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  • 1
    Publication Date: 2005-01-08
    Description: Dehalococcoides ethenogenes is the only bacterium known to reductively dechlorinate the groundwater pollutants, tetrachloroethene (PCE) and trichloroethene, to ethene. Its 1,469,720-base pair chromosome contains large dynamic duplicated regions and integrated elements. Genes encoding 17 putative reductive dehalogenases, nearly all of which were adjacent to genes for transcription regulators, and five hydrogenase complexes were identified. These findings, plus a limited repertoire of other metabolic modes, indicate that D. ethenogenes is highly evolved to utilize halogenated organic compounds and H2. Diversification of reductive dehalogenase functions appears to have been mediated by recent genetic exchange and amplification. Genome analysis provides insights into the organism's complex nutrient requirements and suggests that an ancestor was a nitrogen-fixing autotroph.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Seshadri, Rekha -- Adrian, Lorenz -- Fouts, Derrick E -- Eisen, Jonathan A -- Phillippy, Adam M -- Methe, Barbara A -- Ward, Naomi L -- Nelson, William C -- Deboy, Robert T -- Khouri, Hoda M -- Kolonay, James F -- Dodson, Robert J -- Daugherty, Sean C -- Brinkac, Lauren M -- Sullivan, Steven A -- Madupu, Ramana -- Nelson, Karen E -- Kang, Katherine H -- Impraim, Marjorie -- Tran, Kevin -- Robinson, Jeffrey M -- Forberger, Heather A -- Fraser, Claire M -- Zinder, Stephen H -- Heidelberg, John F -- New York, N.Y. -- Science. 2005 Jan 7;307(5706):105-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA. rekha@tigr.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15637277" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acids/biosynthesis ; Biodegradation, Environmental ; Chloroflexi/*genetics/*metabolism ; Gene Duplication ; Genes, Bacterial ; *Genome, Bacterial ; Hydrogen/metabolism ; Molecular Sequence Data ; Nitrogenase/genetics/metabolism ; Operon ; Oxidation-Reduction ; Oxidoreductases/genetics/metabolism ; Quinones/metabolism ; Sequence Analysis, DNA ; Tetrachloroethylene/*metabolism ; Transcription Factors/genetics/metabolism ; Water Pollutants, Chemical/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2003-12-13
    Description: The complete genome sequence of Geobacter sulfurreducens, a delta-proteobacterium, reveals unsuspected capabilities, including evidence of aerobic metabolism, one-carbon and complex carbon metabolism, motility, and chemotactic behavior. These characteristics, coupled with the possession of many two-component sensors and many c-type cytochromes, reveal an ability to create alternative, redundant, electron transport networks and offer insights into the process of metal ion reduction in subsurface environments. As well as playing roles in the global cycling of metals and carbon, this organism clearly has the potential for use in bioremediation of radioactive metals and in the generation of electricity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Methe, B A -- Nelson, K E -- Eisen, J A -- Paulsen, I T -- Nelson, W -- Heidelberg, J F -- Wu, D -- Wu, M -- Ward, N -- Beanan, M J -- Dodson, R J -- Madupu, R -- Brinkac, L M -- Daugherty, S C -- DeBoy, R T -- Durkin, A S -- Gwinn, M -- Kolonay, J F -- Sullivan, S A -- Haft, D H -- Selengut, J -- Davidsen, T M -- Zafar, N -- White, O -- Tran, B -- Romero, C -- Forberger, H A -- Weidman, J -- Khouri, H -- Feldblyum, T V -- Utterback, T R -- Van Aken, S E -- Lovley, D R -- Fraser, C M -- New York, N.Y. -- Science. 2003 Dec 12;302(5652):1967-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA. bmethe@tigr.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14671304" target="_blank"〉PubMed〈/a〉
    Keywords: Acetates/metabolism ; Acetyl Coenzyme A/metabolism ; Aerobiosis ; Anaerobiosis ; Bacterial Proteins/genetics/metabolism ; Carbon/metabolism ; Chemotaxis ; Chromosomes, Bacterial/genetics ; Cytochromes c/genetics/metabolism ; Electron Transport ; Energy Metabolism ; Genes, Bacterial ; Genes, Regulator ; *Genome, Bacterial ; Geobacter/*genetics/*metabolism/physiology ; Hydrogen/metabolism ; Metals/*metabolism ; Movement ; Open Reading Frames ; Oxidation-Reduction ; Phylogeny
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2012-08-24
    Description: Antibiotics administered in low doses have been widely used as growth promoters in the agricultural industry since the 1950s, yet the mechanisms for this effect are unclear. Because antimicrobial agents of different classes and varying activity are effective across several vertebrate species, we proposed that such subtherapeutic administration alters the population structure of the gut microbiome as well as its metabolic capabilities. We generated a model of adiposity by giving subtherapeutic antibiotic therapy to young mice and evaluated changes in the composition and capabilities of the gut microbiome. Administration of subtherapeutic antibiotic therapy increased adiposity in young mice and increased hormone levels related to metabolism. We observed substantial taxonomic changes in the microbiome, changes in copies of key genes involved in the metabolism of carbohydrates to short-chain fatty acids, increases in colonic short-chain fatty acid levels, and alterations in the regulation of hepatic metabolism of lipids and cholesterol. In this model, we demonstrate the alteration of early-life murine metabolic homeostasis through antibiotic manipulation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3553221/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3553221/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cho, Ilseung -- Yamanishi, Shingo -- Cox, Laura -- Methe, Barbara A -- Zavadil, Jiri -- Li, Kelvin -- Gao, Zhan -- Mahana, Douglas -- Raju, Kartik -- Teitler, Isabel -- Li, Huilin -- Alekseyenko, Alexander V -- Blaser, Martin J -- 1UL1-RR029893/RR/NCRR NIH HHS/ -- R01 DK090989/DK/NIDDK NIH HHS/ -- T-R01-DK090989/DK/NIDDK NIH HHS/ -- UL1 RR029893/RR/NCRR NIH HHS/ -- UL1 TR000038/TR/NCATS NIH HHS/ -- UL1-TR000038/TR/NCATS NIH HHS/ -- England -- Nature. 2012 Aug 30;488(7413):621-6. doi: 10.1038/nature11400.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Medicine, New York University School of Medicine, New York, New York 10016, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22914093" target="_blank"〉PubMed〈/a〉
    Keywords: Adiposity/*drug effects/physiology ; Age Factors ; Animals ; Anti-Bacterial Agents/*administration & dosage/*pharmacology ; Body Composition/drug effects ; Body Weight/drug effects ; Bone Density/drug effects ; Bone Development/drug effects ; Cecum/drug effects/metabolism ; Cholesterol/metabolism ; Colon/*drug effects/*microbiology ; Fatty Acids, Volatile/metabolism ; Feces/microbiology ; Female ; Gastric Inhibitory Polypeptide/blood/metabolism ; Lipid Metabolism/drug effects ; Liver/drug effects/metabolism ; Male ; Metagenome/*drug effects ; Mice ; Mice, Inbred C57BL ; Polymerase Chain Reaction ; Weaning
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 4
    Publication Date: 2015-07-25
    Description: Microbial life inhabits deeply buried marine sediments, but the extent of this vast ecosystem remains poorly constrained. Here we provide evidence for the existence of microbial communities in ~40 degrees to 60 degrees C sediment associated with lignite coal beds at ~1.5 to 2.5 km below the seafloor in the Pacific Ocean off Japan. Microbial methanogenesis was indicated by the isotopic compositions of methane and carbon dioxide, biomarkers, cultivation data, and gas compositions. Concentrations of indigenous microbial cells below 1.5 km ranged from 〈10 to ~10(4) cells cm(-3). Peak concentrations occurred in lignite layers, where communities differed markedly from shallower subseafloor communities and instead resembled organotrophic communities in forest soils. This suggests that terrigenous sediments retain indigenous community members tens of millions of years after burial in the seabed.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Inagaki, F -- Hinrichs, K-U -- Kubo, Y -- Bowles, M W -- Heuer, V B -- Hong, W-L -- Hoshino, T -- Ijiri, A -- Imachi, H -- Ito, M -- Kaneko, M -- Lever, M A -- Lin, Y-S -- Methe, B A -- Morita, S -- Morono, Y -- Tanikawa, W -- Bihan, M -- Bowden, S A -- Elvert, M -- Glombitza, C -- Gross, D -- Harrington, G J -- Hori, T -- Li, K -- Limmer, D -- Liu, C-H -- Murayama, M -- Ohkouchi, N -- Ono, S -- Park, Y-S -- Phillips, S C -- Prieto-Mollar, X -- Purkey, M -- Riedinger, N -- Sanada, Y -- Sauvage, J -- Snyder, G -- Susilawati, R -- Takano, Y -- Tasumi, E -- Terada, T -- Tomaru, H -- Trembath-Reichert, E -- Wang, D T -- Yamada, Y -- New York, N.Y. -- Science. 2015 Jul 24;349(6246):420-4. doi: 10.1126/science.aaa6882. Epub 2015 Jul 23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi 783-8502, Japan. Research and Development Center for Marine Resources, JAMSTEC, Yokosuka 237-0061, Japan. ; MARUM Center for Marine Environmental Sciences, University of Bremen, D-28359 Bremen, Germany. ; Center for Deep-Earth Exploration, JAMSTEC, Yokohama 236-0061, Japan. Research and Development Center for Ocean Drilling Science, JAMSTEC, Yokohama 236-0001, Japan. ; College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR 97331, USA. ; Research and Development Center for Marine Resources, JAMSTEC, Yokosuka 237-0061, Japan. Department of Subsurface Geobiological Analysis and Research, JAMSTEC, Yokosuka 237-0061, Japan. ; Research and Development Center for Marine Resources, JAMSTEC, Yokosuka 237-0061, Japan. Department of Biogeochemistry, JAMSTEC, Yokosuka 237-0061, Japan. ; Center for Geomicrobiology, Department of Bioscience, Aarhus University, DK-8000 Aarhus C, Denmark. ; Department of Environmental Genomics, J. Craig Venter Institute, Rockville, MD 20850, USA. ; Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8567, Japan. ; Department of Geology and Petroleum Geology, School of Geosciences, University of Aberdeen, Aberdeen AB2A 3UE, UK. ; Department of Applied Geosciences and Geophysics, Montanuniversitat, 8700 Leoben, Austria. ; School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham B15 2TT, UK. ; Environmental Management Research Institute, AIST, Tsukuba, Ibaraki 305-8569, Japan. ; The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing, Jiangsu 210093, China. ; Center for Advanced Marine Core Research, Kochi University, Nankoku, Kochi 783-8502, Japan. ; Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. ; Petroleum and Marine Resources Research Division, Korea Institute of Geoscience and Mineral Resources, Yuseong-gu, Daejeon 305-350, Korea. ; Department of Earth Sciences, University of New Hampshire, Durham, NH 03824, USA. ; Department of Earth and Atmospheric Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588, USA. ; Department of Earth Sciences, University of California Riverside, Riverside, CA 92521, USA. ; Graduate School of Oceanography, University of Rhode Island, Narragansett, RI 02882, USA. ; Department of Earth Science, Rice University, Houston, TX 77005, USA. ; School of Earth Science, University of Queensland, Brisbane Queensland 4072, Australia. ; Department of Subsurface Geobiological Analysis and Research, JAMSTEC, Yokosuka 237-0061, Japan. ; Marine Works Japan, Yokosuka 237-0063, Japan. ; Department of Earth Sciences, Graduate School of Science, Chiba University, Chiba 263-8522, Japan. ; Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA. ; Research and Development Center for Ocean Drilling Science, JAMSTEC, Yokohama 236-0001, Japan. Department of Urban Management, Graduate School of Engineering, Kyoto University, Kyoto 615-8540, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26206933" target="_blank"〉PubMed〈/a〉
    Keywords: Aquatic Organisms/*classification/genetics/metabolism ; Archaea/*classification/genetics/metabolism ; Bacteria/*classification/genetics/metabolism ; Biomarkers/metabolism ; Carbon Dioxide/metabolism ; Coal/*microbiology ; Geologic Sediments/*microbiology ; Japan ; Methane/metabolism ; Methanococcus/classification/genetics/metabolism ; Methanosarcina barkeri/classification/genetics/metabolism ; *Microbial Consortia ; Pacific Ocean ; Seawater/*microbiology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
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    Unknown
    PANGAEA
    In:  Supplement to: Inagaki, F; Hinrichs, Kai-Uwe; Kubo, Y; Bowles, Marshall W; Heuer, Verena B; Hong, W-L; Hoshino, Tatsuhiko; Ijiri, Akira; Imachi, H; Ito, M; Kaneko, Masanori; Lever, Mark A; Lin, Yu-Shih; Methe, B A; Morita, S; Morono, Yuki; Tanikawa, Wataru; Bihan, M; Bowden, Stephen A; Elvert, Marcus; Glombitza, Clemens; Gross, D; Harrington, G J; Hori, T; Li, K; Limmer, D; Liu, Chiung-Hui; Murayama, M; Ohkouchi, Naohiko; Ono, Shuhei; Park, Young-Soo; Phillips, S C; Prieto-Mollar, Xavier; Purkey, M; Riedinger, Natascha; Sanada, Yoshinori; Sauvage, J; Snyder, Glen T; Susilawati, R; Takano, Yoshinori; Tasumi, E; Terada, Takeshi; Tomaru, Hitoshi; Trembath-Reichert, E; Wang, D T; Yamada, Y (2015): Exploring deep microbial life in coal-bearing sediment down to ~2.5 km below the ocean floor. Science, 439 (6246), 420-424, https://doi.org/10.1126/science.aaa6882
    Publication Date: 2023-04-29
    Description: Microbial life inhabits deeply buried marine sediments, but the extent of this vast ecosystem remains poorly constrained. Here we provide evidence for the existence of microbial communities in ~40° to 60°C sediment associated with lignite coal beds at ~1.5 to 2.5 km below the seafloor in the Pacific Ocean off Japan. Microbial methanogenesis was indicated by the isotopic compositions of methane and carbon dioxide, biomarkers, cultivation data, and gas compositions. Concentrations of indigenous microbial cells below 1.5 km ranged from 〈10 to ~10**4 cells cm**-3. Peak concentrations occurred in lignite layers, where communities differed markedly from shallower subseafloor communities and instead resembled organotrophic communities in forest soils. This suggests that terrigenous sediments retain indigenous community members tens of millions of years after burial in the seabed.
    Keywords: Integrated Ocean Drilling Program / International Ocean Discovery Program; IODP
    Type: Dataset
    Format: application/zip, 2 datasets
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  • 6
    Electronic Resource
    Electronic Resource
    Springer
    Hydrobiologia 401 (1999), S. 77-96 
    ISSN: 1573-5117
    Keywords: bacterial diversity ; acidification ; Adirondack lakes ; aluminum
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Bacterial diversity was examined in six lakes located in the Adirondack Mountains of upstate New York. This region receives significant anthropogenic atmospheric inputs of strong mineral acids resulting in decreases in pH and acid neutralizing capacity (ANC) in many of the lakes. Statistical methods including correlation and cluster analysis were used to determine if there were significant associations between phylotypes and water chemistry variables. Direct effects of acidification, pH and ANC, were not significantly correlated with any of the broadest level taxonomic classifications (equivalent to class or order), but may be correlated with subgroups within these classifications. Indirect influences of acidification were suggested by significant correlations of phylotypes with aluminum chemistry. There were positive correlations between the relative abundance of the γ subdivision of the Proteobacteria and total aluminum (r 2= 0.70,p= 0.04), monomeric aluminum (r 2= 0.78, p= 0.02) and non-labile aluminum (r 2= 0.92, p= 0.002). The ACK1 clade of the β-Proteobacteria (Adirondack clade 1) was correlated with monomeric aluminum (r 2= 0.71, p=0.03) and non-labile aluminum (r 2= 0.73, p= 0.03). Significant negative correlations were found between the relative abundance of the Cytophaga-Flexibacter-Bacteroides phylum and total aluminum (r 2= 0.74, p= 0.03), and the High G+C subdivision of the Gram Positive phylum with total aluminum (r 2 0.70, p= 0.04). Dissolved organic carbon (DOC) concentrations may also influence bacteria through amelioration of aluminum toxicity and as a carbon source. There were significant positive correlations between DOC and the relative abundance of the γ (r 2= 0.66, p= 0.05) and β (r 2= 0.78, p= 0.02) subdivisions and the ACK1 clade (r 2= 0.84, p= 0.01). Additional significant correlations were also noted between specific phylotypes and certain macro- and micro-nutrients. The results of this study indicate that water chemistry can have a direct influence on bacterial lake assemblages and that in acid stressed lakes aluminum chemistry and DOC concentrations may play a particularly important role.
    Type of Medium: Electronic Resource
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  • 7
  • 8
    Publication Date: 2003-12-12
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 9
    Publication Date: 2015-07-24
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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