Antonie van Leeuwenhoek

, Volume 94, Issue 1, pp 51–62

An assessment of actinobacterial diversity in the marine environment

Original Paper


The 16S rRNA gene sequence diversity within the Phylum Actinobacteria was assessed from four sources: PCR-generated V6 sequence tags derived from seawater samples, metagenomic data from the Global Ocean Sampling (GOS) expedition, marine-derived sequences maintained in the Ribosomal Database Project (RDP), and select cultured strains for which sequence data is not yet available in the RDP. This meta-analysis revealed remarkable levels of phylogenetic diversity and confirms the existence of major, deeply rooted, and as of yet uncharacterized lineages within the phylum. A dramatic incongruence among cultured strains and those detected using culture-independent techniques was also revealed. Redundancy among the actinobacteria detected using culture-independent techniques suggests that greater sequence coverage or improved DNA extraction efficiencies may be required to detect the rare phylotypes that can be readily cultured from marine samples. Conversely, new strategies need to be developed for the cultivation of frequently observed but yet to be cultured marine actinobacteria.


Marine actinobacteria Bacterial diversity Metagenomics Actinomycetes 


  1. Bérdy J (2005) Bioactive microbial metabolites. J Antibiot 58:1–26PubMedCrossRefGoogle Scholar
  2. Bull AT, Ward AC, Goodfellow M (2000) Search and discovery strategies for biotechnology: the paradigm shift. Microbiol Mol Biol Rev 64: 573–606PubMedCrossRefGoogle Scholar
  3. Fuhrman JA, McCallum K, Davis AA (1993) Phylogenetic diversity of subsurface marine microbial communities from the Atlantic and Pacific Oceans. Appl Environ Microbiol 59:1294–1302PubMedGoogle Scholar
  4. Giovanonni SJ, Stingl U (2005) Molecular diversity and ecology of microbial plankton. Nature 437:343–348CrossRefGoogle Scholar
  5. Gontang EA, Fenical W, Jensen PR (2007) Phylogenetic diversity of Gram-positive bacteria cultured from marine sediments. Appl Environ Microbiol 73:3272–3282PubMedCrossRefGoogle Scholar
  6. 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, Inc., Orlando, pp 453–472Google Scholar
  7. Grein A, Meyers SP (1958) Growth characteristics and antibiotic production of actinomycetes isolated from littoral sediments and materials suspended in sea water. J Bacteriol 76:457–463PubMedGoogle Scholar
  8. Han SK, Nedashkovzkaya OI, Mikhailov VV, Kim SB, Bae KS (2003) Salinibacterium amurkyense gen. nov., sp. nov., a novel genus of the family Microbacteriaceae from the marine environment. Int J Syst Evol Microbiol 53:2061–2066PubMedCrossRefGoogle Scholar
  9. Helmke E, Weyland H (1984) Rhodococcus marinonascens sp. nov., an actinomycete from the sea. Int J Syst Bacteriol 34:127–138CrossRefGoogle Scholar
  10. Hentschel U, Hopke J, Horn M, Friedrich AB, Wagner M, Hacker J, Moore BS (2002) Molecular evidence for a uniform microbial community in sponges from different oceans. Appl Environ Microbiol 68:4431–4440PubMedCrossRefGoogle Scholar
  11. Huber JA, Johnson HP, Butterfield DA, Baross JA (2006) Microbial life in ridge flank crustal fluids. Environ Microbiol 8:88–99PubMedCrossRefGoogle Scholar
  12. Huber JA, Welch DBM, Morrison HG, Huse SM, Neal PR, Butterfield DA, Sogin ML (2007) Microbial population structures in the deep marine biosphere. Science 318:97–100PubMedCrossRefGoogle Scholar
  13. Jensen PR, Dwight R, Fenical W (1991) Distribution of actinomycetes in near-shore tropical marine sediments. Appl Environ Microbiol 57:1102–1108PubMedGoogle Scholar
  14. Jensen PR, Gontang E, Mafnas C, Mincer TJ, Fenical W (2005) Culturable marine actinomycete diversity from tropical Pacific Ocean sediments. Environ Microbiol 7:1039–1048PubMedCrossRefGoogle Scholar
  15. Magarvey NA, Keller JM, Bernan V, Dworkin M, Sherman DH (2004) Isolation and characterization of novel marine-derived actinomycete taxa rich in bioactive metabolites. Appl Environ Microbiol 70:7520–7529PubMedCrossRefGoogle Scholar
  16. Maldonado L, Mincer TJ, Fenical W, Goodfellow M, Jensen PR, Ward AC (2005a) Salinispora gen nov., a home for obligate marine actinomycetes belonging to the family Micromonosporaceae. Int J Syst Evol Microbiol 55:1759–1766PubMedCrossRefGoogle Scholar
  17. Maldonado LA, Stach JEM, Pathom-aree W, Ward AC, Bull AT, Goodfellow M (2005b) Diversity of cultivable actinobacteria in geographically widespread marine sediments. Antonie van Leeuwenhoek 87:11–18PubMedCrossRefGoogle Scholar
  18. Mincer TJ, Jensen PR, Kauffman CA, Fenical W (2002) Widespread and persistent populations of a major new marine actinomycete taxon in ocean sediments. Appl Environ Microbiol 68:5005–5011PubMedCrossRefGoogle Scholar
  19. Mincer TJ, Fenical W, Jensen PR (2005) Cultured and culture-independent diversity within the obligate marine actinomycete genus Salinispora. Appl Environ Microbiol 71:7019–7028PubMedCrossRefGoogle Scholar
  20. Montalvo NF, Mohamed NM, Enticknap JJ, Hill RT (2005) Novel actinobacteria from marine sponges. Antonie van Leeuwenhoek 87:29–36PubMedCrossRefGoogle Scholar
  21. Moran MA, Rutherford LT, Hodson RE (1995) Evidence for indeginous Streptomyces populations in a marine environment determined with a 16S rRNA probe. Appl Environ Microbiol 61:3695–3700PubMedGoogle Scholar
  22. Penn K, Wu D, Eisen JA, Ward N (2006) Characterization of bacterial communities associated with deep-sea corals on the Gulf of Alaska seamounts. Appl Environ Microbiol 72:1680–1683PubMedCrossRefGoogle Scholar
  23. Prieto-Davo A, Fenical W, Jensen PR (accepted) Actinomycete diversity in marine sediments. Aquat Microbial EcolGoogle Scholar
  24. Rappé MS, Kemp PF, Giovannoni SJ (1997) Phylogenetic diversity of marine picoplankton 16S rRNA genes cloned from the continental shelf off Cape Hatteras, North Carolina. Limnol Oceanogr 42:811–826Google Scholar
  25. Rappé MS, Gordon DA, Vergin KL, Giovannoni SJ (1999) Phylogeny of Actinobacteria small subunit (SSU) rRNA gene clones recovered from marine bacterioplankton. Syst Appl Microbiol 22:106–112Google Scholar
  26. Rusch DB, Halpern AL, Sutton G et al (2007) The Sorcerer II global ocean sampling expedition: Northwest Atlantic through Eastern tropical Pacific. PLOS Biol 5:398–431CrossRefGoogle Scholar
  27. Sogin ML, Morrison HG, Huber JA, Welch DM, Huse SM, Neal PR, Arrieta JM, Herndi GJ (2006) Microbial diversity in the deep sea and the underexplored “rare biosphere”. Proc Natl Acad Sci 32:12115–12120CrossRefGoogle Scholar
  28. Stach JE, Maldonado LA, Masson DG, Ward AC, Goodfellow M, Bull AT (2003) Statistical approaches for estimating actinobacterial diversity in marine sediments. Appl Environ Microbiol 69:6189–6200PubMedCrossRefGoogle Scholar
  29. Swofford DL (2002) paup*. Phylogenetic analysis using parsimony (*and other methods), version 4. Sinauer Associates, Sunderland Google Scholar
  30. Takami H, Inoue A, Fuji F, Horikoshi K (1997) Microbial flora in the deepest sea mud of the Mariana T drench. FEMS Microbiol Lett 152:279–285PubMedCrossRefGoogle Scholar
  31. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882PubMedCrossRefGoogle Scholar
  32. Ward AC, Bora N (2006) Diversity and biogeography of marine actinobacteria. Curr Opin Microbiol 9:279–286PubMedCrossRefGoogle Scholar
  33. Weyland H (1969) Actinomycetes in North Sea and Atlantic Ocean sediments. Nature 223:858PubMedCrossRefGoogle Scholar
  34. Whitman WB, Coleman DC, Wiebe WJ (1998) Prokaryotes: the unseen majority. Proc Natl Acad Sci 95:6578–6583PubMedCrossRefGoogle Scholar
  35. Yi H, Schuman P, Sohn K, Chun J (2004) Serinicoccus marinus gen. nov., sp. nov., a novel actinomycete with L-ornithine and L-serine in the peptidoglycan. Int J Syst Evol Microbiol 54:1585–1589PubMedCrossRefGoogle Scholar
  36. Yooseph S, Sutton G, Rusch DB et al (2007) The Sorcerer II global ocean sampling expedition: expanding the universe of protein families. PLOS Biol 5:432–466CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2008

Authors and Affiliations

  1. 1.Scripps Institution of OceanographyUniversity of California San DiegoLa JollaUSA
  2. 2.Environmental Microbiology Initiative, School of Biotechnology and Biomolecular SciencesThe University of New South WalesSydneyAustralia

Personalised recommendations