1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 70, Issue 11

sp. nov., isolated from wetland soil Free

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).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): chemotaxonomic , gene , phylogenetic , Populus euphratica , strain and Streptomyces
Funding
This study was supported by the:
  • Tarim University graduate research and innovation projects (project no.TDGR1201808) (Award TDGR1201808)
    • Principle Award Recipient: Panpan Liu
  • National Natural Science Foundation of China (Award U1703236)
    • Principle Award Recipient: Li-Li Zhang
© 2020 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004430
2020-09-17
2024-04-26
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/11/5613.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004430&mimeType=html&fmt=ahah

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 [View Article][PubMed]
     [Google Scholar]
  2. Anderson AS, Wellington EM. The taxonomy of Streptomyces and related genera. Int J Syst Evol Microbiol 2001; 51:797–814 [View Article][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 [View Article][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 [View Article][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 [View Article][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 [View Article][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 [View Article][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 [View Article][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 [View Article][PubMed]
     [Google Scholar]
  12. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
     [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 [View Article][PubMed]
     [Google Scholar]
  14. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
     [Google Scholar]
  15. Kluge AG, Farris JS. Quantitative Phyletics and the evolution of anurans. Syst Zool 1969; 18:1–32 [View Article]
     [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 [View Article][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 [View Article][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 [View Article]
     [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 [View Article][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 [View Article][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 [View Article][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 [View Article]
     [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 [View Article]
     [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 [View Article]
     [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
Streptomyces arboris sp. nov., isolated from Populus euphratica wetland soil
Int J Syst Evol Microbiol 70, 5613 (2020); https://doi.org/10.1099/ijsem.0.004430
/content/journal/ijsem/10.1099/ijsem.0.004430
/content/journal/ijsem/10.1099/ijsem.0.004430
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed

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