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Diversity of cultivable actinobacteria in geographically widespread marine sediments

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Abstract

Reports describing actinobacteria isolated from marine environments have been dominated by Micromonospora, Rhodococcus and Streptomyces species. Recent culture-independent studies have shown that marine environments contain a high diversity of actinobacterial species that are rarely, if at all, recovered by cultivation-based methods. In this study, it is shown that cultivation-independent methods can be used to guide the application of selective isolation methods. The detection of marine-derived actinobacterial species that have previously only been reported from terrestrial habitats is highlighted. This study provides good evidence that the previously described low diversity of actinobacterial species isolated from marine environments does not reflect an actual low species diversity, and that the use of informed selective isolation procedures can aid in the isolation of members of novel taxa.

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References

  • E. Atalan G.P. Manfio A.C. Ward R.M. Kroppenstedt M. Goodfellow (2000) ArticleTitleBiosystematic studies on novel streptomycetes from soil Antonie van Leeuwenhoek 77 337–353 Occurrence Handle1:CAS:528:DC%2BD3cXmsVSksb0%3D Occurrence Handle10959563

    CAS  PubMed  Google Scholar 

  • M. Athalye J. Lacey M. Goodfellow (1981) ArticleTitleSelective isolation and enumeration of actinomycetes using rifampicin J. Appl. Microbiol. 51 289–297 Occurrence Handle1:CAS:528:DyaL3MXmtVSntbc%3D

    CAS  Google Scholar 

  • M. Banerjee B.A. Whitton D.D. Wynn-Williams (2000) ArticleTitlePhosphatase activities of endolithic communities in rocks of the Antarctic Dry Valleys Microbial. Ecol. 39 80–91 Occurrence Handle1:CAS:528:DC%2BD3cXjsFehsrg%3D

    CAS  Google Scholar 

  • J.A. Breznak (2004) Invertebrates-insects A.T. Bull (Eds) Microbial Diversity and Bioprospecting ASM Press Washington, DC 191–203

    Google Scholar 

  • A.T. Bull (Eds) (2004) Microbial Diversity and Bioprospecting ASM Press Washington, DC 1–496

    Google Scholar 

  • A.T. Bull A.C. Ward M. Goodfellow (2000) ArticleTitleSearch and discovery strategies for biotechnology: the paradigm shift Microbiol. Mol. Biol. Rev. 64 573–606 Occurrence Handle1:CAS:528:DC%2BD3cXntVCgtL8%3D Occurrence Handle10974127

    CAS  PubMed  Google Scholar 

  • F.H. Chapelle K. O’Neill P.M. Bradley B.A. Methe S.A. Ciufo L.L. Knobel D.R. Lovley (2002) ArticleTitleA hydrogen-based subsurface microbial community dominated by methanogens Nature 415 312–315 Occurrence Handle10.1038/415312a Occurrence Handle11797006

    Article  PubMed  Google Scholar 

  • J. Chun M. Goodfellow (1995) ArticleTitleA phylogenetic analysis of the genus Nocardia with 16S rRNA gene sequences Int. J. Syst. Bacteriol. 45 240–245 Occurrence Handle1:CAS:528:DyaK2MXmtFWhsr0%3D Occurrence Handle7537058

    CAS  PubMed  Google Scholar 

  • J.A. Colquhoun J. Mexson M. Goodfellow A.C. Ward K. Horikoshi A.T. Bull (1998) ArticleTitleNovel rhodococci and other mycolate actinomycetes from the deep sea Antonie van Leeuwenhoek 74 27–40 Occurrence Handle1:STN:280:DyaK1M7msl2isw%3D%3D Occurrence Handle10068786

    CAS  PubMed  Google Scholar 

  • J. Felsenstein (1985) ArticleTitleConfidence limits on phylogenies: an approach using the bootstrap Evolution 39 783–791

    Google Scholar 

  • J. Felsenstein (1993) PHYLIP (phylogenetic inference package) Department of Genetics, University of Washington SeattleUSA

    Google Scholar 

  • H.-P. Fiedler C. Bruntner A.T. Bull A.C. Ward M. Goodfellow G. Mihm (2004) ArticleTitleMarine actinomycetes as a source of novel secondary metabolites Antonie van Leeuwenhoek 87 37–42

    Google Scholar 

  • M. Goodfellow J.A. Haynes (1984) Actinomycetes in marine sediments L. Ortiz-Ortiz L.F. Bojalil V. Yakoleff (Eds) Biological, Biochemical and Biomedical Aspects of Actinomycetes Academic Press Orlando 453–472

    Google Scholar 

  • M. Goodfellow S.T. Williams M. Mordarski (Eds) (1988) Actinomycetes in Biotechnology Academic Press Ltd London 1–501

    Google Scholar 

  • R.E. Gordon J.M. Mihm (1962) ArticleTitleIdentification of Nocardia caviae (Erikson) nov. comb Ann. N.Y. Acad. Sci. 98 628–636

    Google Scholar 

  • M. Hayakawa H. Nonomura (1987) ArticleTitleHumic-acid vitamins agara new medium for the selective isolation of soil actinomycetes J. Ferm. Tech. 65 501–509 Occurrence Handle1:CAS:528:DyaL1cXjtlKi

    CAS  Google Scholar 

  • R.T. Hill (2004) Microbes from marine sponges: a treasure trove of biodiversity for natural products AT. Bull (Eds) Microbial Diversity and Bioprospecting ASM Press Washington, DC 191–203

    Google Scholar 

  • P. Hirsch U. Mevs R.M. Kroppenstedt P. Schumann E. Stackebrandt (2004) ArticleTitleCryptoendolithic actinomycetes from antarctic sandstone rock samples: Micromonospora endolithica sp. nov. and two isolates related to Micromonospora coerulea Jensen 1932 Syst. Appl. Microbiol. 27 166–174 Occurrence Handle1:CAS:528:DC%2BD2cXjsFemtr0%3D Occurrence Handle15046305

    CAS  PubMed  Google Scholar 

  • D.W. Hopkins S.J. MacNaughton A.G. O Donnell (1991) ArticleTitleA dispersion and differential centrifugation technique for representatively sampling microorganisms from soil Soil Biol. Biochem. 23 217–225

    Google Scholar 

  • K.L. Jones (1949) ArticleTitleFresh isolates of actinomycetes in which the presence of sporogenous aerial mycelia is a fluctuating characteristic J. Bacteriol. 57 141–145

    Google Scholar 

  • T.H. Jukes C.R. Cantor (1969) Evolution of protein molecules H.N. Munro (Eds) Mammalian Protein MetabolismVol. 3 Academic Press New York 21–132

    Google Scholar 

  • J.K. Kristijanson G.O. Hreggvidson W.D. Grant (2000) Taxonomy of extremophiles F.G. Priest M. Goodfellow (Eds) Applied Microbial Systematics Kluwer Academic Publishers Dordrecht 231–291

    Google Scholar 

  • L.R. Krumholz (2000) ArticleTitleMicrobial communities in the deep sea subsurface Hydrogeol. J. 8 4–10

    Google Scholar 

  • E. Küster (1959) ArticleTitleOutline of a comparative study of criteria used in characterization of the actinomycetes Int. Bull. Bact. Nom. Tax. 9 97–104

    Google Scholar 

  • E. Küster S.T. Williams (1964) ArticleTitleSelective media for isolation of streptomycetes Nature 202 928–929

    Google Scholar 

  • D.J. Lane (1991) 16S/23S rRNA sequencing E. Stackebrandt M. Goodfellow (Eds) Nucleic Acid Techniques in Bacterial Systematics John Wiley and Sons ChichesterUnited Kingdom 115–175

    Google Scholar 

  • H.P. McVeigh M. Divers S. Warwick J. Munro T.M. Embley (1994) ArticleTitleExploration of actinomycete diversity using ribosomal RNA sequences Biotechnologia 7–8 253–260

    Google Scholar 

  • T.J. Mincer P.R. Jensen C.A. Kauffman W. Fenical (2002) ArticleTitleWidespread and persistent populations of a major new marine actinomycete taxon in ocean sediments Appl. Env. Microbiol. 68 5005–5011 Occurrence Handle1:CAS:528:DC%2BD38XnvFClurY%3D

    CAS  Google Scholar 

  • P. Monciardini M. Sosio L. Cavaletti C. Chiocchini S. Donadio (2002) ArticleTitleNew PCR primers for the selective amplification of 16S rDNA from different groups of actinomycetes FEMS Microb. Ecol. 42 419–429 Occurrence Handle1:CAS:528:DC%2BD38XoslGiur8%3D

    CAS  Google Scholar 

  • R. Morón I. Gonzalez O. Genilloud (1999) ArticleTitleNew genus-specific primers for the PCR identification of members of the genera Pseudonocardia Saccharopolyspora Int. J. Syst. Bacteriol. 49 149–162 Occurrence Handle10028256

    PubMed  Google Scholar 

  • R.J. Parkes P. Wellsbury (2004) Deep biospheres A.T. Bull (Eds) Microbial Diversity and Bioprospecting ASM Press Washington, DC 120–129

    Google Scholar 

  • M.A. Pisano M.J. Sommer L. Brancaccio (1989) ArticleTitleIsolation of bioactive actinomycetes from marine sediments using rifampicin Appl. Microbiol. Biotechnol. 31 609–612 Occurrence Handle1:CAS:528:DyaL1MXmtFWltrc%3D

    CAS  Google Scholar 

  • T.J. Rowbotham T. Cross (1977) ArticleTitleEcology of Rhodococcus coprophilusassociated actinomycetes in freshwater and agricultural habitats J. Gen. Microbiol. 100 231–240

    Google Scholar 

  • N. Saitou M. Nei (1987) ArticleTitleThe neighbor-joining method: a new method for reconstructing phylogenetic trees Mol. Biol. Evol. 4 406–425 Occurrence Handle1:STN:280:DyaL1c7ovFSjsA%3D%3D Occurrence Handle3447015

    CAS  PubMed  Google Scholar 

  • L. Sembiring A.C. Ward M. Goodfellow (2000) ArticleTitleSelective isolation and characterisation of members of the Streptomyces violaceusniger clade associated with the roots of Paraserianthes falcataria Antonie van Leeuwenhoek 78 353–366 Occurrence Handle1:CAS:528:DC%2BD3MXktVOgsro%3D Occurrence Handle11386358

    CAS  PubMed  Google Scholar 

  • J.E. Stach L.A. Maldonado D.G. Masson A.C. Ward M. Goodfellow A.T. Bull (2003a) ArticleTitleStatistical approaches to estimating bacterial diversity in marine sediments Appl. Env. Microbiol. 69 6189–6200 Occurrence Handle1:CAS:528:DC%2BD3sXotlKjsLo%3D

    CAS  Google Scholar 

  • J.E. Stach L.A. Maldonado A.C. Ward M. Goodfellow A.T. Bull (2003b) ArticleTitleNew primers for the class Actinobacteria: application to marine and terrestrial environments Env. Microbiol. 5 828–841 Occurrence Handle1:CAS:528:DC%2BD3sXos1Clt7c%3D

    CAS  Google Scholar 

  • E. Stackebrandt F.A. Rainey N.L. Ward-Rainey (1997) ArticleTitleProposal for a new hierarchic classification systemActinobacteria classis nov Int. J. Syst. Bacteriol. 47 479–491 Occurrence Handle10.1099/00207713-47-2-479

    Article  Google Scholar 

  • T.O. Stevens J.P. McKinley (1995) ArticleTitleLithotrophic microbial ecosystems in deep basalt aquifers Science 270 450–454 Occurrence Handle1:CAS:528:DyaK2MXovVersLw%3D

    CAS  Google Scholar 

  • G.Y.A. Tan (2002) Amycolatopsis Systematics: A New Beginning University of Newcastle upon TyneNewcastle upon Tyne UK

    Google Scholar 

  • A. Teske K.U. Hinrichs V. Edgcomb A.D. Gomez D. Kysela S.P. Sylva M.L. Sogin H.W. Jannasch (2002) ArticleTitleMicrobial diversity of hydrothermal sediments in the Guaymas Basin: evidence for anaerobic methanotrophic communities Appl. Env. Microbiol. 68 1994–2007 Occurrence Handle1:CAS:528:DC%2BD38XivFGlu7Y%3D

    CAS  Google Scholar 

  • J.D. Thompson T.J. Gibson F. Plewniak F. Jeanmougin D.G. Higgins (1997) ArticleTitleThe CLUSTAL X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools Nucleic Acids Res. 25 4876–4882 Occurrence Handle1:CAS:528:DyaK1cXntFyntQ%3D%3D Occurrence Handle9396791

    CAS  PubMed  Google Scholar 

  • J.C. Vickers S.T. Williams G.W. Ross (1984) A taxonomic approach to selective isolation of streptomycetes from soil L. Ortiz-Ortiz L.F. Bojalil V. Yakoleff (Eds) Biological, Biochemical and Biomedical Aspects of Actinomycetes Academic Press London 553–551

    Google Scholar 

  • H. Weyland (1969) ArticleTitleActinomycetes in North Sea and Atlantic Ocean sediment Nature 223 858 Occurrence Handle1:STN:280:DyaF1M3lt1Kiug%3D%3D Occurrence Handle5799036

    CAS  PubMed  Google Scholar 

  • H. Weyland (1981) ArticleTitleDistribution of actinomycetes on the sea floor Zentral Bakteriol. supp. 11 185–193

    Google Scholar 

  • W.B. Whitman D.C. Coleman W.J. Wiebe (1998) ArticleTitleProkaryotes: the unseen majority Proc. Nat. Acad. Sci. USA 95 6578–6583 Occurrence Handle1:CAS:528:DyaK1cXjslyntro%3D Occurrence Handle9618454

    CAS  PubMed  Google Scholar 

  • K. Zengler G. Toledo M. Rappe J. Elkins E.J. Mathur J.M. Short M. Keller (2002) ArticleTitleCultivating the uncultured Proc. Nat. Acad. Sci. USA 99 15681–15686 Occurrence Handle1:CAS:528:DC%2BD3sXjvFSh Occurrence Handle12438682

    CAS  PubMed  Google Scholar 

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Correspondence to Luis A. Maldonado.

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Maldonado, L.A., Stach, J. ., Pathom-aree, W. et al. Diversity of cultivable actinobacteria in geographically widespread marine sediments. Antonie Van Leeuwenhoek 87, 11–18 (2005). https://doi.org/10.1007/s10482-004-6525-0

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  • DOI: https://doi.org/10.1007/s10482-004-6525-0

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