Table of Contents Author Guidelines Submit a Manuscript
Archaea
Volume 2013, Article ID 723871, 11 pages
http://dx.doi.org/10.1155/2013/723871
Research Article

Archaeal Community Structures in the Solfataric Acidic Hot Springs with Different Temperatures and Elemental Compositions

Division of Environmental Engineering for Symbiosis, Graduate School of Engineering, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo 192-8577, Japan

Received 31 October 2012; Revised 20 January 2013; Accepted 24 March 2013

Academic Editor: Yoshizumi Ishino

Copyright © 2013 Tomoko Satoh et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. N. R. Pace, “Origin of life—facing up to the physical setting,” Cell, vol. 65, no. 4, pp. 531–533, 1991. View at Publisher · View at Google Scholar · View at Scopus
  2. S. L. Miller and A. Lazcano, “The origin of life—did it occur at high temperatures?” Journal of Molecular Evolution, vol. 41, no. 6, pp. 689–692, 1995. View at Google Scholar · View at Scopus
  3. J. A. Baross, “Do the geological and geochemical records of the early earth support the prediction from global phylogenetic models of a thermophilic cenancestor,” in Thermophiles: The Keys to Molecular Evolution and the Origin of Life, pp. 3–18, Taylor & Francis, Boca Raton, Fla, USA, 1998. View at Google Scholar
  4. N. R. Pace, “A molecular view of microbial diversity and the biosphere,” Science, vol. 276, no. 5313, pp. 734–740, 1997. View at Publisher · View at Google Scholar · View at Scopus
  5. S. M. Barns, R. E. Fundyga, M. W. Jeffries, and N. R. Pace, “Remarkable archaeal diversity detected in a Yellowstone National Park hot spring environment,” Proceedings of the National Academy of Sciences of the United States of America, vol. 91, no. 5, pp. 1609–1613, 1994. View at Google Scholar · View at Scopus
  6. S. M. Barns, C. F. Delwiche, J. D. Palmer, and N. R. Pace, “Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences,” Proceedings of the National Academy of Sciences of the United States of America, vol. 93, no. 17, pp. 9188–9193, 1996. View at Publisher · View at Google Scholar · View at Scopus
  7. P. Hugenholtz, C. Pitulle, K. L. Hershberger, and N. R. Pace, “Novel division level bacterial diversity in a Yellowstone hot spring,” Journal of Bacteriology, vol. 180, no. 2, pp. 366–376, 1998. View at Google Scholar · View at Scopus
  8. A. L. Reysenbach, M. Ehringer, and K. Hershberger, “Microbial diversity at 83°C in Calcite Springs, Yellowstone National Park: another environment where the Aquificales and “Korarchaeota” coexist,” Extremophiles, vol. 4, no. 1, pp. 61–67, 2000. View at Google Scholar · View at Scopus
  9. C. E. Blank, S. L. Cady, and N. R. Pace, “Microbial composition of near-boiling silica-depositing thermal springs throughout Yellowstone National Park,” Applied and Environmental Microbiology, vol. 68, no. 10, pp. 5123–5135, 2002. View at Publisher · View at Google Scholar · View at Scopus
  10. D. R. Meyer-Dombard, E. L. Shock, and J. P. Amend, “Archaeal and bacterial communities in geochemically diverse hot springs of Yellowstone National Park, USA,” Geobiology, vol. 3, no. 3, pp. 211–227, 2005. View at Publisher · View at Google Scholar · View at Scopus
  11. A. A. Perevalova, T. V. Kolganova, N. K. Birkeland, C. Schleper, E. A. Bonch-Osmolovskaya, and A. V. Lebedinsky, “Distribution of Crenarchaeota representatives in terrestrial hot springs of Russia and Iceland,” Applied and Environmental Microbiology, vol. 74, no. 24, pp. 7620–7628, 2008. View at Publisher · View at Google Scholar · View at Scopus
  12. N. P. Burton and P. R. Norris, “Microbiology of acidic, geothermal springs of Montserrat: environmental rDNA analysis,” Extremophiles, vol. 4, no. 5, pp. 315–320, 2000. View at Google Scholar · View at Scopus
  13. L. M. Stout, R. E. Blake, J. P. Greenwood, A. M. Martini, and E. C. Rose, “Microbial diversity of boron-rich volcanic hot springs of St. Lucia, Lesser Antilles,” FEMS Microbiology Ecology, vol. 70, no. 3, pp. 402–412, 2009. View at Publisher · View at Google Scholar · View at Scopus
  14. T. Kvist, B. K. Ahring, and P. Westermann, “Archaeal diversity in Icelandic hot springs,” FEMS Microbiology Ecology, vol. 59, no. 1, pp. 71–80, 2007. View at Publisher · View at Google Scholar · View at Scopus
  15. K. Takai and Y. Sako, “A molecular view of archaeal diversity in marine and terrestrial hot water environments,” FEMS Microbiology Ecology, vol. 28, no. 2, pp. 177–188, 1999. View at Publisher · View at Google Scholar · View at Scopus
  16. S. Kato, T. Itoh, and A. Yamagishi, “Archaeal diversity in a terrestrial acidic spring field revealed by a novel PCR primer targeting archaeal 16S rRNA genes,” FEMS Microbiology Letters, vol. 319, no. 1, pp. 34–43, 2011. View at Publisher · View at Google Scholar · View at Scopus
  17. T. Kvist, A. Mengewein, S. Manzei, B. K. Ahring, and P. Westermann, “Diversity of thermophilic and non-thermophilic crenarchaeota at 80°C,” FEMS Microbiology Letters, vol. 244, no. 1, pp. 61–68, 2005. View at Publisher · View at Google Scholar · View at Scopus
  18. P. Kanokratana, S. Chanapan, K. Pootanakit, and L. Eurwilaichitr, “Diversity and abundance of Bacteria and Archaea in the Bor Khlueng Hot Spring in Thailand,” Journal of Basic Microbiology, vol. 44, no. 6, pp. 430–444, 2004. View at Publisher · View at Google Scholar · View at Scopus
  19. A. M. Childs, B. W. Mountain, R. O'Toole, and M. B. Stott, “Relating microbial community and physicochemical parameters of a hot spring: champagne pool, wai-o-tapu, New Zealand,” Geomicrobiology Journal, vol. 25, no. 7-8, pp. 441–453, 2008. View at Publisher · View at Google Scholar · View at Scopus
  20. Z. Q. Song, J. Q. Chen, H. C. Jiang et al., “Diversity of Crenarchaeota in terrestrial hot springs in Tengchong, China,” Extremophiles, vol. 14, no. 3, pp. 287–296, 2010. View at Publisher · View at Google Scholar · View at Scopus
  21. K. Goko, “Structure and hydrology of the Origi field, West Kirishima geothermal area, Kyushu, Japan,” Geothermics, vol. 29, no. 2, pp. 127–149, 2000. View at Publisher · View at Google Scholar · View at Scopus
  22. T. Tsuyuki, “Geological study of hot springs in Kyushu, Japan (5). Some hot springs in the Kagoshima graben, with special references to thermal water reservoir. Reports of the Faculty of Science, Kagoshima University,” Earth Science and Biology, vol. 2, pp. 85–101, 1969 (Japanese). View at Google Scholar
  23. R. Imura, T. Kobayashi, and C. C. S. Sentā, Geological Map of Kirishima Volcano, (Japanese), Geological Survey of Japan, 2001.
  24. K. Tamura, D. Peterson, N. Peterson, G. Stecher, M. Nei, and S. Kumar, “MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods,” Molecular Biology and Evolution, vol. 28, pp. 2731–2739, 2011. View at Google Scholar
  25. S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, “Basic local alignment search tool,” Journal of Molecular Biology, vol. 215, no. 3, pp. 403–410, 1990. View at Publisher · View at Google Scholar · View at Scopus
  26. J. D. Thompson, D. G. Higgins, and T. J. Gibson, “CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice,” Nucleic Acids Research, vol. 22, no. 22, pp. 4673–4680, 1994. View at Google Scholar · View at Scopus
  27. S. H. Hurlbert, “The nonconcept of species diversity: a critique and alternative parameters,” Ecology, vol. 52, pp. 577–586, 1971. View at Google Scholar
  28. G. Stirling and B. Wilsey, “Empirical relationships between species richness, evenness, and proportional diversity,” American Naturalist, vol. 158, no. 3, pp. 286–299, 2001. View at Publisher · View at Google Scholar · View at Scopus
  29. C. E. Shannon, W. Weaver, R. E. Blahut, and B. Hajek, The Mathematical Theory of Communication, University of Illinois Press, Urbana, Ill, USA, 1949.
  30. E. H. Simpson, “Measurement of diversity,” Nature, vol. 163, no. 4148, article 688, 1949. View at Google Scholar · View at Scopus
  31. R. K. Colwell, 2006, EstimateS: Statistical estimation of species richness and shared species from samples, Version 8, http://purl.oclc.org/estimates.
  32. E. C. Pielou, “Association tests versus homogeneity tests: their use in subdividing quadrats into groups,” Vegetatio, vol. 18, no. 1–6, pp. 4–18, 1969. View at Publisher · View at Google Scholar · View at Scopus
  33. A. Chao, “Estimating the population size for capture—recapture data with unequal catchability,” Biometrics, vol. 43, no. 4, pp. 783–791, 1987. View at Google Scholar · View at Scopus
  34. A. Chao, W. H. Hwang, Y. C. Chen, and C. Y. Kuo, “Estimating the number of shared species in two communities,” Statistica Sinica, vol. 10, no. 1, pp. 227–246, 2000. View at Google Scholar · View at Scopus
  35. I. J. Good, “The population frequencies of species and the estimation of population parameters,” Biometrika, vol. 40, pp. 237–264, 1953. View at Google Scholar
  36. D. R. Singleton, M. A. Furlong, S. L. Rathbun, and W. B. Whitman, “Quantitative comparisons of 16S rRNA gene sequence libraries from environmental samples,” Applied and Environmental Microbiology, vol. 67, no. 9, pp. 4374–4376, 2001. View at Publisher · View at Google Scholar · View at Scopus
  37. H. Kimura, K. Mori, T. Tashiro et al., “Culture-independent estimation of optimal and maximum growth temperatures of archaea in subsurface habitats based on the G plus C content in 16S sequences,” Geomicrobiology Journal, vol. 27, no. 2, pp. 114–122, 2010. View at Publisher · View at Google Scholar · View at Scopus
  38. T. Itoh, K. I. Suzuki, P. C. Sanchez, and T. Nakase, “Caldivirga maquilingensis gen. nov., sp. nov., a new genus of rod- shaped crenarchaeote isolated from a hot spring in the Philippines,” International Journal of Systematic Bacteriology, vol. 49, no. 3, pp. 1157–1163, 1999. View at Google Scholar · View at Scopus
  39. T. Itoh, K. I. Suzuki, and T. Nakase, “Vulcanisaeta distributa gen. nov., sp. nov., and Vulcanisaeta souniana sp. nov., novel hyperthermophilic, rod-shaped crenarchaeotes isolated from hot springs in Japan,” International Journal of Systematic and Evolutionary Microbiology, vol. 52, no. 4, pp. 1097–1104, 2002. View at Publisher · View at Google Scholar · View at Scopus
  40. W. Zillig, K. O. Stetter, and S. Wunderl, “The Sulfolobus-“Caldariella” group: taxonomy on the basis of the structure of DNA-dependent RNA polymerases,” Archives of Microbiology, vol. 125, no. 3, pp. 259–269, 1980. View at Google Scholar · View at Scopus
  41. G. Huber, C. Spinnler, A. Gambacorta, and K. O. Stetter, “Metallosphaera sedula gen. and sp. nov. represents a new genus of aerobic, metal-mobilizing, thermoacidophilic archaebacteria,” Systematic and Applied Microbiology, vol. 12, pp. 38–47, 1989. View at Google Scholar
  42. A. Segerer, A. Neuner, J. K. Kristjansson, and K. O. Stetter, “Acidianus infernus gen. nov., sp. nov., and Acidianus brierleyi comb. nov.: facultatively aerobic, extremely acidophilic thermophilic sulfur-metabolizing archaebacteria,” International Journal of Systematic Bacteriology, vol. 36, no. 4, pp. 559–564, 1986. View at Google Scholar · View at Scopus
  43. T. Itoh, K. Suzuki, P. C. Sanchez, and T. Nakase, “Caldisphaera lagunensis gen. nov., sp. nov., a novel thermoacidophilic crenarchaeote isolated from a hot spring at Mt Maquiling, Philippines,” International Journal of Systematic and Evolutionary Microbiology, vol. 53, no. 4, pp. 1149–1154, 2003. View at Publisher · View at Google Scholar · View at Scopus
  44. H. Huber and K. O. Stetter, “Order III. Sulfolobales,” in Bergey’s Manual of Systematic Bacteriology, J. T. Staley, M. P. Bryant, E. N. Pfenning, and J. G. Holt, Eds., vol. 1, pp. 198–210, Williams and Wilkins, Baltimore, Md, USA, 2nd edition, 2001. View at Google Scholar
  45. M. O. Schrenk, D. S. Kelley, J. R. Delaney, and J. A. Baross, “Incidence and diversity of microorganisms within the walls of an active deep-sea sulfide chimney,” Applied and Environmental Microbiology, vol. 69, no. 6, pp. 3580–3592, 2003. View at Google Scholar · View at Scopus
  46. T. Nunoura, H. Hirayama, H. Takami et al., “Genetic and functional properties of uncultivated thermophilic crenarchaeotes from a subsurface gold mine as revealed by analysis of genome fragments,” Environmental Microbiology, vol. 7, no. 12, pp. 1967–1984, 2005. View at Publisher · View at Google Scholar · View at Scopus
  47. T. Itoh, K. I. Suzuki, and T. Nakase, “Thermocladium modestius gen. nov., sp. nov., a new genus of rod-shaped, extremely thermophilic crenarchaeote,” International Journal of Systematic Bacteriology, vol. 48, no. 3, pp. 879–887, 1998. View at Google Scholar · View at Scopus
  48. E. S. Boyd, R. A. Jackson, G. Encarnacion et al., “Isolation, characterization, and ecology of sulfur-respiring Crenarchaea inhabiting acid-sulfate-chloride-containing geothermal springs in Yellowstone National Park,” Applied and Environmental Microbiology, vol. 73, no. 20, pp. 6669–6677, 2007. View at Publisher · View at Google Scholar · View at Scopus
  49. K. Takai and K. Horikoshi, “Genetic diversity of archaea in deep-sea hydrothermal vent environments,” Genetics, vol. 152, no. 4, pp. 1285–1297, 1999. View at Google Scholar · View at Scopus
  50. F. Inagaki, K. Takai, H. Hirayama, Y. Yamato, K. H. Nealson, and K. Horikoshi, “Distribution and phylogenetic diversity of the subsurface microbial community in a Japanese epithermal gold mine,” Extremophiles, vol. 7, no. 4, pp. 307–317, 2003. View at Publisher · View at Google Scholar · View at Scopus
  51. C. Vetriani, H. W. Jannasch, B. J. Macgregor, D. A. Stahl, and A. L. Reysenbach, “Population structure and phylogenetic characterization of marine benthic Archaea in deep-sea sediments,” Applied and Environmental Microbiology, vol. 65, no. 10, pp. 4375–4384, 1999. View at Google Scholar · View at Scopus
  52. K. Takai, D. P. Moser, M. DeFlaun, T. C. Onstott, and J. K. Fredrickson, “Archaeal diversity in waters from deep South African gold mines,” Applied and Environmental Microbiology, vol. 67, no. 12, pp. 5750–5760, 2001. View at Publisher · View at Google Scholar · View at Scopus
  53. A. Teske, K. U. Hinrichs, V. Edgcomb et al., “Microbial diversity of hydrothermal sediments in the Guaymas Basin: evidence for anaerobic methanotrophic communities,” Applied and Environmental Microbiology, vol. 68, no. 4, pp. 1994–2007, 2002. View at Publisher · View at Google Scholar · View at Scopus
  54. E. F. DeLong, “Archaea in coastal marine environments,” Proceedings of the National Academy of Sciences of the United States of America, vol. 89, no. 12, pp. 5685–5689, 1992. View at Publisher · View at Google Scholar · View at Scopus
  55. G. Jurgens and A. Saano, “Diversity of soil Archaea in boreal forest before, and after clear-cutting and prescribed burning,” FEMS Microbiology Ecology, vol. 29, no. 2, pp. 205–213, 1999. View at Publisher · View at Google Scholar · View at Scopus
  56. M. I. Prokofeva, N. A. Kostrikina, T. V. Kolganova et al., “Isolation of the anaerobic thermoacidophilic crenarchaeote Acidilobus saccharovorans sp. nov. and proposal of Acidilobales ord. nov., including Acidilobaceae fam. nov. and Caldisphaeraceae fam. nov,” International Journal of Systematic and Evolutionary Microbiology, vol. 59, no. 12, pp. 3116–3122, 2009. View at Publisher · View at Google Scholar · View at Scopus