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Streptomyces chengbuensis sp. nov., isolated from the rhizosphere soil of Cathaya argyrophylla

Abstract

Strain HUAS CB01T was a novel actinobacterium which was isolated from the rhizosphere soil of Cathaya argyrophylla, Chengbu Miao Autonomous County of Hunan Province, China. The strain formed well-growing substrate mycelium, diffusible pigments, and aerial mycelium, and differentiated into spiral-type spore chains composed of smooth-surface rod-shaped spores. Phylogenetic analysis on account of 16 S rRNA gene sequence demonstrated the strain HUAS CB01T was a member of the genus Streptomyces and had a close relationship with Streptomyces wuyuanensis CGMCC 4.7042 T (100%) and Streptomyces marianii ICN19T (99.86%). Genome-based comparisons indicated that strain HUAS CB01T could be distinctly different from its closest species, Streptomyces wuyuanensis CGMCC 4.7042 T, Streptomyces marianii ICN19T, with ANIm and dDDH results of 92.78% and 45.90%, 92.22% and 43.30%, respectively, far less than 96.7 and 70% cut-off points recommended for delineating species. The main cellular fatty acids concluded anteiso-C15:0, iso-C14:0, iso-C16:0, C16:0 and C16:1 2OH. The menaquinones were MK-9(H4), MK-9(H6) and MK-9(H8) and the whole-cell sugars consisted of ribose and mannose. The polar lipids included phosphatidyl ethanolamine, diphosphatidylglycerol, phosphatidylglycerol, mannosides and unidentified phospholipids. According to these genotypic and phenotypic characteristics, strain HUAS CB01T can be distinguished and representative to be a novel species of the genus Streptomyces, for which the name Streptomyces chengbuensis is proposed. The type strain is HUAS CB01T ( = MCCC 1K08666T = JCM 36277 T).

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References

  1. Igwaran A, Kayode AJ, Moloantoa KM, Khetsha ZP, Unuofin JO. Cyanobacteria harmful algae blooms: causes, impacts, and risk management. Water Air Soil Pollut. 2024;235:71.

    Article  CAS  Google Scholar 

  2. Kavagutti VS, Bulzu PA, Chiriac CM, Salcher MM, Mukherjee I, et al. High-resolution metagenomic reconstruction of the freshwater spring bloom. Microbiome. 2023;11:15.

    Article  PubMed  PubMed Central  Google Scholar 

  3. Iiames JS, Salls WB, Mehaffey MH, Nash MS, Christensen JR, Schaeffer BA. Modeling anthropogenic and environmental influences on freshwater harmful algal bloom development detected by meris over the central United States. Water Resour Res. 2021;10:57.

    Google Scholar 

  4. Roberts VA, Vigar M, Backer L, Veytsel GE, Esschert KLV. Surveillance for harmful algal bloom events and associated human and animal illnesses-one health harmful algal bloom system, United States. Morb Mortal Wkly Rep. 2020;69:1889–94.

    Article  Google Scholar 

  5. Howard A, Kirkby MJ, Kneale PE, Mcdonald AT. Modelling the growth of cyanobacteria (GrowSCUM). Hydrol Process. 1995;9:809–20.

    Article  Google Scholar 

  6. Sun R, Sun PF, Zhang JH, Sofia EE, Wu Y. Microorganisms-based methods for harmful algal blooms control: a review. Bioresour Technol. 2017;248:12–20.

    Article  PubMed  Google Scholar 

  7. Liting C, Jun Z, Siyi T, Dai G, Song L, Gan N. Progress in control of cyanobacteria by microorganism. J Wuhan Univ. 2019;65:401–10.

    Google Scholar 

  8. Tang SS, Lin WT, Li JY, Cai XL, Li HQ. Isolation and algicidal characteristics of the algicidal components from actinomycete strain L74. Microbiol China. 2011;38:654–9.

    CAS  Google Scholar 

  9. Wang SQ, Luo CQ, Zhu XM, Yang PH, Luo YS, Gan NQ. Isolation and identification of an efficient algicidal actinomycetes strain LW9 and Its algicidal characteristics. J Wuhan Univ. 2021;67:93–102.

    Article  Google Scholar 

  10. Xiao CQ, Jiang HC, Cheng K, Zhao YJ. Selection of algae lysing Actinomycetes AN02 and optimization of its cultural conditions. J Microbiol. 2007;4:11–12.

    Google Scholar 

  11. Luo JF, Wang Y, Tang SH, Liang JW, Lin WT, et al. Isolation and identification of algicidal compound from Streptomyces and algicidal mechanism to microcystis aeruginosa. PLoS ONE. 2013;8:1–14.

    Google Scholar 

  12. Somdee T, Sumalai N, Somdee A. A novel actinomycete Streptomyces aurantiogriseus with algicidal activity against the toxic cyanobacterium Microcystis aeruginosa. J Appl Phycol. 2013;25:1587–94.

    Article  CAS  Google Scholar 

  13. An XL, Zhang BZ, Zhang HJ, Li Y, Zheng W, et al. Discovery of an algicidal compound from Brevibacterium sp. BS01 and its effect on a harmful algal bloom-causing species, Alexandrium tamarense. Front Microbiol. 2015;6:1235.

    Article  PubMed  PubMed Central  Google Scholar 

  14. Kim MJ, Jeong SY, Lee SJ. Isolation, identification, and algicidal activity of marine bacteria against Cochlodinium polykrikoides. J Appl Phycol. 2008;20:1069–78.

    Article  Google Scholar 

  15. Mo P, Zhao JR, Li KQ, Tang XK, Gao J. Streptomyces manganisoli sp. nov., a novel actinomycete isolated from manganese-contaminated soil. Int J Syst Evol Microbiol. 2018;68:1890–5.

    Article  CAS  PubMed  Google Scholar 

  16. Atlas RM Handbook of microbiological media. 1993 Edited by Parks LC CRC Press, Boca Raton.

  17. Shirling EB, Gottlieb D. Methods for characterisation of Streptomyces species. Int J Syst Bacteriol. 1966;16:313–40.

    Article  Google Scholar 

  18. Ridgway R. Color standards and color nomenclature. 1912 Published by the author, Washington, DC. 1-43, plate I–LII.

  19. Xu LH, Li WJ, Liu ZH, Jiang CL. Actinomycetes systematics: principles, methods and practices. Beijing: Science Press; 2007.

    Google Scholar 

  20. Ruan J, Huang Y. Rapid Identification and systematics of actinobacteria. Beijing: Science Press; 2011.

    Google Scholar 

  21. Hasegawa T, Takizawa M, Tanida S. A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Appl Microbiol. 1983;29:319–22.

    Article  CAS  Google Scholar 

  22. Lechevalier MP, Lechevalier H. Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol. 1970;20:435–43.

    Article  CAS  Google Scholar 

  23. Mo P, Li K, Zhou JH, Zhou FM, He J, Zou WS, Gao J. Nocardiopsis changdeensis sp. nov., an endophytic actinomycete isolated from the roots of Eucommia ulmoides Oliv. J Antibiot. 2023;76:191–7.

    Article  CAS  Google Scholar 

  24. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, Chun J. Introducing EzBioCloud: a taxonomically united database of 16S rRNA and whole genome assemblies. Int J Syst Evol Microbiol. 2017;67:1613–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987;4:406–25.

    CAS  PubMed  Google Scholar 

  26. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol. 1981;17:368–76.

    Article  CAS  PubMed  Google Scholar 

  27. Kluge AG, Farris JS. Quantitative phyletics and the evolution of anurans. Syst Zool. 1969;18:1–32.

    Article  Google Scholar 

  28. Tamura K, Stecher G, Kumar S. MEGA11: molecular evolutionary genetics analysis version 11. Mol Biol Evol. 2021;38:3022–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Meier-Kolthoff JP, Göker M. TYGS is an automated high-through-put platform for state-of-the-art genome-based taxonomy. Nat Commun. 2019;10:2182.

    Article  PubMed  PubMed Central  Google Scholar 

  30. 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;32:929–31.

    Article  CAS  PubMed  Google Scholar 

  31. Meier-Kolthoff JP, Auch AF, Klenk HP, Goker M. Genome sequence based species delimitation with confidence intervals and improved distance functions. BMC Bioinforma. 2013;14:1–14.

    Article  Google Scholar 

  32. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, et al. The RAST server: rapid annotations using subsystems technology. BMC Genom. 2008;9:75.

    Article  Google Scholar 

  33. 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. 2019;48:D517–25.

    PubMed Central  Google Scholar 

  34. Makarova KS, Wolf YI, Iranzo J, Shmakov SA, Alkhnbashi OS, et al. Evolutionary classification of CRISPR–Cassystems: a burst of class 2 and derived variants. Nat Rev Microbiol. 2019;18:67–83.

    Article  PubMed  PubMed Central  Google Scholar 

  35. Claire B, Laird MR, Williams KP, Lau BY, Hoad G, et al. IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets. Nucleic Acids Res. 2017;45:W30–5.

    Article  Google Scholar 

  36. Hu SR, Li KQ, Zhang YF, Wang YF, Li FU, Yan X, Tang XK, Gao J. New insights into the threshold values of multilocus sequence analysis, average nucleotide identity and digital DNA–DNA hybridization in delineating Streptomyces species. Front Microbiol. 2022;13:910277.

    Article  PubMed  PubMed Central  Google Scholar 

  37. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE, Stackebrandt E, Starr MP, Trüper HG. International Committee on Systematic Bacteriology. Report of the ad hoc committee on the reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol. 1987;37:463–4.

    Article  Google Scholar 

  38. Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today. 2006;4:6–9.

    Google Scholar 

  39. Farris JS. Estimating phylogenetic trees from distance matrices. Am Nat. 1972;106:645–68.

    Article  Google Scholar 

  40. Vincent L, Richard D, Olivier G. FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program. Mol Biol Evol. 2015;32:2798–800.

    Article  Google Scholar 

  41. Zhang X, Zhang J, Zheng J, Xin D, Xin Y, Pang H. Streptomyces wuyuanensis sp. nov. an actinomycete from soil. Int J Syst Bacteriol. 2013;63:2945–50.

    Article  CAS  Google Scholar 

  42. Iniyan AM, Wink J, Landwehr W, Ramprasad EVV, Sasikala C, Ramana CV, Schumann P, Spröer C, Bunk B, Joseph FJRS, Joshua SA, Shyl ENSGD, Kannan RR, Vincent SGP. Streptomyces marianii sp. nov. a novel marine actinomycete from southern coast of India. J Antibiot. 2020;74:1–11.

    Google Scholar 

Download references

Acknowledgements

The authors sincerely thank Zeng Zhihong and Xu Wangjie (Wuhan Benagen Technology Co., Ltd, Hubei, China) for giving great help in gene sequencing.

Funding

This research was funded by the project of Hunan Provincial Education Department (23B0659), Hunan Provincial Natural Science Foundation (2023JJ40464 and 2024JJ7300), Research start-up fee for Hunan University of Arts and Sciences (22BSQD27), Central guidance local science and technology development fund projects (2023ZYC012), the Innovation and Entrepreneurship Training Program for College Students, and Innovation Team of Microbial Technology in Hunan University of Arts and Science (202026).

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YX Z, P M and CX L designed the study, ZB Z and P M developed and implemented the program, YX Z, ZF Z and KR H performed the experiments, P M, HX Z and Y W analyzed the data, ZB Z, CX L, YX Z and P M wrote the manuscript, Y W, KR H and P M revised a paper.

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Correspondence to Ping Mo or Kerui Huang.

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The NCBI accession numbers for the 16 S rRNA gene sequence and genome sequence of strain HUAS CB01T are OR237576 and CP129137, respectively.

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Zheng, Y., Mo, P., Li, C. et al. Streptomyces chengbuensis sp. nov., isolated from the rhizosphere soil of Cathaya argyrophylla. J Antibiot (2024). https://doi.org/10.1038/s41429-024-00745-z

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