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Streptomyces klenkii sp. nov., isolated from deep marine sediment

Abstract

A novel actinomycete strain, designated S2704T, was isolated from a deep sediment sample, collected from the southern Black Sea coast, Turkey and characterized using a polyphasic approach. Comparison of 16S rRNA gene sequences showed that strain S2704T is a member of the genus Streptomyces, exhibiting highest similarity with Streptomyces specialis GW 41-1564T (97.1 %). Strain S2704T could be distinguished from all other Streptomyces species with validly published names by sequence similarity values less than 97.0 %. The isolate was found to contain LL-diaminopimelic acid as the diagnostic diamino acid. Whole cell hydrolysates were found to contain glucose, mannose and ribose. The polar lipids were identified as diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylinositol, glycophospholipid, a phospholipid and two unknown glycolipids. The predominant menaquinones were identified as MK-9(H8) and MK-10(H6). The major fatty acids were found to be anteiso-C17:0, iso-C16:0 and anteiso-C15:0. The G+C content of the DNA was determined to be 72.2 mol%. On the basis of its phenotypic and molecular properties, strain S2704T is considered to be a novel species of the genus Streptomyces, for which the name Streptomyces klenkii sp. nov. is proposed. The type strain is S2704T (=DSM 42104T = KCTC 29202T).

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References

  • Chun J, Goodfellow M (1995) A phylogenetic analysis of the genus Nocardia with 16S rRNA gene sequences. Int J Syst Bacteriol 45:240–245

    CAS  PubMed  Article  Google Scholar 

  • Clement BG, Luther GWIII, Tebo BM (2009) Rapid, oxygen-dependent microbial Mn(II) oxidation kinetics at sub-micromolar oxygen concentrations in the Black Sea suboxic zone. Geochim Cosmochim Acta 73:1878–1889

    CAS  Article  Google Scholar 

  • Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376

    CAS  PubMed  Article  Google Scholar 

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

    Article  Google Scholar 

  • Fiedler HP, Brunner C, Bull AT, Ward AC, Goodfellow M, Mihm G (2005) Marine actinomycetes as a source of novel secondary metabolites. Antonie Van Leeuwenhoek 87(1):37–42

    CAS  PubMed  Article  Google Scholar 

  • Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416

    Article  Google Scholar 

  • Gonzalez JM, Saiz-Jimenez C (2005) A simple fluorimetric method for the estimation of DNA–DNA relatedness between closely related microorganisms by thermal denaturation temperatures. Extremophiles 9:75–79

    CAS  PubMed  Article  Google Scholar 

  • Hasegawa T, Takizawa M, Tanida S (1983) A rapid analysis for chemical grouping of aerobic Actinomycetes. J Gen Appl Microbiol 29:319–322

    CAS  Article  Google Scholar 

  • Jensen PR, Mincer TJ, Williams PG, Fenical W (2005) Marine actinomycete diversity and natural product discovery. Antonie Van Leeuwenhoek 87(1):43–48

    CAS  PubMed  Article  Google Scholar 

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

    CAS  PubMed Central  PubMed  Google Scholar 

  • Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro HN (ed) Mammalian protein metabolism, vol vol. 3. Academic Press, New York, pp 21–132

    Chapter  Google Scholar 

  • Kämpfer P, Kroppenstedt RM (1996) Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 42:989–1005

    Article  Google Scholar 

  • Kelly KL (1964) Inter-Society Color Council-National Bureau of Standards color-name charts illustrated with centroid colors published in US

  • Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, Park SC, Jeon YS, Lee JH, Yi H, Won S, Chun J (2012) Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62:716–721

    CAS  PubMed  Article  Google Scholar 

  • Kluge AG, Farris FS (1969) Quantitative phyletics and the evolution of anurans. Syst Zool 18:1–32

    Article  Google Scholar 

  • Kuypers MMM, Sliekers AO, Lavik G, Schmid M, Jørgensen BB, Sinninghe Damsté JS et al (2003) Anaerobic ammonium oxidation by anammox bacteria in the Black Sea. Nature 422:608–611

    CAS  PubMed  Article  Google Scholar 

  • Lam P, Jensen MM, Lavik G, McGinnis DF, Müller B, Schubert CJ et al (2007) Linking crenarchaeal and bacterial nitrification to anammox in the Black Sea. Proc Natl Acad Sci USA 104:7104–7109

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  • Lechevalier MP, De Bièvre C, Lechevalier HA (1977) Chemotaxonomy of aerobic actinomycetes: phospholipid composition. Biochem Syst Ecol 5:249–260

    CAS  Article  Google Scholar 

  • Manske AK, Glaeser J, Kuypers MM, Overmann J (2005) Physiology and phylogeny of green sulfur bacteria forming a monospecific phototrophic assemblage at a depth of 100 m in the Black Sea. Appl Environ Microbiol 71:8049–8060

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  • Murray JW, Codispoti LA, Friedrich GE (1995) Oxidation-reduction environments: the suboxic zone in the Black Sea. In Aquatic Chemistry: interfacial and interspecies processes ACS advances in chemistry series, Oxford University Press, New York, 244: 157–176

  • Nash P, Krent MM (1991) Culture media. In: Ballows A, Hauser WJ, Herrmann KL, Isenberg HD, Shadomy HJ (eds) Manual Of Clinical Microbiology, 5th edn. American Society for Microbiology, Washington DC, pp 1268–1270

    Google Scholar 

  • Oakley BO, Francis CA, Roberts KJ, Fuchsman CA, Srinivasan S, Staley JT (2007) Analysis of nitrite reductase (nirK and nirS) genes and cultivation reveal depauperate community of denitrifying bacteria unique to the Black Sea suboxic zone. Environ Microbiol 9:118–130

    CAS  PubMed  Article  Google Scholar 

  • Saitou N, Nei M (1987) The neighbor-joining method. A new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    CAS  PubMed  Google Scholar 

  • Sanglier JJ, Whitehead D, Saddler GS, Ferguson EV, Goodfellow M (1992) Pyrolisis mass spectrometry as a method for the classification, identification and selection of actinomycetes. Gene 115:235–242

    CAS  PubMed  Article  Google Scholar 

  • Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. Technical Note 101. Newark, DE: MIDI Inc

  • Shirling EB, Gottlieb D (1966) Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16:313–340

    Article  Google Scholar 

  • Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Bio Evol 28:2731–2739

    CAS  Article  Google Scholar 

  • Tindall BJ (1990a) A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 13:128–130

    CAS  Article  Google Scholar 

  • Tindall BJ (1990b) Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 66:199–202

    CAS  Article  Google Scholar 

  • Veyisoglu A, Sahin N (2014) Streptomyces hoynatensis sp. nov., isolated from deep marine sediment. Int J Syst Evol Microbiol 64:819–826

    CAS  PubMed  Article  Google Scholar 

  • Veyisoglu A, Sazak A, Cetin D, Guven K, Sahin N (2013) Saccharomonospora amisosensis sp. nov., isolated from Black Sea deep sediment. Int J Syst Evol Microbiol 63:3782–3786

    CAS  PubMed  Article  Google Scholar 

  • Waksman SA (1967) The Actinomycetes A Summary of Current Knowledge. Ronald Press, New York

    Google Scholar 

  • Williams ST, Goodfellow M, Alderson G, Wellington EMH, Sneath PHA, Sackin MJ (1983) Numerical classification of Streptomyces and related genera. J Gen Microbiol 129:1743–1813

    CAS  PubMed  Google Scholar 

  • Xu Y, He J, Tian XP, Li J, Yang LL, Xie Q, Tang SK, Chen YG, Zhang S, Li WJ (2012) Streptomyces glycovorans sp. nov., Streptomyces xishensis sp. nov. and Streptomyces abyssalis sp. nov., isolated from marine sediments. Int J Syst Evol Microbiol 62:2371–2377

    CAS  PubMed  Article  Google Scholar 

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Acknowledgments

This research was supported by Ondokuz Mayis University (OMU), project no. PYO. FEN. 1901.12.014.

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Correspondence to Nevzat Sahin.

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Veyisoglu, A., Sahin, N. Streptomyces klenkii sp. nov., isolated from deep marine sediment. Antonie van Leeuwenhoek 107, 273–279 (2015). https://doi.org/10.1007/s10482-014-0325-y

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  • DOI: https://doi.org/10.1007/s10482-014-0325-y

Keywords

  • Streptomycetaceae
  • Streptomyces klenkii
  • Polyphasic taxonomy
  • Southern Black Sea coast