• 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

  • Ancient invaders -

    Bacterial symbionts of amoebae

    and the evolution of the intracellular lifestyle

  • The human microbiome -

    Our own social network of microbial friends

  • 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

Crenothrix are major methane consumers in stratified lakes

Methane-oxidizing bacteria represent a major biological sink for methane (Oremland and Culbertson 1992) and are thus Earth’s natural protection against this potent greenhouse gas. Here we show that in two stratified freshwater lakes a substantial part of upward-diffusing methane was oxidized by filamentous gamma-proteobacteria related to Crenothrix polyspora. These filamentous bacteria have been known as contaminants of drinking water supplies since 1870 (Cohn 1870) but their role in the environmental methane removal has remained unclear. While oxidizing methane, these organisms were assigned an ‘unusual’ methane monooxygenase (MMO) which was only distantly related to ‘classical’ MMO of gamma-proteobacterial methanotrophs (Stoecker et al., 2006). We now correct this assignment and show that C. polyspora as well as its lacustrine relative encode a typical gamma-proteobacterial pmoA. Stable-isotope labeling in combination with single-cell imaging mass spectrometry revealed methane-dependent growth of the lacustrine Crenothrix with oxygen as well as under oxygen-deficient conditions. Concurrently, Crenothrix genomes encoded pathways for the respiration of oxygen as well as for the reduction of nitrate to N2O. Due to their large biomass and rapid planktonic growth Crenothrix might constitute a major biological sink for methane and should be considered in the context of environmental removal of methane. 

Oswald K, Graf JS, Liftmann S, Tierken D, Brand A, Wehrli B, Albertsen M, Daims H, Wagner M, Kuypers MMM, Schubert CJ, Milucka J
2017 - ISME J, in press

Variant profiling of evolving prokaryotic populations.

Genomic heterogeneity of bacterial species is observed and studied in experimental evolution experiments and clinical diagnostics, and occurs as micro-diversity of natural habitats. The challenge for genome research is to accurately capture this heterogeneity with the currently used short sequencing reads. Recent advances in NGS technologies improved the speed and coverage and thus allowed for deep sequencing of bacterial populations. This facilitates the quantitative assessment of genomic heterogeneity, including low frequency alleles or haplotypes. However, false positive variant predictions due to sequencing errors and mapping artifacts of short reads need to be prevented. We therefore created VarCap, a workflow for the reliable prediction of different types of variants even at low frequencies. In order to predict SNPs, InDels and structural variations, we evaluated the sensitivity and accuracy of different software tools using synthetic read data. The results suggested that the best sensitivity could be reached by a union of different tools, however at the price of increased false positives. We identified possible reasons for false predictions and used this knowledge to improve the accuracy by post-filtering the predicted variants according to properties such as frequency, coverage, genomic environment/localization and co-localization with other variants. We observed that best precision was achieved by using an intersection of at least two tools per variant. This resulted in the reliable prediction of variants above a minimum relative abundance of 2%. VarCap is designed for being routinely used within experimental evolution experiments or for clinical diagnostics. The detected variants are reported as frequencies within a VCF file and as a graphical overview of the distribution of the different variant/allele/haplotype frequencies. The source code of VarCap is available at https://github.com/ma2o/VarCap. In order to provide this workflow to a broad community, we implemeted VarCap on a Galaxy webserver, which is accessible at http://galaxy.csb.univie.ac.at.

Zojer M, Schuster LN, Schulz F, Pfundner A, Horn M, Rattei T
2017 - PeerJ, e2997

Capturing the genetic makeup of the active microbiome in situ

More than any other technology, nucleic acid sequencing has enabled microbial ecology studies to be complemented with the data volumes necessary to capture the extent of microbial diversity and dynamics in a wide range of environments. In order to truly understand and predict environmental processes, however, the distinction between active, inactive and dead microbial cells is critical. Also, experimental designs need to be sensitive towards varying population complexity and activity, and temporal as well as spatial scales of process rates. There are a number of approaches, including single cell techniques, that were designed to study in situ microbial activity and that have been successively coupled to nucleic acid sequencing. The exciting new discoveries regarding in situ microbial activity provide evidence that future microbial ecology studies will indispensably rely on techniques that specifically capture members of the microbiome active in the environment. Herein we review those currently used activity-based approaches that can be directly linked to shotgun nucleic acid sequencing, evaluate their relevance to ecology studies, and discuss future directions.

Singer E, Wagner M, Woyke T
2017 - ISME J, in press

Lecture series

Harnessing Bacteria for Drug Discovery: from Bioprospecting to Synthetic Biology

Sergey Zotchev
Department of Pharmacognosy, University of Vienna
26.01.2017
12:00 h
Hörsaal 2. (UZA I), Althanstrasse 14, A-1090 Vienna

The tale of the rumen microbiome – from interaction with the host to plasmid mediated gene mobility

Itzhak Mizrahi
Ben-Gurion University of the Negev, Israel
22.09.2016
12:00 h
Hörsaal 2. (UZA I)

Importance of chemosymbiotic lucinid bivalves in seagrass community functioning

Matthijs van der Geest
Université de Montpellier
20.01.2016
11:00 h
Seminar room DoME (2.309), UZA 1