1887

Abstract

A novel actinobacterium, designated strain H8750, was isolated from sediment sampled at Lugu Lake, southwest PR China and its polyphasic taxonomy was studied. Strain H8750 produced well-developed substrate mycelium, and formed club-shaped and hooked structures borne on the tip of the aerial mycelia. It contained -diaminopimelic, glucose, ribose and madurose in whole-cell hydrolysates. The predominant menaquinones were MK-9(H), MK-9(H) and MK-9(H). The phospholipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, hydroxy-phosphatidylethanolamine, unidentified phospholipids and unidentified aminophospholipids. The major fatty acid (>10 %) were 9 C, iso-C and C. The DNA G+C content was 69.7 mol% based on the whole genome sequence. Phylogenetic analysis based on 16S rRNA gene and whole-genome sequences indicated that strain H8750 was closely related to JCM 10982 (98.0 %), JCM 10983 (97.9 %) and DSM 45867 (97.8 %) and formed a monophyletic clade within the genus in the phylogenetic trees. The average nucleotide identity and digital DNA–DNA hybridization values between strain H8750 and its closely related species were 79.8~87.2 % and 25.9~28.0 %, respectively, which showed that it belonged to a distinct species. Furthermore, the morphological and phenotypic characteristics allowed the isolate to be differentiated from its closely related species. Therefore, it is concluded that strain H8750 can be classified as representing a novel species of the genus , for which the name sp. nov. is proposed. The type strain is H8750 (=JCM 34849=CICC 25116). Moreover, based on the gene prediction results, strain H8750 may have the genetic potential to synthesize many new secondary metabolites, which further increases its bioactive value.

Funding
This study was supported by the:
  • start-up fund of introducing talent of Chengdu University (Award No. 20181915049)
    • Principle Award Recipient: ChaolanLiu
  • Special Program for Basic Research of the Ministry of Science and 568 Technology, China (Award No. 2017FY100301)
    • Principle Award Recipient: YiwenChu
  • Sichuan Science and Technology Program (Award No. 2020YJ0276)
    • Principle Award Recipient: ChaolanLiu
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005526
2022-09-21
2024-12-14
Loading full text...

Full text loading...

References

  1. Tamura T, Suzuki S, Hatano K. Acrocarpospora gen. nov., a new genus of the order Actinomycetales. Int J Syst Evol Microbiol 2000; 50 Pt 3:1163–1171 [View Article] [PubMed]
    [Google Scholar]
  2. Williams ST, Sharples GP. Streptosporangium corrugation sp. nov., an actinomycete with some unusual morphological features. Int J Syst Bacteriol 1976; 26:45–52 [View Article]
    [Google Scholar]
  3. Niemhom N, Suriyachadkun C, Tamura T, Thawai C. Acrocarpospora phusangensis sp. nov., isolated from a temperate peat swamp forest soil. Int J Syst Evol Microbiol 2013; 63:2174–2179 [View Article] [PubMed]
    [Google Scholar]
  4. Tiwari K, Gupta RK. Rare actinomycetes: a potential storehouse for novel antibiotics. Crit Rev Biotechnol 2012; 32:108–132 [View Article] [PubMed]
    [Google Scholar]
  5. Hayakawa M, Nonomura H. Humic acid-vitamin agar, a new medium for the selective isolation of soil actinomycetes. J Ferment Technol 1987; 65:501–509 [View Article]
    [Google Scholar]
  6. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
    [Google Scholar]
  7. Liu C, Guo Y, Li L, Wang X, Lin J et al. Catellatospora sichuanensis sp. nov., a novel actinobacterium isolated from soil. Int J Syst Evol Microbiol 2020; 70:3309–3315 [View Article] [PubMed]
    [Google Scholar]
  8. 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]
  9. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23:2947–2948 [View Article] [PubMed]
    [Google Scholar]
  10. 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]
  11. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article]
    [Google Scholar]
  12. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol 1971; 20:406–416 [View Article]
    [Google Scholar]
  13. 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]
    [Google Scholar]
  14. 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]
    [Google Scholar]
  15. 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]
    [Google Scholar]
  16. Nei M, Kumar S. Molecular Evolution and Phylogenetics New York: Oxford University Press; 2000
    [Google Scholar]
  17. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article]
    [Google Scholar]
  18. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article] [PubMed]
    [Google Scholar]
  19. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article] [PubMed]
    [Google Scholar]
  20. Zuo G, Hao B. CVTree3 web server for whole-genome-based and alignment-free prokaryotic phylogeny and taxonomy. Genomics, Proteomics Bioinf 2015; 13:321–331 [View Article]
    [Google Scholar]
  21. Zuo GH. CVTree: a parallel alignment-free phylogeny and taxonomy tool based on composition vectors of genomes. Genomics, Proteomics Bioinf 2021; 19:662–667 [View Article]
    [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 H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article] [PubMed]
    [Google Scholar]
  24. Xu L, Dong Z, Fang L, Luo Y, Wei Z et al. OrthoVenn2: a web server for whole-genome comparison and annotation of orthologous clusters across multiple species. Nucleic Acids Res 2019; 47:W52–W58 [View Article] [PubMed]
    [Google Scholar]
  25. 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]
  26. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article] [PubMed]
    [Google Scholar]
  27. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article]
    [Google Scholar]
  28. 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 [View Article]
    [Google Scholar]
  29. Kelly KL. Inter-Society Colour Council–National Bureau of Standards Colour–Name Charts Illustrated with Centroid Colours US National Bureau of Standards; 1964
    [Google Scholar]
  30. Jia FY, Liu CX, Wang XJ, Zhao JW, Liu QF et al. A new member of the family micromonosporaceae. Antonie van Leeuwenhoek 2013; 103:399–408 [View Article]
    [Google Scholar]
  31. 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 [View Article]
    [Google Scholar]
  32. Gordon RE, Barnett DA, Handerhan JE, Pang CHN. Nocardia coeliaca, Nocardia autotrophica, and the nocardin strain. Int J Syst Bacteriol 1974; 24:54–63 [View Article]
    [Google Scholar]
  33. Smibert RM, Krieg NR. Methods for general and molecular bacteriology. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. eds Phenotypic Characterization Washington: American Society for Microbiology; 1994 pp 607–654
    [Google Scholar]
  34. Yokota A, Tamura T, Hasegawa T, Huang LH. Catenuloplanes japonicus 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]
  35. Gomori G. Preparation of buffers for use in enzyme studies. Methods Enzymol 1955; 1:138–146 [View Article]
    [Google Scholar]
  36. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974; 28:226–231 [View Article] [PubMed]
    [Google Scholar]
  37. Lechevalier MP, Lechevalier HA. The chemotaxonomy of actinomycetes. In Dietz A, Thayer DW. eds Actinomycete Taxonomy Special Publication vol 6 Arlington: Society of Industrial Microbiology; 1980 pp 277–291
    [Google Scholar]
  38. Uchida K, Kudo T, Suzuki K-I, Nakase T. A new rapid method of glycolate test by diethyl ether extraction, which is applicable to a small amount of bacterial cells of less than one milligram. J Gen Appl Microbiol 1999; 45:49–56 [View Article]
    [Google Scholar]
  39. Minnikin DE, Hutchinson IG, Caldicott AB, Goodfellow M. Thin-layer chromatography of methanolysates of mycolic acid-containing bacteria. J Chromatogr A 1980; 188:221–233 [View Article]
    [Google Scholar]
  40. Komagata K, Suzuki K. 4 lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1988; 19:161–207 [View Article]
    [Google Scholar]
  41. Stackebrandt E, Kroppenstedt RM, Jahnke KD, Kemmerling C, Gürtle H et al. Transfer of Streptosporangium viridogriseum (Okuda et al. 1996), Streptosporangium viridogriseum subsp. kofuense (Nonomura and Ohara 1969), and Streptosporangium albidum (Furumai et al. 1968) to Kutzneria gen. nov. as Kutzneria viridogrisea comb. nov., Kutzneria kofuensis comb. nov., and Kutzneria albida comb. nov., respectively, and emendation of the genus Streptosporangium. Int J Syst Bacteriol 1996 [View Article]
    [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.005526
Loading
/content/journal/ijsem/10.1099/ijsem.0.005526
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