1887

Abstract

A Gram-stain-positive, aerobic actinomycete, designated strain BMP B8144, was isolated from desert soil, in Xinjiang province, northwest China. The isolate produced scanty aerial mycelium and fragmented substrate mycelium on most tested media. Cell-wall hydrolysates contained -diaminopimelic acid, galactose and mannose. The diagnostic phospholipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylhydroxylethanolamine, phosphatidylinositol, and phosphatidylinositol mannosides. The major fatty acids included -C, C 8 and -C. The predominant menaquinones were MK-9(H) and MK-10(H). The DNA G+C content was 70.4 mol% (genome). Based on the 16S rRNA gene sequence analysis on EzBioCloud server, strain BMP B8144 showed the closest similarities to YIM LPA2h (98.9 %) and ‘’ Hhs.015 (98.6 %). However, it can be distinguished from the closest strains based on the low levels of DNA–DNA relatedness (59.3±1.8 and 47.9±2.3 %, respectively). A combination of morphological, chemotaxonomic and phylogenetic characteristics, strain BMP B8144 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is BMP B8144 (=CGMCC 4.7490=KCTC 49001).

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2020-01-22
2020-02-28
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References

  1. Labeda DP, Testa RT, Lechevalier MP, Lechevalier HA. Saccharothrix: a new genus of the Actinomycetales related to Nocardiopsis. Int J Syst Bacteriol 1984;34: 426– 431 [CrossRef]
    [Google Scholar]
  2. Labeda DP, Lechevalier MP et al. Amendment of the Genus Saccharothrix Labeda et al. 1984 and descriptions of Saccharothrix espanaensis sp. nov., Saccharothrix cryophilis sp. nov., and Saccharothrix mutabilis comb. nov. Int J Syst Bacteriol 1984;1989: 420– 423
    [Google Scholar]
  3. Zhi X-Y, Li W-J, Stackebrandt E. An update of the structure and 16S rRNA gene sequence-based definition of higher ranks of the class Actinobacteria, with the proposal of two new suborders and four new families and emended descriptions of the existing higher taxa. Int J Syst Evol Microbiol 2009;59: 589– 608 [CrossRef]
    [Google Scholar]
  4. Labeda DP, Goodfellow M, Chun J, Zhi X-Y, Li W-J. Reassessment of the systematics of the suborder Pseudonocardineae: transfer of the genera within the family Actinosynnemataceae Labeda and Kroppenstedt 2000 emend. Zhi et al. 2009 into an emended family Pseudonocardiaceae Embley et al. 1989 emend. Zhi et al. 2009. Int J Syst Evol Microbiol 2011;61: 1259– 1264 [CrossRef]
    [Google Scholar]
  5. Yassin AF, Rainey FA, Brzezinka H, Jahnke KD, Weissbrodt H et al. Lentzea gen. nov., a new genus of the order Actinomycetales. Int J Syst Bacteriol 1995;45: 357– 363 [CrossRef]
    [Google Scholar]
  6. Labeda DP. Crossiella gen. nov., a new genus related to Streptoalloteichus. Int J Syst Evol Microbiol 2001;51: 1575– 1579 [CrossRef]
    [Google Scholar]
  7. Labeda DP, Hatano K, Kroppenstedt RM, Tamura T. Revival of the genus Lentzea and proposal for Lechevalieria gen. nov. Int J Syst Evol Microbiol 2001;51: 1045– 1050 [CrossRef]
    [Google Scholar]
  8. Labeda DP, Kroppenstedt RM. Goodfellowia gen. nov., a new genus of the Pseudonocardineae related to Actinoalloteichus, containing Goodfellowia coeruleoviolacea gen. nov., comb. nov. Int J Syst Evol Microbiol 2006;56: 1203– 1207 [CrossRef]
    [Google Scholar]
  9. Labeda DP, Kroppenstedt RM. Proposal of Umezawaea gen. nov., a new genus of the Actinosynnemataceae related to Saccharothrix, and transfer of Saccharothrix tangerinus Kinoshita et al. 2000 as Umezawaea tangerina gen. nov., comb. nov. Int J Syst Evol Microbiol 2007;57: 2758– 2761 [CrossRef]
    [Google Scholar]
  10. Takahashi Y, Shinose M, Seino A, Iwai Y, Omura S. Transfer of staurosporine-producing strain Streptomyces staurosporeus AM-2282 to the genus Saccharothrix as Saccharothrix aerocolonigenes (Labeda 1986) subsp. staurosporeus subsp. nov. Actinomycetologica 1995;9: 19– 26 [CrossRef]
    [Google Scholar]
  11. LABEDA DP. Transfer of "Nocardia aerocolonigenes" (Shinobu and Kawato 1960) Pridham 1970 into the genus Saccharothrix Labeda, Testa, Lechevalier, and Lechevalier 1984 as Saccharothrix aerocolonigenes sp. nov. Int J Syst Bacteriol 1986;36: 109– 110 [CrossRef]
    [Google Scholar]
  12. Grund E, Kroppenstedt RM. Transfer of five Nocardiopsis species to the genus Saccharothrix Labeda et al. 1984. Syst Appl Microbiol 1989;12: 267– 274 [CrossRef]
    [Google Scholar]
  13. Kroppenstedt RM, Stackebrandt E, Goodfellow M. Taxonomic revision of the actinomycete genera Actinomadura and Microtetraspora. Syst Appl Microbiol 1990;13: 148– 160 [CrossRef]
    [Google Scholar]
  14. Kim B-Y, Brown R, Labeda DP, Goodfellow M. Reclassification of 'Dactylosporangium variesporum' as Saccharothrix variisporea corrig. (ex Tomita et al. 1977) sp. nov., nom. rev. Int J Syst Evol Microbiol 2011;61: 310– 314 [CrossRef]
    [Google Scholar]
  15. Zitouni A, Lamari L, Boudjella H, Badji B, Sabaou N et al. Saccharothrix algeriensis sp. nov., isolated from Saharan soil. Int J Syst Evol Microbiol 2004;54: 1377– 1381 [CrossRef]
    [Google Scholar]
  16. Boubetra D, Zitouni A, Bouras N, Mathieu F, Lebrihi A et al. Saccharothrix hoggarensis sp. nov., an actinomycete isolated from Saharan soil. Int J Syst Evol Microbiol 2013;63: 549– 553 [CrossRef]
    [Google Scholar]
  17. Boubetra D, Zitouni A, Bouras N, Mathieu F, Lebrihi A et al. Saccharothrix saharensis sp. nov., an actinomycete isolated from Algerian Saharan soil. Int J Syst Evol Microbiol 2013;63: 3744– 3749 [CrossRef]
    [Google Scholar]
  18. Boubetra D, Zitouni A, Bouras N, Schumann P, Spröer C et al. Saccharothrix tamanrassetensis sp. nov., an actinomycete isolated from Saharan soil. Int J Syst Evol Microbiol 2015;65: 1316– 1320 [CrossRef]
    [Google Scholar]
  19. Bull AT, Asenjo JA, Goodfellow M, Gómez-Silva B. The Atacama desert: technical resources and the growing importance of novel microbial diversity. Annu Rev Microbiol 2016;70: 215– 234 [CrossRef]
    [Google Scholar]
  20. Vértesy L, Barbone FP, Cashmen E, Decker H, Ehrlich K et al. Pluraflavins, potent antitumor antibiotics from Saccharothrix sp. DSM 12931. J Antibiot 2001;54: 718– 729 [CrossRef]
    [Google Scholar]
  21. Labeda DP, Kroppenstedt RM. Phylogenetic analysis of Saccharothrix and related taxa: proposal for Actinosynnemataceae fam. nov. Int J Syst Evol Microbiol 2000;50: 331– 336 [CrossRef]
    [Google Scholar]
  22. Labeda DP. Genus XV. Saccharothrix Labeda, Testa, Lechevalier and Lechevalier 1984, 429VP emend. Labeda and Lechevalier1989, 422 In Goodfellow M, Kämpfer P, Busse HJ, Trujillo ME, Suzuki KI. (editors) Bergey's Manual of Systematic Bacteriology New York: Springer; 2012; pp 1415– 1419
    [Google Scholar]
  23. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966;16: 313– 340 [CrossRef]
    [Google Scholar]
  24. Qin S, Bai J-L, Wang Y, Feng W-W, Yuan B et al. Tamaricihabitans halophyticus gen. nov., sp. nov., an endophytic actinomycete of the family Pseudonocardiaceae. Int J Syst Evol Microbiol 2015;65: 4662– 4668 [CrossRef]
    [Google Scholar]
  25. Kelly KL. Inter-Society Color Council – National Bureau of Standards Color Name Charts Illustrated with Centroid Colors Washington, DC: US Government Printing Office; 1964
    [Google Scholar]
  26. Cao C, Sun Y, Wu B, Zhao S, Yuan B et al. Actinophytocola glycyrrhizae sp. nov. isolated from the rhizosphere of Glycyrrhiza inflata. Int J Syst Evol Microbiol 2018;68: 2504– 2508 [CrossRef]
    [Google Scholar]
  27. Gerhardt P, Murray RGE, Wood WA, Krieg NR. Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994
    [Google Scholar]
  28. Kurup PV, Schmitt JA. Numerical taxonomy of Nocardia. Can J Microbiol 1973;19: 1035– 1048 [CrossRef]
    [Google Scholar]
  29. Smibert RM, Krieg NR. Phenotypic characterization In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994; pp 607– 654
    [Google Scholar]
  30. Gordon RE, Barnett DA, Handerhan JE, Pang CHN. Nocardia coeliaca, Nocardia autotrophica, and the Nocardin strain. Int J Syst Bacteriol 1974;24: 54– 63 [CrossRef]
    [Google Scholar]
  31. Hasegawa T, Takizawa M, Tanida S. A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Appl Microbiol 1983;29: 319– 322 [CrossRef]
    [Google Scholar]
  32. 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 [CrossRef]
    [Google Scholar]
  33. 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 [CrossRef]
    [Google Scholar]
  34. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  35. 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 [CrossRef]
    [Google Scholar]
  36. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016;33: 1870– 1874 [CrossRef]
    [Google Scholar]
  37. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4: 406– 425 [CrossRef]
    [Google Scholar]
  38. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981;17: 368– 376 [CrossRef]
    [Google Scholar]
  39. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971;20: 406– 416 [CrossRef]
    [Google Scholar]
  40. Cao C, Xu T, Liu J, Cai X, Sun Y et al. Actinomadura deserti sp. nov., isolated from desert soil. Int J Syst Evol Microbiol 2018;68: 2930– 2935 [CrossRef]
    [Google Scholar]
  41. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39: 783– 791 [CrossRef]
    [Google Scholar]
  42. Marmur J. A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol 1961;3: 208– 218 [CrossRef]
    [Google Scholar]
  43. De Ley J, Cattoir H, Reynaerts A. The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 1970;12: 133– 142 [CrossRef]
    [Google Scholar]
  44. Lim HJ, Lee E-H, Yoon Y, Chua B, Son A. Portable lysis apparatus for rapid single-step DNA extraction of Bacillus subtilis. J Appl Microbiol 2016;120: 379– 387 [CrossRef]
    [Google Scholar]
  45. Li R, Zhu H, Ruan J, Qian W, Fang X et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 2010;20: 265– 272 [CrossRef]
    [Google Scholar]
  46. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008;24: 713– 714 [CrossRef]
    [Google Scholar]
  47. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012;19: 455– 477 [CrossRef]
    [Google Scholar]
  48. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJM et al. ABySS: a parallel assembler for short read sequence data. Genome Res 2009;19: 1117– 1123 [CrossRef]
    [Google Scholar]
  49. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O et al. Report of the ad hoc Committee on Reconciliation of Approaches to Bacterial Systematics. Int J Syst Bacteriol 1987;37: 463– 464 [CrossRef]
    [Google Scholar]
  50. Li Y-Q, Liu L, Cheng C, Shi X-H, Lu C-Y et al. Saccharothrix lopnurensis sp. nov., a filamentous actinomycete isolated from sediment of Lop Nur. Antonie van Leeuwenhoek 2015;108: 975– 981 [CrossRef]
    [Google Scholar]
  51. Yan X, Huang L-L, Tu X, Gao X-N, Kang Z-S et al. Saccharothrix yanglingensis sp. nov., an antagonistic endophytic actinomycete isolated from cucumber plant. Antonie van Leeuwenhoek 2012;101: 141– 146 [CrossRef]
    [Google Scholar]
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