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Estimating and comparing the diversity of marine actinobacteria

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Abstract

This paper reviews the application of species richness estimators to microbial diversity data and describes phylogenetic approaches to comparing microbial communities. The techniques are demonstrated using a community of marine actinobacteria. Results demonstrate that marine environments harbour massive actinobacterial diversity. Furthermore, these predictions are likely to be severe underestimates due to the use of arbitrary OTU definitions.

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References

  • R. Amann W. Ludwig K.-H. Schleifer (1994) ArticleTitleIdentification of uncultured bacteria: a challenging task for molecular taxonomists ASM News 60 360–365

    Google Scholar 

  • Bull A.T., Stach J.E.M., Ward A.C. and Goodfellow M. 2004. Marine Actinobacteria: perspectives, challenges, future directions. Antonie Van Leeuwenhoek (this issue).

  • A. Chao (1987) ArticleTitleEstimating the population-size for capture recapture data with unequal catchability Biometrics 43 783–791 Occurrence Handle1:STN:280:DyaL1c7gsl2qsw%3D%3D Occurrence Handle3427163

    CAS  PubMed  Google Scholar 

  • A. Chao S.M. Lee (1992) ArticleTitleEstimating the number of classes via sample coverage J. Am. Stat. Assoc. 87 210–217

    Google Scholar 

  • J.R. Cole B. Chai T.L. Marsh R.J. Farris Q. Wang S.A. Kulam S. Chandra D.M. McGarrell T.M. Schmidt G.M. Garrity J.M. Tiedje (2003) ArticleTitleThe Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy Nucleic Acids Res. 31 442–443 Occurrence Handle1:CAS:528:DC%2BD3sXhvFSls7o%3D Occurrence Handle12520046

    CAS  PubMed  Google Scholar 

  • T.P. Curtis W.T. Sloan J.W. Scannell (2002) ArticleTitleEstimating prokaryotic diversity and its limits Proc. Natl. Acad. Sci. USA 99 10494–10499 Occurrence Handle1:CAS:528:DC%2BD38Xmt1Chsrc%3D Occurrence Handle12097644

    CAS  PubMed  Google Scholar 

  • J. Dunbar S.M. Barns L.O. Ticknor C.R. Kuske (2002) ArticleTitleEmpirical and theoretical bacterial diversity in four Arizona soils Appl. Environ. Microbiol. 68 3035–3045 Occurrence Handle1:CAS:528:DC%2BD38XksVWqt7k%3D Occurrence Handle12039765

    CAS  PubMed  Google Scholar 

  • W. Fenical D. Baden M. Burg C.V. de Goyet J.D. Grimes M. Katz N.H. Marcus S. Pomponi P. Rhines P. Tester J. Vena (1999) Marine-derived pharmaceuticals and related bioactive compounds W. Fenical (Eds) From Monsoons to Microbes: Understanding the Ocean’s Role in Human Health National Academies Press Washington, DC

    Google Scholar 

  • Fiedler H.-P., Brunner C., Bull A.T., Ward A.C., Goodfellow M. and Mihm G. 2004. Marine actinomycetes as a source of novel secondary metabolites. Antonie Van Leeuwenhoek (This issue).

  • H. Heuer M. Krsek P. Baker K. Smalla E.M.H. Wellington (1997) ArticleTitleAnalysis of actinomycete communities by specific amplification of genes encoding 16S rRNA and gel-electrophoretic separation in denaturing gradients Appl. Environ. Microbiol. 63 3233–3241 Occurrence Handle1:CAS:528:DyaK2sXlt1Wis7c%3D Occurrence Handle9251210

    CAS  PubMed  Google Scholar 

  • J.B. Hughes J.J. Hellmann T.H. Ricketts B.J.M. Bohannan (2001) ArticleTitleCounting the uncountable: Statistical approaches to estimating microbial diversity Appl. Environ. Microbiol. 67 4399–4406 Occurrence Handle1:CAS:528:DC%2BD3MXns1Wisro%3D Occurrence Handle11571135

    CAS  PubMed  Google Scholar 

  • Jensen P.R., Mincer T.J., Williams P.G. and Fenical W. 2004. Marine actinomycete diversity and natural product discovery. Antonie Van Leeuwenhoek (This issue).

  • J. Keswani W.B. Whitman (2001) ArticleTitleRelationship of 16S rRNA sequence similarity to DNA hybridization in prokaryotes Int. J. Syst. Evol. Microbiol. 51 667–678 Occurrence Handle1:CAS:528:DC%2BD3MXivVOru7g%3D Occurrence Handle11321113

    CAS  PubMed  Google Scholar 

  • R. Lande P.J. DeVries T.R. Walla (2000) ArticleTitleWhen species accumulation curves intersect: implications for ranking diversity using small samples Oikos 89 601–605 Occurrence Handle10.1034/j.1600-0706.2000.890320.x

    Article  Google Scholar 

  • A. Lazzarini L. Cavaletti G. Toppo F. Marinelli (2000) ArticleTitleRare genera of actinomycetes as potential producers of new antibiotics Antonie van Leeuwenhoek 78 399–405 Occurrence Handle1:CAS:528:DC%2BD3MXktVOgs70%3D Occurrence Handle11386363

    CAS  PubMed  Google Scholar 

  • A.P. Martin (2002) ArticleTitlePhylogenetic approaches for describing and comparing the diversity of microbial communities Appl. Environ. Microbiol. 68 3673–3682 Occurrence Handle1:CAS:528:DC%2BD38XmtVaqtLY%3D Occurrence Handle12147459

    CAS  PubMed  Google Scholar 

  • H.P. McVeigh J. Munro T.M. Embley (1996) ArticleTitleMolecular evidence for the presence of novel actinomycete lineages in a temperate forest soil J. Ind. Microbiol. 17 197–204 Occurrence Handle1:CAS:528:DyaK2sXltF2jtw%3D%3D

    CAS  Google Scholar 

  • D.N. Miller J.E. Bryant E.L. Madsen W.C. Ghiorse (1999) ArticleTitleEvaluation and optimization of DNA extraction and purification procedures for soil and sediment samples Appl. Environ. Microbiol. 65 4715–4724 Occurrence Handle1:CAS:528:DyaK1MXnt1WmtrY%3D Occurrence Handle10543776

    CAS  PubMed  Google Scholar 

  • T. Palys L.K. Nakamura F.M. Cohan (1997) ArticleTitleDiscovery and classification of ecological diversity in the bacterial world: the role of DNA sequence data Int. J. Syst. Bacteriol. 47 1145–1156 Occurrence Handle1:CAS:528:DyaK2sXntV2qurg%3D Occurrence Handle9336922

    CAS  PubMed  Google Scholar 

  • L. Ranjard D.P.H. Lejon C. Mougel L. Schehrer D. Merdinoglu R. Chassod (2003) ArticleTitleSampling strategy in molecular microbial ecology: influence of soil sample size on DNA fingerprinting analysis of fungal and bacterial communities Environ. Microbiol. 5 1111–1120 Occurrence Handle1:CAS:528:DC%2BD3sXpslGht70%3D Occurrence Handle14641591

    CAS  PubMed  Google Scholar 

  • J.E.M. Stach S. Bathe J.P. Clapp R.G. Burns (2001) ArticleTitlePCR-SSCP comparison of 16S rDNA sequence diversity in soil DNA obtained using different isolation and purification methods FEMS Microbiol. Ecol. 36 139–151 Occurrence Handle1:CAS:528:DC%2BD3MXltVeisro%3D Occurrence Handle11451518

    CAS  PubMed  Google Scholar 

  • J.E.M. Stach R.G. Burns (2002) ArticleTitleEnrichment versus biofilm culture: a functional and phylogenetic comparison of polycyclic aromatic hydrocarbon-degrading microbial communities Environ. Microbiol. 4 169–182 Occurrence Handle12000317

    PubMed  Google Scholar 

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

    CAS  Google Scholar 

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

    CAS  Google Scholar 

  • E. Stackebrandt B.M. Goebel (1994) ArticleTitleTaxonomic note: a place for DNA–DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology Int. J. Syst. Bacteriol. 44 846–849 Occurrence Handle10.1099/00207713-44-4-846 Occurrence Handle1:CAS:528:DyaK2MXitFCnsb4%3D

    Article  CAS  Google Scholar 

  • F. von Wintzingerode U.B. Gobel E. Stackebrandt (1997) ArticleTitleDetermination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis FEMS Microbiol. Rev. 21 213–229 Occurrence Handle1:STN:280:DyaK1c7htlOqtw%3D%3D Occurrence Handle9451814

    CAS  PubMed  Google Scholar 

  • A.C. Ward M. Goodfellow (2004) Phylogeny and functionality – Taxonomy as a roadmap to genes A.T. Bull (Eds) Microbial Diversity and Bioprospecting ASM Press Washington, DC 288–313

    Google Scholar 

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Authors and Affiliations

  1. Research school of Biosciences, University of Kent, Canterbury, CT1 7NJ, Kent, UK

    E.M. Stach & Alan T. Bull

  2. Institute for Research on Environment and Sustainability, School of Biology, Devonshire Building, University of Newcastle, Newcastle upon Tyne, NE1 7RU, UK

    E.M. Stach

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  1. E.M. Stach
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  2. Alan T. Bull
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Correspondence to E.M. Stach.

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Stach, E., Bull, A.T. Estimating and comparing the diversity of marine actinobacteria. Antonie Van Leeuwenhoek 87, 3–9 (2005). https://doi.org/10.1007/s10482-004-6524-1

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  • DOI: https://doi.org/10.1007/s10482-004-6524-1

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