1887

Abstract

A novel actinobacterial strain (TRM 68085) was isolated from soil of wetland. A polyphasic approach was used to study the taxonomy of TRM 68085 and the results showed a range of phylogenetic and chemotaxonomic properties consistent with those of the genus . Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain TRM 68085 showed the highest similarity value to 1H-SSA4 (98.6 %), and phylogenetically clustered with ZX01(97.5 %) and NBRC 13050 (97.4 %). The genomic DNA G+C content of strain TRM 68085 based on the genome sequence was 71.4 mol%. The levels of DNA–DNA relatedness between the genome of the isolate and its nearest phylogenetic neighbours, 1H-SSA4, ZX01 and NBRC 13050, were 19.2±0.4, 21.8±0.5 and 19.3±0.6 %, respectively. Chemotaxonomic data revealed that strain TRM 68085 possessed MK-9(H) and MK-9(H) as the predominant menaquinones. -Diaminopimelic acid and a small amount of -diaminopimelic acid were the diagnostic diamino acids. Ribose, xylose, glucose and galactose were the whole-cell sugars. The major cellular fatty acids were C (25.4 %) and iso-C (18.3 %). On the basis of these genotypic and phenotypic data, it is concluded that strain TRM 68085 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is TRM 68085 (=CCTCC AA2019031=LMG 31492).

Funding
This study was supported by the:
  • Panpan Liu , Tarim University graduate research and innovation projects (project no.TDGR1201808) , (Award TDGR1201808)
  • Li-Li Zhang , National Natural Science Foundation of China , (Award U1703236)
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004430
2020-09-17
2020-10-20
Loading full text...

Full text loading...

References

  1. Zhao F, Qin YH, Zheng X, Zhao HW, Chai DY et al. Biogeography and adaptive evolution of Streptomyces strains from saline environments. Sci Rep 2016; 6:32718 [CrossRef][PubMed]
    [Google Scholar]
  2. Anderson AS, Wellington EM. The taxonomy of Streptomyces and related genera. Int J Syst Evol Microbiol 2001; 51:797–814 [CrossRef][PubMed]
    [Google Scholar]
  3. Manfio GP. Towards minimal standards for the description of Streptomyces species. Biotekhnologiya 1995; 8:228–237
    [Google Scholar]
  4. Lee LH, Zainal N, Azman AS, Eng SK, Ab Mutalib NS et al. Streptomyces pluripotens sp. nov., a bacteriocin-producing streptomycete that inhibits meticillin-resistant Staphylococcus aureus. Int J Syst Evol Microbiol 2014; 64:3297–3306 [CrossRef][PubMed]
    [Google Scholar]
  5. Nguyen TM, Kim J. Streptomyces gilvifuscus sp. nov. a novel actinomycete that produces antibacterial compounds isolated from soil in Pyeongchang-gun, South Korea. Int J Syst Evol Microbiol 2015; 65:3493–3500
    [Google Scholar]
  6. Mao J, Wang J, Dai HQ, Zhang ZD, Tang QY et al. Yuhushiella deserti gen. nov., sp. nov., a new member of the suborder Pseudonocardineae. Int J Syst Evol Microbiol 2011; 61:621–630 [CrossRef][PubMed]
    [Google Scholar]
  7. Law JW, Chan KG, He Y-W, Khan TM, Ab Mutalib N-S et al. Diversity of Streptomyces spp. from mangrove forest of Sarawak (Malaysia) and screening of their antioxidant and cytotoxic activities. Sci Rep 2019; 9:15262 [CrossRef][PubMed]
    [Google Scholar]
  8. Khieu TN, Liu MJ, Nimaichand S, Quach NT, Chu-Ky S et al. Characterization and evaluation of antimicrobial and cytotoxic effects of Streptomyces sp. HUST012 isolated from medicinal plant Dracaena cochinchinensis Lour. Front Microbiol 2015; 6:574 [CrossRef][PubMed]
    [Google Scholar]
  9. Abdel-Mageed WM, Milne BF, Wagner M, Schumacher M, Sandor P et al. Dermacozines, a new phenazine family from deep-sea dermacocci isolated from a Mariana Trench sediment. Org Biomol Chem 2010; 8:2352–2362 [CrossRef][PubMed]
    [Google Scholar]
  10. Wang DS, Xue QH, Ma YY, Wei XL, Chen J, He F et al. Oligotrophy is helpful for the isolation of bioactive actinomycetes. Indian J Microbiol 2014; 54:178–184 [CrossRef][PubMed]
    [Google Scholar]
  11. Mingma R, Duangmal K, Thamchaipenet A, Trakulnaleamsai S, Matsumoto A et al. Streptomyces oryzae sp. nov., an endophytic actinomycete isolated from stems of rice plant. J Antibiot 2015; 68:368–372 [CrossRef][PubMed]
    [Google Scholar]
  12. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [CrossRef]
    [Google Scholar]
  13. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [CrossRef][PubMed]
    [Google Scholar]
  14. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  15. Kluge AG, Farris JS. Quantitative Phyletics and the evolution of anurans. Syst Zool 1969; 18:1–32 [CrossRef]
    [Google Scholar]
  16. Sudhir K, Glen S, Koichiro T. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology & Evolution 2016; 7:1870–1874
    [Google Scholar]
  17. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119–0 [CrossRef][PubMed]
    [Google Scholar]
  18. Zuo G, Hao B. CVTree3 web server for Whole-genome-based and alignment-free prokaryotic phylogeny and taxonomy. Genomics Proteomics Bioinformatics 2015; 13:321–331 [CrossRef][PubMed]
    [Google Scholar]
  19. Ezaki T, Hashimoto Y, Yabuuchi E. 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 1989; 39:224–229 [CrossRef]
    [Google Scholar]
  20. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [CrossRef][PubMed]
    [Google Scholar]
  21. Yoon S-H, Ha S-M, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [CrossRef][PubMed]
    [Google Scholar]
  22. Wayne LG, Brenner DJ, Colwell RR. International Committee on systematic bacteriology. Report of the ad hoc Committee on reconciliation of approaches to bacterial Systematics. Int J Syst Bacteriol 1987; 37:463–464
    [Google Scholar]
  23. Richter M, Rosselló-Móra R, Rossellȯ-Mȯra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [CrossRef][PubMed]
    [Google Scholar]
  24. Jones KL. Fresh isolates of actinomycetes in which the presence of sporogenous aerial mycelia is a fluctuating characteristic. J Bacteriol 1949; 57:141–145 [CrossRef]
    [Google Scholar]
  25. Shepard Anna O. The iscc-nbs method of designating colors and a dictionary of color names. American Antiquity 1955; 22:158–310
    [Google Scholar]
  26. Williams ST, Cross T. Actinomycetes. Methods Microbiol 1971; 4:295–334
    [Google Scholar]
  27. Gordon RE, Barnett DA, Handerhan JE, Pang C, Pang CH. Nocardia coeliaca, Nocardia autotrophica, and the Nocardin strain. Int J Syst Bacteriol 1974; 24:54–63 [CrossRef]
    [Google Scholar]
  28. Minnikin DE, O'Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2:233–241 [CrossRef]
    [Google Scholar]
  29. Wu C, Lu X, Qin M, Ruan J. Analysis of menaquinonecompound in microbial cells by HPLC. Microbiology 1964; 16:176–178
    [Google Scholar]
  30. Lepage G, Roy CC. Improved recovery of fatty acid through direct transesterification without prior extraction or purification. J Lipid Res 1984; 25:1391–1396[PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004430
Loading
/content/journal/ijsem/10.1099/ijsem.0.004430
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error