Department of Limnology and Biological Oceanography



The microbiome of coral surface mucus is decisive for coral health

In a recently published paper in the ISME Journal, our former MSc student Bettina Glasl and PostDoc Pedro Frade, both now at AIMS, Townsville, Australia, describe the microbial community composition in the mucus layer of several coral species. This research highlights the decisive contribution of microbes associated with the surface mucus layer of corals to the health and homeostasis of their hosts.


Full text available here:


Bettina Glasl, Gerhard J Herndl and Pedro R Frade (2016) The microbiome of coral surface mucus has a key role in mediating holobiont health and survival upon disturbance. The ISME Journal 1-13; doi:10.1038/ismej.2016.9

Manuela Trobej won the Algological studies prize

Manuela Trobej (center) of Michael Schagerl´s Team Phycology won the Algological studies prize for the best master talk at the Phycology meeting in Leipzig (Germany). Title: Island in the landscape – travertine springs and their algal communities

Foto: Kerstin Hoef-Emden


Aquatic Viruses and Global Climate Change

A recent chapter by Peter Peduzzi summarizes the current state of research in the new book “Climate Change and Microbial Ecology: Current Research and Future Trends”, edited by J. Marxsen, Caister Academic Press (; March 2016


The viral component in aquatic systems clearly needs to be incorporated into future ocean and inland water climate models. Viruses have the potential to influence carbon and nutrient cycling in aquatic ecosystems significantly. Changing climate likely has both direct and indirect influence on virus-mediated processes, among them an impact on food webs, biogeochemical cycles and on the overall metabolic performance of whole ecosystems. Here I synthesize current knowledge on potential climate-related consequences for viral assemblages, virus-host interactions and virus function, and in turn, viral processes contributing to climate change. There is a need to increase the accuracy of predictions of climate change impacts on virus-driven processes, particularly of those linked to biological production and biogeochemical cycles. Comprehension of the relationships between microbial/viral processes and global phenomena is essential to predict the influence on as well as the response of the biosphere to global change.

New paper in PLoS ONE

We published a new paper on the inhibition of bacterial growth by the trophosome of the giant deep-sea tubeworm Riftia pachyptila.


Julia Klose, Karin Aistleitner, Matthias Horn, Liselotte Krenn, Verena Dirsch, Martin Zehl, Monika Bright: Trophosome of the deep-sea tubeworm Riftia pachyptila inhibits bacterial growth Endosymbionts escape dead hydrothermal vent tubeworms to enrich the free-living population. PLoS ONE 11(1): e0146446. doi:10.1371/journal.pone.0146446


The giant deep-sea tubeworm Riftia pachyptila lives in a mutualistic association with the chemoautotrophic gammaproteobacterium Cand. Endoriftia persephone, harbored in the host’s trophosome. Symbiont transmission is horizontal in each host generation. Escape of symbionts happens after the host dies. Surprisingly, no microbial fouling was found in degrading trophosome tissue. In high-pressure incubation experiments we could show, the antimicrobial effect of the tubeworm’s trophosome. Mainly Gram-positive bacterial strains were inhibited in growth. We could identify lysophospholipids and free fatty acids, well known antimicrobial and anitfouling substances by a liquid chromatography-mass spectrometric analysis. As a result of tissue autolysis, the abundance of the free fatty acids increased with time and correlated with an increased growth inhibition of two bacterial strains. After death, the host cannot provide nutrients to the chemoautotrophic symbiont. Therefore, it is tempting to speculate that under post mortem host conditions, Endoriftia switches to a heterotrophic life style to feed on the dead host until it escapes.


Renate Degen received the three-year Hertha Firnberg grant from the Austrian Science Fund (FWF) to study the functions of macro- and megabenthic communities in the Arctic Ocean. While in recent years some information was gathered about the structural variability of Arctic benthos, information on the functional variability is currently still lacking. The aim of this project is to fill these knowledge gaps by means of a pan-Arctic, integrated approach, including i) the analysis of benthic functioning on Arctic shelves and basins and along a shelf-slope-basin gradient in the Eurasian and the Amerasian part of the Arctic, ii) the identification of functions and regions most susceptible to changes, and iii) the prediction of benthic ecosystem functioning in a future, seasonally ice free Arctic Ocean.


Barbara Bayer, Jana Vojvoda, Pierre Offre, Ricardo J. E. Alves, Nathalie H. Elisabeth, Juan A. L. Garcia, Jean-Marie Volland, Abhishek Srivastava, Christa Schleper, and Gerhard J. Herndl

The ISME Journal, Nov 3, 2015; (in Press), doi: 10.1038/ismej.2015.200.

Ammonia-oxidizing Archaea (AOA) are ubiquitous throughout the oceanic water column; however, our knowledge on their physiological and ecological diversity in different oceanic regions is rather limited. Here, we report the cultivation and characterization of two novel Nitrosopumilus strains, originating from coastal surface waters of the Northern Adriatic Sea. The combined physiological and genomic information revealed that each strain exhibits different metabolic and functional traits, potentially reflecting contrasting life modes. Strain NF5 contains many chemotaxis-related genes and is able to express archaella, suggesting that it can sense and actively seek favorable microenvironments such as nutrient-rich particles. In contrast, strain D3C is non-motile and shows higher versatility in substrate utilization, being able to use urea as an alternative substrate in addition to ammonia. Furthermore, it encodes a divergent, second copy of the AmoB subunit of the key enzyme ammonia monooxygenase, which might have an additional catalytic function and suggests further metabolic versatility. However, the role of this gene requires further investigation. Our results provide evidence for functional diversity and metabolic versatility among phylogenetically closely related thaumarchaeal strains, and point toward adaptations to free-living versus particle-associated life styles and possible niche differentiation among AOA in marine ecosystems


for the project "Significance of selected major microbial groups in the oxygenated deep ocean".

This fellowship program is an individual scholarship financed by the University of Vienna aiming at supporting excellent doctoral candidates for a three years period. The fellowship provides early stage researchers with conditions that allow them to focus exclusively on their research to make substantial contributions to science.

In her PhD thesis, Barbara will investigate the metabolic potential and activities of selected, thus far uncharacterized groups of Bacteria and Archaea in the deep ocean. Due to the enormous volume of the deep-sea, the metabolic processes of these uncharacterized microbial groups may be of great importance for global biogeochemical cycles.

Research project ‘Architecture of marine snow-associated prokaryotic communities (ARTEMIS)’ funded by the Austrian Science Fund (FWF)

Gerhard J. Herndl received funding for investigating coastal and open ocean marine snow. In ARTEMIS, focus will be put on the architecture of marine snow-associated microbial communities during the successional stages of marine snow by combining metagenomic and –proteomic analyses of physically and chemically characterized habitats within marine snow with metabolic rate measurements. Using advanced image analysis, microspatial coexistence of individual microbial taxa will be investigated. Quantification of functional genes indicative for C, N and S cycling will be performed on sections through marine snow particles and related to the physical and chemical microenvironment. Taken together, ARTEMIS should elucidate the microspatial architecture of microbial communities during the succession of marine snow, particularly the changes related to increasing oxygen depletion in the interior of marine snow. Funding is provided for one Post Doc and one PhD student for three years.

Else Richter grant on "Exo-proteomics of marine dissolved organic matter” to Roberta Hansman

Roberta Hansman received a four-year Else Richter grant from the Austrian Science Fund (FWF) to analyze dissolved proteins found in seawater. Proteins comprise about 50% of all living organisms, including the millions of microbes present in every liter of seawater, and thus become a major component of the dissolved organic material found in the ocean. This work will identify and quantify proteins dissolved in seawater in order to gain insight into what organic material in the ocean is composed of and what role microorganisms play in structuring dissolved organic matter composition. The project will be conducted within the ViMe (Vienna Metabolomics Center; research platform here at the University of Vienna.

Experimental Work on streamside Flumes on stream c-cycling Featured in ORF 2 State TV Program

Experimental work of the Stream Biofilm and Biogeochmistry Group at the Lunzer:::Rinnen Experimental Flumes was featured in a TV program aired on the ORF2 TV Channel on Suturday, 2015-11-2. Please visit the ORF website to watch the program (in German, availiable till 2015-12-11).

Maria Pinto received the prestigious DOC-grant

from the Austrian Academy of Sciences to work on her PhD thesis on the microbial colonization and biodegradation of microplastics in the ocean. The amount of plastic produced globally has doubled from the year 2001 to 2014 amounting at present 280 million tons per year. A considerable fraction of this plastic production ends up in the ocean forming plastic islands in the oceanic gyres. A substantial part of this plastic, however, sinks apparently into the ocean’s interior. In her PhD thesis, Maria will investigate the dynamics of the microbial biofilm on plastic material in different depth layers of the open ocean and in the northern Adriatic and the interaction between solar radiation and microbial activity in degrading plastic material in the sea. 

A hairy case: The evolution of filtering carnivorous caddisflies

Molecular Phylogenetics and Evolution 93 (2015): 249–260, by Simon Vitecek, Wolfram Graf, Ana Previšič, Mladen Kucinič, János Oláh, Miklós Bálint , Lujza Keresztes, Steffen U. Pauls & Johann Waringer

The caddisfly subfamily Drusinae BANKS comprises roughly 100 species inhabiting mountain ranges in Europe, Asia Minor and the Caucasus. A 3-gene phylogeny of the subfamily previously identified three major clades that were corroborated by larval morphology and feeding ecologies: scraping grazers, omnivorous shredders and filtering carnivores. Larvae of filtering carnivores exhibit unique head capsule complexities, unknown from other caddisfly larvae. Here we assess the species-level relationships within filtering carnivores, hypothesizing that head capsule complexity is derived from simple shapes observed in the other feeding groups. We summarize the current systematics and taxonomy of the group, clarify the systematic position of Cryptothrix nebulicola, and present a larval key to filtering carnivorous Drusinae. We infer relationships of all known filtering carnivorous Drusinae and 34 additional Drusinae species using Bayesian species tree analysis and concatenated Bayesian phylogenetic analysis of 3805 bp of sequence data from six gene regions (mtCOI5-P, mtCOI3-P, 16S mrDNA, CADH, WG, 28S nrDNA), morphological cladistics from 308 characters, and a total evidence analysis. All analyses support monophyly of the three feeding ecology groups but fail to fully resolve internal relationships. Within filtering carnivores, variation in head setation and frontoclypeus structure may be associated with progressive niche adaptation, with less complex species recovered at a basal position. We propose that diversification of complex setation and frontoclypeus shape represents a recent evolutionary development, hypothetically enforcing speciation and niche specificity within filtering carnivorous Drusinae.

Endosymbionts escape dead hydrothermal vent tubeworms to enrich the free-living population.

Proceedings of the National Academy of Sciences, Aug, 17, 2015; (in Press), doi:10.1073/pnas.1501160112,  by Julia Klose, Martin F. Polz, Michael Wagner, Mario P. Schimak, Sabine Gollner, Monika Bright


The giant tubeworm Riftia pachyptila is nourished by a bacterial endosymbiont, which is acquired by each new generation of worm larvae. Maintaining this arrangement requires the symbionts to be able to escape from their hosts and replenish the free-living bacterial population. The article describes the bacterial release from dead host tissue under simulated deep-sea and hydrothermal vent conditions in the laboratory. This suggests that several million to over one billion bacteria escape upon host death of a single tubeworm clump. The escaped bacteria settled on surfaces where they proliferated.  Monitoring of tubeworm clumps at a hydrothermal vent field at the East Pacific Rise following a volcanic eruption exhibited rapid turnover within two years, suggesting that large numbers of bacteria could be released over a relatively short time. The connection between the host-associated and free-living bacterial populations might explain how the symbiotic relationship between tubeworms and bacteria has remained stable over evolutionary time scales.



Virus ecology of fluvial systems: a blank spot on the map?

Biological Reviews, Juni 2015 (doi: 10.1111/brv.12202)

A recent review by Peter Peduzzi on virus ecology of fluvial systems summarizes the current state of research in the journal BIOLOGICAL REVIEWS. Although viruses are present in high numbers in all aquatic systems, their role in flowing waters (as important part of the global water cycle) are still largely unexplored. Here, physical and biological drivers seem to act in concert, strongly linked to the often very variable environmental settings (lotic and lentic conditions). Also the effect of anthropogenic alterations of fluvial systems on viruses-related processes requires attention. The identification of existing considerable knowledge gaps should foster future research efforts. The outcome of such studies can be expected to contribute significantly to modern concepts of fluvial systems.

Link zu Artikel:

Outstanding Editor Award for the journal Biogeosciences to Gerhard J. Herndl


Gerhard J. Herndl receives the First Outstanding Editor Award for the journal Biogeosciences.

Message from Biogeosciences:  Gerhard has handled 37 manuscripts last year. Not only has he handled the biggest load among all of us last year, he has done so with admirable efficiency and effectiveness. Despite his heavy work load, Gerhard didn't miss a decision deadline and he seems to apply the right personal touch when motivating reviewers to provide their assessment and to do so on time. The official EGU certificate recognizing his contributions will be presented to Gerhard at the 2016 EGU meeting. 

Congratulations to Prof. Ott on receiving the ‘Goldenes Verdienstzeichen'


Prof. Jörg Ott, former head of the Department of Marine Biology, was awarded with the highly honored ‘Goldenes Verdienstzeichen des Landes Wien' on April 16, 2015. The presentation of the medal and the celebration took place in the presence of the major of Vienna, Dr. Michael Häupl, at the town hall of Vienna on April, 16, 2015.

More on the ceremony can be found here.

One of the Thousand


on April 16th, 2015 Julia Klose was ‘One of the Thousand' at the 650 Year Anniversary Concert of the University of Vienna playing Gustav Mahlers Symphonie Nr. 8.


From the lab coat to the running shirt - Vom Laborkittel ins Laufshirt


LimBO runners are on track, as the uni:view magazine reports. Read more here.

The dissolved organic carbon soup of the deep ocean isn’t too refractory for microbes it’s too thin.


This is the conclusion of a recent study published in Science on deep-water dissolved organic carbon utilization by heterotrophic microbes. The major part of the study was performed during the MEDEA cruise in the North Atlantic in the frame of the ERC Advanced Grant awarded to Gerhard J. Herndl.


Arrieta, J.M., E Mayol, R.L. Hansman, G.J. Herndl, T. Dittmar, C.M. Duarte: Dilution limits dissolved organic carbon utilization in the deep ocean. Science DOI: 10.1126/science.1258955. Link.

Position for a full Professor of Limnology open at the department


The The Faculty of Life Sciences of the University of Vienna is opening a position for a  Full Professor (Chair) of Limnology. For more information please follow the link to the official announcement.



The Faculty Research Focus Symbiosis will hold the next workshop at the seminar room DOME, April, 17, 2015. A flyer can be found here.


Registration deadline is March 27. Please register by email to Andrea Nussbaumer.



A study authored by Anna Sieczko, Maria Maschek and Prof. Peter Peduzzi on the fate of organic matter in Danube floodplains has been published in the journal 'Frontiers in Microbiology'. Please visit the link to the journal.


Two new species of caddisflies identified


A study Co-authored by Simon Vitecek and Prof. Johann Waringer identified two new endemic species from the Western Balkans by means of comparative morphology and molecular methods. The study is published in the journal 'Arthropod Systematics & Phylogeny'. Read and download the article here.


Master Thesis of Irene Teubner awarded as 'best Masters' by Springer


The Master thesis of Irene Teubner entiteld 'Viruses in the Danube Floodplains', supervised by Prof. Peter Peduzzi was selected for the 'Best Masters' series by Springer.


See more on the Springer website (in German).

Guest Lecture by Paul del Giorgio, University of Quebec at Montreal, Canada

Title: The taxonomic and functional biogeography of bacterial communities across boreal aquatic networks.

December 2nd, 2014, 12:00 pm (noon), Lecture Hall 5, UZA II, Althanstrasse 14.


You may also download the flyer as a pdf file.

De Bary Lecture by Christoph Hauert, University of British Columbia

the 'Research Focus Symbiosis' presents a De Bary Lecture by

Christoph Hauert, University of British Columbia, Canada with the
title: "Dynamics of Social Dilemmas: An evolutionary game theory perspective".

December 2, 1014 16.00 s.t., Seminar Room Limnology


Article Unifying River Ecosystem Concepts published in BioScience


A new article that unifies river ecosystem concepts has been published in the journal Bioscience. Title: "The River Wave Concept: Integrating River Ecosystem Models".


Link to journal article:


Tom Battin appointed Full Professor in Ecohydraulics at EPFL Lausanne


Tom Battin appointed Full Professor in Ecohydraulics at the Ecole Polytechnique Fédérale de Lausanne (EPFL), Switzerland. Tom will leave the University of Vienna in January 2015 to start his new position in Lausanne.



New Website of the 'Stream Biofilm and Biogeochemistry' Group launched.


The Stream Biofilm and Biogeochemistry Lab headed by Prof. Tom J. Battin has launched its new website!


Curious? Here's the link:


Article on microbial Co-occurence in fluvial Networks published in PNAS!


Widder, S., K. Besemer, G. A. Singer, S. Ceola, E. Bertuzzo, C. Quince, W. T. Sloan, A. Rinaldo, and T. J. Battin (2014): Fluvial network organization imprints on microbial co-occurrence networks, Proceedings of the National Academy of Sciences (in press).


Link to journal article.

Science Day - Biology 2014

PhD and MSc students of the departments present their research. The lectures are followed by a summer party.

Tuesday, July 1, 09:00a.m.-07:00p.m., Lecture Hall I, UZA 1


Guest Lectures:

Victor Smetacek, Alfred Wegener Institute, Bremerhaven

Gaspar Jekely, Max-Planck-Institute for Developmental Biology, Tübingen

Download program

Margalef Lecture by Alan Decho, University of South Carolina


Title: Biofilms Remixed: Microbial Mats and Stromatolites


Wednesday, May 14th 2014, 15:00 s.t.
Seminar Room Limnology

Article on food assimilation in rotifers published in Freshwater biology

Alfred Burian, Martin J. Kainz, Michael Schagerl and Andrew Yasindi, 2014: Species-specific separation of lake plankton reveals divergent food assimilation patterns in rotifers. Freshwater Biology 59: 1257–1265; doi: 10.1111/fwb.12345


More on this work :

Link to journal article.
Download article as pdf file (open access).

review by Monika Bright and co-authors published in Frontiers in Microbiology

Monika Bright, Salvador Espada-Hinojosa, Ilias Lagkouvardos, Jean-Marie Volland: The giant ciliate Zoothamnium niveum and its thiotrophic epibiont Candidatus Thiobios zoothamnicoli: a model system to study interspecies cooperation. Frontiers in Microbiology, online, April 7, 2014; doi:10.3389/fmicb.2014.00145


Read more on Monika Brights work here.


More on this work:

Link to journal article and download article as pdf file (open access).

Mia Bengtsson receives a Back-to-Research Grant

"I wanted to be able to see and experience the things that are invisible because they are so small", says the microbiologist Mia Bengtsson who received a Back-to-Research Grant and works at the Department of Limnology and Oceanography of the University of Vienna.


Read more about Mia here. You may also visit her personal page.

Katharina Besemer receives Erwin-Schrödinger stipend

Katharina Besemer received a Erwin-Schrödinger stipend from the Austrian Science Fund (FWF) to work with Christopher Quince at the University of Glasgow on the metagenomics and community modelling of microbial biofilms in streams.

Gerhard Herndl receives the 2014 G. Evelyn Hutchinson Award by the Association for the Sciences of Limnology and Oceanography (ASLO)

Gerhard Herndl has received this years G. Evelyn Hutchinson Award from the Association forthe Sciences of Limnology and Oceanography’s (ASLO) for his contributions to the development of oceanography and aquatic microbial ecology, for broadening our understanding of the interactions between microbes and marine biogeochemical cycles, for spearheading the exploration of the dark ocean, and for his excellence and dedication to training and community service.                              

The G. Evelyn Hutchinson award is given by ASLO to honor a limnology and oceanography scientist who has made considerable contributions to knowledge, and whose future work promises a continuing legacy of scientific excellence. The award was presented at the 17th biennial Ocean Sciences Meeting at the Hawaii Convention Center in Honolulu, Hawaii, on 26 February 2014.


More on Gerhard Herndls work can be found here.


International Conference on Biofilms hosted at the University of Vienna

The 6th International Conference on Biofilms will take place at the University of Vienna, Austria, 11-13 May 2014.

„Understanding biofilms“ with a focus on environmental and technical systems and on general biofilm research is the theme of this International Conference.


For more information please visit the conference website:

The virus’s tooth - cyanophages affect an African flamingo population in a bottom up cascade

A recent study by Peter Peduzzi and Co-authors links flamingo abundance to virus infections of cyanobacteria, the base of a short food chain.


Peter Peduzzi, Martin Gruber, Michael Gruber & Michael Schagerl, 2014. The ISME Journal, advance online, January 16, 2014; doi:10.1038/ismej.2013.241


Trophic cascade effects occur when a food web is disrupted by loss or significant reduction of one or more of its members. In East African Rift Valley lakes, the Lesser Flamingo is on top of a short food chain. At irregular intervals, the dominance of their most important food source, the cyanobacterium Arthrospira fusiformis, is interrupted. Bacteriophages are known as potentially controlling photoautotrophic bacterioplankton. In Lake Nakuru (Kenya), we found the highest abundance of suspended viruses ever recorded in a natural aquatic system. We document that cyanophage infection and the related breakdown of A. fusiformis biomass led to a dramatic reduction in flamingo abundance. This documents for the first time that virus infection at the very base of a food chain can affect, in a bottom-up cascade, the distribution of end-consumers. We anticipate this as an important example for virus-mediated cascading effects, potentially occurring also in various other aquatic food webs.


Link to journal article:

Donwload article as .pdf file (open access):


Microbial diversity in stream networks

Besemer, K Singer GA, Quince C, E Bertuzzo, W Sloan and  TJ Battin, 2013. Headwaters are critical reservoirs of microbial diversity for fluvial networks Proceedings of the Royal Society B.


Streams and rivers form conspicuous networks and life therein figures among the most diverse on Earth. The common wisdom has been that biodiversity in these fluvial networks accumulates downstream similar to water and sediments. Combing sequencing with ecology, the freshwater scientists have now shown together with colleagues from Switzerland and the United Kingdom that this does not hold for microorganisms, which show their highest diversity in headwaters. Their findings highlight headwaters as vital for the microbial biodiversity in entire fluvial networks. These findings are critical given the numerous ecosystem functions microbes fulfil and the fact that headwaters are increasingly under thread worldwide.


Link to journal article:

Microbial control of the dark end of the biological pump

Herndl, G. J., and T. Reinthaler, 2013. Microbial control of the dark end of the biological pump. Nature Geoscience 6: 718–724, doi:10.1038/ngeo1921


A fraction of the carbon captured by phytoplankton in the sunlit surface ocean sinks to depth as dead organic matter and faecal material. The microbial breakdown of this material in the subsurface ocean generates carbon dioxide. Collectively, this microbially mediated flux of carbon from the atmosphere to the ocean interior is termed the biological pump. In recent decades it has become clear that the composition of the phytoplankton community in the surface ocean largely determines the quantity and quality of organic matter that sinks to depth. This settling organic matter, however, is not sufficient to meet the energy demands of microbes in the dark ocean. Two additional sources of organic matter have been identified: non-sinking organic particles of debated origin that escape capture by sediment traps and exhibit stable concentrations throughout the dark ocean, and microbes that convert inorganic carbon into organic matter. Whether these two sources can together account for the significant mismatch between organic matter consumption and supply in the dark ocean remains to be seen. It is clear, however, that the microbial community of the deep ocean works in a fundamentally different way from surface water communities.


Link to journal article:


What a merger!

The former Department of Marine Biology and the Department of Limnology merged into the new Department of Limnology and Oceanography. This marriage will greatly hasten research in aquatic ecology and biogeochemistry at the University of Vienna