1887

Abstract

A novel actinomycete, designated strain NEAU-YY374, was isolated from root of wheat and a polyphasic taxonomic study was carried out. 16S rRNA gene sequence analysis indicated that strain NEAU-YY374 was closely related to NEAU-Jh2-17 (99.3 %) and 12A09 (98.6%). Phylogenetic analysis based on 16S rRNA gene sequences demonstrated that strain NEAU-YY374 formed a stable clade with NEAU-Jh2-17 and 12A09 in trees generated with two algorithms. Key morphological and chemotaxonomic properties also confirmed the affiliation of strain NEAU-YY374 to the genus . The differences of DNA G+C contents among these three strains were all less than 1 %, and the digital DNA-DNA hybridization and the average nucleotide identity values were higher than the circumscription thresholds of species and subspecies, clearly indicating that the three strains should belong to the same species. Therefore, we concluded that strain NEAU-YY374 is a new strain of . Meanwhile, should be reclassified as a later heterotypic synonym of according to the priority of publication and validation of the name.

Funding
This study was supported by the:
  • the National Natural Science Foundation of China (Award 31972291)
    • Principle Award Recipient: XiangjingWang
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2022-11-23
2024-12-13
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References

  1. Stackebrandt E, Rainey FA, Ward-rainey NL. Proposal for a new hierarchic classification system, Actinobacteria classis nov. Int J Syst Bacteriol 1997; 47:479–491 [View Article]
    [Google Scholar]
  2. Cui XL, Mao PH, Zeng M, Li WJ, Zhang LP et al. Streptimonospora salina gen. nov., sp. nov., a new member of the family Nocardiopsaceae. Int J Syst Evol Microbiol 2001; 51:357–363 [View Article]
    [Google Scholar]
  3. Li W-J, Xu P, Zhang L-P, Tang S-K, Cui X-L et al. Streptomonospora alba sp. nov., a novel halophilic actinomycete, and emended description of the genus Streptomonospora Cui et al. 2001. Int J Syst Evol Microbiol 2003; 53:1421–1425 [View Article] [PubMed]
    [Google Scholar]
  4. Zhang D-F, Pan H-Q, He J, Zhang X-M, Zhang Y-G et al. Description of Streptomonospora sediminis sp. nov. and Streptomonospora nanhaiensis sp. nov., and reclassification of Nocardiopsis arabia Hozzein & Goodfellow 2008 as Streptomonospora arabica comb. nov. and emended description of the genus Streptomonospora. Int J Syst Evol Microbiol 2013; 63:4447–4455 [View Article]
    [Google Scholar]
  5. Cai M, Zhi X-Y, Tang S-K, Zhang Y-Q, Xu L-H et al. Streptomonospora halophila sp. nov., a halophilic actinomycete isolated from a hypersaline soil. Int J Syst Evol Microbiol 2008; 58:1556–1560 [View Article] [PubMed]
    [Google Scholar]
  6. Cai M, Tang S-K, Chen Y-G, Li Y, Zhang Y-Q et al. Streptomonospora amylolytica sp. nov. and Streptomonospora flavalba sp. nov., two novel halophilic actinomycetes isolated from a salt lake. Int J Syst Evol Microbiol 2009; 59:2471–2475 [View Article] [PubMed]
    [Google Scholar]
  7. Meklat A, Bouras N, Riba A, Zitouni A, Mathieu F et al. Streptomonospora algeriensis sp. nov., a halophilic actinomycete isolated from soil in Algeria. Antonie van Leeuwenhoek 2014; 106:287–292 [View Article] [PubMed]
    [Google Scholar]
  8. Zhao J, Guo L, Liu C, Sun P, Li J et al. Streptomonospora halotolerans sp. nov., an actinomycete isolated from soil. Int J Syst Evol Microbiol 2015; 65:3183–3189 [View Article] [PubMed]
    [Google Scholar]
  9. Tatar D, Guven K, Inan K, Cetin D, Belduz AO et al. Streptomonospora tuzyakensis sp. nov., a halophilic actinomycete isolated from saline soil. Antonie van Leeuwenhoek 2016; 109:35–41 [View Article] [PubMed]
    [Google Scholar]
  10. Wang X, Zhao J, Liu C, Wang J, Shen Y et al. Nonomuraea solani sp. nov., an actinomycete isolated from eggplant root (Solanum melongena L.). Int J Syst Evol Microbiol 2013; 63:2418–2423 [View Article] [PubMed]
    [Google Scholar]
  11. Atlas RM. Handbook of Microbiological Media Boca Raton: CRC Press; 2004 pp 364–365 [View Article]
    [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. Jones KL. Fresh isolates of actinomycetes in which the presence of sporogenous aerial mycelia is a fluctuating characteristic. J Bacteriol 1949; 57:141–145 [View Article]
    [Google Scholar]
  14. Waksman SA. The Actinomycetes. A Summary of Current Knowledge New York: Ronald Press; 1967
    [Google Scholar]
  15. Waksman SA. Classification, identification and descriptions of genera and species. In The Actinomycetes vol 2 Baltimore: Williams and Wilkins; 1961
    [Google Scholar]
  16. 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]
  17. 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:E360 [View Article]
    [Google Scholar]
  18. 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 [View Article]
    [Google Scholar]
  19. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. eds Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp 607–654
    [Google Scholar]
  20. Gordon RE, Barnett DA, Handerhan JE, Pang C-N. Nocardia coeliaca, Nocardia autotrophica, and the nocardin strain. Int J Syst Bacteriol 1974; 24:54–63 [View Article]
    [Google Scholar]
  21. 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 [View Article]
    [Google Scholar]
  22. Kim ES, Kim B-S, Kim K-Y, Woo H-M, Lee S-M et al. Aerobic and anaerobic cellulose utilization by Paenibacillus sp. CAA11 and enhancement of its cellulolytic ability by expressing a heterologous endoglucanase. J Biotechnol 2018; 268:21–27 [View Article] [PubMed]
    [Google Scholar]
  23. 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 [View Article] [PubMed]
    [Google Scholar]
  24. Lechevalier MP, Lechevalier HA. The chemotaxonomy of actinomycetes. In Dietz A, Thayer DW. eds Actinomycete Taxonomy vol 6 Arlington: Society of Industrial Microbiology; 1980 pp 227–291
    [Google Scholar]
  25. 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 [View Article]
    [Google Scholar]
  26. Collins MD. Isoprenoid quinone analyses in bacterial classification and identification. In Goodfellow M, Minnikin DE. eds Chemical Methods in Bacterial Systematics London: Academic Press; 1985 pp 267–284
    [Google Scholar]
  27. Wu C, Lu X, Qin M, Wang Y, Ruan J. Analysis of menaquinone compound in microbial cells by HPLC. Microbiology China 1989; 16:176–178
    [Google Scholar]
  28. Song J, Qiu S, Zhao J, Han C, Wang Y et al. Pseudonocardia tritici sp. nov., a novel actinomycete isolated from rhizosphere soil of wheat (Triticum aestivum L.). Antonie van Leeuwenhoek 2019; 112:765–773 [View Article] [PubMed]
    [Google Scholar]
  29. 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 [View Article] [PubMed]
    [Google Scholar]
  30. 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 [View Article] [PubMed]
    [Google Scholar]
  31. Chun J, Goodfellow M. A phylogenetic analysis of the genus Nocardia with 16S rRNA gene sequences. Int J Syst Bacteriol 1995; 45:240–245 [View Article] [PubMed]
    [Google Scholar]
  32. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22:4673–4680 [View Article] [PubMed]
    [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. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article] [PubMed]
    [Google Scholar]
  35. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article] [PubMed]
    [Google Scholar]
  36. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article]
    [Google Scholar]
  37. 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 [View Article] [PubMed]
    [Google Scholar]
  38. Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 1993; 10:512–526 [View Article] [PubMed]
    [Google Scholar]
  39. 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 [View Article]
    [Google Scholar]
  40. Nikodinovic J, Barrow KD, Chuck JA. High yield preparation of genomic DNA from Streptomyces. Biotechniques 2003; 35:932–934 [View Article]
    [Google Scholar]
  41. 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 [View Article] [PubMed]
    [Google Scholar]
  42. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008; 24:713–714 [View Article] [PubMed]
    [Google Scholar]
  43. 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 [View Article]
    [Google Scholar]
  44. Medema MH, Blin K, Cimermancic P, de Jager V, Zakrzewski P et al. antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Res 2011; 39:W339–46 [View Article]
    [Google Scholar]
  45. 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 [View Article]
    [Google Scholar]
  46. Yoon SH, Ha SM, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article]
    [Google Scholar]
  47. Thayer DW, Lowther SV, Phillips JG. Cellulolytic activities of strains of the genus Cellulomonas. Int J Syst Bacteriol 1984; 34:432–438 [View Article]
    [Google Scholar]
  48. Henrissat B, Claeyssens M, Tomme P, Lemesle L, Mornon JP. Cellulase families revealed by hydrophobic cluster analysis. Gene 1989; 81:83–95 [View Article] [PubMed]
    [Google Scholar]
  49. Krichevsky MI, Moore LH, Moore WEC. 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]
  50. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci 2009; 106:19126–19131 [View Article]
    [Google Scholar]
  51. Meier-Kolthoff JP, Hahnke RL, Petersen J, Scheuner C, Michael V et al. Complete genome sequence of DSM 30083(T), the type strain (U5/41(T)) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy. Stand Genomic Sci 2014; 9:2 [View Article]
    [Google Scholar]
  52. Meier-Kolthoff JP, Klenk HP, Göker M. Taxonomic use of DNA G+C content and DNA-DNA hybridization in the genomic age. Int J Syst Evol Microbiol 2014; 64:352–356 [View Article] [PubMed]
    [Google Scholar]
  53. Parker CT, Tindall BJ, Garrity GM. International Code of Nomenclature of Prokaryotes. Int J Syst Evol Microbiol 2019; 69:S1–S111 [View Article]
    [Google Scholar]
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