1887

Abstract

A novel thermophilic and lithoautotrophic sulfate-reducing archaeon was isolated from black rust formed on the steel surface of a borehole observatory (CORK 1026B) retrieved during IODP Expedition 301 on the eastern flank of Juan de Fuca Ridge, eastern Pacific Ocean. Cells of the strain were lobe-shaped or triangular. The optimum temperature, pH and NaCl concentration for growth were 75 °C, pH 7 and 2 % (w/v), respectively. The isolate was strictly anaerobic, growing lithoautotrophically on H and CO using sulfate, sulfite or thiosulfate as electron acceptors. Lactate and pyruvate could serve as alternative energy and carbon sources. The G+C content of the genomic DNA was 42 mol%. Phylogenetic analyses of the 16S rRNA gene indicated that the isolate was closely related to members of the family , with sequence similarities of 90.3–94.4 %. Physiological and molecular properties showed that the isolate represents a novel species of the genus . The name sp. nov. is proposed; the type strain is PM70-1 (=DSM 19444=JCM 14716).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.016105-0
2010-12-01
2020-09-29
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/60/12/2745.html?itemId=/content/journal/ijsem/10.1099/ijs.0.016105-0&mimeType=html&fmt=ahah

References

  1. Altschul S. F., Madden T. L., Schäffer A. A., Zhang J. H., Zhang Z., Miller W., Lipman D. J. 1997; Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402 [CrossRef]
    [Google Scholar]
  2. Balch W. E., Fox G. E., Magrum L. J., Woese C. R., Wolfe R. S. 1979; Methanogens: reevaluation of a unique biological group. Microbiol Rev 43:260–296
    [Google Scholar]
  3. Burggraf S., Jannasch H. W., Nicolaus B., Stetter K. O. 1990; Archaeoglobus profundus sp. nov., represents a new species within the sulfur-reducing Archaebacteria . Syst Appl Microbiol 13:24–28 [CrossRef]
    [Google Scholar]
  4. Campanella J. J., Bitincka L., Smalley J. 2003; MatGAT: an application that generates similarity/identity matrices using protein or DNA sequences. BMC Bioinformatics 4:29–32 [CrossRef]
    [Google Scholar]
  5. Castresana J. 2000; Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17:540–552 [CrossRef]
    [Google Scholar]
  6. Castro H. F., Williams N. H., Ogram A. 2000; Phylogeny of sulfate-reducing bacteria. FEMS Microbiol Ecol 31:1–9
    [Google Scholar]
  7. Cord-Ruwisch R. 1985; A quick method for the determination of dissolved and precipitated sulfides in cultures of sulfate-reducing bacteria. J Microbiol Methods 4:33–36 [CrossRef]
    [Google Scholar]
  8. Cowen J. P., Giovannoni S. J., Kenig F., Johnson H. P., Butterfield D., Rappé M. S., Hutnak M., Lam P. 2003; Fluids from aging ocean crust that support microbial life. Science 299:120–123 [CrossRef]
    [Google Scholar]
  9. Dereeper A., Guignon V., Blanc G., Audic S., Buffet S., Chevenet F., Dufayard J.-F., Guindon S., Lefort V. other authors 2008; Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res 36: Web Server issue W465–W469 [CrossRef]
    [Google Scholar]
  10. Edwards U., Rogall T., Blöcker H., Emde M., Böttger E. C. 1989; Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA. Nucleic Acids Res 17:7843–7853 [CrossRef]
    [Google Scholar]
  11. Felsenstein J. 1985; Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791 [CrossRef]
    [Google Scholar]
  12. Fisher A. T., Urabe T., Klaus A. Expedition 301 Scientists 2005; Proceedings of the Integrated Ocean Drilling Program . vol 301 College Station TX: Integrated Ocean Drilling Program Management International, Inc; [CrossRef]
  13. Guindon S., Gascuel O. 2003; A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52:696–704 [CrossRef]
    [Google Scholar]
  14. Hafenbradl D., Keller M., Dirmeier R., Rachel R., Roßnagel P., Burggraf S., Huber H., Stetter K. O. 1996; Ferroglobus placidus gen. nov., sp. nov. a novel hyperthermophilic archaeum that oxidizes Fe2+ at neutral pH under anoxic conditions. Arch Microbiol 166:308–314 [CrossRef]
    [Google Scholar]
  15. Hartzell P., Reed D. W. 2006; The genus Archaeoglobus . In The Prokaryotes, 3rd edn. vol 3 pp 82–100 Edited by Dworkin M., Falkow S., Rosenberg E., Schleifer K.-H., Stackebrandt E. New York: Springer;
    [Google Scholar]
  16. Huber H., Jannasch H., Rachel R., Fuchs T., Stetter K. O. 1997; Archaeoglobus veneficus sp. nov., a novel facultative chemolithoautotrophic hyperthermophilic sulfite reducer, isolated from abyssal black smokers. Syst Appl Microbiol 20:374–380 [CrossRef]
    [Google Scholar]
  17. Huelsenbeck J. P., Ronquist F. 2001; mrbayes: Bayesian inference of phylogenetic trees. Bioinformatics 17:754–755 [CrossRef]
    [Google Scholar]
  18. Itoh T., Suzuki K., Sanchez P. C., Nakase T. 1999; Caldivirga maquilingensis gen. nov., sp. nov., a new genus of rod-shaped crenarchaeote isolated from a hot spring in the Philippines. Int J Syst Bacteriol 49:1157–1163 [CrossRef]
    [Google Scholar]
  19. Jukes T. H., Cantor C. R. 1969; Evolution of protein molecules. In Mammalian Protein Metabolism vol 3 pp 211–232 Edited by Munro H. N. New York: Academic Press;
    [Google Scholar]
  20. Kashefi K., Tor J. M., Holmes D. E., Gaw Van Praagh C. V., Reysenbach A.-L., Lovley D. R. 2002a; Geoglobus ahangari gen. nov., sp. nov., a novel hyperthermophilic archaeon capable of oxidizing organic acids and growing autotrophically on hydrogen with Fe(III) serving as the sole electron acceptor. Int J Syst Evol Microbiol 52:719–728 [CrossRef]
    [Google Scholar]
  21. Kashefi K., Holmes D. E., Reysenbach A.-L., Lovley D. R. 2002b; Use of Fe(III) as an electron acceptor to recover previously uncultured hyperthermophiles: isolation and characterization of Geothermobacterium ferrireducens gen. nov., sp. nov.. Appl Environ Microbiol 68:1735–1742 [CrossRef]
    [Google Scholar]
  22. Lovley D. R. 2006; Dissimilatory Fe(III)- and Mn(IV)-reducing prokaryotes. In The Prokaryotes, 3rd edn. vol 2 pp 635–658 Edited by Dworkin M., Falkow S., Rosenberg E., Schleifer K.-H., Stackebrandt E. New York: Springer;
    [Google Scholar]
  23. Ludwig W., Strunk O., Westram R., Richter L., Meier H., Yadhukumar Buchner. A., Lai T., Steppi S. other authors 2004; arb: a software environment for sequence data. Nucleic Acids Res 32:1363–1371 [CrossRef]
    [Google Scholar]
  24. Lysnes K., Thorseth I. H., Steinsbu B. O., Øvreås L., Torsvik T., Pedersen R. B. 2004; Microbial community diversity in seafloor basalt from the Arctic spreading ridges. FEMS Microbiol Ecol 50:213–230 [CrossRef]
    [Google Scholar]
  25. Mandel M., Igambi L., Bergendahl J., Dodson M. L., Scheltgen E. (1970; Correlation of melting temperature and cesium chloride buoyant density of bacterial deoxyribonucleic acid. J Bacteriol 101:333–338
    [Google Scholar]
  26. Marmur J. 1963; A procedure for the isolation of deoxyribonucleic acid from microorganisms. Methods Enzymol 6:726–728
    [Google Scholar]
  27. Massana R., Murray A. E., Preston C. M., DeLong E. F. 1997; Vertical distribution and phylogenetic characterization of marine planktonic Archaea in the Santa Barbara Channel. Appl Environ Microbiol 63:50–56
    [Google Scholar]
  28. Mori K., Maruyama A., Urabe T., Suzuki K., Hanada S. 2008; Archaeoglobus infectus sp. nov., a novel thermophilic, chemolithoheterotrophic archaeon isolated from a deep-sea rock collected at Suiyo Seamount, Izu-Bonin Arc, western Pacific Ocean. Int J Syst Evol Microbiol 58:810–816 [CrossRef]
    [Google Scholar]
  29. Nakagawa S., Inagaki F., Suzuki Y., Steinsbu B. O., Lever M. A., Takai K., Engelen B., Sako Y., Wheat C. G., Horikoshi K. Integrated Ocean Drilling Program Expedition 301 Scientists; 2006; Microbial community in black rust exposed to hot ridge flank crustal fluids. Appl Environ Microbiol 72:6789–6799 [CrossRef]
    [Google Scholar]
  30. Pruesse E., Quast C., Knittel K., Fuchs B. M., Ludwig W., Peplies J., 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 [CrossRef]
    [Google Scholar]
  31. Reynolds E. S. 1963; The use of lead citrate at high pH as an electron-opaque stain in electron microscopy. J Cell Biol 17:208–212 [CrossRef]
    [Google Scholar]
  32. Saitou N., Nei M. 1987; The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
    [Google Scholar]
  33. Shen Y., Buick R. 2004; The antiquity of microbial sulfate reduction. Earth Sci Rev 64:243–272 [CrossRef]
    [Google Scholar]
  34. Slobodkina G. B., Kolganova T. V., Querellou J., Bonch-Osmolovskaya E. A., Slobodkin A. I. 2009; Geoglobus acetivorans sp. nov., an iron(III)-reducing archaeon from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 59:2880–2883 [CrossRef]
    [Google Scholar]
  35. Stackebrandt E., Ebers J. 2006; Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 33:152–155
    [Google Scholar]
  36. 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]
  37. Stetter K. O. 1988; Archaeoglobus fulgidus gen. nov., sp. nov. a new taxon of extremely thermophilic archaebacteria. Syst Appl Microbiol 10:172–173 [CrossRef]
    [Google Scholar]
  38. Stetter K. O., Lauerer G., Thomm M., Neuner A. 1987; Isolation of extremely thermophilic sulfate reducers: evidence for a novel branch of archaebacteria. Science 236:822–824 [CrossRef]
    [Google Scholar]
  39. Stetter K. O., Huber R., Blöchl E., Kurr M., Eden R. D., Fielder M., Cash H., Vance I. 1993; Hyperthermophilic archaea are thriving in deep North Sea and Alaskan oil reservoirs. Nature 365:743–745 [CrossRef]
    [Google Scholar]
  40. 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]
    [Google Scholar]
  41. Tor J. M., Lovley D. R. 2001; Anaerobic degradation of aromatic compounds coupled to Fe(III) reduction by Ferroglobus placidus . Environ Microbiol 3:281–287 [CrossRef]
    [Google Scholar]
  42. Tor J. M., Kashefi K., Lovley D. R. 2001; Acetate oxidation coupled to Fe(III) reduction in hyperthermophilic microorganisms. Appl Environ Microbiol 67:1363–1365 [CrossRef]
    [Google Scholar]
  43. Widdel F., Bak F. 1992; Gram-negative mesophilic sulfate-reducing bacteria. In The Prokaryotes, 2nd edn. pp 3352–3378 Edited by Balows A., Trüper H. G., Dworkin M., Harder W., Schleifer K.-H. New York: Springer;
    [Google Scholar]
  44. Yarza P., Richter M., Peplies J., Euzéby J., Amann R., Schleifer K.-H., Ludwig W., Glöckner F. O., Rosselló-Móra R. 2008; The all-species living tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol 31:241–250 [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.016105-0
Loading
/content/journal/ijsem/10.1099/ijs.0.016105-0
Loading

Data & Media loading...

Most cited this month Most Cited RSS feed

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