• Centre for Microbiology and Environmental Systems Science

  • CUBE - Computational Systems Biology

  • DOME - Microbial Ecology

  • EDGE - Environmental Geosciences

  • TER - Terrestrial Ecosystem Research


  • 21st Genomic Standards Consortium Meeting in Vienna


    The 21st meeting of the Genomic Standards Consortium was hosted by the University of Vienna and CUBE. The meeting from May 20-23, and additional workshops on May ...

  • New FWF Project for Fatima Pereira


    Fatima has been awarded a Young Investigator Researcher Group project from the FWF, entitled “Adjusting the base: (Epi)transcriptomic RNA modification in inflammation & host-microbiome crosstalk”. The project will address relevant aspects and implications of RNA editing in inflammatory bowel diseases, ...

  • New FWF project for Astrid Collingro


    Astrid received funding for her project "Towards functional ecology of environmental chlamydiae" from the Austrian Science Fund. Congratulations!

  • Sung-Keun Rhee

    Prof. Sung-Keun Rhee visiting professor at DOME


    Sung-Keun Rhee, professor at the Department of Microbiology of the Chungbuk National University, South Korea will spend the next 6 months at our division as a visiting professor. We are very much looking forward to many exciting collaborations on ammonia-oxidizing archaea and ...

Latest publications

Mitigating anticipated effects of systematic errors supports sister-group relationship between Xenacoelomorpha and Ambulacraria

Xenoturbella and the acoelomorph worms (Xenacoelomorpha) are simple marine animals with controversial affinities. They have been placed as the sister group of all other bilaterian animals (Nephrozoa hypothesis), implying their simplicity is an ancient characteristic; alternatively, they have been linked to the complex Ambulacraria (echinoderms and hemichordates) in a clade called the Xenambulacraria, suggesting their simplicity evolved by reduction from a complex ancestor. The difficulty resolving this problem implies the phylogenetic signal supporting the correct solution is weak and affected by inadequate modeling, creating a misleading non-phylogenetic signal. The idea that the Nephrozoa hypothesis might be an artifact is prompted by the faster molecular evolutionary rate observed within the Acoelomorpha. Unequal rates of evolution are known to result in the systematic artifact of long branch attraction, which would be predicted to result in an attraction between long-branch acoelomorphs and the outgroup, pulling them toward the root. Other biases inadequately accommodated by the models used can also have strong effects, exacerbated in the context of short internal branches and long terminal branches. We have assembled a large and informative dataset to address this problem. Analyses designed to reduce or to emphasize misleading signals show the Nephrozoa hypothesis is supported under conditions expected to exacerbate errors, and the Xenambulacraria hypothesis is preferred in conditions designed to reduce errors. Our reanalyses of two other recently published datasets produce the same result. We conclude that the Xenacoelomorpha are simplified relatives of the Ambulacraria.

Philippe H, Poustka AJ, Chiodin M, Hoff KJ, Dessimoz C, Tomiczek B, Schiffer PH, Müller S, Domman D, Horn M, Kuhl H, Timmermann B, Satoh N, Hikosaka-Katayama T, Nakano H, Rowe ML, Elphick MR, Thomas-Chollier M, Hankeln T, Mertes F, Wallberg A, Rast JP, Copley RR, Martinez P, Telford MJ
2019 - Curr. Biol., in press

Global diversity and biogeography of bacterial communities in wastewater treatment plants

Microorganisms in wastewater treatment plants (WWTPs) are essential for water purification to protect public and environ- mental health. However, the diversity of microorganisms and the factors that control it are poorly understood. Using a systematic global-sampling effort, we analysed the 16S ribosomal RNA gene sequences from ~1,200 activated sludge samples taken from 269 WWTPs in 23 countries on 6 continents. Our analyses revealed that the global activated sludge bacterial communities contain ~1 billion bacterial phylotypes with a Poisson lognormal diversity distribution. Despite this high diversity, activated sludge has a small, global core bacterial community (n=28 operational taxonomic units) that is strongly linked to activated sludge performance. Meta-analyses with global datasets associate the activated sludge microbiomes most closely to freshwater populations. In contrast to macroorganism diversity, activated sludge bacterial communities show no latitudinal gradient. Furthermore, their spatial turnover is scale-dependent and appears to be largely driven by stochastic processes (dispersal and drift), although deterministic factors (temperature and organic input) are also important. Our findings enhance our mechanistic understanding of the global diversity and biogeography of activated sludge bacterial communities within a theoretical ecology framework and have important implications for microbial ecology and wastewater treatment processes.

Wu L, Ning D, Zhang B, Li Y, Zhang P, Shan X, Zhang Q, Brown M, Li Z, Van Nostrand JD, Ling F, Xiao N, Zhang Y, Vierheilig J, Wells GF, Yang Y, Deng Y, Tu Q, Wang A, Global Water Microbiome Consortium, Zhang T, He Z, Keller J, Nielsen PH, Alvarez PJJ, Criddle CS, Wagner M, Tiedje JM, He Q, Curtis TP, Stahl DA, Alvarez-Cohen L, Rittmann BE, Wen X, Zhou J
2019 - Nat Microbiol, in press

Symbiont-mediated defense against Legionella pneumophila in amoebae

Legionella pneumophila is an important opportunistic pathogen for which environmental reservoirs are crucial for the infection of humans. In the environment, free-living amoebae represent key hosts providing nutrients and shelter for highly efficient intracellular proliferation of L. pneumophila, which eventually leads to lysis of the protist. However, the significance of other bacterial players for L. pneumophila ecology is poorly understood. In this study, we used a ubiquitous amoeba and bacterial endosymbiont to investigate the impact of this common association on L. pneumophilainfection. We demonstrate that L. pneumophila proliferation was severely suppressed in Acanthamoeba castellanii harboring the chlamydial symbiont Protochlamydia amoebophila. The amoebae survived the infection and were able to resume growth. Different environmental amoeba isolates containing the symbiont were equally well protected as different L. pneumophila isolates were diminished, suggesting ecological relevance of this symbiont-mediated defense. Furthermore, protection was not mediated by impaired L. pneumophila uptake. Instead, we observed reduced virulence of L. pneumophila released from symbiont-containing amoebae. Pronounced gene expression changes in the presence of the symbiont indicate that interference with the transition to the transmissive phase impedes the L. pneumophila infection. Finally, our data show that the defensive response of amoebae harboring P. amoebophila leaves the amoebae with superior fitness reminiscent of immunological memory. Given that mutualistic associations between bacteria and amoebae are widely distributed, P. amoebophila and potentially other amoeba endosymbionts could be key in shaping environmental survival, abundance, and virulence of this important pathogen, thereby affecting the frequency of human infection.

König L, Wentrup C, Schulz F, Wascher F, Escola S, Swanson MS, Buchrieser C, Horn M
2019 - mBio, 10: e00333-19

Lecture series

Deciphering population-specific activities of marine microbes with quantitative stable isotope probing

William Orsi
Ludwig-Maximilians-Universität München, Germany
12:00 h
Lecture Hall HS4, UZA2, Althanstrasse 14, 1090 Wien

Nanomaterials : Not the next asbestos or What 20 years of nanomaterial implication research has taught us

Prof. Dr. Mark Wiesner
Professor of Civil and Environmental Engineering, Pratt School of Engineering, Duke University, USA
16:30 h
Eberhard Clar-Saal (2B 204), Althanstrasse 14 UZA II, 1090 Vienna

Viral Intrahost Evolution – a Race in Space and Time

Andreas Bergthaler
CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences
12:00 h
Lecture Hall 2, UZA 1, Althanstr. 14, 1090 Wien