Astrobiology is a multidisciplinary topic that addresses the origin, distribution and evolution of life in the universe. One of the key questions relates to whether life could have evolved on other planetary bodies, and Mars has been the major focus. Biologists contribute to this question by studying the ecology of extreme environments on Earth that share closest analogy to Mars’ past or present environment. In this thesis, molecular-level interrogations were used to address some aspects of microbial biodiversity, ecology and stress tolerance in two such extreme environments. The high-altitude cold and intense UV irradiance of central Tibet was selected as an analogue for Mars surface today, whilst cold alkaline high-carbonate freshwater lakes were chosen as an analogue for Mars’ previous late wet phase. Biological soil crusts from central Tibet supported a diverse microflora and these were variously bacteria or eukarya dominated. The relatively well-developed eukarya-dominated crusts were characterized and showed they comprised of Stichococcus bacillaris, plus alphaproteobacteria, betaproteobacteria, bacteroidetes and gemmatimonadetes. In order to evaluate the diversity of radiation-tolerant taxa in these soils, samples were exposed to ionizing radiation and viability, physiology and phylogenetic identity determined. The most radio-tolerant taxa isolated and characterized were from the radiation tolerant phylum Deinococci (15kGy), whilst a relatively diverse range of Actinobacteria, Bacilli, Cyanobacteria and Proteobacteria were also recovered after exposure to doses up to 10kGy. This implies the high-radiation environment has selected for tolerance among diverse phyla, with tolerances that far exceed environmental exposure. It is not known at this stage if they all employ similar protective strategies. Microbial reefs that have developed in cold alkaline lakes in British Columbia were studied as analogues for a late-wet Mars environment. Molecular ecological analysis revealed that communities consisted largely of of Proteobacteria (alpha), Cyanobacteria (Leptolyngbya) and Acidobacteria, with similarities in community assembly to marine stromatolites. Microbial diversity varied spatially and temporally within microbialites, and indicated that geographically proximal structures can develop with different communities. Significant changes also occur between summer and winter when the lake surface is frozen. Investigation of other nearby lakes with similar geochemistry but not supporting microbialites revealed extensive microbial mats. These developed in the presence of relatively high concentrations of methane or sulfate, and their biodiversity reflected this with several putative methanotrophic and sulphate utilizing taxa identified. No obvious cues that inhibit or promote microbialite formation were observed in this study. / published_or_final_version / Biological Sciences / Doctoral / Doctor of Philosophy

Thesis (Ph.D.)--Biology, Georgia Institute of Technology, 2008. / Committee Chair: Patricia Sobecky; Committee Member: Ellery Ingall; Committee Member: Jim Spain; Committee Member: Martial Taillefert; Committee Member: Thomas DiChristina.

Extreme environments created through natural and anthropogenic processes harbor microbes with diverse physiologies capable of catalyzing chemical reactions which are environmentally beneficial on local and global scales. This work focused on two unique environments, the Gulf of Mexico (GoM) submarine mud volcano systems and the subsurface soils at the Department of Energy s (DOE) Field Research Center (FRC) located in the Oak Ridge National Laboratory Reservation (Oak Ridge, TN). In addition to the physical and chemical extremes present within mud volcano sediments and FRC subsurface soils, these environments are sources of greenhouse gases as well as metal/radionuclide contaminants, respectively. Within the previously uncharacterized mud volcano cold seep sediments, culture-independent analyses of microbial community structure via DNA and RNA clone libraries indicated Gammaproteobacteria and anaerobic methane oxidizing Archaea as the dominant methane oxidizing taxa. Culture-dependent studies of FRC subsurface Arthrobacter and Bacillus isolates demonstrated extensive lateral gene transfer of the PIB-type ATPase metal resistance genes. Additionally, FRC Bacillus and Rahnella isolates demonstrated U(VI) sequestration capabilities as up to 95% soluble U(VI) was immobilization via biogenic phosphate mineral production resulting from constitutive nonspecific phosphohydrolase activity. Findings from these studies identify the prokaryotic diversity within aquatic and terrestrial sediments that contribute to the geochemical cycling of carbon, metals, and radionuclides.

Metagenomics has revealed that the marine microbial biosphere is immensely more diverse than originally considered, and is an almost untapped reservoir for the potential discovery of microbial natural products. Despite numerous advances in culturing, biosynthetic engineering and genomic-based screening efforts to uncover much of this diversity in relatively accessible environments, a high rediscovery rate has resulted in the investigation of unique, relatively unexplored ecosystems harboring phylogenetically diverse communities of marine organisms. The focus of this research was to establish a culture repository of microorganisms collected from the Red Sea and from deep-sea hydrothermal vents, and to assess their biosynthetic potential for the production of new chemical scaffolds. Cultivation of marine cyanobacteria from the Red Sea has led to the identification of five new cyclic depsipeptides, apratoxin H, grassypeptolides D and E, Ibu-epidemethoxylyngbyastin 3 and leptochelin, the latter possessing a unique chemical scaffold capable of binding metals. A collection of deep-sea hydrothermal vent sediment and microbial mat samples led to the isolation of 64 unique bacterial strains, with eight assigned as members of the order Actinomycetales. Importantly, these isolates, along with a collection of deep-vent invertebrates and microbes, have led to the development of methods for the collection, culturing and biological screening of organisms from this extreme environment for future natural products research. / Graduation date: 2013

"June, 2008". / Thesis (PhD)--Macquarie University, Division of Environmental & Life Sciences, Dept. of Chemistry & Biomolecular Sciences, 2009. / Bibliography: p. 227-259. / Literature review -- Materials and methods -- Sampling sites and sampling material -- Enrichment cultures and molecular analyses -- Optical and binding characterisation of the QDs -- Applications of the QDs -- Concluding remarks. / White island, the most active volcano in New Zealand, is a poorly studied environment that represents an ideal site for the investigation of acidophilic thermophiles. The microorganisms present on here are continually exposed to extreme environmental conditions as they are surrounded by steamy sulphurous fumaroles and acidic streams. The sediment temperature ranges from 38°C to 104°C whilst maintaining pH values below 3. A survey of the volcanic hydrothermal system of White Island was undertaken in order to gain insights onto the microbial diversity using culture-dependant techniques and molecular and phylogenetic analyses. A novel liquid medium based on "soil-extract" was designed which supported growth of bacterial and archaeal mixed cultures. Molecular analyses revealed that the dominant culturable bacterial species belong to the Bacteroidetes, Firmicutes and α-Proteobacteria groups. Several previously uncultured archaeal species were also present in the mixed cultures. The knowledge gained from these studies was intended to help in the development of a novel microbial detection technique suitable for community analysis. -- Conventional molecular techniques used to study microbial biodiversity in environmental samples are both time-consuming and expensive. A novel bead-based assay employing Quantum dots (QDs) was considered to have many advantages over standard molecular techniques. These include high detection speeds, sensitivity, specificity, flexibility and the capability for multiplexed analysis. QDs are inorganic semiconductor nanoparticles made up of crystals about the size of proteins. It has been claimed that the physical and chemical properties of the QDs have significant advantages compared to organic dyes, including brighter fluorescence and resistance to photo-bleaching. Their optical properties facilitate the simultaneous imaging of multiple colours due to their flexible excitation and narrow band emission. Functionalised QDs are able to bind to different biological targets such as DNA, allowing high-throughput analysis for rapid detection and quantification of genes and cells. -- The optical and physical characteristics of the QDs as well their interaction with biomolecules are shown to be suitable for the development of a novel bead-based technique able to target the key microbial species and identify them by flow cytometric measurements (FCM). The broad absorption and narrow emission spectra of the QDs, as well as their fluorescence intensity and specify to target biomolecules, was compared to other organic fluorophores. The potential advantages and limitations of QDs as a fluorophores for biological applications are discussed. -- The data acquired during this study provides a broad overview of the microbial diversity and ecology of the volcanically-active hydrothermal systems of White Island and constitutes the baseline for the development of a novel bead-based technique based on QDs. / Mode of access: World Wide Web. / xvii, 259 p. ill. (some col.)