Department of Ecogenetics and Systems Biology - Division of Archaea Biology and Ecogenomics


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Research > Ongoing Projects

TACK and Lokiarchaeota Evolution: Dissecting the Ecology and Evolution of Archaea to Elucidate the Prokaryote to Eukaryote Transition

The emergence of complex eukaryotic life forms on Earth from prokaryotic cells is one of the most fundamental questions in biology and also one of the least understood transitions in evolution. Phylogenomic studies recently indicated that the eukaryotic line of descent arose from within the TACK+L superphylum of Archaea.
This project addresses the systematic analysis of two newly discovered, but largely uncharacterized lineages of Archaea from this superphylum that mark crucial evolutionary transitions.
This project will give fundamental insights into the ecological success of Archaea in commonplace environments and into the biology of the closest living prokaryotic relatives of Eukaryotes. Reconstructing the ancestral gene repertoire and biological features of lineages of the TACK+L superphylum will help resolve the enigma of the emergence of eukaryotes.

Pan-metabolic profiling of Archaea: The ecology of genomics

The Archaea are a goldmine of discoveries, with fundamentally new forms regularly being discovered through metagenomics. We are beginning to realize the vast diversity of archaeal ecological adaptations, and how much we do not know regarding their metabolism. Uncharacterized genes of Archaea present a plethora of opportunities to, at the cutting edge of the field, identify new metabolic traits. Yet, to detect which gene innovations form the base for the ecological success of specific groups we have to look to the entire genomic space.
This project aims at using genomic data to forge robust links between physiological phenotypes among modern Archaea and their genomic adaptations and how those are evolving. By performing large-scale whole-genomic comparisons complemented with thorough phylogenetic analysis of all single gene trees, we will be able to define archaeal metabolic profiles, clusters of genes conserved among organisms with similar phenotypic traits, and identify what makes them so special. The metabolic profiles, defined at a pan-phenotypic level, will serve not only to develop a classification-tool aiming at an automatic metabolic classification of newly sequenced genomes, but also to pinpoint unknown archaeal conserved genes, potentially linked to metabolism, to be functional characterized. By extending this strategy to eukaryotes, the role of Archaea in Eukarya origin and evolution can be evaluated, and additional testable predictions will be made.
The metabolic profiles will serve to disentangling both specialist and generalist adaptation strategies first within archaeal groups, later in eukaryotes, thereby increasing our understanding in microbial ecological adaptations and evolution.

Microbial Nitrogen Cycling - From Single Cells to Ecosystems

Understanding the contribution of microorganisms to ecosystem processes remains one of the most compelling challenges in ecology and requires a high degree of interdisciplinary research.
The Faculty of Life Sciences at the University of Vienna has gathered an exceptional number of renowned experts over the past years with complementary research areas in microbial ecology, functional genomics and aquatic and terrestrial ecosystem research.
Ten faculty members from three departments propose here a joint PhD program with highly integrated, interdisciplinary and international education, training and research, dedicated to creating knowledge and expertise in both microbial ecology and ecosystems research.
All proposed PhD projects focus on the nitrogen cycle and its microbial components, a topic to which most members of the faculty have already made significant contributions. We have identified two major themes: (I) Terrestrial Ecosystems and Eukaryote - Microbe Interactions and (II) Metabolic flexibility and niche differentiation, that will be tackled in the 22 proposed PhD research topics.

Growth and septation of animal-attached bacteria

Up to now, the study of bacterial reproduction focused on a handful of model microorganisms. On the other hand, cell biological studies of environmental bacteria such as those thriving on animal surfaces are scarce. In this research proposal we want to determine the molecular and cell biological mechanisms underlying the reproductive anomalies of four Gammaproteobacteria stably associated to animals. The ultimate goal is the identification of cell growth and septum positioning mechanisms conserved among this ecologically and medically important group of microorganisms. We will study selected cell division proteins in cell-free systems and apply a wide palette of state-of-the-art and classic microscopic techniques to both live and fixed nematode-bacteria consortia (e.g. Selective Plane Illumination Microscopy, 3D structured illumination microscopy, cryo-EM and confocal laser scanning microscopy).

RE-ATTACH: REproduction Mechanisms of Host ATTACHed Bacteria

The molecular basis of cell division is well studied only in model microorganisms. Yet, the vast majority of these are not cultivable and their reproduction modes are unexplored. In the course of my dissertation I will focus on environmental Gammaproteobacteria that coat the surface of two marine nematodes Laxus oneistus and Robbea sp.3. Both of these rod-shaped microbial symbionts display extraordinarily reproductive strategies as they grow in width and set their constricting rings longitudinally. We want to understand the molecular and cell biological mechanisms by which these two nematode symbionts grow and reproduce. Do longitudinally dividing bacteria share the same cell division molecules with model Gammaproteobacteria or do, instead, utilize different ones? Which are the core septum positioning mechanisms and molecules conserved in all Gammaproteobacteria? We will address these questions by using a wide palette of microscopy-based techniques (e.g. negative stain electron microscopy and confocal laser scanning microscopy), biochemical approaches such as peptidoglycan composition analysis and in vitro reconstitution of bacterial cytoskeletal components, as well as ectopic expression of symbiont cell division proteins in E. coli and fission yeast. In order to possess the complete repertoire of cell division proteins of the aforementioned symbionts, their complete genomes will be sequenced. This will also allow us to gain insights about their evolution and ecology.

Metabolic and Genomic Studies of Ammonia Oxidizing Archaea from Soil - AOA

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.

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.

Ammonia Oxidizing Archaea in Arctic Tundra Soils - ARC


The functioning of Arctic soil ecosystems is crucially important for the global climate. Permafrost soils contain nearly twice as much carbon as the atmosphere and it is assumend that large quantities of carbon are lost (in the form of methane and carbon dioxide) when these soils thaw. Understanding the composition and functioning of the microbial communities in arctic soils is therefore crucial in order to be able to predict their vulnerability and reactions in a changing climate. Nitrification is considered important for ecosystem functioning in the arctic, because the availability of nitrogen, the major limiting nutrient in the system, is directly dependent on it. But the major drivers of nitrification in the arctic are currently unknown. We have recently measured different gross situand potential nitrification rates in arctic soils that were dominated by distinct phylogenetic clades of ammonia oxidizing archaea (AOA) suggesting differences in the activities of various clades and also dominance of AOA over ammonia oxidizing bacteria (AOB) in most soils or even their exclusive presence in some. Furthermore, an enrichment of an arctic AOA of an uncharacterized lineage was obtained that is abundant in the European arctic tundra. overall goal of this proposal is to get insight into the distribution and activity of AOA in arctic ecosystems. To achieve this we will follow two experimental paths: One involves the study of AOA in diverse arctic ecosystems and the second the characterization of Nitrosovradea arctica, an organism representing one of the abundant lineages in arctic soils. will study the distribution and abundance of the six major AOA clades in various arctic soils, using deep sequencing and a clade-specific quantitative PCR assay and will link these to environmental parameters and gross nitrification rates. Samples will be obtained in the frame of two international projects studying terrestrial arctic ecosystems, in which we participate (CryoCarb, ESF) or collaborate (CryoN/PAGE21, EU). The direct and indirect contribution of AOA to NO production and nitrification will be studied in incubation experiments with various inhibitors. Metatranscriptomics will be employed in order to investigate their activity in soils at situand increased temperatures. In the second part of the project, the enrichment culture of the arctic strain will be used to study growth characteristics, inhibitors, and NO emission. Furthermore, the genomic sequence will be determined and transcription studies will be performed in order to analyse adaptations and physiological characteristics. Both project parts will be closely interlinked.total, we will contribute to a better understanding of arctic ammonia oxidizers including their direct or indirect influence on nitrification and NO production and we will contribute to a better understanding of the physiology of ammonia oxidizing archaea in general.

Thaumarchaeota in Marine Sediments

Marine sediments host the largest reservoir of organic carbon in the world as well as a huge number of microorganisms. These complex microbial communities and their associated metabolic activities have a profound impact onglobal biogeochemical cycles. Understanding their structure and function is crucial for predicting the fate of carbon and other essential elements in the marine system. However, the vast majority of subsurface microorganisms are poorly characterized and their physiological activities remain unknown. One of the most widespread and abundant microbial groups in oceanic sediments are thaumarchaeota, a phylum of archaea formerly referred to as mesophilic crenarchaeota. Thaumarchaeota in aerobic environments, i.e. in the oceanic plankton and in soils and freshwater are capable of aerobic ammonia oxidation and therefore contribute to global nitrogen cycling by performing the first step in nitrification. While the metabolism of thaumarchaeota in marine sediments is unknown, their metabolic activities are expected to be different and probably more versatile since they reside in large numbers in anaerobic horizons of the deep sediments. this study we will investigate the genomic potential of different thaumarchaeotal clades that typically occur in marine sediments and we will also attempt to cultivate and physiologically characterize representatives of them. Our study builds on an earlier intense investigation of two highly stratified marine sediment cores from the ultra-slow spreading ridge of the North Atlantic (PNAS 2012, 109(42):E2846-55). The 3 m cores exhibited an unusually strong and compressed geochemical layering allowing us to find quantitative correlations between the sediment geochemistry and changes in the microbial communities. Eight out of 15 horizons in these cores were dominated by thaumarchaeota of various subclades typical for deep marine sediments. Samples from these horizons will be used in this project to directly extract DNA for metagenomic investigations and to extract cells for cell sorting and subsequent single cell genomics. In parallel we will set up a variety of enrichments based on the geochemical context data available. Along the project, genomic information will feed into the cultivation strategies and enrichment cultures will in turn be used as starting material for single cell genomics. In addition isotopic studies on actively growing archaeal enrichments will be performed using NanoSIMS imaging (nano secondary ion mass spectrometry) to investigate the assimilation of substrates by certain archaeal clades. Comparative genomic studies of thaumarchaeota from marine sediments will be performed to tackle their specific genomic and physiological adaptations and their evolutionary relationship with other thaumarchaeota and related archaeal clades.
Our study will provide insights into the physiological and metabolic potential, genetic setup and evolution of one of the most widespread and abundant, but very little studied microbial groups on this planet.

4ME - RuMEn MEthanoplasmatales as target for MEthane mitigation: eco-physiology and interactions assessed by integrated MEta-omics

Methane (CH4) is a very potent greenhouse gas. Most global CH4 emissions are caused by human activities, with farming of cows and other ruminant animals being the largest anthropogenic CH4 source. Rumen Methanoplasmatales (RMp) belong to a recently discovered and poorly characterised group of methanogenic archaea that produce CH4 as a metabolic end-product. RMp can constitute up to 80% of ruminant methanogen populations, perform a unique type of methanogenesis and can be inhibited via dietary rapeseed oil (RSO) supplementation. This makes them a promising target for CH4 mitigation strategies - much-needed to ensure ecologically and economically sustainable milk and meat production especially in times of global climate change. This PhD project wants to answer pressing questions about the poorly characterised RMp: With whom and how do RMp metabolically interact? What is their ecological niche in the complex rumen ecosystem? What is the role of RMp in the rumen nitrogen cycle? What are the inhibitory effects of RSO compounds? I will apply cutting-edge microbial ecology technologies (e.g. integrated meta-omics and FISH-nanoSIMS) combined with state-of-the-art in vivo and in vitro experiments. Interdisciplinary collaborations with excellent national and international experts will ensure that 4ME contributes new knowledge about these widespread, yet poorly understood methanogens and can pave the way for novel CH4 mitigation strategies in agriculture.

BioHyMe: Entwicklung eines Hochdruckproduktionsverfahrens für die gekoppelte biologische Wasserstoff- und Methanproduktion

Um eine sichere Versorgung mit Treibstoffen und Energie zu gewährleisten werden Verfahren zur regenerativen Elektrizitätsproduktion in Europa ausgebaut. Teilweise kann aber die erzeugte Elektrizität nicht gespeichert werden, da die Netzkapazitäten des Stromnetzes nicht ausreichen. Zudem benötigt die Gesellschaft Treibstoffe für die Mobilität. Um beide vorhergenannten Themenfelder sinnvoll zu kombinieren kann man aus Wasser elektrolytisch mittels der „Power-to-Gas“ Technologie Überschussstrom in Wasserstoff (H2) umwandeln. H2 kann dann mit Kohlendioxid mittels biologischer Methanproduktion (BMP) in Methan umgewandelt werden. Für das BMP Verfahren werden derzeit nur hydrogenotrophe Methanogene genutzt. Viele Mikroorganismen sind jedoch bioprozesstechnisch noch nicht unter Hochdruckbedingungen charakterisiert worden. Das Projekt BioHyMe unterscheidet sich von den herkömmlichen Methanisierungsverfahren, sowohl chemisch als auch biologisch, da hier Mikroorganismen bei verschiedenen Druckniveaus bioprozesstechnisch mittels „closed batch“, „fed-batch“ und in kontinuierlicher Kultur charakterisiert werden. Durch die Optimierung der Prozessbedingungen, und durch die gezielte Priorisierung von Mikroorganismen, sollen signifikante wissenschaftliche Entwicklungen im Bereich der Hochdruckbiologie erreicht werden.

H2.at: Extremophile mikrobielle Zellfabriken zur hocheffizienten Produktion von Biowasserstoff

Wasserstoff (H2) stellt einen wichtigen erneuerbaren Energieträger der Zukunft dar und kann u.a. biologisch durch anaerobe Fermentation hergestellt werden. Zurzeit sind allerdings die dabei erzielten Umsatzraten und Ausbeuten unbefriedigend. Für eine energieeffiziente, umweltschonende Form der Bio-H2 Produktion im industriellen Maßstab ist es notwendig, neue H2-Produktionstechnologien zu entwickeln.
Extremophile Mikroorganismen bieten neuartige Optionen zur erheblichen Verbesserung der biogenen H2 Produktion. Durch ihre außergewöhnlichen Stoffwechselwege eignen sich Extremophile hervorragend für neuartige biotechnologische Anwendungen. Extremophile (z.B. Thermophile) finden sich v.a. in der Gruppe der Archaea, welche neben den Bakterien und Eukaryoten eine eigene, dritte Domäne des Lebens bilden. Gegenstand des Projektes ist die Entwicklung eines innovativen Fermentationsprozesses zur H2 Produktion mittels thermophilen Extremophilen - insbesondere Archaea. Im ersten Schritt erfolgt der Aufschluss von organischem Substrat durch Stämme, deren H2-Produktion endproduktinhibiert wird. Neben H2 wird dabei CO2 und Acetat gebildet. In einem zweiten Schritt wird das zuvor gebildete Acetat durch syntrophe Mikroorganismen für die H2 Produktion genutzt.
Im Projekt H2.AT werden die geeignetsten Extremophilen ausgewählt, zu einen effektiven mikrobiellen Konsortium zusammengestellt und in Form eines Biofilms immobilisiert. Zur Unterstützung der Biowasserstoffproduktion wird der strukturierte Biofilm mit innovativen Verfahren zur H2-Enfernung gekoppelt, um hohe H2-Produktionsraten und Ausbeuten erzielen zu können. Die Kombination aus innovativen Verfahren zur H2-Entfernung mit dem mikrobiellen Konsortium des strukturierten Biofilms soll eine maßgeschneiderte und effiziente H2-Produktion ermöglichen.
Das Endziel des Projektes H2.AT ist eine komplette biologische Konversion des eingesetzten organischen Materials in H2.

Evolutionary history and ecological adaptations of ammonia oxidizing Thaumarchaeota

Ammonia oxidizing archaea (AOA), a clade of the Thaumarchaeota phylum, diversified in a variety of marine and terrestrial environments. Due to their abundance, AOA are deemed major players in the global cycle of nitrogen. They also produce greenhouse gasses. Despite their ecological importance, the nature and origin of ammonia oxidizing metabolism and the reasons for the ecological success of AOA are still unknown. This project aims at performing the first comprehensive evolutionary and comparative genomic analysis of Thaumarchaeota to identify crucial metabolic and genomic features. Metagenomic data produced in the laboratory will give access to genomes of crucial taxa for this project. These genomes will be completed, and analysed together with AOA genomes available in the databanks with a sophisticated model of genome evolution to reconstruct the species tree of Thaumarchaeota and the events (gene duplications, transfers and losses) that occurred along their evolution. The genome of the AOA's ancestor will be inferred, and the minimal gene set required for ammonia oxidation identified. The sets of evolutionary events and the ancestral genome will be linked to metabolic and ecological transitions to obtain the scenario of ammonia oxidation emergence and of the adaptation of AOA to various environments, thus addressing key questions in the fields of ecology, evolution, and archaea biology.

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