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Volume 2013 (2013), Article ID 136714, 13 pages
http://dx.doi.org/10.1155/2013/136714
Research Article

Microbial Diversity and Biochemical Potential Encoded by Thermal Spring Metagenomes Derived from the Kamchatka Peninsula

1Department of Genomic and Applied Microbiology and Goettingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Goettingen, Grisebachstraße 8, 37077 Goettingen, Germany
2Section of Agricultural Entomology, Department for Crop Sciences, Georg-August-University Goettingen, Grisebachstraße 6, 37077 Goettingen, Germany

Received 21 November 2012; Accepted 6 January 2013

Academic Editor: Michael Hoppert

Copyright © 2013 Bernd Wemheuer 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. 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 Scopus
  2. V. T. Marteinsson, S. Hauksdóttir, C. F. V. Hobel, H. Kristmannsdóttir, G. O. Hreggvidsson, and J. K. Kristjánsson, “Phylogenetic diversity analysis of subterranean hot springs in Iceland,” Applied and Environmental Microbiology, vol. 67, no. 9, pp. 4242–4248, 2001. View at Publisher · View at Google Scholar · View at Scopus
  3. 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
  4. G. J. Olsen, C. R. Woese, and R. Overbeek, “The winds of (evolutionary) change: breathing new life into microbiology,” Journal of Bacteriology, vol. 176, no. 1, pp. 1–6, 1994. View at Scopus
  5. C. R. Woese, O. Kandler, and M. L. Wheelis, “Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya,” Proceedings of the National Academy of Sciences of the United States of America, vol. 87, no. 12, pp. 4576–4579, 1990. View at Publisher · View at Google Scholar · View at Scopus
  6. J. Handelsman, “Metagenomics: application of genomics to uncultured microorganisms,” Microbiology and Molecular Biology Reviews, vol. 68, no. 4, pp. 669–685, 2004. View at Publisher · View at Google Scholar · View at Scopus
  7. R. Daniel, “The soil metagenome—a rich resource for the discovery of novel natural products,” Current Opinion in Biotechnology, vol. 15, no. 3, pp. 199–204, 2004. View at Publisher · View at Google Scholar · View at Scopus
  8. W. R. Streit, R. Daniel, and K. E. Jaeger, “Prospecting for biocatalysts and drugs in the genomes of non-cultured microorganisms,” Current Opinion in Biotechnology, vol. 15, no. 4, pp. 285–290, 2004. View at Publisher · View at Google Scholar · View at Scopus
  9. Y. Hotta, S. Ezaki, H. Atomi, and T. Imanaka, “Extremely stable and versatile carboxylesterase from a hyperthermophilic archaeon,” Applied and Environmental Microbiology, vol. 68, no. 8, pp. 3925–3931, 2002. View at Publisher · View at Google Scholar · View at Scopus
  10. J. L. Arpigny, D. Jendrossek, and K. E. Jaeger, “A novel heat-stable lipolytic enzyme from Sulfolobus acidocaldarius DSM 639 displaying similarity to polyhydroxyalkanoate depolymerases,” FEMS Microbiology Letters, vol. 167, no. 1, pp. 69–73, 1998. View at Publisher · View at Google Scholar · View at Scopus
  11. R. I. Amann, W. Ludwig, and K. H. Schleifer, “Phylogenetic identification and in situ detection of individual microbial cells without cultivation,” Microbiological Reviews, vol. 59, no. 1, pp. 143–169, 1995. View at Scopus
  12. P. Lorenz, K. Liebeton, F. Niehaus, and J. Eck, “Screening for novel enzymes for biocatalytic processes: accessing the metagenome as a resource of novel functional sequence space,” Current Opinion in Biotechnology, vol. 13, no. 6, pp. 572–577, 2002. View at Publisher · View at Google Scholar · View at Scopus
  13. C. Elend, C. Schmeisser, C. Leggewie et al., “Isolation and biochemical characterization of two novel metagenome-derived esterases,” Applied and Environmental Microbiology, vol. 72, no. 5, pp. 3637–3645, 2006. View at Publisher · View at Google Scholar · View at Scopus
  14. C. Elend, C. Schmeisser, H. Hoebenreich, H. L. Steele, and W. R. Streit, “Isolation and characterization of a metagenome-derived and cold-active lipase with high stereospecificity for (R)-ibuprofen esters,” Journal of Biotechnology, vol. 130, no. 4, pp. 370–377, 2007. View at Publisher · View at Google Scholar · View at Scopus
  15. C. Simon, A. Wiezer, A. W. Strittmatter, and R. Daniel, “Phylogenetic diversity and metabolic potential revealed in a glacier ice metagenome,” Applied and Environmental Microbiology, vol. 75, no. 23, pp. 7519–7526, 2009. View at Publisher · View at Google Scholar · View at Scopus
  16. 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
  17. J. Zhou, M. A. Bruns, and J. M. Tiedje, “DNA recovery from soils of diverse composition,” Applied and Environmental Microbiology, vol. 62, no. 2, pp. 316–322, 1996. View at Scopus
  18. G. Muyzer, A. Teske, C. O. Wirsen, and H. W. Jannasch, “Phylogenetic relationships of Thiomicrospira species and their identification in deep-sea hydrothermal vent samples by denaturing gradient gel electrophoresis of 16S rDNA fragments,” Archives of Microbiology, vol. 164, no. 3, pp. 165–172, 1995. View at Publisher · View at Google Scholar · View at Scopus
  19. A. Wilmotte, G. Van Der Auwera, and R. De Wachter, “Structure of the 16 S ribosomal RNA of the thermophilic cyanobacterium Chlorogloeopsis HTF (Mastigocladus laminosus HTF) strain PCC7518, and phylogenetic analysis,” FEBS Letters, vol. 317, no. 1-2, pp. 96–100, 1993. View at Publisher · View at Google Scholar · View at Scopus
  20. T. V. Kolganova, B. B. Kuznetsov, and T. P. Turova, “Designing and testing oligonucleotide primers for amplification and sequencing of archaeal 16S rRNA genes,” Mikrobiologiya, vol. 71, no. 2, pp. 283–286, 2002. View at Scopus
  21. 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
  22. 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
  23. J. G. Caporaso, J. Kuczynski, J. Stombaugh et al., “QIIME allows analysis of high-throughput community sequencing data,” Nature Methods, vol. 7, no. 5, pp. 335–336, 2010. View at Publisher · View at Google Scholar · View at Scopus
  24. R. Staden, K. F. Beal, and J. K. Bonfield, “The Staden package, 1998,” Methods in Molecular Biology, vol. 132, pp. 115–130, 2000. View at Scopus
  25. K. E. Ashelford, N. A. Chuzhanova, J. C. Fry, A. J. Jones, and A. J. Weightman, “New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras,” Applied and Environmental Microbiology, vol. 72, no. 9, pp. 5734–5741, 2006. View at Publisher · View at Google Scholar · View at Scopus
  26. T. Huber, G. Faulkner, and P. Hugenholtz, “Bellerophon: a program to detect chimeric sequences in multiple sequence alignments,” Bioinformatics, vol. 20, no. 14, pp. 2317–2319, 2004. View at Publisher · View at Google Scholar · View at Scopus
  27. J. R. Cole, B. Chai, T. L. Marsh et al., “The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy,” Nucleic Acids Research, vol. 31, no. 1, pp. 442–443, 2003. View at Publisher · View at Google Scholar · View at Scopus
  28. R. C. Edgar, “Search and clustering orders of magnitude faster than BLAST,” Bioinformatics, vol. 26, no. 19, Article ID btq461, pp. 2460–2461, 2010. View at Publisher · View at Google Scholar · View at Scopus
  29. C. Camacho, G. Coulouris, V. Avagyan et al., “BLAST+: architecture and applications,” BMC Bioinformatics, vol. 10, article 421, 2009. View at Publisher · View at Google Scholar · View at Scopus
  30. E. Pruesse, C. Quast, K. Knittel et al., “SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB,” Nucleic Acids Research, vol. 35, no. 21, pp. 7188–7196, 2007. View at Publisher · View at Google Scholar · View at Scopus
  31. C. E. Shannon, “A mathematical theory of communication,” SIGMOBILE Mobile Computing and Communications Review, vol. 5, no. 1, pp. 3–55, 2001.
  32. A. Chao and J. Bunge, “Estimating the number of species in a stochastic abundance model,” Biometrics, vol. 58, no. 3, pp. 531–539, 2002. View at Scopus
  33. W. Ludwig, O. Strunk, R. Westram et al., “ARB: a software environment for sequence data,” Nucleic Acids Research, vol. 32, no. 4, pp. 1363–1371, 2004. View at Publisher · View at Google Scholar · View at Scopus
  34. C. Simon, J. Herath, S. Rockstroh, and R. Daniel, “Rapid identification of genes encoding DNA polymerases by function-based screening of metagenomic libraries derived from glacial ice,” Applied and Environmental Microbiology, vol. 75, no. 9, pp. 2964–2968, 2009. View at Publisher · View at Google Scholar · View at Scopus
  35. A. Henne, R. A. Schmitz, M. Bömeke, G. Gottschalk, and R. Daniel, “Screening of environmental DNA libraries for the presence of genes conferring lipolytic activity on Escherichia coli,” Applied and Environmental Microbiology, vol. 66, no. 7, pp. 3113–3116, 2000. View at Publisher · View at Google Scholar · View at Scopus
  36. T. Waschkowitz, S. Rockstroh, and R. Daniel, “Isolation and characterization of metalloproteases with a novel domain structure by construction and screening of metagenomic libraries,” Applied and Environmental Microbiology, vol. 75, no. 8, pp. 2506–2516, 2009. View at Publisher · View at Google Scholar · View at Scopus
  37. K. Rutherford, J. Parkhill, J. Crook et al., “Artemis: sequence visualization and annotation,” Bioinformatics, vol. 16, no. 10, pp. 944–945, 2000. View at Scopus
  38. U. K. Laemmli, “Cleavage of structural proteins during the assembly of the head of bacteriophage T4,” Nature, vol. 227, no. 5259, pp. 680–685, 1970. View at Publisher · View at Google Scholar · View at Scopus
  39. D. Tillett and B. A. Neilan, “Enzyme-free cloning: a rapid method to clone PCR products independent of vector restriction enzyme sites,” Nucleic Acids Research, vol. 27, no. 19, pp. e26–e28, 1999. View at Scopus
  40. K. Rashamuse, T. Ronneburg, F. Hennessy et al., “Discovery of a novel carboxylesterase through functional screening of a pre-enriched environmental library,” Journal of Applied Microbiology, vol. 106, no. 5, pp. 1532–1539, 2009. View at Publisher · View at Google Scholar · View at Scopus
  41. R Development Core Team, R: a Language and Environment for Statistical Computing, R Foundation for Statistical Computing, Vienna, Austria, 2005.
  42. S. Banerji and A. Flieger, “Patatin-like proteins: a new family of lipolytic enzymes present in Bacteria?” Microbiology, vol. 150, no. 3, pp. 522–525, 2004. View at Scopus
  43. J. L. Arpigny and K. E. Jaeger, “Bacterial lipolytic enzymes: classification and properties,” Biochemical Journal, vol. 343, part 1, pp. 177–183, 1999. View at Publisher · View at Google Scholar · View at Scopus
  44. N. D. Rawlings, A. J. Barrett, and A. Bateman, “MEROPS: the peptidase database,” Nucleic Acids Research, vol. 38, supplement 1, pp. D227–D233, 2010. View at Publisher · View at Google Scholar · View at Scopus
  45. I. V. Kublanov, S. K. Bidjieva, A. V. Mardanov, and E. A. Bonch-Osmolovskaya, “Desulfurococcus kamchatkensis sp. nov., a novel hyperthermophilic protein-degrading archaeon isolated from a Kamchatka hot spring,” International Journal of Systematic and Evolutionary Microbiology, vol. 59, no. 7, pp. 1743–1747, 2009. View at Publisher · View at Google Scholar · View at Scopus
  46. C. R. Jackson, H. W. Langner, J. Donahoe-Christiansen, W. P. Inskeep, and T. R. McDermott, “Molecular analysis of microbial community structure in an arsenite-oxidizing acidic thermal spring,” Environmental Microbiology, vol. 3, no. 8, pp. 532–542, 2001. View at Publisher · View at Google Scholar · View at Scopus
  47. N. Byrne, M. Strous, V. Crépeau et al., “Presence and activity of anaerobic ammonium-oxidizing Bacteria at deep-sea hydrothermal vents,” ISME Journal, vol. 3, no. 1, pp. 117–123, 2009. View at Publisher · View at Google Scholar · View at Scopus
  48. Q. Huang, C. Dong, R. Dong et al., “Archaeal and bacterial diversity in hot springs on the Tibetan Plateau, China,” Extremophiles, vol. 15, no. 5, pp. 549–563, 2011.
  49. C. Brochier-Armanet, S. Gribaldo, and P. Forterre, “Spotlight on the Thaumarchaeota,” The ISME Journal, vol. 6, no. 2, pp. 227–230, 2012.
  50. A. Spang, R. Hatzenpichler, C. Brochier-Armanet et al., “Distinct gene set in two different lineages of ammonia-oxidizing archaea supports the phylum Thaumarchaeota,” Trends in Microbiology, vol. 18, no. 8, pp. 331–340, 2010. View at Publisher · View at Google Scholar · View at Scopus
  51. 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
  52. J. K. Rhee, D. G. Ahn, Y. G. Kim, and J. W. Oh, “New thermophilic and thermostable esterase with sequence similarity to the hormone-sensitive lipase family, cloned from a metagenomic library,” Applied and Environmental Microbiology, vol. 71, no. 2, pp. 817–825, 2005. View at Publisher · View at Google Scholar · View at Scopus
  53. P. Tirawongsaroj, R. Sriprang, P. Harnpicharnchai et al., “Novel thermophilic and thermostable lipolytic enzymes from a Thailand hot spring metagenomic library,” Journal of Biotechnology, vol. 133, no. 1, pp. 42–49, 2008. View at Publisher · View at Google Scholar · View at Scopus
  54. X. Chu, H. He, C. Guo, and B. Sun, “Identification of two novel esterases from a marine metagenomic library derived from South China Sea,” Applied Microbiology and Biotechnology, vol. 80, no. 4, pp. 615–625, 2008. View at Publisher · View at Google Scholar · View at Scopus
  55. V. Delorme, R. Dhouib, S. Canaan, F. Fotiadu, F. Carrière, and J. F. Cavalier, “Effects of surfactants on lipase structure, activity, and inhibition,” Pharmaceutical Research, vol. 28, no. 8, pp. 1831–1842, 2011. View at Publisher · View at Google Scholar · View at Scopus
  56. S. Kocabiyik and B. Demirok, “Cloning and overexpression of a thermostable signal peptide peptidase (SppA) from Thermoplasma volcanium GSS1 in E. coli,” Biotechnology Journal, vol. 4, no. 7, pp. 1055–1065, 2009. View at Publisher · View at Google Scholar · View at Scopus
  57. E. Burgess, J. Unrine, G. Mills, C. Romanek, and J. Wiegel, “Comparative geochemical and microbiological characterization of two thermal pools in the Uzon Caldera, Kamchatka, Russia,” Microbial Ecology, vol. 63, no. 3, pp. 471–489, 2012.
  58. R. Cavicchioli, M. Z. DeMaere, and T. Thomas, “Metagenomic studies reveal the critical and wide-ranging ecological importance of uncultivated archaea: the role of ammonia oxidizers,” BioEssays, vol. 29, no. 1, pp. 11–14, 2007. View at Publisher · View at Google Scholar · View at Scopus
  59. L. J. Reigstad, A. Richter, H. Daims, T. Urich, L. Schwark, and C. Schleper, “Nitrification in terrestrial hot springs of Iceland and Kamchatka,” FEMS Microbiology Ecology, vol. 64, no. 2, pp. 167–174, 2008. View at Publisher · View at Google Scholar · View at Scopus
  60. M. Pester, C. Schleper, and M. Wagner, “The Thaumarchaeota: an emerging view of their phylogeny and ecophysiology,” Current Opinion in Microbiology, vol. 14, no. 3, pp. 300–306, 2011. View at Publisher · View at Google Scholar · View at Scopus