1887

Abstract

A taxonomic study employing a polyphasic approach was performed on a novel anaerobic bacterium isolated from natural gas production-water. The bacterium stained Gram-negative and consisted of non-motile, non-spore-forming, rod-shaped cells. Products of glucose or starch fermentation were ethanol, CO, formate, acetate and H2. The predominant fatty acids were C ALDE and summed feature 3 comprising Cω7 and/or Cω6. The DNA G+C content was 45.5 mol%. 16S rRNA gene sequence analysis demonstrated that the nearest phylogenetic neighbours of the novel strain were DSM 6139 (98.5 %) and JCM 14817 (95.4 %). The DNA–DNA hybridization value between the novel organism and PeC1 DSM 6139 was determined to be only 30.2 %, demonstrating the separateness of the two species. Based on phylogenetic, phenotypic and chemotaxonomic evidence that clearly distinguished strain 232.1 from and other close relatives, it is proposed that the novel isolate be classified as representing a novel species of a new genus within the family , gen. nov., sp. nov. The type strain of the type species is 232.1 ( = ATCC BAA-2257 = DSM 24749). In addition, is proposed to be reclassified as comb. nov.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.053728-0
2014-01-01
2019-10-22
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/64/1/198.html?itemId=/content/journal/ijsem/10.1099/ijs.0.053728-0&mimeType=html&fmt=ahah

References

  1. Allen T. D. , Kraus P. F. , Lawson P. A. , Drake G. R. , Balkwill D. L. , Tanner R. S. . ( 2008; ). Desulfovibrio carbinoliphilus sp. nov., a benzyl alcohol-oxidizing, sulfate-reducing bacterium isolated from a gas condensate-contaminated aquifer. . Int J Syst Evol Microbiol 58:, 1313–1317. [CrossRef] [PubMed]
    [Google Scholar]
  2. Allen T. D. , Caldwell M. E. , Lawson P. A. , Huhnke R. L. , Tanner R. S. . ( 2010; ). Alkalibaculum bacchi gen. nov., sp. nov., a CO-oxidizing, ethanol-producing acetogen isolated from livestock-impacted soil. . Int J Syst Evol Microbiol 60:, 2483–2489. [CrossRef] [PubMed]
    [Google Scholar]
  3. Aziz R. K. , Bartels D. , Best A. A. , DeJongh M. , Disz T. , Edwards R. A. , Formsma K. , Gerdes S. , Glass E. M. . & other authors ( 2008; ). The rast Server: Rapid Annotations using Subsystems Technology. . BMC Genomics 9:, 75. [CrossRef] [PubMed]
    [Google Scholar]
  4. Baena S. , Patel B. K. C. . ( 2009; ). Genus V. Caloramator Collins, Lawson, Cordoba, Fernandez-Garayzabel, Garcia, Cai, Hippe and Farrow 1994, 812VP emend. Chrisostomos, Patel, Dwivedi and Denman 1996, 497. . In Bergey’s Manual of Systematic Bacteriology, , 2nd edn., Vol 3, The Firmicutes, pp. 834–838. Edited by De Vos P. , Garrity G. M. , Jones D. , Krieg N. R. , Ludwig W. , Rainey F. A. , Schleifer K.-H. , Whitman W. B. . . New York:: Springer;.
    [Google Scholar]
  5. Beveridge T. J. , Lawrence J. R. , Murray R. G. E. . ( 2007; ). Sampling and staining for light microscopy. . In Methods for General and Molecular Microbiology, , 3rd edn., pp. 19–33. Edited by Reddy C. A. , Beveridge T. J. , Breznak J. A. , Marzluf G. A. , Schmidt T. M. , Snyder R. L. . . Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  6. Boisvert S. , Raymond F. , Godzaridis É. , Laviolette F. , Corbeil J. . ( 2012; ). Ray Meta: scalable de novo metagenome assembly and profiling. . Genome Biol 13:, R122. [CrossRef] [PubMed]
    [Google Scholar]
  7. Bryant M. P. , Robinson I. M. . ( 1962; ). Some nutritional characteristics of predominant culturable ruminal bacteria. . J Bacteriol 84:, 605–614.[PubMed]
    [Google Scholar]
  8. Collins M. D. , Lawson P. A. , Willems A. , Cordoba J. J. , Fernandez-Garayzabal J. , Garcia P. , Cai J. , Hippe H. , Farrow J. A. . ( 1994; ). The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations. . Int J Syst Bacteriol 44:, 812–826. [CrossRef] [PubMed]
    [Google Scholar]
  9. De Ley J. , Cattoir H. , Reynaerts A. . ( 1970; ). The quantitative measurement of DNA hybridization from renaturation rates. . Eur J Biochem 12:, 133–142. [CrossRef] [PubMed]
    [Google Scholar]
  10. Duda V. I. , Lebedinsky A. V. , Mushegjan M. S. , Mitjushina L. L. . ( 1987; ). A new anaerobic bacterium, forming up to five endospores per cell –Anaerobacter polyendosporus gen. et spec. nov.. Arch Microbiol 148:, 121–127. [CrossRef]
    [Google Scholar]
  11. Engle M. , Li Y. , Rainey F. , DeBlois S. , Mai V. , Reichert A. , Mayer F. , Messner P. , Wiegel J. . ( 1996; ). Thermobrachium celere gen. nov., sp. nov., a rapidly growing thermophilic, alkalitolerant, and proteolytic obligate anaerobe. . Int J Syst Bacteriol 46:, 1025–1033. [CrossRef] [PubMed]
    [Google Scholar]
  12. Felter R. A. , Colwell R. R. , Chapman G. B. . ( 1969; ). Morphology and round body fermation in Vibrio marinus . . J Bacteriol 99:, 326–335.[PubMed]
    [Google Scholar]
  13. Fraj B. , Ben Hania W. , Postec A. , Hamdi M. , Ollivier B. , Fardeau M.-L. . ( 2013; ). Fonticella tunisiensis gen. nov., sp. nov., isolated from a hot spring. . Int J Syst Evol Microbiol 63:, 1947–1950. [CrossRef] [PubMed]
    [Google Scholar]
  14. Grabowski A. , Nercessian O. , Fayolle F. , Blanchet D. , Jeanthon C. . ( 2005; ). Microbial diversity in production waters of a low-temperature biodegraded oil reservoir. . FEMS Microbiol Ecol 54:, 427–443. [CrossRef] [PubMed]
    [Google Scholar]
  15. Gupta R. S. , Gao B. . ( 2009; ). Phylogenomic analyses of clostridia and identification of novel protein signatures that are specific to the genus Clostridium sensu stricto (cluster I). . Int J Syst Evol Microbiol 59:, 285–294. [CrossRef] [PubMed]
    [Google Scholar]
  16. Jarrell K. F. , Colvin J. R. , Sprott G. D. . ( 1982; ). Spontaneous protoplast formation in Methanobacterium bryantii . . J Bacteriol 149:, 346–353.[PubMed]
    [Google Scholar]
  17. Kim O.-S. , Cho Y.-J. , Lee K. , Yoon S.-H. , Kim M. , Na H. , Park S.-C. , Jeon Y. S. , Lee J.-H. . & other authors ( 2012; ). Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. . Int J Syst Evol Microbiol 62:, 716–721. [CrossRef] [PubMed]
    [Google Scholar]
  18. Kimura M. . ( 1980; ). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. . J Mol Evol 16:, 111–120. [CrossRef] [PubMed]
    [Google Scholar]
  19. Krumholz L. R. , Bryant M. P. . ( 1985; ). Clostridium pfennigii sp. nov. uses methoxyl groups of monobenzenoids and produces butyrate. . Int J Syst Bacteriol 35:, 454–456. [CrossRef]
    [Google Scholar]
  20. Levin R. E. , Vaughn R. H. . ( 1968; ). Spontaneous spheroplast formation by Desulfovibrio aestuarii . . Can J Microbiol 14:, 1271–1276. [CrossRef] [PubMed]
    [Google Scholar]
  21. Liou J. S. , Balkwill D. L. , Drake G. R. , Tanner R. S. . ( 2005; ). Clostridium carboxidivorans sp. nov., a solvent-producing clostridium isolated from an agricultural settling lagoon, and reclassification of the acetogen Clostridium scatologenes strain SL1 as Clostridium drakei sp. nov.. Int J Syst Evol Microbiol 55:, 2085–2091. [CrossRef] [PubMed]
    [Google Scholar]
  22. Ludwig W. , Schleifer K.-H. , Whitman W. B. . ( 2009; ). Revised road map to the phylum Firmicutes . . In Bergey’s Manual of Systematic Bacteriology , , 2nd edn., vol. 3 The Firmicutes, pp. 1–13. Edited by De Vos P. , Garrity G. M. , Jones D. , Krieg N. R. , Ludwig W. , Rainey F. A. , Schleifer K.-H. , Whitman W. B. . . New York:: Springer;. [CrossRef]
    [Google Scholar]
  23. Miller L. T. . ( 1982; ). Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. . J Clin Microbiol 16:, 584–586.[PubMed]
    [Google Scholar]
  24. Myers E. W. , Miller W. . ( 1988; ). Optimal alignments in linear space. . Comput Appl Biosci 4:, 11–17.[PubMed]
    [Google Scholar]
  25. Ogg C. D. , Patel B. K. C. . ( 2010; ). Fervidicella metallireducens gen. nov., sp. nov., a thermophilic, anaerobic bacterium from geothermal waters. . Int J Syst Evol Microbiol 60:, 1394–1400. [CrossRef] [PubMed]
    [Google Scholar]
  26. Patel B. K. C. , Monk C. , Littleworth H. , Morgan H. W. , Daniel R. M. . ( 1987; ). Clostridium fervidus sp. nov., a new chemoorganotrophic acetogenic thermophile. . Int J Syst Bacteriol 37:, 123–126. [CrossRef]
    [Google Scholar]
  27. Pearson W. R. , Lipman D. J. . ( 1988; ). Improved tools for biological sequence comparison. . Proc Natl Acad Sci U S A 85:, 2444–2448. [CrossRef] [PubMed]
    [Google Scholar]
  28. Rainey F. A. . ( 2009; ). Genus III. Acetivibrio Patel, Khan, Agnew, and Colvin 1980, 184VP (emend. Robinson and Ritchie 1981 335; emend. Khan, Meek, Sowden and Colvin 1984 420; emend. Murray 1986, 316). . In Bergey’s Manual of Systematic Bacteriology, , 2nd edn., vol 3 The Firmicutes, pp. 1020–1021. Edited by De Vos P. , Garrity G. M. , Jones D. , Krieg N. R. , Ludwig W. , Rainey F. A. , Schleifer K.-H. , Whitman W. B. . . New York:: Springer;.
    [Google Scholar]
  29. Rainey F. A. , Hollen B. J. , Small A. . ( 2009; ). Genus I. Clostridium Prazmowski 1880, 23AL . . In Bergey’s Manual of Systematic Bacteriology, , 2nd edn., vol 3 The Firmicutes, pp. 738–828. Edited by De Vos P. , Garrity G. M. , Jones D. , Krieg N. R. , Ludwig W. , Rainey F. A. , Schleifer K.-H. , Whitman W. B. . . New York:: Springer;.
    [Google Scholar]
  30. Ravot G. , Magot M. , Fardeau M. L. , Patel B. K. , Thomas P. , Garcia J. L. , Ollivier B. . ( 1999; ). Fusibacter paucivorans gen. nov., sp. nov., an anaerobic, thiosulfate-reducing bacterium from an oil-producing well. . Int J Syst Bacteriol 49:, 1141–1147. [CrossRef] [PubMed]
    [Google Scholar]
  31. Saitou N. , Nei M. . ( 1987; ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4:, 406–425.[PubMed]
    [Google Scholar]
  32. Sasser M. . ( 1990; ). Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. Newark, DE:: MIDI, Inc;.
    [Google Scholar]
  33. Stackebrandt E. , Ebers J. . ( 2006; ). Taxonomic parameters revisited: tarnished gold standards. . Microbiol Today 33:, 152–155.
    [Google Scholar]
  34. Stackebrandt E. , Goebel B. M. . ( 1994; ). Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. . Int J Syst Bacteriol 44:, 846–849. [CrossRef]
    [Google Scholar]
  35. Strąpoć D. , Mastalerz M. , Eble C. , Schimmelmann A. . ( 2007; ). Characterization of the origin of coalbed gases in southeastern Illinois Basin by compound-specific carbon and hydrogen stable isotope ratios. . Org Geochem 38:, 267–287. [CrossRef]
    [Google Scholar]
  36. Tamura K. , Dudley J. , Nei M. , Kumar S. . ( 2007; ). mega4: molecular evolutionary genetics analysis (mega) software version 4.0. . Mol Biol Evol 24:, 1596–1599. [CrossRef] [PubMed]
    [Google Scholar]
  37. Tanaka K. , Nakamura K. , Mikami E. . ( 1991; ). Fermentation of cinnamate by a mesophilic strict anaerobe, Acetivibrio multivorans sp. nov.. Arch Microbiol 155:, 120–124. [CrossRef]
    [Google Scholar]
  38. Tanner R. S. . ( 2007; ). Cultivation of bacteria and fungi. . In Manual of Environmental Microbiology, , 3rd edn., pp. 69–78. Edited by Hurst C. J. , Crawford R. L. , Mills A. L. , Garland J. L. , Stetzenbach L. D. , Lipson D. A. . . Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  39. Tanner R. S. , Wolfe R. S. . ( 1988; ). Nutritional requirements of Methanomicrobium mobile . . Appl Environ Microbiol 54:, 625–628.[PubMed]
    [Google Scholar]
  40. Taylor B. F. , Campbell W. L. , Chinoy I. . ( 1970; ). Anaerobic degradation of the benzene nucleus by a facultatively anaerobic microorganism. . J Bacteriol 102:, 430–437.[PubMed]
    [Google Scholar]
  41. Thompson J. D. , Higgins D. G. , Gibson T. J. . ( 1994; ). clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. . Nucleic Acids Res 22:, 4673–4680. [CrossRef] [PubMed]
    [Google Scholar]
  42. Tindall B. J. , Sikorski J. , Smibert R. A. , Krieg N. R. . ( 2007; ). Phenotypic characterization and the principles of comparative systematics. . In Methods for General and Molecular Microbiology, pp. 330–393. Edited by Reddy C. A. , Beveridge T. J. , Breznak J. A. , Marzluf G. A. , Schmidt T. M. , Snyder R. L. . . Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  43. Wawrik B. , Mendivelso M. , Parisi V. A. , Suflita J. M. , Davidova I. A. , Marks C. R. , Van Nostrand J. D. , Liang Y. , Zhou J. . & other authors ( 2012; ). Field and laboratory studies on the bioconversion of coal to methane in the San Juan Basin. . FEMS Microbiol Ecol 81:, 26–42. [CrossRef] [PubMed]
    [Google Scholar]
  44. Wayne L. G. , Brenner D. J. , Colwell R. R. , Grimont P. A. D. , Kandler O. , Krichevsky M. I. , Moore L. H. , Moore W. E. C. , Murray R. G. E. . & other authors ( 1987; ). International Committee on Systematic Bacteriology. R eport of the ad hoc committee on reconciliation of approaches to bacterial systematics. . Int J Syst Bacteriol 37:, 463–464. [CrossRef]
    [Google Scholar]
  45. Widdel F. , Bak F. . ( 1992; ). Gram-negative mesophilic sulfate-reducing bacteria. . In The Prokaryotes, pp. 3352–3378. Edited by Barlows A. , Truper H. G. , Dworkin M. , Harder W. , Schleifer K.-H. . . New York:: Springer;.[CrossRef]
    [Google Scholar]
  46. Youssef N. , Elshahed M. S. , McInerney M. J. . ( 2009; ). Microbial processes in oil fields: culprits, problems, and opportunities. . Adv Appl Microbiol 66:, 141–251. [CrossRef] [PubMed]
    [Google Scholar]
  47. Zhang K. , Song L. , Dong X. . ( 2010; ). Proteiniclasticum ruminis gen. nov., sp. nov., a strictly anaerobic proteolytic bacterium isolated from yak rumen. . Int J Syst Evol Microbiol 60:, 2221–2225. [CrossRef] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.053728-0
Loading
/content/journal/ijsem/10.1099/ijs.0.053728-0
Loading

Data & Media loading...

Supplements

Supplementary material 

PDF

Most Cited This Month

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error