Showing papers by "Tatiana A. Vishnivetskaya published in 2009"

The Exiguobacterium genus: biodiversity and biogeography.

Abstract: Bacteria of the genus Exiguobacterium are low G + C, Gram-positive facultative anaerobes that have been repeatedly isolated from ancient Siberian permafrost. In addition, Exiguobacterium spp. have been isolated from markedly diverse sources, including Greenland glacial ice, hot springs at Yellowstone National Park, the rhizosphere of plants, and the environment of food processing plants. Strains of this hereto little known bacterium that have been retrieved from such different (and often extreme) environments are worthy of attention as they are likely to be specifically adapted to such environments and to carry variations in the genome which may correspond to psychrophilic and thermophilic adaptations. However, comparative genomic investigations of Exiguobacterium spp. from different sources have been limited. In this study, we employed different molecular approaches for the comparative analysis of 24 isolates from markedly diverse environments including ancient Siberian permafrost and hot springs at Yellowstone National Park. Pulsed-field gel electrophoresis (PFGE) with I-CeuI (an intron-encoded endonuclease), AscI and NotI were optimized for the determination of genomic fingerprints of nuclease-producing isolates. The application of a DNA macroarray for 82 putative stress-response genes yielded strain-specific hybridization profiles. Cluster analyses of 16S rRNA gene sequence data, PFGE I-CeuI restriction patterns and hybridization profiles suggested that Exiguobacterium strains formed two distinct divisions that generally agreed with temperature ranges for growth. With few exceptions (e.g., Greenland ice isolate GIC31), psychrotrophic and thermophilic isolates belonged to different divisions.

Controlling accumulation of fermentation inhibitors in biorefinery recycle water using microbial fuel cells

Abstract: Background: Microbial fuel cells (MFC) and microbial electrolysis cells are electrical devices that treat water using microorganisms and convert soluble organic matter into electricity and hydrogen, respectively. Emerging cellulosic biorefineries are expected to use large amounts of water during production of ethanol. Pretreatment of cellulosic biomass results in production of fermentation inhibitors which accumulate in process water and make the water recycle process difficult. Use of MFCs to remove the inhibitory sugar and lignin degradation products from recycle water is investigated in this study. Results: Use of an MFC to reduce the levels of furfural, 5-hydroxymethylfurfural, vanillic acid, 4hydroxybenzaldehyde and 4-hydroxyacetophenone while simultaneously producing electricity is demonstrated here. An integrated MFC design approach was used which resulted in high power densities for the MFC, reaching up to 3700 mW/m 2 (356 W/m 3 net anode volume) and a coulombic efficiency of 69%. The exoelectrogenic microbial consortium enriched in the anode was characterized using a 16S rRNA clone library method. A unique exoelectrogenic microbial consortium dominated by δ-Proteobacteria (50%), along with β-Proteobacteria (28%), αProteobacteria (14%), γ-Proteobacteria (6%) and others was identified. The consortium demonstrated broad substrate specificity, ability to handle high inhibitor concentrations (5 to 20 mM) with near complete removal, while maintaining long-term stability with respect to power production. Conclusion: Use of MFCs for removing fermentation inhibitors has implications for: 1) enabling higher ethanol yields at high biomass loading in cellulosic ethanol biorefineries, 2) improved water recycle and 3) electricity production up to 25% of total biorefinery power needs.

Microbial Communities in Subpermafrost Saline Fracture Water at the Lupin Au Mine, Nunavut, Canada

Abstract: We report the first investigation of a deep subpermafrost microbial ecosystem, a terrestrial analog for the Martian subsurface. Our multidisciplinary team analyzed fracture water collected at 890 and 1,130 m depths beneath a 540-m-thick permafrost layer at the Lupin Au mine (Nunavut, Canada). 14C, 3H, and noble gas isotope analyses suggest that the Na–Ca–Cl, suboxic, fracture water represents a mixture of geologically ancient brine, ~25-kyr-old, meteoric water and a minor modern talik-water component. Microbial planktonic concentrations were ~103 cells mL−1. Analysis of the 16S rRNA gene from extracted DNA and enrichment cultures revealed 42 unique operational taxonomic units in 11 genera with Desulfosporosinus, Halothiobacillus, and Pseudomonas representing the most prominent phylotypes and failed to detect Archaea. The abundance of terminally branched and midchain-branched saturated fatty acids (5 to 15 mol%) was consistent with the abundance of Gram-positive bacteria in the clone libraries. Geochemical data, the ubiquinone (UQ) abundance (3 to 11 mol%), and the presence of both aerobic and anaerobic bacteria indicated that the environment was suboxic, not anoxic. Stable sulfur isotope analyses of the fracture water detected the presence of microbial sulfate reduction, and analyses of the vein-filling pyrite indicated that it was in isotopic equilibrium with the dissolved sulfide. Free energy calculations revealed that sulfate reduction and sulfide oxidation via denitrification and not methanogenesis were the most thermodynamically viable consistent with the principal metabolisms inferred from the 16S rRNA community composition and with CH4 isotopic compositions. The sulfate-reducing bacteria most likely colonized the subsurface during the Pleistocene or earlier, whereas aerobic bacteria may have entered the fracture water networks either during deglaciation prior to permafrost formation 9,000 years ago or from the nearby talik through the hydrologic gradient created during mine dewatering. Although the absence of methanogens from this subsurface ecosystem is somewhat surprising, it may be attributable to an energy bottleneck that restricts their migration from surface permafrost deposits where they are frequently reported. These results have implications for the biological origin of CH4 on Mars.

Viable Cyanobacteria and Green Algae from the Permafrost Darkness

Abstract: This review represents an overview of the existence, distribution and abundance of the photoautotrophic microorganisms in the deep subsurface permafrost of the Northeast Russia and McMurdo Dry Valleys, Antarctica. The morphology, growth rate, spectral properties, phylogenetic position of the viable permafrost green algae and cyanobacteria have been studied. Viable photoautotrophs were represented by unicellular green algae and filamentous cyanobacteria with low growth rate. Spectral studies of ancient cyanobacteria and green algae did not reveal any significant differences between them and their contemporary relatives. Phylogenetic analyses have shown that permafrost photoautotrophs were closely related to strains and more often to uncultured environmental clones from cold regions.

Donor-dependent extent of uranium reduction for bioremediation of contaminated sediment microcosms.

Abstract: Bioremediation of uranium was investigated in microcosm experiments containing contaminated sediments from Oak Ridge, Tennessee to explore the importance of electron donor selection for uranium reduction rate and extent. In these experiments, all of the electron donors, including ethanol, glucose, methanol, and methanol with added humic acids, stimulated the reduction and immobilization of aqueous uranium by the indigenous microbial community. Uranium loss from solution began after the completion of nitrate reduction but essentially concurrent with sulfate reduction. When electron donor concentrations were normalized for their equivalent electron donor potential yield, the rates of uranium reduction were nearly equivalent for all treatments (0.55-0.95 micromol L(-1) d(-1)). Uranium reduction with methanol proceeded after a 15-d longer lag time relative to that of ethanol or glucose. Significant differences were not found with the inclusion of humic acids. The extent of U reduction in sediment slurries measured by XANES at various time periods after the start of the experiment increased in the order of ethanol (5-7% reduced at 77 and 153 d), glucose (49% reduced at 53 d), and methanol (93% reduced at 90 d). The microbial diversity of ethanol- and methanol-amended microcosms in their late stage of U reduction was analyzed with 16S rRNA gene amplification. Members of the Geobacteraceae were found in all microcosms as well as other potential uranium-reducing organisms, such as Clostridium and Desulfosporosinus. The effectiveness of methanol relative to ethanol at reducing aqueous and sediment-hosted uranium suggests that bioremediation strategies that encourage fermentative poising of the subsurface to a lower redox potential may be more effective for long-term uranium immobilization as compared with selecting an electron donor that is efficiently metabolized by known uranium-reducing microorganisms.

Proteomic Insights: Cryoadaptation of Permafrost Bacteria

Abstract: The permafrost microbial community has been described as 'a community of survivors' (Friedman 1994). Because of the permanently cold condition and the long term isolation of the permafrost sediments, the permafrost microorganisms have acquired various adaptive features in the membrane, enzymes, and macromolecular synthesis. This chapter reviews the different adaptive mechanisms used by permafrost microorganisms with a focus on the proteomic level of cryoadaptation that have recently been identified during the low temperature growth in permafrost bacteria.

Effect of Growth Temperature and Culture Medium on the Cryotolerance of Permafrost Exiguobacterium Sibiricum 255-15 by Proteome-Wide Mass Mapping

Abstract: Exiguobacterium sibiricum 255-15 has shown significantly improved cryotolerance after liquid broth growth at 4 o C and agar surface growth at both 4 o C and 25 o C compared with liquid broth growth at 25 o C. The ability to survive freeze-thaw stress is expected to depend on the physiological state and protein composition of cells prior to freezing. Using 2-D liquid separation and an ESI-TOF MS-based mass mapping technique, we examined the differences in the pro- teomic profiles of the permafrost bacterium E. sibiricum 255-15 grown at two temperatures (4 o C and 25 o C) and two media (liquid broth and agar surface) before freeze-thawing treatments. In this study, a total of 330 proteins were identified. The cells cultured under the growth conditions associated with the improved cryotolerance have revealed a general down- regulation of enzymes involved in major metabolic processes (glycolysis, anaerobic respiration, ATP synthesis, fermenta- tion, electron transport, and sugar metabolism) as well as in the metabolism of lipids, amino acids, nucleotides and nucleic acids. In addition, eight proteins (2'-5' RNA ligase, hypoxanthine phosphoribosyl transferase, FeS assembly ATPase SufC, thioredoxin reductase and four hypothetical proteins) were observed to be up-regulated. This suggests these eight proteins might have a potential role to induce the improved cryotolerance.