Skip to main content

Streptomyces xiaopingdaonensis sp. nov., a novel marine actinomycete isolated from the sediment of Xiaopingdao in Dalian, China

Abstract

A novel streptomycete, designated as strain DUT 180T, was isolated from a marine sediment sample collected from a sea cucumber farm in Dalian, northeast China. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain DUT 180T is phylogenetically affiliated to the genus Streptomyces where it formed a distinct phyletic line with recognized Streptomyces species. Morphological and chemotaxonomic data also supported the affiliation of this isolate to the genus Streptomyces. Strain DUT 180T was found to exhibit highest sequence similarities of 99.52 and 99.36 % to Streptomyces halophytocola KLBMP 1284T and Streptomyces sulphureus NRRL B-1627T, respectively. However, strain DUT 180T could be distinguished from these two closest neighbours by a range of phenotypic properties. The DNA–DNA hybridization analyses between strain DUT 180T and the type strains of the phylogenetic neighbours revealed 54.8 ± 1.4 and 52.4 ± 2.8 % relatedness. Based on the phenotypic, chemotaxonomic and phylogenetic evidence, we suggest that the isolate DUT 180T represents a novel species of the genus Streptomyces, for which the name Streptomyces xiaopingdaonensis sp. nov. is proposed, with the type strain DUT 180T (= KCTC 29679T = CGMCC 4.7208T).

This is a preview of subscription content, access via your institution.

Fig. 1
Fig. 2

References

  • Bull AT, Stach JE (2007) Marine actinobacteria: new opportunities for natural product search and discovery. Trends Microbiol 15:491–499

    CAS  PubMed  Article  Google Scholar 

  • Collins MD, Pirouz T, Goodfellow M, Minnikin DE (1977) Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 100:221–230

    CAS  PubMed  Article  Google Scholar 

  • Embley T, Stackebrandt E (1994) The molecular phylogency and systematics of the actinomycetes. Annu Rev Microbiol 48:257–289

    CAS  PubMed  Article  Google Scholar 

  • Ezaki T, Hashimoto Y, Yabuuchi E (1989) Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 39:224–229

    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 phylogenies: an approach using the bootstrap. Evolution 39:783–791

    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 

  • Goodfellow M, Fiedler HP (2010) A guide to successful bioprospecting: informed by actinobacterial systematic. Antonie Van Leeuwenhoek 98:119–142

    PubMed  Article  Google Scholar 

  • Gordon RE, Barnett DA, Handerhan JE, Pang CHN (1974) Nocardia coeliaca, Nocardia autotrophica, and the nocardin strain. Int J Syst Bacteriol 24:54–63

    Article  Google Scholar 

  • Groth I, Schumann P, Rainey FA, Martin K, Schuetze B, Augsten K (1997) Demetria terragena gen. nov., sp. nov., a new genus of actinomycetes isolated from compost soil. Int J Syst Bacteriol 47:1129–1133

    CAS  PubMed  Article  Google Scholar 

  • He L, Li W, Huang Y, Wang L, Liu Z, Lanoot B, Vancanneyt M, Swings J (2005) Streptomyces jietaisiensis sp. nov., isolated from soil in northern China. Int J Syst Evol Microbiol 55:1939–1944

    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

  • Kelly KL (1964) Color-name charts illustrated with centroid colors. Inter-Society Color Council-National Bureau of Standards, Chicago

    Google Scholar 

  • 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 

  • Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120

    CAS  PubMed  Article  Google Scholar 

  • Labeda DP, Goodfellow M, Brown R, Ward AC, Lanoot B, Vanncanneyt M, Swings J, Kim SB, Liu Z, Chun J, Tamura T, Oguchi A, Kikuchi T, Kikuchi H, Nishii T, Tsuji K, Yamaguchi Y, Tase A, Takahashi M, Sakane T, Suzuki KI, Hatano K (2012) Phylogenetic study of the species within the family Streptomycetaceae. Antonie Van Leeuwenhoek 101:73–104

    CAS  PubMed  Article  Google Scholar 

  • Lechevalier MP, Lechevalier HA (1980) The chemotaxonomy of actinomycetes. In: Dietz A, Thayer DW (eds) Actinomycete taxonomy. Society for Industrial Microbiology, Arlington, pp 22–291

    Google Scholar 

  • Li WJ, Xu P, Schumann P, Zhang YQ, Pukall R, Xu LH, Stackebrandt E, Jiang CL (2007) Georgenia ruanii sp. nov., a novel actinobacterium isolated from forest soil in Yunnan (China) and emended description of the genus Georgenia. Int J Syst Evol Microbiol 57:1424–1428

    PubMed  Article  Google Scholar 

  • Marmur J (1961) A procedure for the isolation of deoxyribonucleic acid from microorganisms. J Mol Biol 3:208–218

    CAS  Article  Google Scholar 

  • Mesbah M, Premachandran U, Whitman WB (1989) Precise measurement of the G + C content of deoxyribonucleic acid by high performance liquid chromatography. Int J Syst Bacteriol 39:159–167

    CAS  Article  Google Scholar 

  • Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M, Schaal A, Parlett JK (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241

    CAS  Article  Google Scholar 

  • Newman DJ, Cragg GM (2012) Natural products as sources of new drugs over the 30 years from 1981 to 2010. J Nat Prod 75:311–335

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  • Parte AC (2014) LPSN—list of prokaryotic names with standing in nomenclature. Nucleic Acids Res 42(Database issue):D613–6

  • Phongsopitanun W, Thawai C, Suwanborirux K, Kudo T, Ohkuma M, Tanasupawat S (2014) Streptomyces chumphonensis sp. nov., isolated from marine sediments. Int J Syst Evol Microbiol 64:2605–2610

    CAS  PubMed  Article  Google Scholar 

  • Qin S, Bian GK, Tamura T, Zhang YJ, Zhang WD, Cao CL, Jiang JH (2013) Streptomyces halophytocola sp. nov., an endophytic actinomycete isolated from the surface-sterilized stems of a coastal halophyte Tamarix chinensis Lour. Int J Syst Evol Microbiol 63:2770–2775

    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 

  • Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids, MIDI technical note 101. MIDI Inc, Newark

    Google Scholar 

  • 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, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  • Tian XP, Xu Y, Zhang J, Li J, Chen Z, Kim CJ, Li WJ, Zhang CS, Zhang S (2012) Streptomyces oceani sp. nov., a new obligate marine actinomycete isolated from a deep-sea sample of seep authigenic carbonate nodule in South China Sea. Antonie Van Leeuwenhoek 102:335–343

    CAS  PubMed  Article  Google Scholar 

  • Waksman SA (1967) The actinomycetes. A summary of current knowledge. Ronald Press, New York

    Google Scholar 

  • Waksman SA, Henrici AT (1943) The nomenclature and classification of the actinomycetes. J Bacteriol 46:337–341

    CAS  PubMed Central  PubMed  Google Scholar 

  • Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE, Stackebrandt E, Starr MP, Trüper HG (1987) Report of the Ad Hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464

    Article  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 P, Li WJ, Tang SK, Zhang YQ, Chen GZ, Chen HH, Xu LH, Jiang CL (2005) Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family ‘Oxalobacteraceae’ isolated from China. Int J Syst Evol Microbiol 55:1149–1153

    CAS  PubMed  Article  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 62:2371–7237

    CAS  PubMed  Article  Google Scholar 

  • Zhao XQ, Yang TH (2011) Draft genome sequence of the marine derived actinomycete Streptomyces xinghaiensis NRRL B24674T. J Bacteriol 193:5543

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  • Zhao XQ, Li WJ, Jiao WC, Li Y, Yuan WJ, Zhang YQ, Klenk HP, Suh JW, Bai FW (2009) Streptomyces xinghaiensis sp. nov., a new marine actinomycete derived from a marine sediment sample. Int J Syst Evol Microbiol 59:2870–2874

    CAS  PubMed  Article  Google Scholar 

  • Zhao XQ, Geng X, Chen C, Chen LY, Jiao WC, Yang C (2012a) Draft genome sequence of the marine actinomycete Streptomyces sulphureus L180, isolated from marine sediment. J Bacteriol 194:4482

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  • Zhao XQ, Jiao WC, Xu XN (2012b) Harnessing the chemical and genetic diversities of marine microorganisms for medical applications In: Marine Microbiology: bioactive compounds and their application, Edited by Se-kwon Kim, Wiley

Download references

Acknowledgments

The authors are grateful to the financial support by Open Funding Project of State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, China, and Qing Lan Project of Jiangsu Province (2014), China.

Author information

Authors and Affiliations

Authors

Corresponding authors

Correspondence to Sheng Qin or Xin-Qing Zhao.

Additional information

Chao Chen and Wei-Wei Feng have contributed equally to this work.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOCX 102 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Chen, C., Feng, WW., Qin, S. et al. Streptomyces xiaopingdaonensis sp. nov., a novel marine actinomycete isolated from the sediment of Xiaopingdao in Dalian, China. Antonie van Leeuwenhoek 107, 511–518 (2015). https://doi.org/10.1007/s10482-014-0347-5

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10482-014-0347-5

Keywords

  • Streptomyces xiaopingdaonensis sp. nov.
  • Marine sediment
  • Polyphasic taxonomy
  • 16S rRNA gene
  • Streptomyces halophytocola