News archive

Postdoctoral fellowships
"Interdisciplinary Cancer Research" (INDICAR)

Postdoctoral Fellowships for the Marie Curie project "Interdisciplinary Cancer Research" (INDICAR) at the University of Vienna are available. We welcome applications of postdocs interested in intestinal microbiota and cancer research.
Please contact David Berry or Alexander Loy.
Further information

Movember at DoME
Thirteen Bros and Sistas from DoME joined
this year's Movember movement.


Open Postdoc and PhD student positions in Microbial Experimental Evolution
Two positions are available in the group of Matthias Horn within the ERC StG Project EVOCHLAMY. The project comprises aspects of evolutionary biology, microbiology, genomics, and bioinformatics.
Job advertisement Postdoc [PDF]
Job advertisement PhD student[PDF]

Two new FWF projects

Dagmar Woebken and David Berry received funding for new projects from the Austrian Science Fund. Dagmar will be "Investigating the function of the ubiquitous Acidobacteria in terrestrial environments". David will work on "The boundary keepers: Intestinal mucus-associated microbes".
 FWF Project database


DoME at castle Riegersburg
The DoME team visited a famous chocolate factory in Styria and conquered castle Riegersburg.

New collaborative large-scale project with the JGI
Michael Wagner and Holger Daims together with members of the Joint Genome Institute will sequence and analyze the whole genome amplification (WGA) products of 100 nitrifier microcolonies from a single activated sludge sample. The microcolonies will be identified by Raman microspectroscopy and sorted by optical tweezing for WGA. The major goal of this project is to understand the evolutionary history and ecological consequences of nitrifier microdiversity. This project will be funded in the framework of the community science program (CSP) of the JGI.
 CSP Sequencing Plans 2014 of DOE JGI

EMI cover image
The cover of the November issue of Environmental Microbiology features an image taken by Barbara Sixt. The cover page shows chlamydiae infecting terrestrial isopods after recovery in insect cell lines and immunofluorescence staining. The corresponding article is entitled "Developmental cycle and host interaction of Rhabdochlamydia porcellionis, an intracellular parasite of terrestrial isopods".

New Master curriculum Microbial Ecology
We have revised and updated the master curriculum Microbial Ecology. Studying microbial ecology is now part of the master studies Molecular Microbiology, Microbial Ecology, and Immunobiology. The new master is held completely in English; students are trained in microbial ecology, symbiosis research, molecular biology & evolution, genetics, environmental chemistry, and bioinformatics.
 Program overview and courses
 Announcement [German]

New paper in the American Journal of Gastroenterology
Together with colleagues from the Medical University of Vienna, Alexander Loy and David Berry explored if and how fecal microbiota transplantation support microbial recolonization of the gut of ulcerative colitis patients. They show that temporal bacterial community dynamics and therapy success varied strongly among individual patients that received this unusual treatment.
 News release
 Der Standard [German]
 Ö1 radio report in "Dimensionen" [MP3] [German]

New Paper in PLoS Pathogens
Chlamydial elementary bodies have mostly been thought of as dormant, spore-like particles. However, Barbara Sixt, Alexander Siegl, Matthias Horn and colleagues now demonstrate metabolic activity in chlamydial elementary bodies that is linked to infectivity. Challenging textbook knowledge, these results suggest that the infective stage is much more dependent on its environment (and thus potentially vulnerable) than previously recognized.
 uni:view Magazin [German]


DOME partnership with
DOE Joint Genome Institute (JGI)

The DOE JGI has recently launched the Emerging Technologies Opportunity Program (ETOP) in order to develop partnerships with groups developing new technologies that DOE JGI could establish to add value to the high throughput sequencing it currently carries out for its users. Six initiatives were chosen including a project proposed by Michael Wagner and Roman Stocker from the M.I.T. (Boston, USA) entitled "High-throughput sorting of microbial cells with specific functional traits for single cell genomics by combining labeling with heavy water, Raman microspectroscopy, microfluidics and flow cytometry". JGI will invest approximately $3.5 million over the next two years in this and the other ETOP projects.
 News release at DOE JGI website


New paper in FEMS Microbiology Reviews
Novel avenues are available for the analysis of intestinal ecophysiology to yield new insights into complex host-symbiotic microbiota-pathogen processes, such colonization resistance against infections. This review summarizes bioinformatics tools for revealing hypothetical interactions from metagenomic data and highlights the value of gnotobiotic mouse models and new single-cell approaches for testing these hypotheses and studying the in vivo physiology of the gut microbiota.
Stecher B, Berry D, Loy A. 2013. Colonization resistance and microbial ecophysiology: Using gnotobiotic mouse models and single-cell technology to explore the intestinal jungle. FEMS Microbiol. Rev. Early online publication.


Chinese Academy of Sciences honors Michael Wagner with 2013 Einstein Professorship
The Chinese Academy of Sciences has named Michael Wagner an Einstein Professor for 2013. As part of the professorship, Michael will visit several institutes in China early next year. He subsequently will host two Chinese scholars for several months at DoME.
 uni:view [German]


DoME to be member of the new Department of Microbiology
and Ecosystem Science

DoME joins forces with the Division of Terrestrial Ecosystem Research and the Division of Computational Systems Biology to form the new Department of Microbiology and Ecosystem Science. Michael Wagner will serve as head of the new department for the first two year term.


Dr. rer. nat. Barbara Sixt
Barbara successfully defended her PhD thesis entitled "Host-free metabolic activity of chlamydial symbionts of amoebae and their interaction with the cellular suicide machinery of metazoan host cells". The board of examiners included Jan Rupp, Thomas Decker, and Matthias Horn. Congratulations!

Federal Minister Töchterle visits DoME
Austrian Federal Minister for Science and Research Karlheinz Töchterle visited DoME today. Together with Eva Nowotny, head of the executive board of the University of Vienna, Heinz W. Engl, rector of the University of Vienna, Karl Schwaha, vice rector, and Horst Seidler, dean of the Faculty of Life Sciences, he was introduced by the DoME team to current research at the department.
 Press report [German]
 uni:view [German]


New FWF project
Dagmar Woebken and Stephanie Eichorst received funding for a new project from the Austrian Science Fund. The project will focus on the active free-living diazotrophs in terrestrial ecosystems and the factors influencing their activity using a single cell approach.
 FWF Project database


New paper in PNAS
A DOME team encompassing David Berry, Alexander Loy, Arno Schintlmeister, Jochen Reichert, and Michael Wagner used NanoSIMS to identify mucus-degrading bacteria in the mouse gut. Together with collaborators providing expertise in IR-MS measurements and animal experiments, they showed that this important process is influenced also by non-degrading community members. The technique presented in this paper allows for the first time direct functional investigation of microbes in the gut on a single cell level.
 Article text
 Press report [German]


New papers in Environmental Microbiology and Frontiers in Microbiology
DOME teams around Michael Wagner and Holger Daims led two genome projects of nitrifying microorganisms representing lineages of global importance. The ammonium-oxidizing archaeon Ca. Nitrososphaera gargensis is the first member of the so-called soil group or group I.1b whose genome was sequenced. This analysis showed that these organisms are metabolically much more flexible than their marine counterparts. The second study reports on the genome of the major marine nitrite oxidizer Nitrospina gracilis and demonstrates that this widespread organism represents a novel bacterial phylum challenging its previous classification.
 Article on Nitrososphaera gargensis
 Article on Nitrospina gracilis


Acanthamoeba sp. trophozoite21.02.13
New paper in Genome Biology
In this international collaboration Ilias Lagkouvardos and Matthias Horn contributed the analysis of the impact of lateral gene transfer on the evolution of amoeboid genomes to suggest that in amoebae, lateral gene transfer is reflective of trophic strategy and driven by the selective pressure of new ecological niches.
 Article text

Michael Wagner elected as fellow in the American Academy of Microbiology
The American Academy of Microbiology is the leadership group of the American Society for Microbiology, the world's oldest and largest life-science organization. Academy fellows are elected annually through a highly selective, peer-review process, based on their records of scientific achievement and original contributions that have advanced microbiology. As a fellow, Michi joins a group of eminent leaders in the field of microbiology recognized for their excellence, originality, creativity and exemplary careers in basic and applied research, teaching, clinical and public health, industry or government service. The academy relies on fellows for authoritative advice and information on critical issues in microbiology, from responding to congressional inquiries to organizing meetings and workshops.
 Homepage of the American Academy of Microbiology


New daime version released
daime is our digital image analysis and visualization software for analyzing 2D and 3D microscopy datasets of fluorescence- labeled microorganisms. Version 2.0 is a major update with many new features and improvements.
 daime website

Two new FWF projects
Holger Daims and Alex Loy received funding for new projects from the Austrain Science Fund. Alex will work on "The cold microbial majority - marine sulfate-reducing microorganisms". Holger aims at "Illuminating the Ecology of Nitrite-Oxidizing Bacteria".
 FWF Project database


Karin Aistleitner, Alex Siegl win Pecha Kucha contest
Karin Aistleitner and Alex Siegl won the Pecha Kucha contest "Biology on Stage - 400 Seconds of Life" with her presentation "Training in the gym pays off: Amoebae as training ground for bacterial pathogens".
 Event homepage


City of Vienna Award for Alex Loy
Alex Loy was awarded with the "Förderungspreis der Stadt Wien 2012" from the City of Vienna.


New paper in Nature
Milucka J, Ferdelman TG, Polerecky L, Franzke D, Wegener G, Schmid M, Lieberwirth I, Wagner M, Widdel F and Kuypers MMM. 2012. Zero-valent sulphur is a key intermediate in marine methane oxidation. Nature doi:10.1038/nature11656
Markus Schmid and Michael Wagner contributed Raman microspectrometry analyses in this international collaboration to discover that the archaea responsible for the anaerobic oxidation of methane also reduce sulfate. Disulphide formed in this reaction is then consumed by deltaproteobacterial partners rendering the archaeal sulfate reduction more energy efficient. Thus, the metabolic model of anaerobic methane oxidation has to be revised by integrating the two newly described metabolic processes.
 Article text
 Press report [German]


New WWTF project
Alex Loy and David Berry received funding for a new project from the Vienna Science and Technology Fund: Nutrition and the intestinal microbiota-host symbiosis -- A holistic stable isotope-labeling approach to decipher key microbial players and quantitatively link single cell activity to system function.
 WWTF Life Science Call 2012


Encarsia pergandiella, the host of Cardinium hertigii25.10.12
New paper in PLoS Genetics
Penz T, Schmitz-Esser S, Kelly SE, Cass BN, Müller A, Woyke T, Malfatti SE, Hunter MS, Horn M. 2012. Comparative genomics suggests an independent origin of cytoplasmic incompatibility in Cardinium hertigii. PLoS Genetics 8: e1003012.
Together with an international team Thomas Penz and Matthias Horn deciphered the biology of a bacterial symbiont able to manipulate reproduction of its insect host and analysed the evolutionary history of this unusual trait.
 Full text
 Press report [German]

Dr. rer. nat. Elena Tönshoff
Elena successfully defended her PhD thesis entitled "Diversity and ecology of bacteriocyte-associated symbionts in adelgids" and received the biggest doctoral cap ever. The board of examiners included Monika Bright, Wolfgang Miller, and Matthias Horn. Congratulations!

David Berry, Assistant Professor
David Berry was promoted to the position of an Assistant Professor (tenure track) and will start a new group at DoME.
Congratulations, great to have you on board!
 David's homepage

DoME up in the trees
This summer the DoME team followed the tracks of our great ape ancestors in a high ropes course
in the Vienna Woods.

DoME at the KinderuniWien 2012
For the sixth time the DoME team held an interactive lecture for children between the age of seven and 12 at the KinderuniWien. The KinderuniWien is an annual summer school for children interested in science and the arts, with more than 4000 registered participants this year.

 Homepage KinderuniWien [German]
 DoME an der KinderuniWien

International FISH Course 2013: Vienna, February 18-22. Registration is now open!
more ...

Ö1 Radio feature about environmental chlamydiae and apoptosis
Barbara Sixt and Matthias Horn talk about a recent study demonstrating that the development of the ability to inhibit apoptosis was a key step in the evolution of chlamydiae as pathogens of humans and animals.
 Ö1 radio report in "Dimensionen" [MP3] [German]
 Full text of the paper at PLoS One
 uni:view [German]

Habilitation awarded to Holger Daims
After a public lecture on Friday, April 20, the habilitation was awarded to Holger. Congratulations!


EMI cover image
The cover of the May issue of Environmental Microbiology features an image taken by Elena Toenshoff. The image shows a 3-D reconstruction of bacteriocyte-associated symbionts in adelgids. In her study she describes the role of co-evolution and symbiont replacement during evolution of this symbiosis.
 Full text

Habilitation awarded to Alexander Loy
After a public lecture on Friday, April 13, the habilitation was awarded to Alex. Congratulations!


A full dozen
Since establishment of DoME in 2003 members of DoME had 11 children. The 12th was born yesterday. Welcome, and congratulations to the parents!


Welcome, Dagmar!
DoME welcomes Dr. Dagmar Woebken as leader of the new NanoSIMS Group. She did her postdoctoral work at Stanford University/NASA Ames/Lawrence Livermore National Laboratory and is with DoME since January.
 Dagmar's homepage

ERC Advanced Grant for Michael Wagner
Michael Wagner has received an ERC Advanced Grant for his project "Nitrification Reloaded – a Single Cell Approach (NITRICARE)". This is the second ERC grant for a member of DoME this year.
 Press release [German]
 European Research Council

Doc.Award for Roland Hatzenpichler
Roland Hatzenpichler received a Doc.Award from the City of Vienna for his doctoral thesis entitled "Identification and characterization of novel ammonia-oxidizing archaea and bacteria". After his PhD at DoME, Roland is now at the California Institute of Technology.
 Roland Hatzenpichler


DOC Fellowship for Frederik Schulz
Frederik Schulz received a PhD (DOC) fellowship from the Austrian Academy of Sciences for funding of his PhD project "Life inside the nucleus – an unusual symbiont of amoebae related to rickettsiae".
 DOC - Doctoral Fellowship Programme
    of the Austrian Academy of Sciences

 Project summary


New paper in PNAS
Mußmann M, Brito I, Pitcher A, Damsté JSS, Hatzenpichler R, Richter A, Nielsen JL, Nielsen PH, Müller A, Daims H, Wagner M, Head IM. 2011. Thaumarchaeotes abundant in refinery nitrifying sludges express amoA but are not obligate autotrophic ammonia oxidizers. Proc. Natl. Acad. Sci. U. S. A., in press.
 Full text
 Der Standard [German]
   uni:view [German]

DoME goes Monsterroller
Fear is not an option - the DoME team drove down mountain Hirschkogel on Monsterrollers during this year's summer trip.     Join Thomas on his Monsterroller in this video [WMV]

ERC Starting Grant for Matthias Horn
Matthias Horn has received an ERC Starting Grant for his project "The Evolution of the Chlamydiae - an Experimental Approach (EVOCHLAMY)".
 Press release [German]
 European Research Council

DoME at the KinderuniWien 2011
For the fifth time the DoME team held an interactive lecture for children between the age of seven and 12 at the KinderuniWien. The KinderuniWien is an annual summer school for children interested in science and the arts, with more than 4400 registered participants this year.
 Homepage KinderuniWien [German]
 DoME an der KinderuniWien
The lecture of DoME at the KinderuniWien was kindly supported by

New paper in PNAS
Gruber-Vodicka HR, Dirks U, Leisch N, Baranyi C, Stoecker K, Bulgheresi S, Heindl NR, Horn M, Lott C, Loy A, Wagner M, Ott J. 2011. Paracatenula, an ancient symbiosis between thiotrophic Alphaproteobacteria and catenulid flatworms. Proc. Natl. Acad. Sci. U. S. A. , in press.
Members of DoME have contributed Raman microspectroscopy analyses among other things to characterize at the single cell level the bacterial symbionts investigated in this collaboration with the Department of Marine Biology at the University of Vienna.
 Full text

Dr. rer. nat. Roland Hatzenpichler
Roland successfully defended his PhD thesis. The board of examiners included James Prosser, Thomas Rattei and Michael Wagner. Roland will start to work as postdoc at the Division of Geological and Planetary Sciences, California Institute of Technology.


New paper in MBE
Collingro A, Tischler P, Weinmaier T, Penz T, Heinz E, Brunham RC, Read TD, Bavoil PM, Sachse K, Kahane S, Friedman MG, Rattei T, Myers GSA, Horn M. (2011) Unity in variety – the pan-genome of the Chlamydiae. Mol. Biol. Evol., online early.
An international collaboration led by Matthias Horn reports on novel insights into the evolution of chlamydiae by phylogenomic anaysis.
 Full text

New paper in PNAS
Tourna M, Stieglmeier M, Spang A, Koenneke M, Schintlmeister A, Urich T, Engel M, Schloter M, Wagner M, Richter R, Schleper C. Nitrososphaera viennensis, an ammonia oxidizing archaeon from soil. Proc. Natl. Acad. Sci. USA , in press.
Michael Wagner and Arno Schintlmeister from DoME and the NanoSIMS Lab have contributed in this collaboration with the Department of Genetics in Ecology at the University of Vienna to the first isolation and in-depth characterization of an ammonia oxidizing archaeon from soil.
     Press release
     NanoSIMS Lab at the University of Vienna

Michael Wagner elected vice-president of the International Society for Microbial Ecology (ISME), to become ISME president in 2012
The International Society for Microbial Ecology is the principle scientific society for the burgeoning field of Microbial Ecology and its related disciplines. ISME fosters the exchange of scientific information by organizing international symposia as well as specific workshops, sponsoring publications, and promoting education and research. The ISME symposia, organized every two years, are the largest international meetings addressing the wide range of topics in Microbial Ecology.
     Homepage ISME
     Die Universität Online [German]

International Year of Biodiversity
DoME celebrates the United Nations' International Year of Biodiversity and contributes to a symposium on biodiversity research in Austria.
Symposium homepage
United Nations Int. Year of Biodiversity

Symposium "Symbiotic Interactions"
November 25/26

Internationally renowned scientists and students of the graduate school Symbiotic Interactions present an interdisciplinary symposium on symbiosis. Symposium homepage

Major probeCheck update
After the melt down of the original probeCheck server due to a failure of our air conditioning system, probeCheck runs on new, 64 bit hardware now. The current releases of Silva (102) can be queried; other databases will be included again soon. probeCheck web server

International FISH Course 2011: Vienna, February 21-25. Registration is now open!
more ...

New paper in PNAS
Lücker S, Wagner M, Maixner F, Pelletier E, Koch H, Vacherie B, Rattei T, Sinninghe Damsté JS, Spieck E, Le Paslier D, Daims H. 2010. A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria. Proc. Natl. Acad. Sci. USA , in press.
     Full text
     Press release [German]
     Der Standard [German]
     Die Presse [German]

Opening of the new NanoSIMS facility
Analytical nano secondary ion mass spectrometry (NanoSIMS) imaging is perfectly suited to measure, visualize and quantify the distribution of elements and their stable isotopes in environmental samples or at the sub-cellular level in biological material. The Nano SIMS lab of the Core Facility for Advanced Isotope Research offers access to one of the most modern secondary ion mass spectrometers currently available, the NanoSIMS 50L (CAMECA).
 Homepage of the new NanoSIMS lab
 Press release [German]
 Die Universität Online [German]

pCOMP - Predicted Chlamydia Outer Membrane Proteins
This new database presents a browsable and searchable collection of putative outer membrane proteins of chlamydiae predicted by a comprehensive and multiphasic in silico approach as described in Heinz et al. 2009. BMC Genomics 10:634.

Michael Wagner elected member of the German Academy of Sciences Leopoldina
The Academy was founded in 1652 and is the world’s oldest continuously existing academy of medicine and natural sciences. In 2008 it officially became the National Academy of Sciences of Germany. The Leopoldina has more than 1.300 members all over the world. Members are elected in a free and secret ballot by the Presidium based on demonstrated academic excellence.
     Homepage Leopoldina
     Der Standard [German]
     Wiener Zeitung [German]
     Die Universität Online [German]


Holger Daims awarded with the "Wiener Zukunftspreis"
Holger Daims made the second place in the category "Newcomer & Start-ups" of the "Wiener Zukunftspreis", which is awarded annually by the city of Vienna and the magazine News.
     die Universität Online [German]
     Report in "News" [German]

8. Deutscher Chlamydien Workshop
The upcoming German work shop on all aspects of chlamydia research, from basic science to clinical research, diagnostics and therapy, will take place in Munich from February 24-26, 2010.
    Plenary speaker are Agathe Subtil (Institut Pasteur) and Jürgen Heesemann (Max von Pettenkofer-
    Institut für Hygiene und Medizinische Mikrobiologie). Registration is now open!
      Conference Homepage [German]

New paper in Science
Hubert C, Loy A, Nickel M, Arnosti C, Baranyi C, Brüchert V, Ferdelman T, Finster K, Christensen FM, Rosa de Rezende J, Vandieken V, Jørgensen BB. 2009. A constant flux of diverse thermophilic bacteria into the cold Arctic seabed. Science 325: 1541-1544.
     Abstract and full text
     Press release [German]
     Der Standard [German]
     Die Universität Online [German]


On the trail of Nitrospira
A recent article in "die universität online" reports on a new WWTF project of Holger Daims and his team.
 Auf den Spuren der geheimnisvollen Nitrospira-Bakterien

Wintersemester 2009
Alle Lehrveranstaltungen im WS09 im Überblick  mehr...
Infobroschüre Lehrveranstaltungen am Department für Mikrobielle Ökologie  PDF-Download

International FISH Course 2010 (February 22-26)
Preliminary program and application form now available!
Application deadline is November, 13. more...

1st DoME Poker Championship
The first DoME Poker Championship took place on August 17. After three rounds of Texas Hold'em (No Limit) on four tables the first DoME Poker Champion was ... Chrissy! Congratulations.


DoME at the KinderuniWien 2009
For the third time the DoME team held an interactive lecture for children between the age of seven and 12 at the KinderuniWien 2009. The KinderuniWien is an annual program for children interested in science and the arts, with more than 3700 registered participants this year.
 Homepage KinderuniWien 2009
 DoME an der KinderuniWien


New paper in Annual Review of Microbiology
Wagner M. 2009. Single-cell ecophysiology of microbes as revealed by Raman microspectroscopy or secondary ion mass spectrometry imaging. Ann. Rev. Microbiol., in press.
 Abstract and full text

New paper in PLoS Pathogens
Arnold R, Brandmaier S, Kleine F, Tischler P, Heinz E, Behrens S, Niinikoski A, Mewes HW, Horn M, Rattei T. 2009. Sequence-based prediction of type III secreted proteins. PLoS Pathogens 5: e1000376.
      Full text article
      The signal for signaling, found (Grynberg M and Godzik A, PLoS Pathog 5: e1000398)

© ÖAW / R. Herbs03.06.09
Michael Wagner, Matthias Horn new members
of the Austrian Academy of Sciences (ÖAW)

At the Ceremonial Meeting 2009, Michael Wagner was accepted as a corresponding member of the Austrian Academy of Sciences , and Matthias Horn was accepted as a member of the "Young Academy"
    of the Austrian Academy of Sciences.
     Homepage of the Austrian Academy of Sciences


7. Deutscher Chlamydien Workshop
The annual German work shop on all aspects of chlamydia research, from basic science to clinical research, diagnostics and therapy, this time takes place in Lübeck from March 4-6, 2009.
      Conference Homepage [German]

City of Vienna Award for Michael Wagner
The City of Vienna Awards are awarded anually to individuals with major achievements in either of nine different categories ranging from architecture, literature and art to humanities and natural sciences. Michael Wagner received the City of Vienna Award 2008 in the category Natural Sciences.
 Die Universität Online [German]

Nichts für schwache Nasen
Michael Wagner und Holger Daims im TV-Feature "Forschen und Entdecken" über die Rolle von Mikroorganismen bei der Abwasserbehandlung.  Video [WMV]

DoME an der KinderUni Wien 2008
Auch dieses Jahr wieder war DoME mit der Vorlesung "Warum sind Bakterien für uns so wichtig? - Erstaunliches und Unerwartetes aus dem unsichtbaren Reich der Bakterien" an der Kinderuni Wien vertreten.
Ö1 Kinderuni, DoME im Radiointerview

New paper in Nature Rev. Microbiology
Decisions on the existence of species and methods to define them should be guided by a method-free species concept that is based on cohesive evolutionary forces. This review summarizes current approaches to defining species and the problems of these approaches, and presents selected examples of the population genetic patterns at and below the species level.
Achtman M, Wagner M. 2008. Microbial diversity and the genetic nature of microbial species. Nature Rev. Microbiol., in press. Advance Online Publication

New paper in Ann. Rev. Microbiology
Although Chlamydiae are major pathogens of humans and animals, they were long recognized only as a phylogenetically well-separated, small group of closely related microorganisms. Today, several chlamydia-like bacteria have been described as symbionts of free-living amoebae and other eukaryotic hosts. Some of these environmental chlamydiae might also be of medical relevance for humans. Their analysis has contributed to a broader understanding of chlamydial biology and to novel insights into the evolution of these unique microorganisms.
Horn M. 2008. Chlamydiae as symbionts in eukaryotes. Ann. Rev. Microbiol. 62: 113-131.
Reviews in Advance

DoME at the Vienna City Marathon
DoME was part of the relay team of the University of Vienna
at the Vienna City Marathon 2008.
 Die Universität Online

New paper in PNAS
Thermophilic ammonia-oxidizing archaea have recently been discovered, in an enrichment from a geothermal spring, by researchers of the University of Vienna, the University of Hamburg, and the Winogradsky Institute of Microbiology. Single-cell metabolic analysis revealed that this archaeon is active at low ammonium concentrations, but highly sensitive to slightly increased amounts of this substrate. Its preference for elevated temperatures supports the hypothesis that ammonia-oxidizing archaea originated from a thermophilic ancestor.
Hatzenpichler R, Lebedeva EV, Spieck E, Stoecker K, Richter A, Daims H, Wagner M. 2008. A moderately thermophilic ammonia-oxidizing crenarchaeote from a hot spring. Proc. Natl. Acad. Sci. USA 105: 2134-2139.  Abstract (PNAS website)     PDF
 Unerwarteter Mikroorganismus in heißer Quelle (Die Universität Online)
 Ö1 radio report in "Wissen Aktuell" [MP3]
 Wiener entdecken neue Mikroorganismen (Der Standard)

Alexander Loy received Focus of Excellence Award
The Focus of Excellence Award of the Faculty of Life Sciences at the University of Vienna is granted annualy to promote young research scientists. DoME's group leader Alexander Loy received this year's award for his work on diagnostic microarrays and sulfate reducing bacteria.
 Fakultät für Lebenswissenschaften wählt Jungwissenschafter 2007 (Die Universität Online)
 Hitzeliebende Sulfatreduzierer auch in der Arktis (Die Universität Online)
 Ressourcenkampf der Mikroben im Fichtelgebirge (Die Universität Online)

DoME contributes cover page for
"Brock - Biology of Microorganisms"

The twelfth edition of "Brock - Biology of Microorganisms" (Madigan, Martinko, Dunlap, Clark, eds.) features on the cover a figure showing the filamentaous methane oxidizer Crenothrix polyspora, contributed by Kilian Stoecker, Holger Daims, and Michael Wagner. The figure was created from a confocal image stack processed and rendered using the image analysis software daime. Brock is among the most widely used, authoritative text books for introductory microbiology.
 Software daime
 Original paper on Crenothrix polsypora

Graduate school "Symbiotic Interactions" started
The Graduate school ("Initiativkolleg") Symbiotic Interactions has started. Nine Ph.D. students are enrolled in nine different projects focusing on the interaction among microbes and between microbes and animals or humans.
 Die Universität Online [German]
 Homepage of the graduate school "Symbiotic Interactions"

6. Deutscher Chlamydien Workshop
Ulm, 27.-29. Februar
 Offizielle Tagungshomepage
 Flyer [PDF]

New paper in PLoS Biology: Trentmann O, Horn M, van Scheltinga AC, Neuhaus HE, Haferkamp I. 2007. Enlightening energy parasitism by analysis of an ATP/ADP transporter from chlamydiae. PLoS Biol. 9: e231.
 PLoS Biology

probeCheck beta test
We are proud to announce the beta test of probecheck, a new web server for convenient testing of probe and primer specificity and coverage. probeCheck uses an extendable list of established sequence databases including the rRNA database Silva, RDP-II, and Greengenes, and the functional gene databases of FGPR.
 probeCheck webserver

DoME at the KinderuniWien: It is the 5th anniversary of the KinderUniWien, a university for children between the age of 7 and 12, that exists for only few weeks each year during the official school holidays. This year, more than 3,000 children have registered, and the Department of Microbial Ecology has contributed an interactive lecture on the importance of bacteria for life on planet earth entitled "Warum sind Bakterien für uns so wichtig? - Erstaunliches und Unerwartetes aus dem unsichtbaren Reich der Bakterien".
Homepage of the KinderuniWien 2007 [German]
DoME an der KinderuniWien [German]


Bank Austria Creditanstalt Award: Six students and scientists from the University of Vienna have recieved awards from the Bank Austria Creditanstalt for their innovative research or education projects. Among them was our postdoc Kilian Stoecker. Die Universität Online [German]

International FISH Course 2008: Vienna, February 25-29. Registration is now open!
more ...

New paper in Microbiol. Mol. Biol. Rev.
Taylor M, Radax R, Steger D, Wagner M. 2007. Sponge-associated microorganisms: evolution, ecology and biotechnological potential. Microbiol. Mol. Biol. Rev. 71: 295-347.
Download ARB database

Call for applications: Ph.D. positions in the graduate school ("Initiativkolleg") "Symbiotic Interactions"
The graduate school "Symbiotic Interactions" at the University of Vienna, an interdisciplinary Ph.D. program focusing on the interaction among microbes and between microbes and protozoa, animals, and humans, awards up to nine doctoral positions to highly qualified and motivated students starting October 1, 2007. Application deadline: June 30, 2007
Homepage of the graduate school "Symbiotic Interactions"

Erregern auf der Spur
Wiener Forscher untersuchen Umwelt-Chlamydien. Mehr im Standard ...

Unbequeme Untermieter - Bakterien, die in Zellen leben
Bakterien haben im Laufe der Evolution die seltsamsten Lebensräume und Nischen besiedelt. Manche von ihnen leben sogar in den Zellen anderer Lebewesen. Solche intrazellulären "Mitbewohner" beeinflussen das Leben vieler Pflanzen, Tiere und Menschen entscheidend. Ein kürzlich gestartetes Projekt im Rahmen eines universitären Forschungsschwerpunktes widmet sich den "Bösewichten" unter ihnen. Mehr auf Die Universität Online ...

Research focus "Symbiosis": The research focus "Symbiosis" of the Faculty of Life Sciences at the University of Vienna, coordinated by the Department of Microbial Ecology, launched a new website.
 Homepage of the research focus

5. Deutscher Chlamydien Workshop
Hannover, 7.-9. März
 Offizielle Tagungshomepage

New paper in Nature Reviews Microbiology:
Battin TJ, Sloan WT, Kjelleberg S, Daims H, Head IM, Curtis TP, Eberl L (2007). Microbial landscapes: new paths to biofilm research. Nature Rev. Microbiol. 5: 76
Die Universität Online [in German]
Nature Reviews Microbiology

Radio feature in Ö1: Mikrostadt Biofilm
 Teil 1 [MP3];  Teil 2 [MP3];  Teil 3 [MP3]

Radio feature in Ö1: Trickreiche Kleinstlebewesen
 Teil 1 [MP3];  Teil 2 [MP3];  Teil 3 [MP3];  Teil 4 [MP3];  Teil 5 [MP3]

Geistesblitz: Freund oder Feind
Matthias Horn erforscht Symbiosen von Bakterien und Amöben. Mehr im Standard ...

Nützliche Parallelwelt
Mikrobiologe Michael Wagner unter Top Ten bei Publikationen und damit der bestplatzierte in Österreich arbeitende Naturwissenschafter - ein Geistesblitz. Mehr im Standard ...


11th International Symposium on Microbial Ecology, Vienna, August 20-25, 2006
Congress Homepage, Die Universität Online [in German], Der Standard [in German] ...

International FISH Course 2007. Preliminary program and application form now available! Application deadline is November, 17. more...


5th International Symbiosis Society (ISS) Congress, Vienna, August 4-10, 2006
Congress Homepage, Die Universität Online [in German]

Crenothrix polyspora and Amoebophilus asiaticus genome projects
The Department of Microbial Ecology participates with two projects in the Community Sequencing Program at the Joint Genome Institute (JGI). In this framework, the whole genome of the Acanthamoeba symbiont Amoebophilus asiaticus and the filamentous methanotroph Crenothrix polyspora will be sequenced.
Crenothrix polyspora project description
Amoebophilus asisaticus project description
Press release [in German]
Die Universität Online [in German]
Wiener Zeitung [in German]

Forschung an trickreichen Bakterien
Seit drei Jahren forscht Matthias Horn an der Universität Wien, seit Februar 2006 hat er eine Professur für Mikrobielle Symbiosen am Biozentrum Althanstraße der Fakultät für Lebenswissenschaften inne. In der Scientific Community hat er sich mit seinen Untersuchungen zu bestimmten Bakterien – den Umweltchlamydien, die mit Amöben in Symbiose leben – einen Namen gemacht. Im Gespräch erzählt er über seine aktuelle Forschung, die Perspektiven für junge WissenschafterInnen und den neuen Bachelor Biologie an der Universität Wien. Mehr auf Die Universität Online ...

Michael Wagner ranked 3rd and 8th in rankings of microbiologists and evolutionary biologists, respectively, in Germany, Austria, and Switzerland. Laborjournal [PDF, in German]
Die Universität Online [in German],  Der Standard Online [in German],  Kurier [in German]
 Die Presse [in German]

Ressourcenkampf der Mikroben
So gut sulfatreduzierende Mikroorganismen im Meer untersucht sind, so wenig weiß man über ihre Rolle in terrestrischen Feuchtgebieten. Offenbar vollkommen neue Vertreter dieser Spezies haben Mikrobiologen der Universität Wien in einem bayerischen Moor entdeckt. Ein soeben begonnenes FWF-Projekt am Department für Mikrobielle Ökologie soll klären, wie diese Organismen es schaffen, dort zu überleben. Mehr auf Die Universität Online ...

20.4.06 Our website can now also be reached at

New paper in Nature: Strous M, Pelletier E, Mangenot S, Rattei T, Lehner A, Taylor MW, Horn M, Daims H, Bartol-Mave D, Wincker P, Barbe V, Fonknechten N, Vallenet D, Segurens B, Schenowitz-Truong C, Médigue C, Collingro A, Snel B, Dutilh BE, Op den Camp HJM, van der Drift C, Cirpus I, van de Pas-Schoonen KT, Harhangi HR, van Niftrik L, Schmid M, Keltjens J, van de Vossenberg J, Kartal B, Meier H, Frishman D, Huynen MA, Mewes HW, Weissenbach J, Jetten MSM, Wagner M, Le Paslier D (2006). Deciphering the evolution and metabolism of an anammox bacterium from a community genome. Nature 440: 790.
Press release [in German]
Forschungsnewsletter der Universität Wien [in German]
Der Standard [in German]
Die Presse [in German]

Wissenschaftstag 2006: Freitag, 31. März. Der wissenschaftliche Nachwuchs des Vienna Ecology Centre präsentiert aktuelle Forschungsprojekte; Abstract Deadline 17. März more...

New paper in PNAS: Stoecker K, Bendinger B, Schöning B, Nielsen PH, Nielsen JL, Baranyi C, Toenshoff ER, Daims H, Wagner M. (2006) Cohn’s Crenothrix is a filamentous methane oxidizer with an unusual methane monooxygenase, published online on February 1 (Track II).
PNAS Open Access Article
Press release [in German]
Ö1 radio report [MP3 audio file, 6 MB, in German]


4. Deutscher Chlamydienworkshop: 1.-3. März, in Düsseldorf more...

First release of daime available: This new software for digital image analysis in microbial ecology is now available for Linux and Windows operating systems. more...

START Award for Matthias Horn. FWF press release [German]; Der Standard [German]; Forschungsnewsletter der Universität Wien [German]

TV feature in Modern Times (ORF): Molecular analysis of complex microbial communities.
 view video [Windows Media Player, 8MB, in German]

New paper in PLoS Biology: Sabehi G, Loy A, Jung KH, Partha R, Spudich JL, Isaacson T, Hirschberg J, Wagner M, Beja O. 2005. New insights into metabolic properties of marine bacteria encoding proteorhodopsins. PLoS Biology 3: e273. more...

Lazy but smart
The discovery of novel transport proteins reveals how bacteria that live inside unicellular microorganisms exploit their host cells.
predicted secondary structure of the NAD transporterResearchers from the Universities of Vienna (M. Horn, M. Wagner) and  Kaiserslautern (I. Haferkamp, E. Neuhaus) have discovered how intracellular bacteria that are closely related with chlamydiae, major pathogens of humans (with more than 60 Million infections per year), exploit their host cells. These symbiotic bacteria thrive within amoebae or human cells and thus can rely on their hosts providing complex and energy-rich nutrients. As a consequence these bacteria have lost the ability to synthesize essential compounds on their own. In the physiological sense, they got "lazy" during evolution.
This reduction of metabolic capability was only possible by simultaneous development of highly specific transport mechanisms. For the first time the research team was able to identify a transport protein for the universal electron carrier and co-factor NAD+ (nicotinamide adenine-dinucleotide). In concert with similar transport proteins the bacteria are able to in addition import energy (as ATP) and further nucleotides, the basic modules of DNA. These transport proteins thus ensure a constant supply of highly valuable substrates from the host cells nutrient pool, the researchers report in the science magazine Nature (December 2nd 2004).
As these transporters are only present in the bacteria but not in the host cells, they might represent promising targets for novel antibiotics. The development of novel drugs for anti-bacterial therapy is one of the major challenges of our time.
 Abstract (Nature)
 Press release [PDF]
 Press release in German [PDF]
Press coverage (in German)
 Die Presse, 6.12.04
 dieUniversitaet, 2.12.04
 Der Standard, 1.12.04

Die Abteilung Mikrobielle Ökologie auf der ScienceWeek
im Museumsquartier



Living Microbial Fossils
© AAAS/Science Genome sequencing of bacteria that have been living in unicellular organisms since primeval times revealed novel insights into the evolution of major bacterial pathogens of humans.
The first complete genome sequence of a bacterium that lives as a symbiont inside amoebae was recently determined by researchers at the Technische Universität München (Germany) and the University of Vienna (Austria).
The investigated bacteria have only recently been discovered and represent the closest living relatives of chlamydiae, according to Michael Wagner and Matthias Horn, lead authors of the study. Chlamydiae are among the most successful bacterial pathogens of humans and cause more than 60 million infections per year.
Deciphering the genetic material of the chlamydia-related symbiont allowed reconstruction of the biology and genetic make-up of the last common ancestor of the symbiont and pathogenic chlamydiae, which had lived in the Precambrian some 700 million years ago. The chlamydial ancestor was already dependent on an animal or plant host cell, presumably an ancient primitive unicellular organism. Long before the first vertebrates roamed the earth, primeval chlamydiae were colonising protozoa and exploiting them as host cells. Today these same strategies of host colonization enable modern chlamydiae and other bacterial pathogens to infect animals and humans. Protozoa (such as amoeba) should thus not be considered merely as predators feeding on bacteria, but also as key players in the evolution of important contemporary pathogens.
The research will be published on 08. April 2004 in Sciencexpress ( and shortly thereafter in the printed version of the journal Science Magazine (Science 304, 728-730).
 Press release [PDF]
 Press release (German) [PDF]
 Advance online publication in Sciencexpress
 Living Microbial Fossils. Movie showing environmental chlamydia UWE25 within
    its amoeba host cells. © AAAS/Science. [Windows Media Player], [Quicktime]
 "Chlamydial evolution probed" in "The Scientist"
 "Zell-Invasion seit 700 Millionen Jahren" in "Die Presse" (German)
 "Mikrobielle Fossilien mit altbewährten Tricks" in "" (German)

Wiener Forschungsfonds WWTF fördert zehn Life Science-Projekte
  Die vollständige APA Pressemitteilung

Amöben: Trojanische Pferde für Bakterien
Die mikrobielle Ökologie ist ein Forschungsgebiet, das nicht zuletzt durch neue molekularbiologische Techniken in den letzten Jahren enorm an Bedeutung gewonnen hat. Beginnend mit einer Reihe neuer Forschungsprojekte will man diesen Forschungszweig auch an der Universität Wien etablieren. Ein interdisziplinäres Projekt zur Symbiose von Bakterien und Amöben wurde nun vom FWF bewilligt.
  Der vollständige Artikel auf

EDGE - Genomanalyse neuartiger Umwelt-Chlamydien
Die Arbeitsgruppe "Mikrobielle Ökologie" der Technischen Universität München unter Leitung von PD Dr. Michael Wagner und die MWG-Biotech AG (Ebersberg) haben sich im Rahmen eines Projekts zur Genomsequenzierung und -analyse eines Vertreters der erst kürzlich entdeckten Umwelt-Chlamydien zusammengeschlossen. Ziel dieser Kooperation, die vom Bundesministerium für Bildung und Forschung gefördert wird, ist das Erlangen eines umfassenden Überblicks über die Biologie dieser neuartigen Mikroorganismen, sowie die Aufklärung der genetischen Unterschiede zwischen den Umwelt-Chlamydien und deren humanpathogenen Verwandten. Damit sollen unter anderem neue Wege bei der Therapie von Chlamydieninfektionen aufgezeigt werden.
Chlamydien sind bedeutende bakterielle Krankheitserreger des Menschen. Deren wichtigsten Vertreter zählen zu den am häufigsten sexuell übertragenen, pathogenen Bakterien (Chlamydia trachomatis) oder verursachen weitverbreitete Atemwegerkrankungen (Chlamydophila pneumoniae). In letzter Zeit gerieten Chlamydien verstärkt ins öffentliche Interesse, nachdem sie zudem mit der Entstehung von Artheriosklerose und Asthma in Zusammenhang gebracht wurden.
Am Lehrstuhl für Mikrobiologie konnten Chlamydien-ähnliche Bakterien erstmals auch in der Umwelt nachgewiesen werden. Inzwischen konnte die Arbeitsgruppe zeigen, dass die Biodiversität der Umwelt-Chlamydien beispielsweise in Kläranlagen noch weit über den heute bekannten Stand hinausgeht. Zudem gibt es eine Reihe von Befunden, die eine medizinische Bedeutung der Umwelt-Chlamydien möglich erscheinen lassen. So wurden bei Patienten mit Atemwegerkrankungen mit Hilfe immunologischer und molekularbiologischer Verfahren Hinweise auf eine Beteiligung von Umwelt-Chlamydien gefunden. Dies deckt sich mit Laborexperimenten, die zeigen, dass zumindest einige der Umwelt-Chlamydien auch Säugetierzellkulturen infizieren können.
Im Rahmen von EDGE, dem "environmental chlamydiae genome project" der Arbeitsgruppe "Mikrobielle Ökologie" am Lehrstuhl für Mikrobiologie soll zusammen mit MWG-Biotech das Genom eines Vertreters der neuartigen Umwelt-Chlamydien sequenziert werden. Die vergleichende Analyse dieser Genomsequenz mit bereits veröffentlichten Genomsequenzen der humanpathogenen Chlamydien soll Aufschlüsse über die Evolution der Chlamydien, sowie über deren Anpassungen an intrazelluläres Leben in höheren eukaryontischen Zellen geben. Im Rahmen der Kooperation werden, basierend auf den gewonnenen Daten, in Zusammenarbeit mit Prof. Dr. Thomas F. Meyer vom Max-Planck Institut für Infektionsbiologie (Berlin) DNA-Chips für die Untersuchung der Genexpression (Transkriptomanalyse) der Umwelt-Chlamydien entwickelt werden. Diese Arbeiten werden wichtige Grundlagen für die Forschung nach neuen Wirkstoffen für die Chlamydien-Therapie liefern und auf diese Weise langfristig zur Bekämpfung der von Chlamydien verursachten Erkrankungen beitragen.
Das Projekt wird vom Bundesministerium für Bildung und Forschung (BMB+F) im Rahmen des Kompetenznetzwerkes "Genome pathogener Bakterien" (Koordination: Prof. Dr. Werner Goebel, Universität Würzburg) unterstützt. Dieses Netzwerk ist Teil einer BMB+F-Initiative zur Förderung der mikrobiellen Genomforschung in Deutschland.

"Ménange à trois" - Neuartige Symbiose zwischen Bakterien und Meereswürmern entdeckt
Nachweis der bakteriellen Symbionten; Wurmquerschnitt; Balken 10 um Symbiosen stellt man sich üblicherweise als Interaktionen zwischen zwei Organismen (einem Symbiont und einem Wirt) vor, die für beide Partner nützlich sind. Generell wird angenommen, dass nur sehr selten mehr als ein Symbiont in einem Wirt vorkommt, da der Wettbewerb zwischen Symbionten um Ressourcen und Raum schädlich für den Wirt wäre.
In einem von Dr. Nicole Dubilier (Max-Planck Institut für Marine Mikrobiologie, Bremen) koordiniertem Projekt wurde nun eine ungewöhnliche Symbiose zwischen dem marinen Wurm Olavius algarvensis und zwei verschiedenen Bakteriensymbionten erforscht. Im Rahmen dieses Projektes, dessen Ergebnisse diese Woche in der Fachzeitschrift Nature veröffentlicht werden, wurden am Lehrstuhl für Mikrobiologie der Technischen Universität München Arbeiten zur Identifizierung und funktionellen Charakterisierung der symbiontischen Bakterien von Dipl.-Biol. Michael Klein unter Leitung von PD Dr. Michael Wagner (Arbeitsgruppe "Mikrobielle Ökologie") durchgeführt. Die nur Millimeter großen Würmer stammen aus Flachwassersedimenten des Mittelmeers unweit der Insel Elba (Italien) und beherbergen in ihrem Inneren zwei verschiedene Bakterienarten, die mit traditionellen Methoden nicht näher charakterisiert werden können. Die Identifikation dieser symbiontischen Bakterien erfolgte durch eine vergleichende Sequenzanalyse ihrer ribosomalen Ribonukleinsäure (rRNS). Mit Hilfe dieses Ansatzes und dem anschließenden Nachweis der Bakterien direkt im Wurm mittels spezifischer rRNS-gerichteter Gensonden und Fluoreszenz in situ Hybridisierung (siehe Abbildung), der an der TU München in Kooperation mit Frau Dubilier durchgeführt wurde, konnte gezeigt werden, dass die beiden Bakterien zu sulfid-oxidierenden bzw. sulfatreduzierenden Bakterien verwandt sind.
Den Forschern an der TU München gelang es zudem in Zusammenarbeit mit der Arbeitsgruppe in Bremen, Gene für die dissimilatorische Sulfitreduktase, ein Schlüsselenzym aller sulfatreduzierenden Bakterien, in einem der Wurmsymbionten nachzuweisen und somit dessen Funktion als sulfatreduzierendes Bakterium zu bestätigen.
Weitere Einblicke in die Physiologie und Aktivität der Symbionten wurden durch immunozytochemische Methoden und Isotopenversuche erhalten. Einer der Symbionten reduziert Sulfat unter Energiegewinn zu Sulfid. Dieses im Wurm gebildete Sulfid wird von dem anderen bakteriellen Symbionten für die Energiegewinnung oxidiert und somit für den sulfatreduzierenden Partner regeneriert. Folglich, konkurrieren beide Symbionten nicht miteinander, sondern katalysieren gemeinsam einen geschlossenen Schwefel-Kreislauf im Inneren des Wurms. Der Wurm bietet den symbiontisch lebenden Bakterien Schutz und Beweglichkeit und profitiert gleichzeitig von deren Anwesenheit, da toxische Stoffwechselprodukte die der Wurm unter anaeroben Bedingungen produziert, den sulfatreduzierenden Bakterien als Nahrung dienen und somit für den Wirt entgiftet werden. Die Sulfatreduzierer stellen zusätzlich eine von der Umgebung unabhängige Quelle reduzierter Schwefelverbindungen dar, die für die schwefeloxidierenden Bakterien lebenswichtig sind. Somit könnte diese Symbiose den Wirt in die Lage versetzt haben neue Lebensräume zu kolonisieren und sich geographisch weiter zu verbreiten.