface-enhanced Raman spectroscopy of microorganisms: Limitations and applicability on the single-cell level

Detection and characterization of microorganisms is essential for both clinical diagnostics and environmental studies. An emerging technique to analyse microbes at single-cell resolution is surface-enhanced Raman spectroscopy (surface-enhanced Raman scattering: SERS). Optimised SERS procedures enable fast analytical read-outs with specific molecular information, providing insight into the chemical composition of microbiological samples. Knowledge about the origin of microbial SERS signals and parameter(s) affecting their occurrence, intensity and/or reproducibility is crucial for reliable SERS-based analyses. In this work, we explore the feasibility and limitations of the SERS approach for characterizing microbial cells and investigate the applicability of SERS for single-cell sorting as well as for three-dimensional visualization of microbial communities. Analyses of six different microbial species (an archaeon, two Gram-positive bacteria, three Gram-negative bacteria) showed thatfor several of these organisms distinct features in their SERS spectra were lacking. As additional confounding factor, the physiological conditions of the cells (as influenced by e.g., storage conditions or deuterium-labelling) were systematically addressed, for which we conclude that the respective SERS signal at the single-cell level is strongly influenced by the metabolic activity of the analysed cells. While this finding complicates the interpretation of SERS data, it may on the other hand enable probing of the metabolic state of individual cells within microbial populations of interest.

Weiss R, Palatinszky M, Wagner M, Niessner R, Elsner M, Seidel M, Ivleva NP
2018 - Analyst, in press

Cyanate and urea are substrates for nitrification by thaumarchaeota in the marine environment

Ammonia-oxidizing archaea of the phylum Thaumarchaeota are among the most abundant marine microorganisms. These organisms thrive in the oceans despite ammonium being present at low nanomolar concentrations. Some Thaumarchaeota isolates have been shown to utilize urea and cyanate as energy and N sources through intracellular conversion to ammonium. Yet, it is unclear whether patterns observed in culture extend to marine Thaumarchaeota, and whether Thaumarchaeota in the ocean directly utilize urea and cyanate or rely on co-occurring microorganisms to break these substrates down to ammonium. Urea utilization has been reported for marine ammonia-oxidizing communities, but no evidence of cyanate utilization exists for marine ammonia oxidizers. Here, we demonstrate that in the Gulf of Mexico, Thaumarchaeota use urea and cyanate both directly and indirectly as energy and N sources. We observed substantial and linear rates of nitrite production from urea and cyanate additions, which often persisted even when ammonium was added to micromolar concentrations. Furthermore, single-cell analysis revealed that the Thaumarchaeota incorporated ammonium-, urea- and cyanate-derived N at significantly higher rates than most other microorganisms. Yet, no cyanases were detected in thaumarchaeal genomic data from the Gulf of Mexico. Therefore, we tested cyanate utilization in Nitrosopumilus maritimus, which also lacks a canonical cyanase, and showed that cyanate was oxidized to nitrite. Our findings demonstrate that marine Thaumarchaeota can use urea and cyanate as both an energy and N source. On the basis of these results, we hypothesize that urea and cyanate are substrates for ammonia-oxidizing Thaumarchaeota throughout the ocean.

Kitzinger K, Padilla CC, Marchant HK, Hach PF, Herbold CW, Kidane AT, Könneke M, Littmann S, Mooshammer M, Niggemann J, Petrov S, Richter A, Stewart FJ, Wagner M, Kuypers MMM, Bristow LA
2018 - Nature Microbiology, in press

Lecture series

O- and N-glycan breakdown by the human gut microbiota

David Bolam
Newcastle University, London, UK
12:00 h
Lecture Hall 2, UZA 1, Althanstr. 14, 1090 Wien

Toward a predictive understanding of microbiome response to environmental change in peatlands

Joel Kostka
Georgia Institute of Technology, Atlanta, USA
13:30 h
Lecture Hall 5, UZA II

Uncovering the metabolic flexibility of aerobic soil bacteria: from enzymes to ecosystems

Chris Greening
Monash University, Melbourne, Australia
12:00 h
Lecture Hall HS2, UZA1, Althanstrasse14, 1090 Vienna