1887

Abstract

Two heterotrophic hyperthermophilic strains, ES1 and CL1, were isolated from sp. polychaete worms collected from active hydrothermal vent chimneys in the north-eastern Pacific Ocean. Both were obligately anaerobic and produced HS in the presence of elemental sulfur and H. Complete genome sequences are available for both strains. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strains are more than 97 % similar to most other species of the genus . Therefore, overall genome relatedness index analyses were performed to establish that these strains are novel species. For each analysis, strain ES1 was determined to be most similar to MP, while strain CL1 was determined to be most similar to 4557. The average nucleotide identity scores for these strains were 84 % for strain ES1 and 81 % for strain CL1, genome-to-genome direct comparison scores were 23 % for strain ES1 and 47 % for strain CL1, and the species identification scores were 89 % for strain ES1 and 88 % for strain CL1. For each analysis, strains ES1 and CL1 were below the species delineation cut-off. Therefore, based on their whole genome sequences, strains ES1 and CL1 are suggested to represent novel species of the genus for which the names sp. nov. and sp. nov. are proposed, respectively. The type strains are ES1 ( = DSM 27261 = KACC 17923) and CL1 ( = DSM 27260 = KACC 17922).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.066100-0
2014-11-01
2019-11-13
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/64/11/3655.html?itemId=/content/journal/ijsem/10.1099/ijs.0.066100-0&mimeType=html&fmt=ahah

References

  1. Adams M. W. W., Holden J. F., Menon A. L., Schut G. J., Grunden A. M., Hou C., Hutchins A. M., Jenney F. E. Jr, Kim C.. & other authors ( 2001;). Key role for sulfur in peptide metabolism and in regulation of three hydrogenases in the hyperthermophilic archaeon Pyrococcus furiosus. . J Bacteriol 183:, 716–724. [CrossRef][PubMed]
    [Google Scholar]
  2. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J.. ( 1990;). Basic local alignment search tool. . J Mol Biol 215:, 403–410. [CrossRef][PubMed]
    [Google Scholar]
  3. Auch A. F., von Jan M., Klenk H. P., Göker M.. ( 2010;). Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. . Stand Genomic Sci 2:, 117–134. [CrossRef][PubMed]
    [Google Scholar]
  4. Bertoldo C., Antranikian G.. ( 2006;). The order Thermococcales. . In The Prokaryotes, vol. 3, pp. 69–81. Edited by Dworkin M., Falkow S., Rosenberg E., Schleifer K. H., Stackerbrandt E... New York:: Springer;. [CrossRef]
    [Google Scholar]
  5. Chun J., Rainey F. A.. ( 2014;). Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea. . Int J Syst Evol Microbiol 64:, 316–324. [CrossRef][PubMed]
    [Google Scholar]
  6. Elmore J. R., Yokooji Y., Sato T., Olson S., Glover C. V. C. III, Graveley B. R., Atomi H., Terns R. M., Terns M. P.. ( 2013;). Programmable plasmid interference by the CRISPR-Cas system in Thermococcus kodakarensis. . RNA Biol 10:, 828–840. [CrossRef][PubMed]
    [Google Scholar]
  7. Goris J., Konstantinidis K. T., Klappenbach J. A., Coenye T., Vandamme P., Tiedje J. M.. ( 2007;). DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. . Int J Syst Evol Microbiol 57:, 81–91. [CrossRef][PubMed]
    [Google Scholar]
  8. Heider J., Ma K., Adams M. W. W.. ( 1995;). Purification, characterization, and metabolic function of tungsten-containing aldehyde ferredoxin oxidoreductase from the hyperthermophilic and proteolytic archaeon Thermococcus strain ES-1. . J Bacteriol 177:, 4757–4764.[PubMed]
    [Google Scholar]
  9. Heider J., Mai X., Adams M. W. W.. ( 1996;). Characterization of 2-ketoisovalerate ferredoxin oxidoreductase, a new and reversible coenzyme A-dependent enzyme involved in peptide fermentation by hyperthermophilic archaea. . J Bacteriol 178:, 780–787.[PubMed]
    [Google Scholar]
  10. Holden J. F., Takai K., Summit M., Bolton S., Zyskowski J., Baross J. A.. ( 2001;). Diversity among three novel groups of hyperthermophilic deep-sea Thermococcus species from three sites in the northeastern Pacific Ocean. . FEMS Microbiol Ecol 36:, 51–60. [CrossRef][PubMed]
    [Google Scholar]
  11. Jeon E. J., Jung J. H., Seo D. H., Jung D. H., Holden J. F., Park C. S.. ( 2014;). Bioinformatic and biochemical analysis of a novel maltose-forming α-amylase of the GH57 family in the hyperthermophilic archaeon Thermococcus sp. CL1. . Enzyme Microb Technol 60:, 9–15. [CrossRef][PubMed]
    [Google Scholar]
  12. Jung J. H., Holden J. F., Seo D. H., Park K. H., Shin H., Ryu S., Lee J. H., Park C. S.. ( 2012;). Complete genome sequence of the hyperthermophilic archaeon Thermococcus sp. strain CL1, isolated from a Paralvinella sp. polychaete worm collected from a hydrothermal vent. . J Bacteriol 194:, 4769–4770. [CrossRef][PubMed]
    [Google Scholar]
  13. Jung J. H., Kim Y. T., Jeon E. J., Seo D. H., Hensley S. A., Holden J. F., Lee J. H., Park C. S.. ( 2014;). Complete genome sequence of hyperthermophilic archaeon Thermococcus sp. ES1. . J Biotechnol 174:, 14–15. [CrossRef][PubMed]
    [Google Scholar]
  14. Larkin M. A., Blackshields G., Brown N. P., Chenna R., McGettigan P. A., McWilliam H., Valentin F., Wallace I. M., Wilm A.. & other authors ( 2007;). clustal w and clustal_x version 2.0. . Bioinformatics 23:, 2947–2948. [CrossRef][PubMed]
    [Google Scholar]
  15. Lee J. E., Kim I. H., Jung J. H., Seo D. H., Kang S. G., Holden J. F., Cha J., Park C. S.. ( 2013;). Molecular cloning and enzymatic characterization of cyclomaltodextrinase from hyperthermophilic archaeon Thermococcus sp. CL1. . J Microbiol Biotechnol 23:, 1060–1069. [CrossRef][PubMed]
    [Google Scholar]
  16. Ma K., Loessner H., Heider J., Johnson M. K., Adams M. W. W.. ( 1995;). Effects of elemental sulfur on the metabolism of the deep-sea hyperthermophilic archaeon Thermococcus strain ES-1: characterization of a sulfur-regulated, non-heme iron alcohol dehydrogenase. . J Bacteriol 177:, 4748–4756.[PubMed]
    [Google Scholar]
  17. McGinnis S., Madden T. L.. ( 2004;). blast: at the core of a powerful and diverse set of sequence analysis tools. . Nucleic Acids Res 32: (Suppl. 2), W20–W25. [CrossRef][PubMed]
    [Google Scholar]
  18. Mende D. R., Sunagawa S., Zeller G., Bork P.. ( 2013;). Accurate and universal delineation of prokaryotic species. . Nat Methods 10:, 881–884. [CrossRef][PubMed]
    [Google Scholar]
  19. Oslowski D. M., Jung J. H., Seo D. H., Park C. S., Holden J. F.. ( 2011;). Production of hydrogen from α-1,4- and β-1,4-linked saccharides by marine hyperthermophilic Archaea. . Appl Environ Microbiol 77:, 3169–3173. [CrossRef][PubMed]
    [Google Scholar]
  20. Pledger R. J., Baross J. A.. ( 1989;). Characterization of an extremely thermophilic archaebacterium isolated from a black smoker polychaete (Paralvinella sp.) at the Juan de Fuca Ridge. . Syst Appl Microbiol 12:, 249–256. [CrossRef]
    [Google Scholar]
  21. Pledger R. J., Crump B. C., Baross J. A.. ( 1994;). A barophilic response by two hyperthermophilic, hydrothermal vent archaea: An upward shift in the optimal temperature and acceleration of growth rate at supra-optimal temperatures by elevated pressure. . FEMS Microbiol Ecol 14:, 233–241. [CrossRef]
    [Google Scholar]
  22. Richter M., Rosselló-Móra R.. ( 2009;). Shifting the genomic gold standard for the prokaryotic species definition. . Proc Natl Acad Sci U S A 106:, 19126–19131. [CrossRef][PubMed]
    [Google Scholar]
  23. Schwartz S., Kent W. J., Smit A., Zhang Z., Baertsch R., Hardison R. C., Haussler D., Miller W.. ( 2003;). Human-mouse alignments with blastz. . Genome Res 13:, 103–107. [CrossRef][PubMed]
    [Google Scholar]
  24. Soderlund C., Bomhoff M., Nelson W. M.. ( 2011;). SyMAP v3.4: a turnkey synteny system with application to plant genomes. . Nucleic Acids Res 39:, e68. [CrossRef][PubMed]
    [Google Scholar]
  25. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S.. ( 2011;). mega5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. . Mol Biol Evol 28:, 2731–2739. [CrossRef][PubMed]
    [Google Scholar]
  26. Wang Q., Garrity G. M., Tiedje J. M., Cole J. R.. ( 2007;). Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. . Appl Environ Microbiol 73:, 5261–5267. [CrossRef][PubMed]
    [Google Scholar]
  27. Ying X., Grunden A. M., Nie L., Adams M. W. W., Ma K.. ( 2009;). Molecular characterization of the recombinant iron-containing alcohol dehydrogenase from the hyperthermophilic Archaeon, Thermococcus strain ES1. . Extremophiles 13:, 299–311. [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.066100-0
Loading
/content/journal/ijsem/10.1099/ijs.0.066100-0
Loading

Data & Media loading...

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