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Item Metagenomes from high-temperature chemotrophic systems reveal geochemical controls on microbial community structure and function(2010-03) Inskeep, William P.; Rusch, Douglas B.; Jay, Zackary J.; Herrgard, Markus J.; Kozubal, Mark A.; Richardson, Toby H.; Macur, Richard E.; Hamamura, Natsuko; Jennings, Ryan deM.; Fouke, Bruce W.; Reysenbach, Anna-Louise; Roberto, Frank; Young, Mark J.; Schwartz, Ariel; Boyd, Eric S.; Badger, Jonathan H.; Mathur, Eric J.; Ortmann, Alice C.; Bateson, Mary M.; Geesey, Gill G.; Frazier, MarvinThe Yellowstone caldera contains the most numerous and diverse geothermal systems on Earth, yielding an extensive array of unique high-temperature environments that host a variety of deeply-rooted and understudied Archaea, Bacteria and Eukarya. The combination of extreme temperature and chemical conditions encountered in geothermal environments often results in considerably less microbial diversity than other terrestrial habitats and offers a tremendous opportunity for studying the structure and function of indigenous microbial communities and for establishing linkages between putative metabolisms and element cycling. Metagenome sequence (14–15,000 Sanger reads per site) was obtained for five high-temperature (>65°C) chemotrophic microbial communities sampled from geothermal springs (or pools) in Yellowstone National Park (YNP) that exhibit a wide range in geochemistry including pH, dissolved sulfide, dissolved oxygen and ferrous iron. Metagenome data revealed significant differences in the predominant phyla associated with each of these geochemical environments. Novel members of the Sulfolobales are dominant in low pH environments, while other Crenarchaeota including distantly-related Thermoproteales and Desulfurococcales populations dominate in suboxic sulfidic sediments. Several novel archaeal groups are well represented in an acidic (pH 3) Fe-oxyhydroxide mat, where a higher O2 influx is accompanied with an increase in archaeal diversity. The presence or absence of genes and pathways important in S oxidation-reduction, H2-oxidation, and aerobic respiration (terminal oxidation) provide insight regarding the metabolic strategies of indigenous organisms present in geothermal systems. Multiple-pathway and protein-specific functional analysis of metagenome sequence data corroborated results from phylogenetic analyses and clearly demonstrate major differences in metabolic potential across sites. The distribution of functional genes involved in electron transport is consistent with the hypothesis that geochemical parameters (e.g., pH, sulfide, Fe, O2) control microbial community structure and function in YNP geothermal springs.Item Microbes in mercury-enriched geothermal springs in western North America(2016-11) Geesey, Gill G.; Barkay, Tamar; King, SueBecause geothermal environments contain mercury (Hg) from natural sources, microorganisms that evolved in these systems have likely adapted to this element. Knowledge of the interactions between microorganisms and Hg in geothermal systems may assist in understanding the long-term evolution of microbial adaptation to Hg with relevance to other environments where Hg is introduced from anthropogenic sources. A number of microbiological studies with supporting geochemistry have been conducted in geothermal systems across western North America. Approximately 1 in 5 study sites include measurements of Hg. Of all prokaryotic taxa reported across sites with microbiological and accompanying physicochemical data, 42% have been detected at sites in which Hg was measured. Genes specifying Hg reduction and detoxification by microorganisms were detected in a number of hot springs across the region. Archaeal-like sequences, representing two crenarchaeal orders and one order each of the Euryarchaeota and Thaumarchaeota, dominated in metagenomes\' MerA (the mercuric reductase protein) inventories, while bacterial homologs were mostly found in one deeply sequenced metagenome. MerA homologs were more frequently found in metagenomes of microbial communities in acidic springs than in circumneutral or high pH geothermal systems, possibly reflecting higher bioavailability of Hg under acidic conditions. MerA homologs were found in hot springs prokaryotic isolates affiliated with Bacteria and Archaea taxa. Acidic sites with high Hg concentrations contain more of Archaea than Bacteria taxa, while the reverse appears to be the case in circumneutral and high pH sites with high Hg concentrations. However, MerA was detected in only a small fraction of the Archaea and Bacteria taxa inhabiting sites containing Hg. Nevertheless, the presence of MerA homologs and their distribution patterns in systems, in which Hg has yet to be measured, demonstrates the potential for detoxification by Hg reduction in these geothermal systems, particularly the low pH springs that are dominated by Archaea.Item Use of dcode system to detect the food-borne bacterial pathogen listeria monocytogenes(1998) Schmolker, N.; van Ommen Kloeke, F.; Geesey, Gill G.Item Influence of divalent cations and ph on adsorption of a bacterial polysaccharide adhesin(1998-09) Bhosle, N.; Suci, Peter A.; Baty, Ace M.; Weiner, R. M.; Geesey, Gill G.Hyphomonas MHS-3 (MHS-3) elaborates a diffuse capsular material, primarily composed of polysaccharide, which has been implicated to serve as the holdfast of this prosthecate marine bacterium. A purified polysaccharide (fr2ps) from this capsular material exhibits a relatively large affinity for (Ge), or more precisely for the Ge oxide surface film. In its natural habitat MHS-3 attaches to marine sediments. This suggests that molecular properties of fr2ps have evolved to render it adhesive toward mineral oxides. In order to characterize these molecular interactions, the effect of divalent cations and pH on the adsorption of fr2ps to Ge has been measured using attenuated total internal reflection Fourier transform infrared (ATR/FT-IR) spectroscopy. The effect of adsorption of fr2ps on the Ge oxide film has been investigated using X-ray photoelectron spectroscopy (XPS). The results indicate that divalent cations participate in binding of fr2ps to Ge oxide and that atomic size of the cation is important. Evidence for significant participation of hydrogen bonding to the oxide surface is lacking.Item Bacterial colonization of artificial substrate in the vicinity of deep-sea hydrothermal vents(1998-06) Guezennec, J.; Ortega-Morales, O.; Raguenes, G.; Geesey, Gill G.Artificial substrata of different material composition were deployed at deep-sea hydrothermal areas on the Mid-Atlantic Ridge for exposure times ranging from 1 to 12 days. After 4 days of exposure, a very thick but loosely-bound biofilm formed on all surfaces. Two bacterial morphotypes dominated the attached microbial community: rod-shaped bacteria sometimes several cell layers thick and large filamentous forms attached to the substratum at one end of the filament. Quantitative extraction of biofilm lipids associated with the substratum surface indicated the accumulation of a large amount of bacterial biomass after 4 days of exposure for all substrata. Microbial biomass accumulated at different rates on the different substrata. The greatest biomass was associated with 316L stainless steel and titanium substrata. Polar lipid fatty acid (PLFA) analysis of lipid extracts contained signatures of sulfate reducing bacteria and fatty acids (FA) previously reported in filamentous sulfur-oxidizing bacteria. The results demonstrate rapid in situ colonization of artificial substrata by hydrothermal vent microbial populations irrespective of the nature of the substratum.Item Observations and interpretations of the performance of engineered materials for containment of spent nuclear fuels during interim wet storage: a need for improved corrosion monitoring capabilities?(1998) Geesey, Gill G.; Zhang, Hong-Ji; Suci, Peter A.; Davidson, D.; Baty, Ace M.; van Ommen Kloeke, F.Item Function of bacterial (hyphomonas spp.) capsular exopolymers in biofouling(1997) Weiner, R. M.; Langille, S. E.; Geesey, Gill G.; Quintero, Ernesto J.Item Characterization of extracellular chitinolytic activity in biofilms(2001) Baty, Ace M.; Diwu, Zhenjun; Dunham, G.; Eastburn, Callie C.; Geesey, Gill G.; Goodman, Amanda E.; Suci, Peter A.; Techkarnjanaruk, SomkietItem Combined light microscopy and attenuated total reflection fourier transform infrared spectroscopy for integration of biofilm structure, distribution, and chemistry at solid-liquid interfaces(1997-11) Suci, Peter A.; Siedlecki, Kevin J.; Palmer, R. J.; White, D. C.; Geesey, Gill G.Item Adsorption of adhesive proteins from the marine mussel, mytilus edulis, on polymer films in the hydrated state using angle dependent x-ray photoelectron spectroscopy and atomic force microscopy(1997-10) Baty, Ace M.; Leavitt, P. K.; Siedlecki, C. A.; Tyler, Bonnie J.; Suci, Peter A.; Marchant, R. E.; Geesey, Gill G.The adsorption of mussel adhesive protein (MAP) from the marine mussel Mytilus edulis has been investigated on polystyrene (PS) and poly(octadecyl methacrylate) (POMA) surfaces using angle dependent X-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM). AFM images previously published in the dehydrated state using contact mode are compared with images acquired in the hydrated state using fluid Tapping Mode to assess the contribution that hydration has on the architecture of the adsorbed proteins. To further characterize the adsorbed protein layer, XPS analysis was performed at liquid nitrogen (LN2) temperature without dehydrating the samples and at room temperature after the surfaces were dehydrated. The differences observed upon dehydration can be attributed to the strength of the interactions between MAP and the two surfaces. The AFM and XPS data indicate that adsorbed MAP is stabilized on the surface of the PS through interactions that prevent the protein layer from being disrupted upon dehydration. The adsorbed MAP on the POMA surface is representative of a loosely bound protein layer that becomes highly perturbed upon dehydration.