Thermococcus onnurineus sp. nov., a Hyperthermophilic Archaeon Isolated from a Deep-Sea Hydrothermal Vent Area at the PACMANUS Field

  • Bae, Seung-Seob (Marine Biotechnology Center, Korea Ocean Research & Development Institute) ;
  • Kim, Yun-Jae (Marine Biotechnology Center, Korea Ocean Research & Development Institute) ;
  • Yang, Sung-Hyun (Marine Biotechnology Center, Korea Ocean Research & Development Institute) ;
  • Lim, Jae-Kyu (Marine Biotechnology Center, Korea Ocean Research & Development Institute) ;
  • Jeon, Jeong-Ho (Marine Biotechnology Center, Korea Ocean Research & Development Institute) ;
  • Lee, Hyn-Sook (Marine Biotechnology Center, Korea Ocean Research & Development Institute) ;
  • Kang, Sung-Gyun (Marine Biotechnology Center, Korea Ocean Research & Development Institute) ;
  • Kim, Sang-Jin (Marine Biotechnology Center, Korea Ocean Research & Development Institute) ;
  • Lee, Jung-Hyun (Marine Biotechnology Center, Korea Ocean Research & Development Institute)
  • Published : 2006.11.30

Abstract

A novel hyperthermophilic, anaerobic, heterotrophic archaeon, designated strain $NA1^T$, was isolated from a deep-sea hydrothermal vent area (depth, 1,650 m) within the Papua New Guinea-Australia-Canada-Manus (PACMANUS) field. Cells of this strain were motile by means of polar flagella, coccoid-shaped with a diameter of approximately $0.5-1.0{\mu}m$, and occurred as single cells. Optimal temperature, pH, and NaCl concentration for growth were $80^{\circ}C$, 8.5, and 3.5%, respectively. The new isolate was an obligate heterotroph that utilized yeast extract, beef extract, tryptone, peptone, casein, and starch as carbon and energy sources. Elemental sulfur was required for growth and was reduced to hydrogen sulfide. The G+C content of the genomic DNA was 52.0 mol%. Phylogenetic analysis of the 16S rRNA gene indicated that strain $NA1^T$ belongs to the genus Thermococcus, and the organism is most closely related to T. gorgonarius, T. peptonophilus, and T. celer; however, no significant homology was observed among species by DNA-DNA hybridization. Strain $NA1^T$ therefore represents a novel species for which the name Thermococcus onnurineus sp. novo is proposed. The type strain is $NA1^T$ (=KCTC 10859, =JCM 13517).

Keywords

References

  1. Atomi, H., T. Fukui, T. Kanai, M. Morikawa, and T. Imanaka. 2004. Description of Thermococcus kodakarensis sp. nov., a well studied hyperthermophilic archeaon previously reported as Pyrococcus sp. KOD1. Archaea 1: 263-267 https://doi.org/10.1155/2004/204953
  2. Bae, S. S., J.-H. Lee, and S.-J. Kim. 2005. Bacillus alveayuensis sp. nov., a thermophilic bacterium isolated from deep-sea sediments of the Ayu Trough. Int. J. Syst. Evol. Microbiol. 55: 1211-1215 https://doi.org/10.1099/ijs.0.63424-0
  3. Balch, W. E. and R. S. Wolfe. 1976. New approach to the cultivation of methanogenic bacteria: 2-Mercaptoethane-sulfonic acid (HS-CoM)-dependent growth of Methanobacterium ruminantium in a pressurized atmosphere. Appl. Environ. Microbiol. 32: 781-791
  4. Bazylinski, D. A., C. O. Wirsen, and H. W. Jannasch. 1989. Microbial utilization of naturally-occurring hydrocarbon at the Guaymas Basin hydrothermal vent site. Appl. Environ. Microbiol. 55: 2832-2836
  5. Choi, J. J. and S.-T. Kwon. 2004. Cloning, expression, and characterization of DNA polymerase from hyperthermophilic bacterium Aquifex pyrophilus. J. Microbiol. Biotechnol. 14: 1022-1030
  6. De Ley, J., H. Cattoir, and A. Reynaerts. 1970. The quantitative measurement of DNA hybridization from renaturation rates. Eur. J. Biochem. 12: 133-142 https://doi.org/10.1111/j.1432-1033.1970.tb00830.x
  7. Delong, E. 1992. Archaea in coastal marine environments. Proc. Natl. Acad. Sci. USA 89: 5685-5689
  8. Felsenstein, J. 1993. PHYLIP (Phylogeny Inference Package), version 3.5c. Department of Genetics, University of Washington, Seattle, WA, U.S.A
  9. Fiala, G. and K. Stetter. 1986. Pyrococcus furiosus sp. nov. represents a new genus of marine heterotrophic archaebacteria growing optimally at $100^{\circ}C$. Arch. Microbiol. 145: 338-349
  10. Fitch, W. M. 1972. Toward defining the course of evolution: Minimum change for a specific tree topology. Syst. Zool. 20: 406-416 https://doi.org/10.2307/2412116
  11. Fitch, W. M. and E. Margoliash. 1967. Construction of phylogenetic trees. Science 155: 279-284 https://doi.org/10.1126/science.155.3760.279
  12. Godfroy, A., F. Lesongeur, G. Raguenes, J. Quérellou, E. Antoine, J.-R. Meunier, J. Guezennec, and G. Barbier. 1997. Thermococcus hydrothermalis sp. nov., a new hyperthermophilic archaeon isolated from a deep-sea hydrothermal vent. Int. J. Syst. Bacteriol. 47: 622-626 https://doi.org/10.1099/00207713-47-3-622
  13. Gonzalez, J. M., C. Kato, and K. Horikoshi. 1995. Thermococcus peptonophilus sp. nov., a fast-growing, extremely thermophilic archaebacterium isolated from deep-sea hydrothermal vents. Arch. Microbiol. 164: 159-164 https://doi.org/10.1007/BF02529966
  14. Holden, J. F., K. Takai, M. Summit, S. Bolton, J. Zyskowski, and J. Baross. 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 https://doi.org/10.1111/j.1574-6941.2001.tb00825.x
  15. Jukes, T. H. and C. R. Cantor. 1969. Evolution of protein molecules, pp. 21-32. In H. N. Munro. (ed.). Mammalian Protein Metabolism, Vol. 3. Academic Press, New York
  16. Lee, S.-H., H. R. Oh, J.-H. Lee, S.-H. Kim, and J.-C. Cho. 2004. Cold-seep sediment harbors phylogenetically diverse uncultured bacteria. J. Microbiol. Biotechnol. 14: 906-913
  17. Mandel, M., L. Igambi, J. Bergendahl, M. L. Dodson, and E. Scheltgen Jr. 1970. Correlation of melting temperature and cesium chloride buoyant density of bacterial deoxyribonucleic acid. J. Bacteriol. 101: 333-338 https://doi.org/10.1002/path.1711010406
  18. Marmur, J. and P. Doty. 1962. Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. J. Mol. Biol. 5: 109-118 https://doi.org/10.1016/S0022-2836(62)80066-7
  19. Miroshnichenko, M. L., G. M. Gongadze, F. A. Rainey, A. S. Kostyukova, A. M. Lysenko, N. A. Chernyh, and E. A. Bonch-Osmolovskaya. 1998. Thermococcus gorgonarius sp. nov. and Thermococcus pacificus sp. nov.: Heterotrophic extremely thermophilic archaea from New Zealand submarine hot vents. Int. J. Syst. Bacteriol. 48: 23-29 https://doi.org/10.1099/00207713-48-1-23
  20. Miroshnichenko, M. L., H. Hippe, E. Stackebrandt, N. A. Kostrikina, A. M. Lysenko, N. A. Chernyh, C. Jeanthon, T. N. Nazina, S. S. Belyaev, and E. A. Bonch-Osmolovskaya. 2001. Isolation and characterization of Thermococcus sibiricus sp. nov., from a Western Siberia high-temperature oil reservoir. Extremophiles 5: 85-91 https://doi.org/10.1007/s007920100175
  21. Porter, K. G. and Y. S. Feig. 1980. The use of DAPI for identifying and counting microflora. Limnol. Oceanogr. 25: 943-948 https://doi.org/10.4319/lo.1980.25.5.0943
  22. Ronimus, R. S., A.-L. Reysenbach, D. R. Musgrave, and H. W. Morgan. 1997. The phylogenetic position of the Thermococcus isolate AN1 based on 16S rRNA gene sequence analysis: A proposal that AN1 represents a new species, Thermococcus zilligii sp. nov. Arch. Microbiol. 168: 245-248 https://doi.org/10.1007/s002030050495
  23. Saitou, N. and M. Nei. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425
  24. Schonheit, P. and T. Schafer. 1995. Metabolism of hyperthermophiles. World J. Microbiol. Biotechnol. 11: 26-57 https://doi.org/10.1007/BF00339135
  25. Shin, H.-J., S.-K. Lee, J. J. Choi, S. H. Koh, J.-H. Lee, S.-J. Kim, and S.-T. Kwon. 2005. Cloning, expression, and characterization of a family B-type DNA polymerase from the hyperthermophilic crenarchaeon Pyrobaculum arsenaticum and its application to PCR. J. Microbiol. Biotechnol. 15: 1359-1367
  26. Sohn, J. H., K. Y. Kwon, J.-H. Kang, H. B. Jung, and S.-J. Kim. 2004. Novosphingobium pentaromativorans sp. nov., a high-molecular-mass polycyclic aromatic hydrocarbon-degrading bacterium isolated from estuarine sediment. Int. J. Syst. Evol. Microbiol. 54: 1483-1487 https://doi.org/10.1099/ijs.0.02945-0
  27. Stackebrandt, E. and B. M. Goebel. 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 https://doi.org/10.1099/00207713-44-4-846
  28. Stetter, K. O. 1999. Extremophiles and their adaptation to hot environments. FEBS Lett. 452: 22-25 https://doi.org/10.1016/S0014-5793(99)00663-8
  29. Takai, K., A. Sugai, T. Itoch, and K. Horikoshi. 2000. Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney. Int. J. Syst. Evol. Microbiol. 50: 489-500 https://doi.org/10.1099/00207713-50-2-489
  30. Takai, K., T. Komatsu, F. Inagaki, and K. Horikoshi. 2001. Distribution of archaea in a black smoker chimney structure. Appl. Environ. Microbiol. 67: 3618-3629 https://doi.org/10.1128/AEM.67.8.3618-3629.2001
  31. Wayne, L. G., D. J. Brenner, R. R. Colwell, P. A. D. Grimont, P. Kandler, M. I. Krichevsky, L. H. Moore, W. E. C. Moore, R. G. E. Murray, E. Stackebrandt, M. P. Starr, and H. G. Trper. 1987. Report of the Ad Hoc Committee on reconciliation of approaches of bacterial systematics. Int. J. Syst. Bacteriol. 37: 463-464 https://doi.org/10.1099/00207713-37-4-463
  32. Zillig, W. and A.-L. Reysenbach. 2001. Class IV. Thermococci class. nov., pp. 342-346 In D. R. Boone and R. W. Castenholz (eds.). Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 1. Springer, New York
  33. Zillig, W., I. Holz, D. Janekovic, W. Schafer, and W. D. Reiter. 1983. The archaebacterium Thermococcus celer represents a novel genus within the thermophilic branch of the archaebacteria. Syst. Appl. Microbiol. 4: 88-94 https://doi.org/10.1016/S0723-2020(83)80036-8