1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 70, Issue 10

sp. nov., an endogenous actinomycete isolated from Free

Abstract

A novel endogenous actinobacteria strain, designated TRM 66187, was isolated from sampled at Alar, Xinjiang, Northwest PR China, and characterized using a polyphasic taxonomic approach. Phylogenetic analysis based on 16S rRNA gene sequences affiliated strain TRM 66187 with the genus . The whole-cell sugar pattern of TRM 66187 consisted of galactose, glucose and ribose. The predominant menaquinones were MK-9(H) and MK-9(H). Major cellular fatty acids were iso-C, iso-C, anteiso-C and anteiso-C. The detected polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside and two unidentified polar lipids. The G+C content of strain TRM 66187 was 71.8 mol%. Results of phylogenetic analysis showed that strain TRM 66187 had 98.48% 16S rRNA gene sequence similarity to the closest described species DSM 42035. The average nucleotide identity value between strain TRM 66187 and the closest related strain DSM 42035 was calculated to be 77.2%. The digital DNA–DNA hybridization value between them was 22.4%. Multilocus sequence analyses based on five housekeeping genes (, , , and ) also indicated that strain TRM 66187 should be assigned to the genus . On the basis of evidence from this polyphasic study, strain TRM 66187 should be designated as representing a novel species of the genus , for which the name sp. nov. is proposed. The type strain is TRM 66187 (=LMG 31493=CCTCC AA 2018094).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): actinomycete , endogenous , new species and Streptomyces
Funding
This study was supported by the:
  • Graduate Innovation Project of Xinjiang Autonomous Region (Award XJ2019G269)
    • Principle Award Recipient: Liran Ma
  • Microbial Resources Utilization Innovation Team in the Key Field of Xingjiang Production and Construction Crops (Award 2017CB014)
    • Principle Award Recipient: Chuanxing Wan
  • Key Projects of National Natural Science Foundation of China (Award U1703236)
    • Principle Award Recipient: Lili Zhang
© 2020 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004372
2020-08-21
2024-04-19
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/10/5197.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004372&mimeType=html&fmt=ahah

References

  1. Waksman SA, Henrici AT. The nomenclature and classification of the actinomycetes. J Bacteriol 1943; 46:337–341 [View Article][PubMed]
     [Google Scholar]
  2. Také A, Matsumoto A, Ōmura S, Takahashi Y. Streptomyces lactacystinicus sp. nov. and Streptomyces cyslabdanicus sp. nov., producing lactacystin and cyslabdan, respectively. J Antibiot 2015; 68:322–327 [View Article][PubMed]
     [Google Scholar]
  3. Katz L, Baltz RH. Natural product discovery: past, present, and future. J Ind Microbiol Biotechnol 2016; 43:155–176 [View Article][PubMed]
     [Google Scholar]
  4. Goodfellow M, Fiedler H-P. A guide to successful bioprospecting: informed by actinobacterial Systematics. Antonie van Leeuwenhoek 2010; 98:119–142 [View Article][PubMed]
     [Google Scholar]
  5. Veyisoglu A, Sahin N. Streptomyces hoynatensis sp. nov., isolated from deep marine sediment. Antonie van Leeuwenhoek 2015; 107:273–279 [View Article][PubMed]
     [Google Scholar]
  6. Goodfellow M, Busarakam K, Idris H, Labeda DP, Nouioui I et al. Streptomyces asenjonii sp. nov., isolated from hyper-arid Atacama desert soils and emended description of Streptomyces viridosporus Pridham et al. 1958. Antonie van Leeuwenhoek 2017; 110:1133–1148 [View Article][PubMed]
     [Google Scholar]
  7. Akshatha VJ, Nalini MS, D'Souza C, Prakash HS. Streptomycete endophytes from anti-diabetic medicinal plants of the Western Ghats inhibit alpha-amylase and promote glucose uptake. Lett Appl Microbiol 2014; 58:433–439 [View Article][PubMed]
     [Google Scholar]
  8. Guo YY, Yu HY, Kong DS, Yan F, Zhang YJ et al. Effects of drought stress on growth and chlorophyll fluorescence of Lycium ruthenicum Murr. seedlings. Photosynthetica 2016; 54:524–531 [View Article]
     [Google Scholar]
  9. Lin L, Jin L, Li X-J, Cui Z-J, Wang Z-H et al. [Survey and protective utilization of Lycium ruthenicum resources distributed in middle and lower reaches of Heihe river]. Zhongguo Zhong Yao Za Zhi 2017; 42:4419–4425 [View Article][PubMed]
     [Google Scholar]
  10. Chen H-kui, Zhong Y. Microsatellite markers for Lycium ruthenicum (Solananeae). Mol Biol Rep 2014; 41:5545–5548 [View Article]
     [Google Scholar]
  11. Mocan A, Zengin G, Simirgiotis M, Schafberg M, Mollica A et al. Functional constituents of wild and cultivated Goji (L. barbarum L.) leaves: phytochemical characterization, biological profile, and computational studies. J Enzyme Inhib Med Chem 2017; 32:153–168 [View Article][PubMed]
     [Google Scholar]
  12. Liu Y-H, Wei Y-Y, Mohamad OAA, Salam N, Zhang Y-G et al. Diversity, community distribution and growth promotion activities of endophytes associated with halophyte Lycium ruthenicum Murr. 3 Biotech 2019; 9:144 [View Article][PubMed]
     [Google Scholar]
  13. Liu F, Zhang H, Qin Y, Dong J, Xu E et al. Semi-natural areas of Tarim Basin in northwest China: linkage to desertification. Sci Total Environ 2016; 573:178–188 [View Article][PubMed]
     [Google Scholar]
  14. Passari AK, Mishra VK, Saikia R, Gupta VK, Singh BP et al. Isolation, abundance and phylogenetic affiliation of endophytic actinomycetes associated with medicinal plants and screening for their in vitro antimicrobial biosynthetic potential. Front Microbiol 2015; 6:273–286 [View Article][PubMed]
     [Google Scholar]
  15. Taechowisan T, Peberdy JF, Lumyong S. Isolation of endophytic actinomycetes from selected plants and their antifungal activity. World J Microbiol Biotechnol 2003; 19:381–385 [View Article]
     [Google Scholar]
  16. Chun J, Goodfellow M. A phylogenetic analysis of the genus Nocardia with 16S rRNA gene sequences. Int J Syst Bacteriol 1995; 45:240–245 [View Article][PubMed]
     [Google Scholar]
  17. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically United database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article][PubMed]
     [Google Scholar]
  18. 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]
  19. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
     [Google Scholar]
  20. Nei M, Kumar S. Molecular evolution and phylogenetics. Mol Phylogenet Evol 2002; 25:567–568
     [Google Scholar]
  21. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S et al. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013; 30:2725–2729 [View Article][PubMed]
     [Google Scholar]
  22. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
     [Google Scholar]
  23. Liu H, Xin B, Zheng J et al. Build a bioinformatics analysis platform and apply it to routine analysis of microbial genomics and comparative genomics. Protoc Exch. 2020
     [Google Scholar]
  24. Lee I, Ouk Kim Y, Park S-C, Chun J, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article][PubMed]
     [Google Scholar]
  25. Labeda DP, Doroghazi JR, Ju K-S, Metcalf WW. Taxonomic evaluation of Streptomyces albus and related species using multilocus sequence analysis and proposals to emend the description of Streptomyces albus and describe Streptomyces pathocidini sp. nov. Int J Syst Evol Microbiol 2014; 64:894–900 [View Article][PubMed]
     [Google Scholar]
  26. Guo Y, Zheng W, Rong X, Huang Y. A multilocus phylogeny of the Streptomyces griseus 16S rRNA gene clade: use of multilocus sequence analysis for streptomycete systematics . Int J Syst Evol Microbiol 2008; 58:149–159 [View Article][PubMed]
     [Google Scholar]
  27. Rong X, Huang Y. Taxonomic evaluation of the Streptomyces hygroscopicus clade using multilocus sequence analysis and DNA–DNA hybridization, validating the MLSA scheme for systematics of the whole genus. Syst Appl Microbiol 2012; 35:7–18 [View Article]
     [Google Scholar]
  28. Kai B, Simon S, Katharina S et al. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res 2019; 47:81–87
     [Google Scholar]
  29. Böszörményi E, Ersek T, Fodor A, Fodor AM, Földes LS et al. Isolation and activity of Xenorhabdus antimicrobial compounds against the plant pathogens Erwinia amylovora and Phytophthora nicotianae . J Appl Microbiol 2009; 107:746–759 [View Article][PubMed]
     [Google Scholar]
  30. Matsuo Y, Kanoh K, Jang J-H, Adachi K, Matsuda S et al. Streptobactin, a tricatechol-type siderophore from marine-derived Streptomyces sp. YM5-799. J Nat Prod 2011; 74:2371–2376 [View Article][PubMed]
     [Google Scholar]
  31. Kang H-S, Brady SF. Arixanthomycins A-C: Phylogeny-guided discovery of biologically active eDNA-derived pentangular polyphenols. ACS Chem Biol 2014; 9:1267–1272 [View Article][PubMed]
     [Google Scholar]
  32. Microorganisms WSA. Book reviews: the actinomycetes. A summary of current knowledge). Science 1967; 157:1028
     [Google Scholar]
  33. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
     [Google Scholar]
  34. Xu P, Li W-J, Tang S-K, Zhang Y-Q, Chen G-Z et al. Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family 'Oxalobacteraceae' isolated from China. Int J Syst Evol Microbiol 2005; 55:1149–1153 [View Article][PubMed]
     [Google Scholar]
  35. Hu H, Lin H-P, Xie Q, Li L, Xie X-Q et al. Streptomyces qinglanensis sp. nov., isolated from mangrove sediment. Int J Syst Evol Microbiol 2012; 62:596–600 [View Article][PubMed]
     [Google Scholar]
  36. Kamlage B. Methods for general and molecular bacteriology. edited by P. Gerhardt, R. G. E. Murray, W. A. wood and N. R. Krieg. Mol Nut Food Res 2010; 40:103
     [Google Scholar]
  37. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974; 28:226–231 [View Article]
     [Google Scholar]
  38. Yokota A, Tamura T, Hasegawa T et al. Catenuloplanes japonicus gen. nov., sp. nov., nom.rev., a new genus of the order actinomycetales. Int J Syst Evol Microbiol 1993; 43:805–812
     [Google Scholar]
  39. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974; 28:226–231 [View Article][PubMed]
     [Google Scholar]
  40. Hasegawa T, Takizawa M, Tanida S. A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Appl Microbiol 1983; 29:319–322 [View Article]
     [Google Scholar]
  41. 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]
  42. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [View Article][PubMed]
     [Google Scholar]
  43. Kroppenstedt RM. Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded Ion exchanger as stationary phases. J Liq Chromatogr 1982; 5:2359–2367 [View Article]
     [Google Scholar]
  44. Athalye M, Noble WC, Minnikin DE. Analysis of cellular fatty acids by gas chromatography as a tool in the identification of medically important coryneform bacteria. J Appl Bacteriol 1985; 58:507–512 [View Article][PubMed]
     [Google Scholar]
  45. Li L, Wang J, Zhou Y-J, Lin H-W, Lu Y-H et al. Streptomyces reniochalinae sp. nov. and Streptomyces diacarni sp. nov., from marine sponges. Int J Syst Evol Microbiol 2019; 69:99–104 [View Article][PubMed]
     [Google Scholar]
  46. Cui Y, Baek S-H, Wang L, Lee H-G, Cui C et al. Streptomyces panacagri sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 2012; 62:780–785 [View Article][PubMed]
     [Google Scholar]
  47. Xu C, Wang L, Cui Q, Huang Y, Liu Z et al. Neutrotolerant acidophilic Streptomyces species isolated from acidic soils in China: Streptomyces guanduensis sp. nov., Streptomyces paucisporeus sp. nov., Streptomyces rubidus sp. nov. and Streptomyces yanglinensis sp. nov. Int J Syst Evol Microbiol 2006; 56:1109–1115 [View Article][PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004372
Loading
Streptomyces lycii sp. nov., an endogenous actinomycete isolated from Lycium ruthenicum
Int J Syst Evol Microbiol 70, 5197 (2020); https://doi.org/10.1099/ijsem.0.004372
/content/journal/ijsem/10.1099/ijsem.0.004372
/content/journal/ijsem/10.1099/ijsem.0.004372
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