1887

Abstract

A novel actinobacterium, designated strain NEAU-GS14, was isolated from soil of a flower bed in a residential area in Sanya, Hainan Province, China, and characterized using a polyphasic approach. Morphological and chemotaxonomic characteristics of the strain coincided with members of the genus Herbidospora. The 16S rRNA gene sequence analysis showed that strain NEAU-GS14 belongs to the genus and was most closely related to JCM 18061 (98.8 %), other type strains of species of the genus were found to be less than 98.7 %. Phylogenetic analysis using the 16S rRNA gene sequences showed that the strain formed a cluster with JCM 18061. Cell wall contained -diaminopimelic acid as the major diamino acid and the whole-cell hydrolysates were glucose, madurose and ribose. The major polar lipids were diphosphatidylglycerol, hydroxyphosphatidylethanolamine, phosphatidylethanolamine phosphatidylmethylethanolamine, phosphoglycolipids and two phosphatidylinositol mannosides. The predominant menaquinone was MK-10(H). Major fatty acids were 10-methly C and C , these chemotaxonomic data supported the affiliation of strain NEAU-GS14 to the genus . The DNA G+C content was 70.6 mol%. Furthermore, the strain could be clearly distinguished by digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) values and some phenotypic characteristics. Therefore, it is proposed that strain NEAU-GS14 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is NEAU-GS14 (=CCTCC AA 2018040=JCM 33459).

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2019-12-12
2020-01-24
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References

  1. Kudo T, Itoh T, Miyadoh S, Shomura T, Seino A. Herbidospora gen. nov., a new genus of the family Streptosporangiaceae Goodfellow et al. 1990. Int J Syst Bacteriol 1993;43: 319– 328 [CrossRef]
    [Google Scholar]
  2. Tseng M, Yang SF, Yuan GF. Herbidospora yilanensis sp. nov. and Herbidospora daliensis sp. nov., from sediment. Int J Syst Evol Microbiol 2010;60: 1168– 1172 [CrossRef]
    [Google Scholar]
  3. Boondaeng A, Suriyachadkun C, Ishida Y, Tamura T, Tokuyama S et al. Herbidospora sakaeratensis sp. nov., isolated from soil, and reclassification of Streptosporangium claviforme as a later synonym of Herbidospora cretacea. Int J Syst Evol Microbiol 2011;61: 777– 780 [CrossRef]
    [Google Scholar]
  4. Ara I, Tsetseg B, Daram D, Suto M, Ando K. Herbidospora mongoliensis sp. nov., isolated from soil, and reclassification of Herbidospora osyris and Streptosporangium claviforme as synonyms of Herbidospora cretacea. Int J Syst Evol Microbiol 2012;62: 2322– 2329 [CrossRef]
    [Google Scholar]
  5. Niemhom N, Thawai C. Herbidospora soli sp. nov., isolated from soil. Int J Syst Evol Microbiol 2018;68: 294– 298 [CrossRef]
    [Google Scholar]
  6. Atlas RM. Handbook of microbiological media. Quarterly Review of Biology 2006;2: 364– 365
    [Google Scholar]
  7. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966;16: 313– 340 [CrossRef]
    [Google Scholar]
  8. Jin L, Zhao Y, Song W, Duan L, Jiang S et al. Streptomyces inhibens sp. nov., a novel actinomycete isolated from rhizosphere soil of wheat (Triticum aestivum L.). Int J Syst Evol Microbiol 2019;69: 688– 695 [CrossRef]
    [Google Scholar]
  9. Jones KL. Fresh isolates of actinomycetes in which the presence of sporogenous aerial mycelia is a fluctuating characteristic. J Bacteriol 1949;57: 141– 145
    [Google Scholar]
  10. Waksman SA. The Actinomycetes A summary of current knowledge, New York: Ronald; 1967
    [Google Scholar]
  11. Waksman SA. The Actinomycetes, Vol. 2, Classification, Identification and Descriptions of Genera and Species Baltimore: Williams and Wilkins; 1961
    [Google Scholar]
  12. Kelly KL. Inter-society color council-national Bureau of standards color-name charts illustrated with centroid colors published in US. 1964
  13. Jia F, Liu C, Wang X, Zhao J, Liu Q et al. Wangella harbinensis gen. nov., sp. nov., a new member of the family Micromonosporaceae. Antonie van Leeuwenhoek 2013;103: 399– 408 [CrossRef]
    [Google Scholar]
  14. Fu Y, Yan R, Liu D, Jiang S, Cui L et al. Trinickia diaoshuihuensis sp. nov., a plant growth promoting bacterium isolated from soil. Int J Syst Evol Microbiol 2019;69: 291– 296 [CrossRef]
    [Google Scholar]
  15. 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]
  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 [CrossRef]
    [Google Scholar]
  17. Yokota A, Tamura T, Hasegawa T, Huang LH. Catenuloplanes japonicas gen. nov., sp. nov., nom. rev., a new genus of the order Actinomycetales. Int J Syst Bacteriol 1993;43: 805– 812 [CrossRef]
    [Google Scholar]
  18. McKerrow J, Vagg S, McKinney T, Seviour EM, Maszenan AM et al. A simple HPLC method for analysing diaminopimelic acid diastereomers in cell walls of Gram-positive bacteria. Lett Appl Microbiol 2000;30: 178– 182 [CrossRef]
    [Google Scholar]
  19. Lechevalier MP, Lechevalier HA. The chemotaxonomy of actinomycetes In Dietz A, Thayer DW. (editors) Actinomycete taxonomy (special publication vol 6 Arlington: Society of Industrial Microbiology; 1980; pp 227– 291
    [Google Scholar]
  20. 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]
  21. Collins MD. Isoprenoid quinone analyses in bacterial classification and identification In Goodfellow M, Minnikin DE. (editors) Chemical Methods in Bacterial Systematics London: Academic Press; 1985; pp 267– 284
    [Google Scholar]
  22. Wu C, Lu X, Qin M, Wang Y, Ruan J. Analysis of menaquinone compound in microbial cells by HPLC. Microbiology [English translation of Microbiology (Beijing)] 1989;16: 176– 178
    [Google Scholar]
  23. Gao R, Liu C, Zhao J, Jia F, Yu C et al. Micromonospora jinlongensis sp. nov., isolated from muddy soil in China and emended description of the genus Micromonospora. Antonie van Leeuwenhoek 2014;105: 307– 315 [CrossRef]
    [Google Scholar]
  24. Xiang W, Liu C, Wang X, Du J, Xi L et al. Actinoalloteichus nanshanensis sp. nov., isolated from the rhizosphere of a fig tree (Ficus religiosa). Int J Syst Evol Microbiol 2011;61: 1165– 1169 [CrossRef]
    [Google Scholar]
  25. Monteiro M, Moreira N, Pinto J, Pires-Luís AS, Henrique R et al. Gc-Ms metabolomics-based approach for the identification of a potential VOC-biomarker panel in the urine of renal cell carcinoma patients. J Cell Mol Med 2017;21: 2092– 2105 [CrossRef]
    [Google Scholar]
  26. Kim SB, Brown R, Oldfield C, Gilbert SC, Iliarionov S et al. Gordonia amicalis sp. nov., a novel dibenzothiophene-desulphurizing actinomycete. Int J Syst Evol Microbiol 2000;50: 2031– 2036 [CrossRef]
    [Google Scholar]
  27. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4: 406– 425
    [Google Scholar]
  28. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981;17: 368– 376 [CrossRef]
    [Google Scholar]
  29. 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]
  30. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39: 783– 791 [CrossRef]
    [Google Scholar]
  31. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980;16: 111– 120 [CrossRef]
    [Google Scholar]
  32. Yoon SH, SM H, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically United database of 16S rRNA and whole genome assemblies. Int J Syst Evol Microbiol 2017;67: 1613– 1617
    [Google Scholar]
  33. Yoon S-H, Ha S-min, 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]
    [Google Scholar]
  34. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013;14: 60 [CrossRef]
    [Google Scholar]
  35. 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]
  36. Li R, Li Y, Kristiansen K, Wang J. Soap: short oligonucleotide alignment program. Bioinformatics 2008;24: 713– 714 [CrossRef]
    [Google Scholar]
  37. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019;10: 2182 [CrossRef]
    [Google Scholar]
  38. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O 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
    [Google Scholar]
  39. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009;106: 19126– 19131 [CrossRef]
    [Google Scholar]
  40. Chun J, Rainey FA. Integrating genomics into the taxonomy and systematics of the bacteria and archaea. Int J Syst Evol Microbiol 2014;64: 316– 324 [CrossRef]
    [Google Scholar]
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