Department of Genetics In Ecology

Metabolic and Genomic Studies of Ammonia Oxidizing Archaea from Soil

Although present in very large numbers, very little is known about the physiology of ammonia oxidizing archaea. Their chemolithoautotrophic growth mode has so far been shown only for a single cultivated isolate from a marine aquarium and for two enrichments from hot environments. Therefore, the physiology of ammonia oxidizing archaea in particular of those from soil has remained elusive and their contribution to nitrification has been debated. We have recently isolated a chemolithoautotrophic ammonia oxidizing archaeon from a garden soil in Vienna that is stably growing in laboratory cultures for three years now. The overall goal of this project is to get a deeper insight into the physiology, general activities, evolution and genomic potential of Candidatus Nitrososphaera viennensis and thus to develop it into a model organism for ammonia oxidizing archaea from soil. For this purpose we will perform detailed physiological characterisations, as well as genomic and functional genomic studies. In total we expect to get a deeper insight into this widely distributed and potentially ecologically significant group of archaea.

Read more

Meta-transcriptomics to study the function and structure of complex microbial communities


We are interested in the characterisation of complex microbial communities with cultivation-independent molecular genomic approaches to disclose the ecological function of uncultured archaea and bacteria. Meta-genomic technologies have been used for many years for this purpose and as a logical next step we have recently established meta-transcriptomic approaches in our laboratory.
Meta-transcriptomics offers the opportunity to reach beyond the community’s genomic potential as assessed in DNA-based methods, towards its in situ activity. In addition, the analysis of the RNA pool of a community links its taxonomic structure and function, as it is naturally enriched not only in functionally but also taxonomically relevant molecules, i.e. mRNA and rRNA, respectively. In addition rRNA can be used for PCR-independent community profiling of all three domains of life.
We have established appropriate experimental and analytical procedures (the “double-RNA” approach) for in-depth characterization of microbial communities by studying mRNA and rRNA molecules simultaneously from the same sample.

Read more

European Project: Sulfolobus, a model archaeon for studying the origin of eukaryotes and the development of their information processing systems.


The evolution of Life on Earth has resulted in three fundamentally distinct classes of organisms: the eukaryotic domain and two prokaryotic domains, the bacteria and the more recently discovered archaea. Comparative genomics and biochemical analyses have indicated that the prokaryotic archaea and the eukaryotes are closely related with respect to cellular information processing systems, such as replication & repair, transcription & translation, as well as protein modification & turnover. The SOLAR project aims at the identification and functional characterization of proteins that play crucial roles in information processing, not only to learn about these systems in archaea, but also to understand the functionality of their more complex eukaryotic counterparts.
Sulfolobus solfataricus is a thermophilic archaeon that serves as a model organism since its complete genome sequence, genetic systems, and functional genomics tools have recently been established by active participation of the applicants’ groups. Key proteins of S. solfataricus will be analysed (i) by monitoring global phenotypes (transcriptome, proteome) wild-type and to-be-generated mutant strains (silenced or enhanced expression of selected target genes), (ii) by identifying in vivo interactions of potential regulators with proteins and DNA fragments, and (iii) by in vitro functional characterization of selected regulatory proteins and their target proteins and/or DNA.

Read more

Sponges as nutrient sources and sinks in the marine ecosystem


Sponges as nutrient sources and sinks in the marine ecosystemSponges are major constitutes of coral reef and deep sea communities. They excrete high amounts of ammonium and, due to the activity of associated microorganisms, nitrite and nitrate; these are essential nutrients, and sponges are thus considered as important nutrient sources in the marine ecosystem. A team of researchers from CGB, the Max Planck Institute for Marine Microbiology in Bremen (Germany) and the University of Vienna (Austria) have recently discovered an alternative role of sponges: under certain conditions, sponges transform these nutrients to elemental nitrogen and thereby remove them from the system; these sponges function as nutrient sinks in the ocean.

Read more

InflammoBiota: Metagenomik und Metatranskriptomik zur Untersuchung der Darm-Mikrobiota chronisch entzündlicher Darmerkrankungen


Link to the webpage of Inflammobiota at the University of Vienna

Der Darm und seine Bewohner
Der menschliche Darm beherbergt eine riesige Zahl von Mikroorganismen, die mit ihren verschiedenen Stoffwechselfunktionen für unsere Gesundheit unentbehrlich sind. Die meisten dieser Symbionten sind aber noch wenig studiert. Ihre Vielfalt wird auf mehrere tausend Spezies geschätzt. Allein die genomische Information, die in der Gesamtheit dieser Mikroben enthalten ist, das sogenannte Metagenom, ist weit größer, als unser eigenes Human-Genom. Gerät das Zusammenspiel des Immunsystems und der komplexen Mikrobiota im Darm aus dem Gleichgewicht, z.B. durch Fehlernährung, so können sich chronische entzündliche Darmerkrankungen (Inflammatory Bowel Disease = IBD) entwickeln.
Entstehung schwerer Darmkrankheiten
Zu diesen Krankheiten gehören Morbus Crohn und Colitis Ulcerosa, die sich insbesondere in hoch industrialisierten Ländern ausbreiten. Etwa 1,5 Millionen Menschen in Europa und mehr als 2 Millionen US-AmerikanerInnen sind von diesen schweren Krankheiten betroffen und diese Zahlen steigen. Da erkrankte Personen eine Veränderung in der Zusammensetzung ihrer Darm-Mikrobiota aufweisen, wird vermutet, dass Mikroorganismen entweder die Krankheit unmittelbar auslösen, oder aber, dass sie zumindest eine wichtige Rolle bei ihrer Entstehung oder ihrem Verlauf spielen.
Die Auslöser finden
Ziel dieses Forschungsprojektes ist, es anhand experimenteller Mausmodelle Mikroorganismen oder mikrobielle Aktivitäten zu identifizieren, die IBD auslösen können oder seine Ausbreitung unterstützen. Hierdurch sollen sowohl molekulare Marker für die Diagnose von IBD identifiziert werden als auch Grundlagen für die Entwicklung wirksamer Therapeutika geschaffen werden.
Für dieses interdisziplinäre Projekt haben sich ExpertInnen aus den Bereichen mikrobielle Ökologie, mikrobielle Genomik, Mausgenetik, Immunbiologie, Maus- und Humanpathologie zusammengeschlossen. Da die Darm-Mikrobiota enorm komplex ist und viele Spezies nicht im Labor kultiviert werden können, ist die Anwendung von neuen Sequenziertechnologien (Hochdurchsatzmethoden) für die Metagenomanalyse und die funktionelle Genomanalyse erforderlich.

Read more

Functional Metagenomics to Study Prokaryotes from Arctic/Sub-Arctic Springs of Hydrothermal Origin

Although prokaryotic in cell structure, Archaea have been recognized as a third primary evolutionary lineage, being as distinct from true Bacteria as they are from Eukaryotes. Phylogenetic and genomic analyses indicate that Archaea and Eucarya are probably sister groups that share a number of homologous factors involved in replication, transcription and translation. Therefore, the study of information processing in the simpler systems of the Archaea is often directly relevant for understanding cellular evolution and the more complex interactions that occur in the eucaryal nucleus.
Most cultivated archaea thrive under extreme environmental conditions, such as temperatures between 70 - 113 °C, low pH or high salt concentrations. However, with molecular ecological methods, specific lineages of archaea have also been detected in common place environments, as for example soils and the marine plankton. Their high abundance indicates, that these archaea should be of global ecological significance. However, their phenotypic and physiological properties are still largely unknown.
Our research interests involve:
- the study of stress-induced transcriptional regulation in the hyperthermophilic archaeon Sulfolobus solfataricus and its virus SSV1 to get insights into global regulatory networks and into regulatory factors interacting with the basic (eucaryotic-like) transcription machinery in hyperthermophilic archaea
- the characterization of as yet uncultivated microorganisms, in particular of archaea, by metagenomic and novel postgenomic techniques

Read more

MOCA: Microbial Oceanography of Chemolithoautotrophic Planktonic Communities


Simulation models predict that the oxygen content of the global ocean will decrease by 25% until the end of the century due to an increased stratification of the oceanic surface waters and a rise in temperature. This loss in oxygen will inevitably lead to an expansion of hypoxic and anoxic areas in the global ocean with major consequences for the oceanic carbon and nitrogen cycling. In this proposal, we assess the functional diversity of chemolithoautotrophic prokaryotic communities in two contrasting marine environments, the deep-water masses of the North Atlantic along a latitudinal gradient and around the redoxcline in the central Baltic Sea. Both environments have been shown previously to harbor highly active chemolithoautotrophic prokaryotic communities with dark carbon dioxide fixation rates approaching surface water phytoplankton activity. Specific focus is put on the functional diversity of prokaryotes in the carbon and nitrogen cycling in both systems, including the sulfur cycle in the central Baltic. Biogeochemical rate measurements are tightly linked to functional gene analyses using among other approaches metagenomics and metatranscriptomics. Information obtained from these analyses will guide the development of primers for QPCR to determine the abundance of genes indicative for geochemically relevant processes in the water column of the two systems. Incubation experiments using stable and radio-isotopes in combination with molecular techniques such as SIP-RNA analyses, single-cell analyses using Raman-FISH, NanoSIMS and MICRO-FISH will allow insights into the dynamics of the functional diversity of chemolithotrophic microbial communities in suboxic and anoxic marine planktonic systems. Field studies will be complemented by laboratory model systems with isolated key players in order to understand the adaptive capacity and performance of chemolithoautotrophs in response to different environmental conditions. The combination of these approaches will provide the base for a significant advancement in our understanding of planktonic chemolithoautotrophy in the dark ocean.

Read more

CryoCarb: Long Term Carbon Storage in Cryoturbated Arctic Soils


The overarching goal of CryoCARB is to advance organic carbon estimates for cryoturbated soils, focusing on the Eurasian Arctic and to understand the vulnerability of these carbon stocks in a future climate. Our vision is that one can build on this knowledge to improve existing models to better predict the responses of cryoturbated soils to future climate conditions. The constraints to our understanding of carbon dynamics in cryogenic soils are currently manifold. First. due to cryoturbation, organic matter is unevenly distributed within the soil, making SOC estimation very difficult. There is evidence that the North American arctic carbon stock is bigger than previously thought, also because of underestimation of carbon stored in distorted, broken and warped horizons. Second, most studies dealing with SOC in arctic soils fail to account for carbon stored in the upper permafrost, although the latter is directly under threat in a rapidly warming Arctic. Thawing of the upper permafrost will also mobilize old, geogenic C, which is rarely addressed. Third, the mechanisms of carbon stabilization are largely unknown thus hampering the prediction of c1imate-C02 feedbacks. Knowledge of the chemical composition of organic matter and the processes on how carbon is stabilized is necessary to predict the magnitude and the time-scale at which SOC will get remobilized from thawing permafrost under climate change.

Read more

Marine nematode symbioses

Stilbonematids (Desmodoridae, Chromadoria) are marine nematodes coated with sulfur-oxidizing bacteria. They are the only known marine metazoans capable of establishing monospecific ectosymbioses. Hundreds of highly specialized hypodermal glandular sensory organs (GSOs) appear to play a fundamental role in symbiosis establishment and maintenance: they produce the mucus the symbionts are embedded in.
In the course of our ongoing research project, we want to study abundantly expressed stilbonematid genes discovered by pyrosequencing-based transcriptome analysis. Among these, some are secreted by the GSOs onto the worm's surface and might play a role in symbiosis. In order to understand their function, we will analyze their expression pattern within the GSO and try to silence them by RNA interference.
Concomitantly, we will start to explore how the microbial partners manage to divide without loosing physical contact with their hosts. This requires a highly unusual division mode in which the fission plan is set longitudinally to the symbiont long axis.
The study of relatively simple, naturally occurring symbioses may be instrumental in understanding how beneficial and pathogenic microbes interact with the mucosal surfaces of higher vertebrates.

Read more

CRISPR-Mediated Virus Defense in Hyperthermophilic Archaea

Sequence analyses of complete bacterial and archaeal genomes have led to the discovery of Clustered Regularly Interspaced Short Palindromic Repeats (in short CRISPR). The potential function of these repeats and their intervening short spacer sequences as well as the function of their associated (Cas-) proteins as constituents of an immune defense system against viruses and other genetic elements, has only recently been recognized. Although CRISPR/Cas systems are found widespread in bacterial and archaeal genomes and exhibit considerable diversity, little insights into the action of most of the CRISPR modules have been obtained in particular in Archaea due to the lack of suitable in vivo test systems. We have recently demonstrated CRISPR/Cas-based immune defense in the hyperthermophilic archaeon Sulfolobus solfataricus. Recombinant variants of the SSV1 virus containing a gene of the conjugative plasmid pNOB8 that represents a target for a corresponding CRISPR spacer in the chromosome were tested in transfection experiments. Almost 100% immunity against the recombinant virus was observed when the chromosomal CRISPR spacer matched perfectly to the protospacer. Different from bacterial systems immunity was still detected, albeit at decreased levels, when mutations distinguished target and spacer. CRISPR/Cas targeting was independent of the transcription of the target gene. Furthermore, a mini CRISPR locus introduced on the viral DNA with spacers targeting the (non-essential) chromosomal beta-galactosidase gene was unstable in host cells and triggered recombination with the indigenous CRISPR locus. Our experiments demonstrate in vivo activity of CRISPR/Cas in archaea for the first time and suggest that – unlike the recently demonstrated in vitro cleavage of RNA in Pyrococcus - DNA is targeted in this archaeon.

Read more