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Volume 68, Issue 1

sp. nov., a novel actinomycete isolated from a coastal soil Free

Abstract

An actinomycete strain, designated KLBMP S0039, was isolated from the rhizosphere soil of Linn., collected from the coastal region in Lianyungang, Jiangsu Province, eastern PR China, and was studied to determine its taxonomic position. The isolate showed a combination of morphological and chemotaxonomic properties typical of the members of the genus . The cell wall contained -diaminopimelic acid as the diagnostic diamino acid and the whole-cell sugars were galactose, arabinose, glucose and ribose. The predominant menaquinone was identified as MK-8(Hω-cycl). The diagnostic phospholipids were found to be diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and unknown lipids. The predominant cellular fatty acids were identified as C, C, Cω9, and 10-methyl C [tuberculostearic acid (TBSA)]. The G+C content of the genomic DNA was determined to be 68.2 mol%. The 16S rRNA gene sequence similarity indicated that KLBMP S0039 was most closely related to NBRC 108232 (99.4 % 16S rRNA gene sequence similarity) and NBRC 15531 (99.2 %), similarities to other type strains of species of the genus were found to be less than 98.6 %. However, DNA–DNA relatedness values and phenotypic data indicated that KLBMP S0039 could be clearly distinguished from the closely related species of the genus . On the basis of polyphasic taxonomic data, it is concluded that KLBMP S0039 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is KLBMP S0039 (=KCTC 39693=CGMCC 4.7329).

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Keyword(s): coastal soil , Nocardia rhizosphaerihabitans sp. nov. and polyphasic taxonomy
© 2018 IUMS
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2018-01-01
2024-04-24
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References

  1. Goodfellow M, Jones AL, Order V. Corynebacteriales ord. nov. In Goodfellow M, Kämpfer P, Busse H-J, Trujillo ME, Suzuki K-I. et al. (editors) Bergey’s Manual of Systematic Bacteriology, 2nd ed. vol. 5 New York: Springer; 2012 pp. 232–243 [Crossref]
     [Google Scholar]
  2. Goodfellow M, Lechevalier MP. Genus Nocardia Trevisan 1889, 9AL . In Williams ST, Sharpe ME, Holt JG. (editors) Bergey’s Manual of Systematic Bacteriology vol. 4 Baltimore: Williams & Wilkins; 1989 pp. 2348–2361
     [Google Scholar]
  3. Goodfellow M, Isik K, Yates E. Actinomycete systematics: an unfinished synthesis. Nova Acta Leopold 1999; 312:47–82
     [Google Scholar]
  4. Qin S, Li J, Chen HH, Zhao GZ, Zhu WY et al. Isolation, diversity, and antimicrobial activity of rare actinobacteria from medicinal plants of tropical rain forests in Xishuangbanna, China. Appl Environ Microbiol 2009; 75:6176–6186 [View Article][PubMed]
     [Google Scholar]
  5. Qin S, Xing K, Jiang JH, Xu LH, Li WJ. Biodiversity, bioactive natural products and biotechnological potential of plant-associated endophytic actinobacteria. Appl Microbiol Biotechnol 2011; 89:457–473 [View Article][PubMed]
     [Google Scholar]
  6. Qin S, Zhang Y-J, Yuan B, Xu P-Y, Xing K et al. Isolation of ACC deaminase-producing habitat-adapted symbiotic bacteria associated with halophyte Limonium sinense (Girard) Kuntze and evaluating their plant growth-promoting activity under salt stress. Plant Soil 2014; 374:753–766 [View Article]
     [Google Scholar]
  7. Rey T, Dumas B. Plenty is no plague: Streptomyces symbiosis with crops. Trends Plant Sci 2017; 22:30–37 [View Article][PubMed]
     [Google Scholar]
  8. Qin S, Feng W-W, Wang T-T, Ding P, Xing K et al. Plant growth-promoting effect and genomic analysis of the beneficial endophyte Streptomyces sp. KLBMP 5084 isolated from halophyte Limonium sinense . Plant Soil 2017; 416:117–132 [View Article]
     [Google Scholar]
  9. Kaewkla O, Franco CM. Nocardia callitridis sp. nov., an endophytic actinobacterium isolated from a surface-sterilized root of an Australian native pine tree. Int J Syst Evol Microbiol 2010; 60:1532–1536 [View Article][PubMed]
     [Google Scholar]
  10. Xing K, Qin S, Fei SM, Lin Q, Bian GK et al. Nocardia endophytica sp. nov., an endophytic actinomycete isolated from the oil-seed plant Jatropha curcas L. Int J Syst Evol Microbiol 2011; 61:1854–1858 [View Article][PubMed]
     [Google Scholar]
  11. Bai JL, Wang Y, Qin S, Ding P, Xing K et al. Nocardia jiangsuensis sp. nov., an actinomycete isolated from coastal soil. Int J Syst Evol Microbiol 2016; 66:4633–4638 [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. Waksman SA. The Actinomycetes. A Summary of Current Knowledge New York: Ronald Press; 1967
     [Google Scholar]
  14. Kelly KL. Inter-Society Color Council-National Bureau of Standards Color-Name Charts Illustrated with Centroid Colors Published in US Washington, DC: US Government Printing Office; 1964
     [Google Scholar]
  15. Xu P, Li WJ, Tang SK, Zhang YQ, Chen GZ 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]
  16. Gordon RE, Barnett DA, Handerhan JE, Pang CH-N. Nocardia coeliaca, Nocardia autotrophica, and the nocardin strain. Int J Syst Bacteriol 1974; 24:54–63 [View Article]
     [Google Scholar]
  17. Williams ST, Goodfellow M, Alderson G, Wellington EMH, Sneath PHA et al. Numerical classification of Streptomyces and related genera. J Gen Microbiol 1983; 129:1743–1813 [View Article][PubMed]
     [Google Scholar]
  18. 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]
  19. Lechevalier MP, Lechevalier H. Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 1970; 20:435–443 [View Article]
     [Google Scholar]
  20. Minnikin DE, Hutchinson IG, Caldicott AB, Goodfellow M. Thin-layer chromatography of methanolysates of mycolic acid-containing bacteria. J Chromatogr A 1980; 188:221–233 [View Article]
     [Google Scholar]
  21. Minnikin DE, Collins MD, Goodfellow M. Fatty acid and polar lipid composition in the classification of Cellulomonas, Oerskovia and related taxa. J Appl Bacteriol 1979; 47:87–95 [View Article]
     [Google Scholar]
  22. Collins MD, Jones D. Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2, 4-diaminobutyric acid. J Appl Bacteriol 1980; 48:459–470 [View Article]
     [Google Scholar]
  23. 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]
  24. Groth I, Schumann P, Rainey FA, Martin K, Schuetze B et al. Demetria terragena gen. nov., sp. nov., a new genus of actinomycetes isolated from compost soil. Int J Syst Bacteriol 1997; 47:1129–1133 [View Article][PubMed]
     [Google Scholar]
  25. Mesbah M, Premachandran U, Whitman WB. Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 1989; 39:159–167 [View Article]
     [Google Scholar]
  26. Qin S, Miao Q, Feng W-W, Wang Y, Zhu X et al. Biodiversity and plant growth promoting traits of culturable endophytic actinobacteria associated with Jatropha curcas L. growing in Panxi dry-hot valley soil. Appl Soil Ecol 2015; 93:47–55 [View Article]
     [Google Scholar]
  27. Takeda K, Kang Y, Yazawa K, Gonoi T, Mikami Y. Phylogenetic studies of Nocardia species based on gyrB gene analyses. J Med Microbiol 2010; 59:165–171 [View Article][PubMed]
     [Google Scholar]
  28. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 25:4876–4882 [View Article][PubMed]
     [Google Scholar]
  29. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012; 62:716–721 [View Article][PubMed]
     [Google Scholar]
  30. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013; 30:2725–2729 [View Article][PubMed]
     [Google Scholar]
  31. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425[PubMed]
     [Google Scholar]
  32. Kluge AG, Farris JS. Quantitative phyletics and the evolution of anurans. Syst Zool 1969; 18:1–32 [View Article]
     [Google Scholar]
  33. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
     [Google Scholar]
  34. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
     [Google Scholar]
  35. 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]
  36. He L, Li W, Huang Y, Wang L, Liu Z et al. Streptomyces jietaisiensis sp. nov., isolated from soil in Northern China. Int J Syst Evol Microbiol 2005; 55:1939–1944 [View Article][PubMed]
     [Google Scholar]
  37. Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article][PubMed]
     [Google Scholar]
  38. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD et al. 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 [View Article]
     [Google Scholar]
  39. Wang Y, Liu W, Feng WW, Zhou XQ, Bai JL et al. Nocardia rhizosphaerae sp. nov., a novel actinomycete isolated from the coastal rhizosphere of Artemisia Linn., China. Antonie van Leeuwenhoek 2015; 108:31–39 [View Article][PubMed]
     [Google Scholar]
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Nocardia rhizosphaerihabitans sp. nov., a novel actinomycete isolated from a coastal soil
Int J Syst Evol Microbiol 68, 192 (2018); https://doi.org/10.1099/ijsem.0.002481
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