1887

Abstract

A novel actinobacterium, designated strain NEAU-D428, was isolated from rhizosphere soil of wheat and characterized using a polyphasic approach. Morphological and chemotaxonomic characteristics of the strain coincided with members of the genus . The 16S rRNA gene sequence analysis showed that the isolate was most closely related to NEAU-TX2-2 (99.2 %). Phylogenetic analysis based on the 16S rRNA gene sequences indicated that the strain clustered with CLES2 (99.1 %), but formed a separate subclade in the phylogenomic tree within the genus . The menaquinones were identified as MK-9(H), MK-9(H) and MK-9(H). The phospholipid profile was found to consist of diphosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, ninhydrin-positive glycophospholipid, phosphatidylinositol and phosphatidylinositol mannoside. The major fatty acids were identified as iso-C, C, 10-methyl C and C. Digital DNA–DNA hybridization and average nucleotide identity values between strain NEAU-D428 and NEAU-TX2-2, 2C-HV3, CLES2, ‘ Gxj-6 and NEAU-HEGS1-5 were 47.6 and 92.2 %, 47.5 and 92.2 %, 55.9 and 94.0 %, 33.1 and 86.8 %, and 33.6 and 87.1 %, respectively. These results and some physiological and biochemical properties demonstrated that the strain could be distinguished from its closest relatives. Therefore, it is proposed that strain NEAU-D428 should be classified as representative of a novel species of the genus , for which the name sp. nov. is proposed. The type strain is NEAU-D428 (=CGMCC 4.7523=DSM 109822).

Funding
This study was supported by the:
  • JunweiZhao , the Heilongjiang Postdoctoral Fund , (Award LBH-Z17015)
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004684
2021-02-02
2021-02-26
Loading full text...

Full text loading...

References

  1. Nonomura H, Ohara Y. Distribution of actinomycetes in soil. II. Microbispora, a new genus of the Streptomycetaceae . J Ferment Technol 1957; 35: 307 311
    [Google Scholar]
  2. Zhao J, Yu B, Han C, Cao P, Yu Z et al. Microbispora fusca sp. nov., a novel actinomycete isolated from the ear of wheat (Triticum aestivum L.). Int J Syst Evol Microbiol 2020; 70: 139 145 [CrossRef] [PubMed]
    [Google Scholar]
  3. Klykleung N, Yuki M, Kudo T, Ohkuma M, Phongsopitanun W et al. Microbispora catharanthi sp. nov., a novel endophytic actinomycete isolated from the root of Catharanthus roseus . Int J Syst Evol Microbiol 2020; 70: 964 970 [CrossRef] [PubMed]
    [Google Scholar]
  4. Han C, Tian Y, Zhao J, Yu Z, Jiang S et al. Microbispora triticiradicis sp. nov., a novel actinomycete isolated from the root of wheat (Triticum aestivum L.). Int J Syst Evol Microbiol 2018; 68: 3600 3605 [CrossRef] [PubMed]
    [Google Scholar]
  5. Kaewkla O, Koomsiri W, Thamchaipenet A, Franco CMM. Microbispora clausenae sp. nov., an endophytic actinobacterium isolated from the surface-sterilized stem of a Thai medicinal plant, Clausena excavala Burm. f. Int J Syst Evol Microbiol 2020; 70: 6213 6219 [CrossRef] [PubMed]
    [Google Scholar]
  6. Han C, Zhao J, Yu B, Shi H, Zhang C et al. Microbispora tritici sp. nov., a novel actinomycete isolated from a root of wheat (Triticum aestivum L.). Antonie van Leeuwenhoek 2019; 112: 1137 1145 [CrossRef] [PubMed]
    [Google Scholar]
  7. Gong X, Xiang W, Cao X, Yu Y, Hao Y et al. Microbispora cellulosiformans sp. nov., a novel actinomycete with cellulase activity isolated from soil in the cold region. Antonie van Leeuwenhoek 2020; 113: 2053 2062 [CrossRef] [PubMed]
    [Google Scholar]
  8. Atlas RM. Handbook of microbiological media. In Parks LC. editor Microbiology Boca Raton: CRC Press; 1993
    [Google Scholar]
  9. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16: 313 340 [CrossRef]
    [Google Scholar]
  10. 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] [PubMed]
    [Google Scholar]
  11. Waksman SA. The Actinomycetes A summary of current knowledge, New York: Ronald; 1967
    [Google Scholar]
  12. Jones KL. Fresh isolates of actinomycetes in which the presence of sporogenous aerial mycelia is a fluctuating characteristic. J Bacteriol 1949; 57: 141 145 [CrossRef] [PubMed]
    [Google Scholar]
  13. Waksman SA. The Actinomycetes, vol. 2, Classification, Identification and Descriptions of Genera and Species Baltimore: Williams and Wilkins; 1961
    [Google Scholar]
  14. Kelly KL. Inter-society color council-national Bureau of standards color-name charts illustrated with centroid colors published in US. 1964
  15. Cao P, Li C, Tan K, Liu C, Xu X et al. Characterization, phylogenetic analyses and pathogenicity of Enterobacter cloacae on rice seedlings in Heilongjiang Province, China. Plant Dis 2020; 104: 1601 1609 [CrossRef] [PubMed]
    [Google Scholar]
  16. Zhao J, Han L, Yu M, Cao P, Li D et al. Characterization of Streptomyces sporangiiformans sp. nov., a novel soil actinomycete with antibacterial activity against Ralstonia solanacearum . Microorganisms 2019; 7: 360 [CrossRef] [PubMed]
    [Google Scholar]
  17. Smibert RM, Krieg NR. Phenotypic characterisation. In Gerhardt P, R. G. E Murray, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology American Society for Microbiology; 1994 pp 607 654
    [Google Scholar]
  18. 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]
  19. 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]
  20. 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] [PubMed]
    [Google Scholar]
  21. Lechevalier MP, Lechevalier HA. The chemotaxonomy of actinomycetes. In Dietz A, Thayer DW. (editors) Actinomycete Taxonomy Special Publication 6 Society of Industrial Microbiology; 1980 pp 227 291
    [Google Scholar]
  22. 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]
  23. 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]
  24. Wu C, Lu X, Qin M, Wang Y, Ruan J. Analysis of menaquinone compound in microbial cells by HPLC. Microbiology 1989; 16: 176 178
    [Google Scholar]
  25. Qu Z, Ruan JS, Hong K. Application of high performance liquid chromatography and gas chromatography in the identification of Actinomyces. Biotechnology Bulletin 2009; s1: 79 82
    [Google Scholar]
  26. Zhuang X, Peng C, Wang Z, Zhao J, Shen Y et al. Actinomadura physcomitrii sp. nov., a novel actinomycete isolated from moss [Physcomitrium sphaericum (Ludw) Fuernr]. Antonie van Leeuwenhoek 2020; 113: 677 685 [CrossRef] [PubMed]
    [Google Scholar]
  27. 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] [PubMed]
    [Google Scholar]
  28. 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] [PubMed]
    [Google Scholar]
  29. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4: 406 425 [CrossRef] [PubMed]
    [Google Scholar]
  30. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20: 406 416 [CrossRef]
    [Google Scholar]
  31. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17: 368 376 [CrossRef] [PubMed]
    [Google Scholar]
  32. 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] [PubMed]
    [Google Scholar]
  33. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39: 783 791 [CrossRef]
    [Google Scholar]
  34. 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] [PubMed]
    [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] [PubMed]
    [Google Scholar]
  36. 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] [PubMed]
    [Google Scholar]
  37. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008; 24: 713 714 [CrossRef] [PubMed]
    [Google Scholar]
  38. Yoon S-H, Ha S-M, 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] [PubMed]
    [Google Scholar]
  39. 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] [PubMed]
    [Google Scholar]
  40. 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] [PubMed]
    [Google Scholar]
  41. De Ley J, Cattoir H, Reynaerts A. The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 1970; 12: 133 142 [CrossRef] [PubMed]
    [Google Scholar]
  42. Huss VA, Festl H, Schleifer KH. Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol 1983; 4: 184 192 [CrossRef] [PubMed]
    [Google Scholar]
  43. Lechevalier MP, De Bièvre C, Lechevalier H. Chemotaxonomy of aerobic actinomycetes: phospholipid composition. Biochem Syst Ecol 1977; 5: 249 260 [CrossRef]
    [Google Scholar]
  44. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57: 81 91 [CrossRef] [PubMed]
    [Google Scholar]
  45. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106: 19126 19131 [CrossRef] [PubMed]
    [Google Scholar]
  46. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O. 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]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004684
Loading
/content/journal/ijsem/10.1099/ijsem.0.004684
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
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