• 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

Long-term transcriptional activity at zero growth by a cosmopolitan rare biosphere member

Microbial diversity in the environment is mainly concealed within the rare biosphere (all species with <0.1% relative abundance). While dormancy explains a low-abundance state very well, the mechanisms leading to rare but active microorganisms remain elusive. We used environmental systems biology to genomically and transcriptionally characterise Candidatus Desulfosporosinus infrequens, a low-abundance sulfate-reducing microorganism cosmopolitan to freshwater wetlands, where it contributes to cryptic sulfur cycling. We obtained its near-complete genome by metagenomics of acidic peat soil. In addition, we analyzed anoxic peat soil incubated under in situ-like conditions for 50 days by Desulfosporosinus-targeted qPCR and metatranscriptomics. The Desulfosporosinus population stayed at a constant low abundance under all incubation conditions, averaging 1.2 × 10⁶ 16S rRNA gene copies per cm³ soil. In contrast, transcriptional activity of Ca.D. infrequens increased at day 36 by 56- to 188-fold when minor amendments of acetate, propionate, lactate, or butyrate were provided with sulfate, as compared to the no-substrate-control. Overall transcriptional activity was driven by expression of genes encoding ribosomal proteins, energy metabolism and stress response but not by expression of genes encoding cell growth-associated processes. Since our results did not support growth of these highly active microorganisms in terms of biomass increase or cell division, they had to invest their sole energy for maintenance, most likely counterbalancing acidic pH conditions. This finding explains how a rare biosphere member can contribute to a biogeochemically relevant process while remaining in a zero growth state over a period of 50 days.

Hausmann B, Pelikan C, Rattei T, Loy A, Pester M
2019 - mBio, In press

Nitrolancea

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 that for 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

Lecture series

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

David Bolam
Newcastle University, London, UK
06.12.2018
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
03.12.2018
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
22.11.2018
12:00 h
Lecture Hall HS2, UZA1, Althanstrasse14, 1090 Vienna