, Volume 10, Issue 3, pp 181–189 | Cite as

Diversity of actinomycetes isolated from Challenger Deep sediment (10,898 m) from the Mariana Trench

  • Wasu Pathom-areeEmail author
  • James E. M. Stach
  • Alan C. Ward
  • Koki Horikoshi
  • Alan T. Bull
  • Michael Goodfellow
Original Paper


Thirty-eight actinomycetes were isolated from sediment collected from the Mariana Trench (10,898 m) using marine agar and media selective for actinomycetes, notably raffinose-histidine agar. The isolates were assigned to the class Actinobacteria using primers specific for members of this taxon. The phylogenetic analysis based on 16S rRNA gene sequencing showed that the isolates belonged to the genera Dermacoccus, Kocuria, Micromonospora, Streptomyces, Tsukamurella and Williamsia. All of the isolates were screened for genes encoding nonribosomal peptide and polyketide synthetases. Nonribosomal peptide synthetase sequences were detected in more than half of the isolates and polyketide synthases type I (PKS-I) were identified in five out of 38 strains. The Streptomyces isolates produced several unusual secondary metabolites, including a PKS-I associated product. In initial testing for piezotolerance, the Dermacoccus strain MT1.1 grew at elevated hydrostatic pressures.


Mariana trench Actinomycetes Deep-sea 16S rRNA genes Phylogenetic analysis NRPS PKS I PKS II Dermacoccus 



We thank the Kaiko operation team and the crew of M.S. Yokosuka for collecting sediment samples and Professor David Manning (School of Civil Engineering and Geomatics, University of Newcastle) for the use of the pressure equipment. Wasu Pathom-aree is also grateful to the Royal Thai Government and to the DPST program for financial support. ATB, MG and ACW also gratefully acknowledge support from the UK Natural Environmental Research Council (grants NER/T/S/2000/00614 and NER/T/S/ 2000/00616). We thank two anonymous reviewers for their constructive comments.


  1. Akimoto K, Hattori M, Uematsu K, Kato C (2001) The deepest living foraminifera, Challenger Deep, Mariana Trench. Mar Micropaleontol 42:95–97CrossRefGoogle Scholar
  2. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410CrossRefPubMedGoogle Scholar
  3. Attwell RW, Colwell RR (1984) Thermoactinomycetes as terrestrial indicators for marine and estuarine waters. In: Ortiz-Ortiz L, Bojalil LF, Yakoleff V (eds) Biological, biochemical and biomedical aspects of actinomycetes. Academic Press, Orlando, pp 441–452Google Scholar
  4. Ayuso-Sacido A, Genilloud O (2005) New PCR primers for the screening of NRPS and PKS-I systems in actinomycetes: detection and distribution of these biosynthetic gene sequences in major taxonomic groups. Microb Ecol 49:10–24CrossRefPubMedGoogle Scholar
  5. Brandão FFB, Bull AT (2003) Nitrile hydrolyzing activities of deep-sea and terrestrial mycolate actinomycetes. Antonie van Leeuwenhoek 84:89–98CrossRefPubMedGoogle Scholar
  6. Brandão PFB, Clapp JP, Bull AT (2002) Discrimination and taxonomy of geographically diverse strains of nitrile-metabolizing actinomycetes using chemometric and molecular sequencing techniques. Environ Microbiol 4:262–276CrossRefPubMedGoogle Scholar
  7. Bull AT (2004) Bountiful oceans: prospecting marine microbial diversity. Screen Trends Drug Discov 5:14–16Google Scholar
  8. Bull AT, Goodfellow M, Slater JH (1992) Biodiversity as a source of innovation in biotechnology. Annu Rev Microbiol 42:219–257CrossRefGoogle Scholar
  9. Bull AT, Stach JEM, Ward AC, Goodfellow M (2005) Marine actinobacteria: perspectives, challenges and future directions. Antonie van Leeuwenhoek 87:65–79CrossRefGoogle Scholar
  10. Colquhoun JA, Mexson J, Goodfellow M, Ward AC, Horikoshi K, Bull AT (1998) Novel rhodococci and other mycolate actinomycetes from the deep sea. Antonie van Leeuwenhoek 74:27–40CrossRefPubMedGoogle Scholar
  11. Courtois S, Cappellano CM, Ball M, Francou FX, Normand P, Helynck G, Martinez A, Kolvek SJ, Hopke J, Osburne MS, August PR, Nalin R, Guerineau M, Jeannin P, Simonet P, Pernodet JL (2003) Recombinant environmental libraries provide access to microbial diversity for drug discovery from natural products. Appl Environ Microbiol 69:49–55CrossRefPubMedGoogle Scholar
  12. Cross T (1968) Thermophilic actinomycetes. J Appl Bacteriol 31:36–53PubMedGoogle Scholar
  13. Duangmal K, Ward AC, Goodfellow M (2005) Selective isolation of members of the Streptomyces violaceoruber clade from soil. FEMS Microbiol Lett 245:321–327CrossRefPubMedGoogle Scholar
  14. Felsenstein J (1985) Confidence limits on phylogeny: an appropriate use of the bootstrap. Evolution 39:783–791Google Scholar
  15. Felsenstein J (1989) PHYLIP—phylogeny inference package (Version 3.2). Cladistics 5:164–166Google Scholar
  16. Fiedler H-P, Bruntner C, Bull AT, Ward AC, Goodfellow M, Mihm G (2005) Marine actinomycetes as a source of novel secondary metabolites. Antonie van Leeuwenhoek 87:37–42CrossRefPubMedGoogle Scholar
  17. Finking R, Marahiel AM (2004) Biosynthesis of nonribosomal peptides. Annu Rev Microbiol 28:453–488CrossRefGoogle Scholar
  18. Ginolhac A, Jarrin C, Gillet B, Robe P, Pujic P, Tuphile K, Bertrand H, Vogel TM, Perriere G, Simonet P, Nalin R (2004) Phylogenetic analysis of polyketide synthase I domains from soil metagenomic libraries allows selection of promising clones. Appl Environ Microbiol 70:5522–5527CrossRefPubMedGoogle Scholar
  19. Goodfellow M, Haynes JA (1984) Actinomycetes in marine sediments. In: Ortiz–Ortiz L, Bojalil LF, Yakoleff V (eds) Biological, biochemical and biomedical aspects of actinomycetes. Academic Press, Orlando, pp 453–472Google Scholar
  20. Gvirtzman Z, Stern RJ (2004) Bathymetry of Mariana trench-arc system and formation of the Challenger Deep as a consequence of weak plate coupling. Tectonics 23(Art no. TC2011)Google Scholar
  21. Han SK, Nedashkovskaya OI, Mikhailov V, Kim SB, Bae KS (2003) Salinibacterium amurskyense gen. nov., sp. nov., a novel genus of the family Microbacteriaceae from the marine environment. Int J Syst Evol Microbiol 53:2061–2066CrossRefPubMedGoogle Scholar
  22. Hayakawa M, Nonomura H (1987) Humic acid vitamin agar, a new medium for the selective isolation of soil actinomycetes. J Ferment Technol 65:501–509CrossRefGoogle Scholar
  23. Heald SC, Brandão PFB, Hardicre R, Bull AT (2001) Physiology, biochemistry and taxonomy of deep-sea nitrile metabolising Rhodococcus strains. Antonie van Leeuwenhoek 80:169–183CrossRefPubMedGoogle Scholar
  24. Janssen PH, Yates PS, Grinton BE, Taylor PM, Sait M (2002) Improved culturability of soil bacteria and isolation in pure culture of novel members of the divisions Acidobacteria, Actinobacteria, Proteobacteria, and Verrucomicrobia. Appl Environ Microbiol 68:2391–2396CrossRefPubMedGoogle Scholar
  25. Jeanmougin F, Thompson JD, Gouy M, et al (1998) Multiple sequence alignment with CLUSTAL X. Trends Biochem Sci 23(10):403–405CrossRefPubMedGoogle Scholar
  26. Jensen PR, Dwight R, Fenical W (1991) Distribution of actinomycetes in near-shore tropical marine sediments. Appl Environ Microbiol 57:1102–1108PubMedGoogle Scholar
  27. Jensen PR, Mincer TJ, Williams PG, Fenical W (2005) Marine actinomycete diversity and natural product discovery. Antonie van Leeuwenhoek 87:43–48CrossRefPubMedGoogle Scholar
  28. Joseph SJ, Hugenholtz P, Sangwan P, Osbone CA, Janssen PH (2003) Laboratory cultivation of widespread and previously uncultured soil bacteria. Appl Environ Microbiol 69:7210–7215CrossRefPubMedGoogle Scholar
  29. Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro HN (ed) Mammalian protein metabolism, vol 3. Academic Press, N Y, pp 21–132Google Scholar
  30. Kato C, Li L, Nogi Y, Nakamura Y, Tamaoka J, Horikoshi K (1998) Extremely barophilic bacteria isolated from the Mariana Trench, Challenger Deep, at a depth of 11,000 meters. Appl Environ Microbiol 64:1510–1513PubMedGoogle Scholar
  31. Kato C, Li L, Tamaoka J, Horikoshi K (1997) Molecular analyses of the sediment of the 11,000-m-deep of the Mariana Trench. Extremophiles 1:117–123Google Scholar
  32. Kelly KL (1958) Centroid notations for the revised ISCC-NBS color name blocks. J Res Nat Bureau Standards USA 61:472Google Scholar
  33. Ketela MM, Virpi S, Halo L, Hautala A, Hakala J, Mantsala P, Ylihonko K (1999) An efficient approach for screening minimal PKS genes from Streptomyces. FEMS Microbiol Lett 180:1–6PubMedGoogle Scholar
  34. Ketela MM, Halo L, Manukka E, Hakala J, Mantsala P, Ylihonko K (2002) Molecular evolution of aromatic polyketides and comparative sequence analysis of polyketide ketosynthase and 16S ribosomal DNA genes from various Streptomyces species. Appl Environ Microbiol 68:4472–4479CrossRefPubMedGoogle Scholar
  35. Kim SB, Falconer C, Williams E, Goodfellow M (1998) Streptomyces thermocarboxydovorans sp. nov. and Streptomyces thermocarboxydus sp. nov., two moderately thermophilic carboxydotrophic species from soil. Int J Syst Bacteriol 48:59–68PubMedGoogle Scholar
  36. Kyo M, Miyazaki E, Tsukioka S, Ochi H, Amitani Y, Tsuchiya T, Aoki T, Takagawa S (1995) The sea trial of “KAIKO”, the full ocean depth research ROV. Oceans 95:1991–1996Google Scholar
  37. Lanoot B, Vancanneyt M, Dawyndt P, Cnockaert M, Zhang J, Huang Y, Liu Z, Swings J (2004) BOX-PCR fingerprinting as a powerful tool to reveal synonymous names in the genus Streptomyces. Emended descriptions are proposed for the species Streptomyces cinereorectus, S. fradiae, S. tricolor, S. colombiensis, S. filamentosus, S. vinaceus and S. phaeopurpureus. Syst Appl Microbiol 27:84–92CrossRefPubMedGoogle Scholar
  38. Liu W, Ahlert J, Gao Q, Pienkowski EW, Shen B, Thorson JS (2003) Rapid PCR amplification of minimal enediyne polyketide synthase cassettes leads to a predictive familial classification model. Proc Natl Acad Sci 100:11959–11963CrossRefPubMedGoogle Scholar
  39. Maldonado LA, Stach JEM, Pathom-aree W, Ward AC, Bull AT, Goodfellow M (2005) Diversity of cultivable actinobacteria in geographically widespread marine sediments. Antonie van Leeuwenhoek 87:11–18CrossRefPubMedGoogle Scholar
  40. Mincer TJ, Jensen PR, Kauffmann CA, Fenical W (2002) Widespread and persistent populations of a major new marine actinomycete taxon in ocean sediments. Appl Environ Microbiol 68:5005–5011CrossRefPubMedGoogle Scholar
  41. National Bureau of Standards (1964) ISCC-NBS color-name charts illustrated with centroid colors (supplement to national bureau of standards USA circular 553). National Bureau of Standards, USAGoogle Scholar
  42. Olive DM, Bean P (1999) Principles and applications of methods for DNA-based typing of microbial organisms. J Clin Microbiol 37:1661–1669PubMedGoogle Scholar
  43. Pearson K (1926) On the coefficient of racial likeness. Biometrika 18:105–117Google Scholar
  44. Sadowsky MJ, Kinnel LL, Bowers JH, Schottel JL (1996) Use of repetitive intergenic DNA sequences to classify pathogenic and disease-suppressive Streptomyces strains. Appl Environ Microbiol 62:3489–3493PubMedGoogle Scholar
  45. Sait M, Hugenholtz P, Janssen PH (2002) Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivation-independent surveys. Environ Microbiol 4:654–666CrossRefPubMedGoogle Scholar
  46. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425PubMedGoogle Scholar
  47. Schaal KP (1977) Nocardia, Actinomadura and Streptomyces. In: CRC handbook series in clinical laboratory science, section E, clinical microbiology. CRC Press, Cleveland, OH, pp 131–158Google Scholar
  48. Shirling EB, Gottlieb D (1966) Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16:313–340Google Scholar
  49. Stach JEM, Maldonado LA, Ward AC, Goodfellow M, Bull AT (2003a) Statistical approaches to estimating bacterial diversity in marine sediments. Appl Environ Microbiol 69:6189–6200CrossRefPubMedGoogle Scholar
  50. Stach JEM, Maldonado LA, Ward AC, Goodfellow M, Bull AT (2003b) New primers for the class Actinobacteria: application to marine and terrestrial environments. Environ Microbiol 5:828–841CrossRefPubMedGoogle Scholar
  51. Taira K, Kitagawa S, Yamashiro T, Yanagimoto D (2004) Deep and bottom currents in the Challenger Deep, Mariana trench, measured with super-deep current meters. J Oceanogr 60:919–926CrossRefGoogle Scholar
  52. Takami H, Inoue A, Fuji F, Horikoshi K (1997) Microbial flora in the deepest sea mud of the Mariana Trench. FEMS Microbiol Lett 152:279–285PubMedGoogle Scholar
  53. Takizawa M, Colwell ER, Hill RT (1993) Isolation and diversity of actinomycetes in Chesapeake Bay. Appl Environ Microbiol 59:997–1002PubMedGoogle Scholar
  54. Van der Peer Y, de Wachter R (1994) TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. Comput Appl Biosci 10:569–570PubMedGoogle Scholar
  55. Versalovic J, Schneider M, de Bruijn FJ, Lupski JR (1994) Genomic fingerprinting of bacteria using repetitive sequence-based polymerase chain reaction. Methods Mol Cell Biol 5:25–40Google Scholar
  56. Vickers JC, Williams ST, Ross GW (1984) A taxonomic approach to selective isolation of streptomycetes from soil. In: Ortiz–Ortiz L, Bojalil LF, Yakoleff V (eds) Biological, biochemical and biomedical aspects of actinomycetes. Academic Press, Orlando, pp 553–561Google Scholar
  57. Ward JH (1963) Hierarchical grouping to optimise an objective function. J Am Statist Assoc 58:236–244Google Scholar
  58. Weyland H (1981) Distribution of actinomycetes on the sea floor. Actinomycetes. Zbl Bakt 11(Suppl):185–193Google Scholar
  59. Yamamura H, Hayakawa M, Nakagawa Y, Iimura Y (2004) Characterization of Nocardia asteroides isolates from different ecological habitats on the basis of repetitive extragenic palindromic-PCR fingerprinting. Appl Environ Microbiol 70:3149–3151CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag 2006

Authors and Affiliations

  • Wasu Pathom-aree
    • 1
    • 4
    Email author
  • James E. M. Stach
    • 1
  • Alan C. Ward
    • 1
  • Koki Horikoshi
    • 2
  • Alan T. Bull
    • 3
  • Michael Goodfellow
    • 1
  1. 1.Division of Biology, Faculty of Science, Agriculture and EngineeringUniversity of NewcastleNewcastle upon TyneUK
  2. 2.The DEEPSTAR GroupJapan Marine Science and Technology Center (JAMSTEC)YokosukaJapan
  3. 3.Research School of BiosciencesUniversity of KentCanterburyUK
  4. 4.Department of Biology, Faculty of ScienceChiang Mai UniversityChiang MaiThailand

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