Christopher R. Omelon

Chemical and Ultrastructural Characterization of High Arctic Cryptoendolithic Habitats

Cryptoendolithic habitats in the Canadian high Arctic are host to a diverse assemblage of microorganisms including cyanobacteria, algae, fungi and heterotrophic bacteria. Communities grow as biofilms attached to mineral surfaces as well as within the open void spaces between grains and in many cases produce extracellular polysaccharides in response to the extreme environmental conditions. In situ observations of the cryptoendolithic habitat as well as ultrastructural examination of microorganisms show that this EPS provides a substrate for accumulation of allochthonous clay particles that enter the system by winds and rain. The lack of evidence for biomineralization within this habitat contrasts with similar environments in the Antarctic Dry Valleys, a consequence of warmer temperatures and wetter conditions that increase erosion rates and subsequent habitat destruction, effectively limiting the time possible for biomineralization by living microorganisms as well as the formation of biosignatures or microfossils.

Inorganic Species Distribution and Microbial Diversity within High Arctic Cryptoendolithic Habitats

Cryptoendolithic habitats in the Canadian high Arctic are associated with a variety of microbial community assemblages, including cyanobacteria, algae, and fungi. These habitats were analyzed for the presence of metal ions by sequential extraction and evaluated for relationships between these and the various microorganisms found at each site using multivariate statistical methods. Cyanobacteria-dominated communities exist under higher pH conditions with elevated concentrations of calcium and magnesium, whereas communities dominated by fungi and algae are characterized by lower pH conditions and higher concentrations of iron, aluminum, and silicon in the overlying surfaces. These results suggest that the activity of the dominant microorganisms controls the pH of the surrounding environment, which in turn dictates rates of weathering or the possibility for surface crust formation, both ultimately deciding the structure of microbial diversity for each cryptoendolithic habitat.

Endolithic Microbial Communities in Polar Desert Habitats

Microorganisms inhabiting terrestrial endolithic habitats are widespread in polar environments including the Antarctic Dry Valleys and the Canadian high Arctic. Their ability to survive in these harsh environments is a result of their finding protection from extremes in temperature, aridity, radiation and winds by colonizing nutrient-rich subsurface habitats that provide more amenable conditions for growth, often developing as vertically stratified communities that include fungi, algae, cyanobacteria and heterotrophic bacteria. Despite finding some refuge from climatic extremes, endolithic microorganisms commonly produce extracellular polysaccharides to avoid desiccation and minimize the damaging effects of freeze-thaw cycles. These microorganisms are geochemically reactive with their endolithic surroundings, observed as heterogeneous concentrations and distributions of metals resulting from mineral dissolution and precipitation reactions as well as element and nutrient release and cycling. Novel microscopy techniques such as SEM-BSE reveal much information about the physiological state of these microorganisms in situ, and show how under specific conditions, microbe-mineral interactions produce unique biosignatures of interest to studies in astrobiology. Their ability to change in situ pH conditions shows that can be directly involved in weathering of endolithic habitats, but the ecology of a given endolithic microbial community can have varying effects on rates of rock weathering. These differences in weathering rates may be an important control on microbial species diversity in polar desert endolithic habitats.

Polar endoliths - an anti-correlation of climatic extremes and microbial biodiversity

We examined the environmental stresses experienced by cyanobacteria living in endolithic gneissic habitats in the Haughton impact structure, Devon Island, Canadian High Arctic (75° N) and compared them with the endolithic habitat at the opposite latitude in the Dry Valleys of Antarctica (76° S). In the Arctic during the summer, there is a period for growth of approximately 2.5 months when temperatures rise above freezing. During this period, freeze–thaw can occur during the diurnal cycle, but freeze–thaw excursions are rare within higher-frequency temperature changes on the scale of minutes, in contrast with the Antarctic Dry Valleys. In the Arctic location rainfall of approximately 3 mm can occur in a single day and provides moisture for endolithic organisms for several days afterwards. This rainfall is an order of magnitude higher than that received in the Dry Valleys over 1 year. In the Dry Valleys, endolithic communities may potentially receive higher levels of ultraviolet radiation than the Arctic location because ozone depletion is more extreme. The less extreme environmental stresses experienced in the Arctic are confirmed by the presence of substantial epilithic growth, in contrast to the Dry Valleys. Despite the more extreme conditions experienced in the Antarctic location, the diversity of organisms within the endolithic habitat, which includes lichen and eukaryotic algal components, is higher than observed at the Arctic location, where genera of cyanobacteria dominate. The lower biodiversity in the Arctic may reflect the higher water flow through the rocks caused by precipitation and the more heterogeneous physical structure of the substrate. The data illustrate an instance in which extreme climate is anti-correlated with microbial biological diversity.

Limestone Corrosion by Neutrophilic Sulfur-Oxidizing Bacteria: A Coupled Microbe-Mineral System

Subsurface karst aquifers receiving sulfidic water can host complex chemolithotrophic microbial communities that are capable of dissolving limestone, forming new karstic habitat. Neutrophilic sulfur-oxidizing bacteria use reduced sulfur compounds as energy rich substrate, potentially producing sulfuric acid as a geochemically reactive byproduct. The physicochemical relationship between a biofilm forming on a limestone surface and the extent of microbial influence on dissolution rate, however, are unknown. We investigated the rate of Madison limestone dissolution by sulfur-oxidizers both in the field at Lower Kane Cave, WY (LKC), and in the laboratory using continuous flow culture reactors and microbial mat collected from LKC. In the field, a microbial consortium rapidly colonized limestone chips forming a thick biofilm, with deep etching of mineral surfaces underneath. In the laboratory we found that a microbial biofilm oxidizing thiosulfate on the limestone surface accelerated dissolution rate up to 7 times faster than the abiotic baseline rate. In contrast, experiments done with H2S or a mixture of H2S and thiosulfate had no effect on dissolution rate. We hypothesize that the laboratory mat community dominated by Thiothrix sp. oxidizes thiosulfate to sulfate and H+, while H2S is partially oxidized to S°. When all sulfur substrate is withheld, the community oxidizes stored intracellular sulfur, briefly accelerating limestone dissolution even in the absence of external supplied substrate. Accelerated corrosion occurs only in the reactive micro-environment under the biofilm, disconnected from the bulk reactor solution. When experiments are repeated where the microbial population is separated from the limestone by a dialysis membrane barrier, measured pH drop is greater, but there is only slight enhancement of rate. This work confirms our working hypothesis that neutrophilic sulfur-oxidizers colonize and rapidly dissolve limestone surfaces, possibly to buffer the production of excess acidity.

Characterization of Microbial Mat Microbiomes in the Modern Thrombolite Ecosystem of Lake Clifton, Western Australia Using Shotgun Metagenomics

Microbialite-forming communities interact with the environment and influence the precipitation of calcium carbonate through their metabolic activity. The functional genes associated with these metabolic processes and their environmental interactions are therefore critical to microbialite formation. The microbiomes associated with microbialite-forming ecosystems are just now being elucidated and the extent of shared pathways and taxa across different environments is not fully known. In this study, we profiled the microbiome of microbial communities associated with lacustrine thrombolites located in Lake Clifton, Western Australia using metagenomic sequencing and compared it to the non-lithifying mats associated with surrounding sediments to determine whether differences in the mat microbiomes, particularly with respect to metabolic pathways and environmental interactions, may potentially contribute to thrombolite formation. Additionally, we used stable isotope biosignatures to delineate the dominant metabolism associated with calcium carbonate precipitation in the thrombolite build-ups. Results indicated that the microbial community associated with the Lake Clifton thrombolites was predominantly bacterial (98.4%) with Proteobacteria, Cyanobacteria, Bacteroidetes, and Actinobacteria comprising the majority of annotated reads. Thrombolite-associated mats were enriched in photoautotrophic taxa and functional genes associated with photosynthesis. Observed δ13C values of thrombolite CaCO3 were enriched by at least 3.5‰ compared to theoretical values in equilibrium with lake water DIC, which is consistent with the occurrence of photoautotrophic activity in thrombolite-associated microbial mats. In contrast, the microbiomes of microbial communities found on the sandy non-lithifying sediments of Lake Clifton represented distinct microbial communities that varied in taxa and functional capability and were enriched in heterotrophic taxa compared to the thrombolite-associated mats. This study provides new insight into the taxa and functional capabilities that differentiate potentially lithifying mats from other non-lithifying types and suggests that thrombolites are actively accreting and growing in limited areas of Lake Clifton.

Isolation and characterization of a CO2-tolerant Lactobacillus strain from Crystal Geyser, Utah, U.S.A.

When CO2 is sequestered into the deep subsurface, changes to the subsurface microbial community will occur. Capnophiles, microorganisms that grow in CO2-rich environments, are some organisms that may be selected for under the new environmental conditions. To determine whether capnophiles comprise an important part of CO2-rich environments, an isolate from Crystal Geyser, Utah, U.S.A., a CO2- rich spring considered a carbon sequestration analogue, was characterized. The isolate was cultured under varying CO2, pH, salinity, and temperature, as well as different carbon substrates and terminal electron acceptors (TEAs) to elucidate growth conditions and metabolic activity. Designated CG-1, the isolate is related (99%) to Lactobacillus casei in 16S rRNA gene identity, growing at PCO2 between 0 to 1.0 MPa. Growth is inhibited at 2.5 MPa, but stationary phase cultures exposed to this pressure survive beyond 5 days. At 5.0 MPa, survival is at least 24 hours. CG-1 grows in neutral pH, 0.25 M NaCl, and between 25° to 45°C andconsumes glucose, lactose, sucrose, or crude oil, likely performing lactic acid fermentation. Fatty acid profiles between 0.1 MPa to 1.0 MPa suggests decreases in cell size and increases in membrane rigidity. Transmission electron microscopy reveals rod shaped bacteria at 0.1 MPa. At 1.0 MPa, cells are smaller, amorphous, and produce abundant capsular material. Its ability to grow in environments regardless of the presence of CO2 suggests we have isolated an organism that is more capnotolerant than capnophilic. Results also show that microorganisms are capable of surviving the stressful conditions created by the introduction of CO2 for sequestration. Furthermore, our ability to culture an environmental isolate indicates that organisms found in CO2 environments from previous genomic and metagenomics studies are viable, metabolizing, and potentially affecting the surrounding environment.

Thermophilic Archaeal Diversity and Methanogenesis from El Tatio Geyser Field, Chile

ABSTRACT The hydrothermal fluid chemistry at El Tatio Geyser Field (ETGF) in northern Chile suggests that biogenic CO2–CH4 cycling may play an important role in water chemistry, and relatively low sulfate (0.6–1 mM) and high molecular hydrogen (H2) concentrations (67–363 nM) suggest that methanogenic Archaea are present in ETGF microbial mats. In this study, δ13C analysis of dissolved inorganic carbon and methane was not indicative of biogenic methane production (δ13CCH4 values ranging from −15‰ to −5.3‰); however, methanogenic Archaea were successfully cultured from each of the hydrothermal sites sampled. Sanger sequencing using universal Archaea primers identified putative methanogenic orders with varying metabolic capabilities, including Methanobacteriales, Methanomicrobiales and Methanosarcinales.

Endolithic Microorganisms and Their Habitats

Endolithic microorganisms are widespread in desert biomes, where hostile environmental conditions limit the majority of life to rock habitats. In these habitats, microorganisms receive light for photosynthesis, moderated and warmer temperatures, protection from UV radiation, and prolonged exposure to liquid water. In general, these microbial communities are composed of phototrophic microorganisms as well as fungi and heterotrophic bacteria. Microbial composition is distinct from soil communities, suggesting these habitats select for microorganisms best suited to this environment. The habitat is not nutrient limited, which explains why these microbial communities colonize a wide range of lithic substrates with different mineralogies; however, greater environmental pressures select for those able to tolerate increasingly harsh conditions. Growth rates vary primarily as a function of moisture availability, resulting in long-lived communities in the driest deserts. While most microorganisms require liquid water for growth, some lichens with an algal phycobiont can photosynthesize with water vapor alone, a significant advantage in these water-limited biomes. Additional strategies against stress include synthesis of pigments, EPS, and osmoprotectants, which significantly offsets the growth of biomass. Microbial activity leads to physical and geochemical weathering, but can also result in stabilization of the lithic habitat. Identification of endolithic biosignatures and microbial fossils has resulted in their study from an astrobiological perspective in the search for life on other planets.