메뉴 건너뛰기




Volumn 2, Issue JAN, 2012, Pages

Metagenomic evidence for H2 oxidation and H2 production by serpentinite-hosted subsurface microbial communities

Author keywords

Alkaline spring; Hydrogenase; Metagenome; Serpentinization; Subsurface

Indexed keywords

BETAPROTEOBACTERIA; BURKHOLDERIALES; CLOSTRIDIA; CLOSTRIDIALES; POSIBACTERIA;

EID: 84862703105     PISSN: None     EISSN: 1664302X     Source Type: Journal    
DOI: 10.3389/fmicb.2011.00268     Document Type: Article
Times cited : (170)

References (65)
  • 1
    • 33645450631 scopus 로고    scopus 로고
    • Brief report statistical methods for characterizing diversity of microbial communities by analysis of terminal restriction fragment length polymorphisms of 16S rRNA genes
    • Abdo, Z., Schüette, U. M., Bent, S. J., Williams, C. J., Forney, L. J., and Joyce, P. (2006). Brief report statistical methods for characterizing diversity of microbial communities by analysis of terminal restriction fragment length polymorphisms of 16S rRNA genes. Environ. Microbiol. 8, 929-938.
    • (2006) Environ. Microbiol. , vol.8 , pp. 929-938
    • Abdo, Z.1    Schüette, U.M.2    Bent, S.J.3    Williams, C.J.4    Forney, L.J.5    Joyce, P.6
  • 5
    • 78649448514 scopus 로고    scopus 로고
    • [FeFe]-Hydrogenase in Yellowstone National Park: evidence for dispersal limitation and phylogenetic niche conservatism
    • Boyd, E. S., Hamilton, T. L., Spear, J. R., Lavin, M., and Peters, J. W. (2010). [FeFe]-Hydrogenase in Yellowstone National Park: evidence for dispersal limitation and phylogenetic niche conservatism. ISME J. 4, 1485-1495.
    • (2010) ISME J , vol.4 , pp. 1485-1495
    • Boyd, E.S.1    Hamilton, T.L.2    Spear, J.R.3    Lavin, M.4    Peters, J.W.5
  • 6
    • 67649621650 scopus 로고    scopus 로고
    • [FeFe] Hydrogenase genetic diversity provides insight into molecular adaptation in a saline microbial mat community
    • Boyd, E. S., Spear, J. R., and Peters, J. W. (2009). [FeFe] Hydrogenase genetic diversity provides insight into molecular adaptation in a saline microbial mat community. Appl. Environ. Microbiol. 75, 4620-4623.
    • (2009) Appl. Environ. Microbiol , vol.75 , pp. 4620-4623
    • Boyd, E.S.1    Spear, J.R.2    Peters, J.W.3
  • 8
    • 72649088719 scopus 로고    scopus 로고
    • Abundant transposases encoded by the metagenome of a hydrothermal chimney biofilm
    • Brazelton, W J., and Baross, J. A. (2009). Abundant transposases encoded by the metagenome of a hydrothermal chimney biofilm. ISME J. 3, 1420-1424.
    • (2009) ISME J , vol.3 , pp. 1420-1424
    • Brazelton, W.J.1    Baross, J.A.2
  • 9
    • 78149422269 scopus 로고    scopus 로고
    • Metagenomic comparison of two thiomicrospira lineages inhabiting contrasting deep-sea hydrothermal environments
    • doi:10.1371/journal.pone.0013530
    • Brazelton, W J., and Baross, J. A. (2010). Metagenomic comparison of two thiomicrospira lineages inhabiting contrasting deep-sea hydrothermal environments. PLoS ONE 5, e13530. doi:10.1371/journal.pone.0013530.
    • (2010) PLoS ONE , vol.5
    • Brazelton, W.J.1    Baross, J.A.2
  • 11
    • 80052574209 scopus 로고    scopus 로고
    • Physiological differentiation within a single-species biofilm fueled by serpentinization
    • 127-11
    • Brazelton, W J., Mehta, M. P., Kelley, D. S., and Baross, J. A. (2011). Physiological differentiation within a single-species biofilm fueled by serpentinization. MBio. 2, e00 127-11.
    • (2011) MBio , vol.2
    • Brazelton, W.J.1    Mehta, M.P.2    Kelley, D.S.3    Baross, J.A.4
  • 12
    • 33748777657 scopus 로고    scopus 로고
    • Methane- and sulfur-metabolizing microbial communities dominate the Lost City hydrothermal field ecosystem
    • Brazelton, W J., Schrenk, M. O., Kelley, D. S., and Baross, J. A. (2006). Methane- and sulfur-metabolizing microbial communities dominate the Lost City hydrothermal field ecosystem. Appl. Environ. Microbiol. 72, 6257-6270.
    • (2006) Appl. Environ. Microbiol. , vol.72 , pp. 6257-6270
    • Brazelton, W.J.1    Schrenk, M.O.2    Kelley, D.S.3    Baross, J.A.4
  • 13
    • 0347823003 scopus 로고    scopus 로고
    • MatGAT: an application that generates similarity/identity matrices using protein or DNA sequences
    • doi:10.1186/1471-2105-4-29
    • Campanella, J. J., Bitincka, L., and Smalley, J. (2003). MatGAT: an application that generates similarity/identity matrices using protein or DNA sequences. BMC Bioinformatics 4, 29. doi:10.1186/1471-2105-4-29.
    • (2003) BMC Bioinformatics , vol.4 , pp. 29
    • Campanella, J.J.1    Bitincka, L.2    Smalley, J.3
  • 15
    • 79953029156 scopus 로고    scopus 로고
    • Correlating carbon monoxide oxidation with cox genes in the abundant Marine Roseobacter Clade
    • Cunliffe, M. (2011). Correlating carbon monoxide oxidation with cox genes in the abundant Marine Roseobacter Clade. ISME J. 5, 685-691.
    • (2011) ISME J , vol.5 , pp. 685-691
    • Cunliffe, M.1
  • 16
    • 46749108474 scopus 로고    scopus 로고
    • Phylogenetic and functional gene analysis of the bacterial and archaeal communities associated with the surface micro -layer of an estuary
    • Cunliffe, M., Schäfer, H., Harrison, E., Cleave, S., Upstill-Goddard, R., and Murrell, J. C. (2008). Phylogenetic and functional gene analysis of the bacterial and archaeal communities associated with the surface micro -layer of an estuary. ISME J. 2, 776-789.
    • (2008) ISME J , vol.2 , pp. 776-789
    • Cunliffe, M.1    Schäfer, H.2    Harrison, E.3    Cleave, S.4    Upstill-Goddard, R.5    Murrell, J.C.6
  • 17
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: multiple sequence alignment with high accuracy and high throughput
    • Edgar, R. C. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792-1797.
    • (2004) Nucleic Acids Res , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 19
    • 55249109000 scopus 로고    scopus 로고
    • The genome organization of Ralstonia eutropha strain H16 and related species of the Burkholderiaceae
    • Fricke, W. F., Kusian, B., and Bowien, B. (2009). The genome organization of Ralstonia eutropha strain H16 and related species of the Burkholderiaceae. J. Mol. Microbiol. Biotechnol. 16, 124-135.
    • (2009) J. Mol. Microbiol. Biotechnol. , vol.16 , pp. 124-135
    • Fricke, W.F.1    Kusian, B.2    Bowien, B.3
  • 21
    • 70350294348 scopus 로고    scopus 로고
    • Systematic artifacts in metagenomes from complex microbial communities
    • Gomez-Alvarez, V., Teal, T. K., and Schmidt, T. M. (2009). Systematic artifacts in metagenomes from complex microbial communities. ISME J. 3, 1314-1317.
    • (2009) ISME J , vol.3 , pp. 1314-1317
    • Gomez-Alvarez, V.1    Teal, T.K.2    Schmidt, T.M.3
  • 22
    • 0036211208 scopus 로고    scopus 로고
    • Temporal changes in archaeal diversity and chemistry in a mid-ocean ridge subseafloor habitat
    • Huber, J. A., Butterfield, D. A., and Baross, J. A. (2002). Temporal changes in archaeal diversity and chemistry in a mid-ocean ridge subseafloor habitat. Appl. Environ. Microbiol. 68, 1585-1594.
    • (2002) Appl. Environ. Microbiol. , vol.68 , pp. 1585-1594
    • Huber, J.A.1    Butterfield, D.A.2    Baross, J.A.3
  • 24
    • 0026599072 scopus 로고
    • The structural genes encoding CO dehydrogenase subunits (cox L, M and S) in Pseudomonas carboxydovorans OM5 reside on plasmid pHCG3 and are, with the exception of Streptomyces thermoautotrophicus, conserved in carboxydotrophic bacteria
    • Hugendieek, I., and Meyer, O. (1992). The structural genes encoding CO dehydrogenase subunits (cox L, M and S) in Pseudomonas carboxydovorans OM5 reside on plasmid pHCG3 and are, with the exception of Streptomyces thermoautotrophicus, conserved in carboxydotrophic bacteria. Arch. Microbiol. 157, 301-304.
    • (1992) Arch. Microbiol. , vol.157 , pp. 301-304
    • Hugendieek, I.1    Meyer, O.2
  • 26
    • 0032885353 scopus 로고    scopus 로고
    • Cloning and molecular characterization of the genes for carbon monoxide dehydrogenase and localization of molybdopterin, flavin adenine dinucleotide, and iron-sulfur centers in the enzyme of Hydrogenophaga pseudoflava
    • Kang, B. S., and Kim, Y. M. (1999). Cloning and molecular characterization of the genes for carbon monoxide dehydrogenase and localization of molybdopterin, flavin adenine dinucleotide, and iron-sulfur centers in the enzyme of Hydrogenophaga pseudoflava. J. Bacteriol. 181, 5581-5590.
    • (1999) J. Bacteriol. , vol.181 , pp. 5581-5590
    • Kang, B.S.1    Kim, Y.M.2
  • 28
    • 0021193863 scopus 로고
    • Effects of cultivation gas phase on hydrogenase of the acetogen Clostridium thermoaceticum
    • Kellum, R., and Drake, H. L. (1984). Effects of cultivation gas phase on hydrogenase of the acetogen Clostridium thermoaceticum. J. Bacteriol. 160, 466-469.
    • (1984) J. Bacteriol. , vol.160 , pp. 466-469
    • Kellum, R.1    Drake, H.L.2
  • 29
    • 2142693754 scopus 로고    scopus 로고
    • Molecular and culture-based analyses of aerobic carbon monoxide oxidizer diversity
    • King, G. M. (2003). Molecular and culture-based analyses of aerobic carbon monoxide oxidizer diversity. Appl. Environ. Microbiol. 69, 7257-7265.
    • (2003) Appl. Environ. Microbiol. , vol.69 , pp. 7257-7265
    • King, G.M.1
  • 30
    • 33645031318 scopus 로고    scopus 로고
    • Nitrate-dependent anaerobic carbon monoxide oxidation by aerobic CO-oxidizing bacteria
    • King, G. M. (2006). Nitrate-dependent anaerobic carbon monoxide oxidation by aerobic CO-oxidizing bacteria. FEMS Microbiol. Ecol. 56, 1-7.
    • (2006) FEMS Microbiol. Ecol. , vol.56 , pp. 1-7
    • King, G.M.1
  • 31
    • 33846476676 scopus 로고    scopus 로고
    • Distribution, diversity and ecology of aerobic CO-oxidizing bacteria
    • King, G. M., and Weber, C. F. (2007). Distribution, diversity and ecology of aerobic CO-oxidizing bacteria. Nat. Rev. Microbiol. 5, 107-118.
    • (2007) Nat. Rev. Microbiol. , vol.5 , pp. 107-118
    • King, G.M.1    Weber, C.F.2
  • 32
    • 72149118443 scopus 로고    scopus 로고
    • Elevated concentrations of formate, acetate and dissolved organic carbon found at the Lost City hydrothermal field
    • Lang, S. Q., Butterfield, D. A., Schulte, M., Kelley, D. S., and Lilley, M. D. (2010). Elevated concentrations of formate, acetate and dissolved organic carbon found at the Lost City hydrothermal field. Geochim. Cosmochim. Acta 74, 941-952.
    • (2010) Geochim. Cosmochim. Acta , vol.74 , pp. 941-952
    • Lang, S.Q.1    Butterfield, D.A.2    Schulte, M.3    Kelley, D.S.4    Lilley, M.D.5
  • 38
    • 33847746181 scopus 로고    scopus 로고
    • Abiotic synthesis of organic compounds in deep-sea hydrothermal environments
    • McCollom, T. M., and Seewald, J. S. (2007). Abiotic synthesis of organic compounds in deep-sea hydrothermal environments. Chem. Rev. 107, 382-401.
    • (2007) Chem. Rev. , vol.107 , pp. 382-401
    • McCollom, T.M.1    Seewald, J.S.2
  • 44
    • 37549027613 scopus 로고    scopus 로고
    • SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
    • Pruesse, E., Quast, C., Knittel, K., Fuchs, B. M., Ludwig, W., Peplies, J., and Glöckner, F. O. (2007). SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 35, 7188-7196.
    • (2007) Nucleic Acids Res , vol.35 , pp. 7188-7196
    • Pruesse, E.1    Quast, C.2    Knittel, K.3    Fuchs, B.M.4    Ludwig, W.5    Peplies, J.6    Glöckner, F.O.7
  • 46
    • 54949153045 scopus 로고    scopus 로고
    • Acetogenesis and the Wood-Ljungdahl pathway of CO2 fixation
    • Ragsdale, S. W., and Pierce, E. (2008). Acetogenesis and the Wood-Ljungdahl pathway of CO2 fixation. Biochim. Biophys. Acta 1784, 1873-1898.
    • (2008) Biochim. Biophys. Acta , vol.1784 , pp. 1873-1898
    • Ragsdale, S.W.1    Pierce, E.2
  • 48
    • 77749245784 scopus 로고    scopus 로고
    • Hitherto unknown [Fe-Fe]-hydrogenase gene diversity in anaerobes and anoxic enrichments from a moderately acidic fen
    • Schmidt, O., Drake, H. L., and Horn, M. A. (2010). Hitherto unknown [Fe-Fe]-hydrogenase gene diversity in anaerobes and anoxic enrichments from a moderately acidic fen. Appl. Environ. Microbiol. 76, 2027-2031.
    • (2010) Appl. Environ. Microbiol. , vol.76 , pp. 2027-2031
    • Schmidt, O.1    Drake, H.L.2    Horn, M.A.3
  • 49
    • 80052762929 scopus 로고    scopus 로고
    • Novel [NiFe]- and [FeFe]-hydrogenase gene transcripts indicative of active facultative aerobes and obligate anaerobes in earthworm gut contents
    • Schmidt, O., Wüst, P. K., Hellmuth, S., Borst, K., Horn, M. A., and Drake, H. L. (2011). Novel [NiFe]- and [FeFe]-hydrogenase gene transcripts indicative of active facultative aerobes and obligate anaerobes in earthworm gut contents. Appl. Environ. Microbiol. 77, 5842-5850.
    • (2011) Appl. Environ. Microbiol. , vol.77 , pp. 5842-5850
    • Schmidt, O.1    Wüst, P.K.2    Hellmuth, S.3    Borst, K.4    Horn, M.A.5    Drake, H.L.6
  • 51
    • 4644245661 scopus 로고    scopus 로고
    • Low archaeal diversity linked to subseafloor geochemical processes at the Lost City Hydrothermal Field, Mid-Atlantic Ridge
    • Schrenk, M. O., Kelley, D. S., Bolton, S. A., and Baross, J. A. (2004). Low archaeal diversity linked to subseafloor geochemical processes at the Lost City Hydrothermal Field, Mid-Atlantic Ridge. Environ. Microbiol. 6, 1086-1095.
    • (2004) Environ. Microbiol. , vol.6 , pp. 1086-1095
    • Schrenk, M.O.1    Kelley, D.S.2    Bolton, S.A.3    Baross, J.A.4
  • 54
    • 70350455960 scopus 로고    scopus 로고
    • Identification of the [FeFe]-hydrogenase responsible for hydrogen generation in Thermoanaerobacterium saccharolyticum and demonstration of increased ethanol yield via hydrogenase knockout
    • Shaw, A. J., Hogsett, D. A., and Lynd, L. R. (2009). Identification of the [FeFe]-hydrogenase responsible for hydrogen generation in Thermoanaerobacterium saccharolyticum and demonstration of increased ethanol yield via hydrogenase knockout. J. Bacteriol. 191, 6457-6464.
    • (2009) J. Bacteriol. , vol.191 , pp. 6457-6464
    • Shaw, A.J.1    Hogsett, D.A.2    Lynd, L.R.3
  • 56
    • 43049156579 scopus 로고    scopus 로고
    • Dethiobacter alkaliphilus gen. nov. sp. nov., and Desulfurivibrio alkaliphilus gen. nov. sp. nov.: two novel representatives of reductive sulfur cycle from soda lakes
    • Sorokin, D. Y., Tourova, T. P., Mussmann, M., and Muyzer, G. (2008). Dethiobacter alkaliphilus gen. nov. sp. nov., and Desulfurivibrio alkaliphilus gen. nov. sp. nov.: two novel representatives of reductive sulfur cycle from soda lakes. Extremophiles 12, 431-439.
    • (2008) Extremophiles , vol.12 , pp. 431-439
    • Sorokin, D.Y.1    Tourova, T.P.2    Mussmann, M.3    Muyzer, G.4
  • 57
    • 33750403801 scopus 로고    scopus 로고
    • RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
    • Stamatakis, A. (2006). RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22, 2688-2690.
    • (2006) Bioinformatics , vol.22 , pp. 2688-2690
    • Stamatakis, A.1
  • 59
    • 35748974830 scopus 로고    scopus 로고
    • Occurrence, classification, and biological function of hydrogenases: an overview
    • Vignais, P. M., and Billoud, B. (2007). Occurrence, classification, and biological function of hydrogenases: an overview. Chem. Rev. 107, 4206-4272.
    • (2007) Chem. Rev. , vol.107 , pp. 4206-4272
    • Vignais, P.M.1    Billoud, B.2
  • 60
    • 0034886919 scopus 로고    scopus 로고
    • Classification and phylogeny of hydrogenases
    • Vignais, P. M., Billoud, B., and Meyer, J. (2001). Classification and phylogeny of hydrogenases. FEMS Microbiol. Rev. 25, 455-501.
    • (2001) FEMS Microbiol. Rev. , vol.25 , pp. 455-501
    • Vignais, P.M.1    Billoud, B.2    Meyer, J.3
  • 61
    • 33847192507 scopus 로고    scopus 로고
    • Physiological, ecological, and phylogenetic characterization of Stappia, a marine CO-oxidizing bacterial genus
    • Weber, C. F., and King, G. M. (2007). Physiological, ecological, and phylogenetic characterization of Stappia, a marine CO-oxidizing bacterial genus. Appl. Environ. Microbiol. 73, 1266-1276.
    • (2007) Appl. Environ. Microbiol. , vol.73 , pp. 1266-1276
    • Weber, C.F.1    King, G.M.2
  • 64
    • 0024333565 scopus 로고
    • Hydrogenophaga, a new genus of hydrogen-oxidizing bacteria that includes Hydrogenophaga flava comb. nov. (Formerly Pseudomonas flava), Hydrogenophaga palleronii (Formerly Pseudomonas palleronii), Hydrogenophaga pseudoflava (Formerly Pseudomonaspseudoflava and "Pseudomonas carboxydoflava"), and Hydrogenophaga taeniospiralis (Formerly Pseudomonas taeniospiralis)
    • Willems, A., Busse, J., Goor, M., Pot, B., Falsen, E., Jantzen, E., Hoste, B., Gillis, M., Kersters, K., Auling, G., and De Ley, J. (1989). Hydrogenophaga, a new genus of hydrogen-oxidizing bacteria that includes Hydrogenophaga flava comb. nov. (Formerly Pseudomonas flava), Hydrogenophaga palleronii (Formerly Pseudomonas palleronii), Hydrogenophaga pseudoflava (Formerly Pseudomonaspseudoflava and "Pseudomonas carboxydoflava"), and Hydrogenophaga taeniospiralis (Formerly Pseudomonas taeniospiralis). Int. J. Syst. Bacteriol. 39, 319-333.
    • (1989) Int. J. Syst. Bacteriol. , vol.39 , pp. 319-333
    • Willems, A.1    Busse, J.2    Goor, M.3    Pot, B.4    Falsen, E.5    Jantzen, E.6    Hoste, B.7    Gillis, M.8    Kersters, K.9    Auling, G.10    De Ley, J.11
  • 65
    • 0027167618 scopus 로고
    • Microbial hydrogenases: primary structure, classification, signatures and phylogeny
    • Wu, L. F., and Mandrand, M. A. (1993). Microbial hydrogenases: primary structure, classification, signatures and phylogeny. FEMS Microbiol. Rev. 10, 243-269.
    • (1993) FEMS Microbiol. Rev. , vol.10 , pp. 243-269
    • Wu, L.F.1    Mandrand, M.A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.