1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 73, Issue 12

sp. nov., isolated from the rhizosphere soil of and healthy leaves of No Access

Abstract

Two actinomycete strains, designated MG62 and CRLD-Y-1, were isolated from rhizosphere soil of and healthy leaves of , respectively, in Hunan province, PR China. They could produce abundant aerial mycelia that generated rod-shaped spores with spiny surfaces. Morphological features of the two strains are typical of the genus . Strains MG62 and CRLD-Y-1 exhibited 99.93 % 16S rRNA gene sequence similarity. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between them were 99.99 and 100 %, respectively, suggesting that they belonged to the same species. 16S rRNA gene sequences analysis revealed that the two strains belonged to the genus and showed highest similarities to NBRC 13104 (99.07–99.29 %) and ISP 5293 (99.21–99.35 %). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strains MG62 and CRLD-Y-1 were closely related to NBRC 13104 and ISP 5293. However, the ANI, dDDH and multilocus sequence analysis evolutionary distance values between the two strains and their relatives provide a robust basis upon which to verify strains MG62 and CRLD-Y-1 as representing a novel species. Moreover, a comprehensive comparison of phenotypic and chemotaxonomic characteristics further confirmed that the two strains were distinct from their relatives. Based on all these data above, strains MG62 and CRLD-Y-1 should represent a novel species, for which the name sp. nov. is proposed. The type strain is MG62 (=JCM 34747=MCCC 1K06175).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): healthy leaves , rhizosphere soil and Streptomyces koelreuteriae sp. nov.
Funding
This study was supported by the:
  • the Hunan Provincial Natural Science Foundation of China and Xiangtan Science and Technology Bureau (Award 2022JJ50125)
    • Principle Award Recipient: JianGao
  • the open fund project of Guangxi Key Laboratory for Polysaccharide Materials and Modification (Award GXPSMM20-7)
    • Principle Award Recipient: JianGao
© 2023 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006196
2023-12-06
2024-05-08
Loading full text...

Full text loading...

References

  1. He PS, Takeuchi T, Yano E. An overview of the China National Tobacco Corporation and State Tobacco Monopoly Administration. Environ Health Prev Med 2013; 18:85–90 [View Article]
     [Google Scholar]
  2. Liu Y, Wu D, Liu Q, Zhang S, Tang Y et al. The sequevar distribution of Ralstonia solanacearum in tobacco-growing zones of China is structured by elevation. Eur J Plant Pathol 2017; 147:541–551 [View Article]
     [Google Scholar]
  3. Jiang G, Wei Z, Xu J, Chen H, Zhang Y et al. Bacterial wilt in China: history, current status, and future perspectives. Front Plant Sci 2017; 8:1549 [View Article]
     [Google Scholar]
  4. Yang L, Wu L, Yao X, Zhao S, Wang J et al. Hydroxycoumarins: new, effective plant-derived compounds reduce Ralstonia pseudosolanacearum populations and control tobacco bacterial wilt. Microbiol Res 2018; 215:15–21 [View Article] [PubMed]
     [Google Scholar]
  5. Peeters N, Guidot A, Vailleau F, Valls M. Ralstonia solanacearum, a widespread bacterial plant pathogen in the post-genomic era. Mol Plant Pathol 2013; 14:651–662 [View Article] [PubMed]
     [Google Scholar]
  6. Karthika S, Midhun SJ, Jisha MS. A potential antifungal and growth-promoting bacterium Bacillus sp. KTMA4 from tomato rhizosphere. Microb Pathog 2020; 142:104049 [View Article] [PubMed]
     [Google Scholar]
  7. Devi S, Sharma M, Manhas RK. Investigating the plant growth promoting and biocontrol potentiality of endophytic Streptomyces sp. SP5 against early blight in Solanum lycopersicum seedlings. BMC Microbiol 2022; 22:285 [View Article] [PubMed]
     [Google Scholar]
  8. Mo P, Zhao J, Li K, Tang X, Gao J. Streptomyces manganisoli sp. nov., a novel actinomycete isolated from manganese-contaminated soil. Int J Syst Evol Microbiol 2018; 68:1890–1895 [View Article]
     [Google Scholar]
  9. Li K, Guo Y, Wang J, Wang Z, Zhao J et al. Streptomyces aquilus sp. nov., a novel actinomycete isolated from a Chinese medicinal plant. Int J Syst Evol Microbiol 2020; 70:1912–1917 [View Article]
     [Google Scholar]
  10. Atlas RM. Handbook of Microbiological Media. 4th edn Boca Raton: CRC Press; 2010 [View Article]
     [Google Scholar]
  11. Rainey FA, Ward-Rainey N, Kroppenstedt RM, Stackebrandt E. The genus Nocardiopsis represents a phylogenetically coherent taxon and a distinct actinomycete lineage: proposal of Nocardiopsaceae fam. nov. Int J Syst Bacteriol 1996; 46:1088–1092 [View Article] [PubMed]
     [Google Scholar]
  12. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173:697–703 [View Article] [PubMed]
     [Google Scholar]
  13. 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] [PubMed]
     [Google Scholar]
  14. 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]
  15. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  16. Kluge AG, Farris JS. Quantitative phyletics and the evolution of anurans. Systematic Zoology 1969; 18:1 [View Article]
     [Google Scholar]
  17. Tamura K, Stecher G, Kumar S. MEGA11: Molecular Evolutionary Genetics Analysis version 11. Mol Biol Evol 2021; 38:3022–3027 [View Article] [PubMed]
     [Google Scholar]
  18. Liu Y, Pei T, Du J, Huang H, Deng M-R et al. Comparative genomic analysis of the genus Novosphingobium and the description of two novel species Novosphingobium aerophilum sp. nov. and Novosphingobium jiangmenense sp. nov. Syst Appl Microbiol 2021; 44:126202 [View Article] [PubMed]
     [Google Scholar]
  19. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [View Article] [PubMed]
     [Google Scholar]
  20. Blin K, Shaw S, Kloosterman AM, Charlop-Powers Z, van Wezel GP et al. antiSMASH 6.0: improving cluster detection and comparison capabilities. Nucleic Acids Res 2021; 49:W29–W35 [View Article] [PubMed]
     [Google Scholar]
  21. Alcock BP, Raphenya AR, Lau TTY, Tsang KK, Bouchard M et al. CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Res 2020; 48:D517–D525 [View Article] [PubMed]
     [Google Scholar]
  22. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [View Article] [PubMed]
     [Google Scholar]
  23. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article]
     [Google Scholar]
  24. Labeda DP, Dunlap CA, Rong X, Huang Y, Doroghazi JR et al. Phylogenetic relationships in the family Streptomycetaceae using multi-locus sequence analysis. Antonie van Leeuwenhoek 2017; 110:563–583 [View Article] [PubMed]
     [Google Scholar]
  25. 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]
  26. Yoon SH, Ha SM, Lim JM, Kwon SJ, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article] [PubMed]
     [Google Scholar]
  27. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
     [Google Scholar]
  28. Ridgway R. Color Standards and Color Nomenclature Washington, D.C: 1912 [View Article]
     [Google Scholar]
  29. Qin S, Li J, Chen H-H, Zhao G-Z, Zhu W-Y et al. Isolation, diversity, and antimicrobial activity of rare actinobacteria from medicinal plants of tropical rain forests in Xishuangbanna, China. Appl Environ Microbiol 2009; 75:6176–6186 [View Article] [PubMed]
     [Google Scholar]
  30. Xu LH, Li WJ, Liu ZH, Jiang CL. Actinomycetes Systematics: Principles, Methods and Practices Beijing, China: Science Press; 2007
     [Google Scholar]
  31. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. In MIDI Technical Note 101 Newark, DE: MIDI inc; 1990
     [Google Scholar]
  32. Collins MD, Faulkner M, Keddie RM. Menaquinone composition of some sporeforming actinomycetes. Syst Appl Microbiol 1984; 5:20–29 [View Article]
     [Google Scholar]
  33. Hasegawa T, Takizawa M, Tanida S. A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Appl Microbiol 1983; 29:319–322 [View Article]
     [Google Scholar]
  34. Lechevalier MP, Lechevalier H. Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 1970; 20:435–443 [View Article]
     [Google Scholar]
  35. 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]
  36. Wright F, Bibb MJ. Codon usage in the G+C-rich Streptomyces genome. Gene 1992; 113:55–65 [View Article] [PubMed]
     [Google Scholar]
  37. Hu S, Li K, Zhang Y, Wang Y, Fu L et al. New insights into the threshold values of multi-locus sequence analysis, average nucleotide identity and digital DNA–DNA hybridization in delineating Streptomyces species. Front Microbiol 2022; 13:910277 [View Article]
     [Google Scholar]
  38. Moore WEC, Stackebrandt E, Kandler O, Colwell RR, Krichevsky MI et al. 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]
  39. Rong X, Huang Y. Taxonomic evaluation of the Streptomyces hygroscopicus clade using multilocus sequence analysis and DNA-DNA hybridization, validating the MLSA scheme for systematics of the whole genus. Syst Appl Microbiol 2012; 35:7–18 [View Article] [PubMed]
     [Google Scholar]
  40. Rautenshtein YI. Biology of antibiotic-producing Actinomycetes (in Russian). Trans Inst Microbiol Acad Sci USSR 1960; 8:1–344
     [Google Scholar]
  41. Pridham TG, Hesseltine CW, Benedict RG. A guide for the classification of streptomycetes according to selected groups; placement of strains in morphological sections. Appl Microbiol 1958; 6:52–79 [View Article] [PubMed]
     [Google Scholar]
  42. Labeda DP, Lyons AJ. Deoxyribonucleic acid relatedness among species of the “Streptomyces cyaneus" cluster. Syst Appl Microbiol 1991; 14:158–164 [View Article]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.006196
Loading
Streptomyces koelreuteriae sp. nov., isolated from the rhizosphere soil of Koelreuteria paniculata and healthy leaves of Xanthium sibiricum
Int J Syst Evol Microbiol 73, 006196 (2023); https://doi.org/10.1099/ijsem.0.006196
/content/journal/ijsem/10.1099/ijsem.0.006196
/content/journal/ijsem/10.1099/ijsem.0.006196
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited 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