메뉴 건너뛰기




Volumn 7, Issue 2, 2012, Pages 304-319

Complete genome sequence of the sulfate-reducing firmicute Desulfotomaculum ruminis type strain (DLT)

(29)  Spring, Stefan a   Visser, Michael b   Lu, Megan c,d   Copeland, Alex c   Lapidus, Alla c   Lucas, Susan c   Cheng, Jan Fang c   Han, Cliff c,d   Tapia, Roxanne c,d   Goodwin, Lynne A c,d   Pitluck, Sam c   Ivanova, Natalia c   Land, Miriam c,e   Hauser, Loren c,e   Larimer, Frank c,e   Rohde, Manfred f   Göker, Markus a   Detter, John C c,d   Kyrpides, Nikos C c   Woyke, Tanja c   more..


Author keywords

Anaerobic; Clostridiales; CSP 2009; Hydrogen sulfide; Incomplete oxidizer; Mesophilic; Mixotrophic; Motile; Peptococcaceae; Sporulating; Sulfate reducer

Indexed keywords

RNA 16S;

EID: 84877868148     PISSN: 19443277     EISSN: None     Source Type: Journal    
DOI: 10.4056/sigs.3226659     Document Type: Article
Times cited : (17)

References (52)
  • 1
    • 76549159301 scopus 로고
    • Classification of the spore-forming sulfate-reducing bacteria
    • PubMed
    • Campbell LL, Postgate JR. Classification of the spore-forming sulfate-reducing bacteria. Bacteriol Rev 1965; 29:359-363. PubMed
    • (1965) Bacteriol Rev , vol.29 , pp. 359-363
    • Campbell, L.L.1    Postgate, J.R.2
  • 2
    • 0040460179 scopus 로고    scopus 로고
    • List of bacterial names with standing in nomenclature: A folder available on the Internet
    • PubMed
    • Euzéby JP. List of bacterial names with standing in nomenclature: A folder available on the Internet. Int J Syst Bacteriol 1997; 47:590-592. PubMed http://dx.doi.org/10.1099/00207713-47-2-590
    • (1997) Int J Syst Bacteriol , vol.47 , pp. 590-592
    • Euzéby, J.P.1
  • 3
    • 77955908592 scopus 로고    scopus 로고
    • NamesforLife. BrowserTool takes expertise out of the database and puts it right in the browser
    • Garrity G. NamesforLife. BrowserTool takes expertise out of the database and puts it right in the browser. Microbiol Today 2010; 37:9.
    • (2010) Microbiol Today , vol.37 , pp. 9
    • Garrity, G.1
  • 4
    • 0343628843 scopus 로고
    • A sulphate-reducing bacterium from the sheep rumen
    • PubMed
    • Coleman GS. A sulphate-reducing bacterium from the sheep rumen. J Gen Microbiol 1960; 22:423-436. PubMed http://dx.doi.org/10.1099/00221287-22-2-423
    • (1960) J Gen Microbiol , vol.22 , pp. 423-436
    • Coleman, G.S.1
  • 5
    • 0342963321 scopus 로고
    • The reduction of sulphate in the rumen of the sheep
    • PubMed
    • Lewis D. The reduction of sulphate in the rumen of the sheep. Biochem J 1954; 56:391-399. PubMed
    • (1954) Biochem J , vol.56 , pp. 391-399
    • Lewis, D.1
  • 6
    • 84877859709 scopus 로고
    • Desulfotomaculum Campbell and Postgate 1965, 361AL
    • 1st ed. Edited by: Holt JG. The Williams and Wilkins Co., Baltimore
    • Campbell LL, Singleton R Jr. Genus IV. Desulfotomaculum Campbell and Postgate 1965, 361AL. In: Bergey's Manual of Systematic Bacteriology, vol. 2. 1st ed. Edited by: Holt JG. The Williams and Wilkins Co., Baltimore; 1974; pp 572-573.
    • (1974) Bergey's Manual of Systematic Bacteriology , vol.2 , pp. 572-573
    • Campbell, L.L.1    Singleton Jr., R.2    Genus, I.V.3
  • 11
    • 0020216528 scopus 로고
    • Isolation and identification of anaerobic contaminants from a machine for producing processed cheese
    • PubMed
    • Savoy de Giori G, Font de Valdéz G, Pesce de Ruiz Holgado A, Oliver G. 1982 Isolation and identification of anaerobic contaminants from a machine for producing processed cheese. Rev Argent Microbiol 1982; 14:105-110. PubMed
    • (1982) Rev Argent Microbiol , vol.14 , pp. 105-110
    • de Giori, S.G.1    de Valdéz, F.G.2    de Ruiz, P.H.3    Oliver, G.4
  • 14
    • 0025300402 scopus 로고
    • Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya
    • PubMed
    • Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 1990; 87:4576-4579. PubMed http://dx.doi.org/10.1073/pnas.87.12.4576
    • (1990) Proc Natl Acad Sci USA , vol.87 , pp. 4576-4579
    • Woese, C.R.1    Kandler, O.2    Wheelis, M.L.3
  • 15
    • 0017843547 scopus 로고
    • Proposals Concerning the Higher Taxa of Bacteria
    • Gibbons NE, Murray RGE. Proposals Concerning the Higher Taxa of Bacteria. Int J Syst Bacteriol 1978; 28:1-6. http://dx.doi.org/10.1099/00207713-28-1-1
    • (1978) Int J Syst Bacteriol , vol.28 , pp. 1-6
    • Gibbons, N.E.1    Murray, R.G.E.2
  • 16
    • 0000685441 scopus 로고    scopus 로고
    • The Road Map to the Manual
    • In: Garrity GM, Boone DR, Castenholz RW, Second Edition, Springer, New York
    • Garrity GM, Holt JG. The Road Map to the Manual. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 1, Springer, New York, 2001, p. 119-169.
    • (2001) Bergey's Manual of Systematic Bacteriology , vol.1 , pp. 119-169
    • Garrity, G.M.1    Holt, J.G.2
  • 17
    • 0344278514 scopus 로고
    • The Higher Taxa, or, a Place for Everything...?
    • In: Holt JG, First Edition, The Williams and Wilkins Co., Baltimore
    • Murray RGE. The Higher Taxa, or, a Place for Everything...? In: Holt JG (ed), Bergey's Manual of Systematic Bacteriology, First Edition, Volume 1, The Williams and Wilkins Co., Baltimore, 1984, p. 31-34.
    • (1984) Bergey's Manual of Systematic Bacteriology , vol.1 , pp. 31-34
    • Murray, R.G.E.1
  • 18
    • 80053365349 scopus 로고    scopus 로고
    • List of new names and new combinations previously effectively, but not validly, published. List no. 132
    • List of new names and new combinations previously effectively, but not validly, published. List no. 132. Int J Syst Evol Microbiol 2010; 60:469-472. http://dx.doi.org/10.1099/ijs.0.022855-0
    • (2010) Int J Syst Evol Microbiol , vol.60 , pp. 469-472
  • 19
    • 80053371233 scopus 로고    scopus 로고
    • Clostridia class nov
    • In: De Vos P, Garrity G, Jones D, Krieg NR, Ludwig W, Rainey FA, Schleifer KH, Whitman WB, Second Edition, Springer-Verlag, New York
    • Rainey FA. Class II. Clostridia class nov. In: De Vos P, Garrity G, Jones D, Krieg NR, Ludwig W, Rainey FA, Schleifer KH, Whitman WB (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 3, Springer-Verlag, New York, 2009, p. 736.
    • (2009) Bergey's Manual of Systematic Bacteriology , vol.3 , pp. 736
    • Rainey, F.A.1    Class, I.I.2
  • 21
    • 84865212442 scopus 로고
    • Hauderoy P, Ehringer G, Guillot G, Magrou. J., Prévot AR, Rosset D, Urbain A (eds), Second Edition, Masson et Cie, Paris
    • Prévot AR. In: Hauderoy P, Ehringer G, Guillot G, Magrou. J., Prévot AR, Rosset D, Urbain A (eds), Dictionnaire des Bactéries Pathogènes, Second Edition, Masson et Cie, Paris, 1953, p. 1-692.
    • (1953) Dictionnaire Des Bactéries Pathogènes , pp. 1-692
    • Prévot, A.R.1
  • 22
    • 0343539959 scopus 로고
    • Peptococcaceae, a new family to include the Gram-positive, anaerobic cocci of the genera Peptococcus, Peptostreptococcus and Ruminococcus
    • Rogosa M. Peptococcaceae, a new family to include the Gram-positive, anaerobic cocci of the genera Peptococcus, Peptostreptococcus and Ruminococcus. Int J Syst Bacteriol 1971; 21:234-237. http://dx.doi.org/10.1099/00207713-21-3-234
    • (1971) Int J Syst Bacteriol , vol.21 , pp. 234-237
    • Rogosa, M.1
  • 23
    • 0022408160 scopus 로고
    • Growth with hydrogen, and further physiological characteristics of Desulfotomaculum species
    • Klemps R, Cypionka H, Widdel F, Pfennig N. Growth with hydrogen, and further physiological characteristics of Desulfotomaculum species. Arch Microbiol 1985; 143:203-208. http://dx.doi.org/10.1007/BF00411048
    • (1985) Arch Microbiol , vol.143 , pp. 203-208
    • Klemps, R.1    Cypionka, H.2    Widdel, F.3    Pfennig, N.4
  • 24
    • 84877844996 scopus 로고    scopus 로고
    • Classification of bacteria and archaea in risk groups
    • BAuA, Bundesanstalt für Arbeitsschutz und Arbeitsmedizin, Germany
    • BAuA. Classification of bacteria and archaea in risk groups. TRBA 466. p. 74. Bundesanstalt für Arbeitsschutz und Arbeitsmedizin, Germany. 2010
    • (2010) TRBA , vol.466 , pp. 74
  • 26
    • 0031055192 scopus 로고    scopus 로고
    • Desulfotomaculum aeronauticum sp. nov., a sporeforming, thiosulfate-reducing bacterium from corroded aluminium alloy in an aircraft
    • Hagenauer A, Hippe H, Rainey FA. Desulfotomaculum aeronauticum sp. nov., a sporeforming, thiosulfate-reducing bacterium from corroded aluminium alloy in an aircraft. Syst Appl Microbiol 1997; 20:65-71. http://dx.doi.org/10.1016/S0723-2020(97)80049-5
    • (1997) Syst Appl Microbiol , vol.20 , pp. 65-71
    • Hagenauer, A.1    Hippe, H.2    Rainey, F.A.3
  • 27
    • 0002426836 scopus 로고
    • Respiratory quinones of sulphate-reducing and sulphur-reducing bacteria: A systematic investigation
    • Collins MD, Widdel F. Respiratory quinones of sulphate-reducing and sulphur-reducing bacteria: a systematic investigation. Syst Appl Microbiol 1986; 8:8-18. http://dx.doi.org/10.1016/S0723-2020(86)80141-2
    • (1986) Syst Appl Microbiol , vol.8 , pp. 8-18
    • Collins, M.D.1    Widdel, F.2
  • 28
    • 84859165788 scopus 로고    scopus 로고
    • The Genomes OnLine Database (GOLD) v.4: Status of genomic and metagenomic projects and their associated metadata
    • PubMed
    • Pagani I, Liolios K, Jansson J, Chen IM, Smirnova T, Nosrat B, Markowitz VM, Kyrpides NC. The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 2012; 40:D571-D579. PubMed http://dx.doi.org/10.1093/nar/gkr1100
    • (2012) Nucleic Acids Res , vol.40
    • Pagani, I.1    Liolios, K.2    Jansson, J.3    Chen, I.M.4    Smirnova, T.5    Nosrat, B.6    Markowitz, V.M.7    Kyrpides, N.C.8
  • 29
    • 84877846208 scopus 로고    scopus 로고
    • List of growth media used at DSMZ
    • List of growth media used at DSMZ: http://www.dsmz.de/catalogues/catalogue-microorganisms/culture-technolog y/list-of-media-for-microorganisms.html
  • 32
    • 84877856800 scopus 로고    scopus 로고
    • JGI website
    • JGI website. http://www.jgi.doe.gov/
  • 33
    • 84877869263 scopus 로고    scopus 로고
    • The Phred/Phrap/Consed software package
    • The Phred/Phrap/Consed software package. http://www.phrap.com
  • 34
    • 43149115851 scopus 로고    scopus 로고
    • Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
    • PubMed
    • Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008; 18:821-829. PubMed http://dx.doi.org/10.1101/gr.074492.107
    • (2008) Genome Res , vol.18 , pp. 821-829
    • Zerbino, D.R.1    Birney, E.2
  • 37
    • 77952299957 scopus 로고    scopus 로고
    • Prodigal: Prokaryotic gene recognition and translation initiation site identification
    • PubMed
    • Hyatt D, Chen GL, LoCascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119. PubMed http://dx.doi.org/10.1186/1471-2105-11-119
    • (2010) BMC Bioinformatics , vol.11 , pp. 119
    • Hyatt, D.1    Chen, G.L.2    Locascio, P.F.3    Land, M.L.4    Larimer, F.W.5    Hauser, L.J.6
  • 39
    • 69949116874 scopus 로고    scopus 로고
    • IMG ER: A system for microbial genome annotation expert review and curation
    • PubMed
    • Markowitz VM, Ivanova NN, Chen IMA, Chu K, Kyrpides NC. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics 2009; 25:2271-2278. PubMed http://dx.doi.org/10.1093/bioinformatics/btp393
    • (2009) Bioinformatics , vol.25 , pp. 2271-2278
    • Markowitz, V.M.1    Ivanova, N.N.2    Chen, I.M.A.3    Chu, K.4    Kyrpides, N.C.5
  • 40
    • 0022531067 scopus 로고
    • Metabolism of L-alanine in Desulfotomaculum ruminis and two marine Desulfovibrio strains
    • Stams AJM, Hansen TA. Metabolism of L-alanine in Desulfotomaculum ruminis and two marine Desulfovibrio strains. Arch Microbiol 1986; 145:277-279. http://dx.doi.org/10.1007/BF00443658
    • (1986) Arch Microbiol , vol.145 , pp. 277-279
    • Stams, A.J.M.1    Hansen, T.A.2
  • 41
    • 0036837968 scopus 로고    scopus 로고
    • Carbon monoxide cycling by Desulfovibrio vulgaris Hildenborough
    • PubMed
    • Voordouw G. Carbon monoxide cycling by Desulfovibrio vulgaris Hildenborough. J Bacteriol 2002; 184:5903-5911. PubMed http://dx.doi.org/10.1128/JB.184.21.59035911.2002
    • (2002) J Bacteriol , vol.184 , pp. 5903-5911
    • Voordouw, G.1
  • 42
    • 80053345905 scopus 로고    scopus 로고
    • Signal P 4.0: Discriminating signal peptides from transmembrane regions
    • PubMed
    • Petersen TN, Brunak S, von Heijne G, Nielsen H. Signal P 4.0: discriminating signal peptides from transmembrane regions. Nat Methods 2011; 8:785-786. PubMed http://dx.doi.org/10.1038/nmeth.1701
    • (2011) Nat Methods , vol.8 , pp. 785-786
    • Petersen, T.N.1    Brunak, S.2    von Heijne, G.3    Nielsen, H.4
  • 43
    • 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
    • PubMed
    • Shaw AJ, Hogsett DA, Lynd LR. Identification of the [FeFe]-hydrogenase responsible for hydrogen generation in Thermoanaerobacterium saccharolyticum and demonstration of increased ethanol yield via hydrogenase knockout. J Bacteriol 2009; 191:6457-6464. PubMed http://dx.doi.org/10.1128/JB.00497-09
    • (2009) J Bacteriol , vol.191 , pp. 6457-6464
    • Shaw, A.J.1    Hogsett, D.A.2    Lynd, L.R.3
  • 44
    • 84871719363 scopus 로고    scopus 로고
    • The membrane QmoABC complex interacts directly with the dissimilatory adenosine 5'- phosphosulfate reductase in sulfate reducing bacteria
    • PubMed
    • Ramos AR, Keller KL, Wall JD, Pereira IA. The membrane QmoABC complex interacts directly with the dissimilatory adenosine 5'- phosphosulfate reductase in sulfate reducing bacteria. Front Microbiol 2012; 3:137. PubMed
    • (2012) Front Microbiol , vol.3 , pp. 137
    • Ramos, A.R.1    Keller, K.L.2    Wall, J.D.3    Pereira, I.A.4
  • 47
    • 57749097713 scopus 로고    scopus 로고
    • The crystal structure of Desulfovibrio vulgaris dissimilatory sulfite reductase bound to DsrC provides novel insights into the mechanism of sulfate respiration
    • PubMed
    • Oliveira TF, Vonrhein C, Matias PM, Venceslau SS, Pereira IA, Archer M. The crystal structure of Desulfovibrio vulgaris dissimilatory sulfite reductase bound to DsrC provides novel insights into the mechanism of sulfate respiration. J Biol Chem 2008; 283:34141-34149. PubMed http://dx.doi.org/10.1074/jbc.M805643200
    • (2008) J Biol Chem , vol.283 , pp. 34141-34149
    • Oliveira, T.F.1    Vonrhein, C.2    Matias, P.M.3    Venceslau, S.S.4    Pereira, I.A.5    Archer, M.6
  • 48
    • 57749097713 scopus 로고    scopus 로고
    • The crystal structure of Desulfovibrio vulgaris dissimilatory sulfite reductase bound to DsrC provides novel insights into the mechanism of sulfate respiration
    • PubMed
    • Oliveira TF, Vonrhein C, Matias PM, Venceslau SS, Pereira IA, Archer M. The crystal structure of Desulfovibrio vulgaris dissimilatory sulfite reductase bound to DsrC provides novel insights into the mechanism of sulfate respiration. J Biol Chem 2008; 283:34141-34149. PubMed http://dx.doi.org/10.1074/jbc.M805643200
    • (2008) J Biol Chem , vol.283 , pp. 34141-34149
    • Oliveira, T.F.1    Vonrhein, C.2    Matias, P.M.3    Venceslau, S.S.4    Pereira, I.A.5    Archer, M.6
  • 49
    • 17644385506 scopus 로고    scopus 로고
    • The hydrogenases of Geobacter sulfurreducens: A comparative genomic perspective
    • PubMed
    • Coppi MV. The hydrogenases of Geobacter sulfurreducens: a comparative genomic perspective. Microbiology 2005; 151:1239-1254. PubMed http://dx.doi.org/10.1099/mic.0.27535-0
    • (2005) Microbiology , vol.151 , pp. 1239-1254
    • Coppi, M.V.1
  • 51
    • 84877862161 scopus 로고    scopus 로고
    • Venn diagram plotter available from the Pacific Northwest National Laboratory Software Distribution Center:
    • Venn diagram plotter available from the Pacific Northwest National Laboratory Software Distribution Center: http://omics.pnl.gov
  • 52
    • 35748974830 scopus 로고    scopus 로고
    • Occurrence, classification, and biological function of hydrogenases: An overview
    • PubMed
    • Vignais PM, Billoud B. Occurrence, classification, and biological function of hydrogenases: an overview. Chem Rev 2007; 107:4206-4272. PubMed http://dx.doi.org/10.1021/cr050196r
    • (2007) Chem Rev , vol.107 , pp. 4206-4272
    • Vignais, P.M.1    Billoud, B.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.