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).

Funding
This study was supported by the:
  • Wensheng Xiang , he National Natural Science Foundation of China , (Award 31872037)
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003922
2019-12-12
2020-11-24
Loading full text...

Full text loading...

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]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003922
Loading
/content/journal/ijsem/10.1099/ijsem.0.003922
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited this month 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