1887

Abstract

A novel actinobacterium, strain ZYX-F-186, was isolated from marine sediment sampled on Yongxing Island, Hainan Province, PR China. Based on the results of 16S rRNA gene sequence analysis, strain ZYX-F-186 belongs to the genus , with high similarity to KK1-3 (98.3 %), K11-0047 (98.1 %), K09-0627 (98.1 %), K11-0057 (97.9 %), K07-0523 (97.7 %), and RD004123 (97.7 %). Phylogenetic analysis of 16S rRNA gene sequences showed that the strain formed a single subclade in the genus . The novel isolate contained -diaminopimelic acid, -glutamic acid, glycine, -alanine, and -lysine in the cell wall. The whole-cell sugars were xylose, arabinose, ribose, and rhamnose. The predominant menaquinones were MK-9(H), MK-9(H), and MK-9(H). The characteristic phospholipids were phosphatidylethanolamine, phosphatidylinositol, phosphatidylmethylethanolamine, phosphatidylglycerol, and an unknown phospholipid. The major fatty acids (>5 %) were iso-C, anteiso-C, and iso-C. Genome sequencing showed a DNA G+C content of 71.9 mol%. Low average nucleotide identity, digital DNA–DNA hybridization, and average amino acid identity values demonstrated that strain ZYX-F-186 could be readily distinguished from its closely related species. Based on its phylogenetic, chemotaxonomic, and physiological characteristics, strain ZYX-F-186 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is ZYX-F-186 (=CGMCC 4.8025=CCTCC AA 2023025=JCM 36507).

Funding
This study was supported by the:
  • Central Public-interest Scientific Institution Basal Research Fund for Chinese Academy of Tropical Agricultural Sciences (Award 1630052024021)
    • Principle Award Recipient: You-XingZhao
  • CARS-Chinese Materia Medica (Award CARS-21)
    • Principle Award Recipient: You-XingZhao
  • Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, P. R. China (Award NFZX2021)
    • Principle Award Recipient: You-XingZhao
  • Natural Science Foundation of Hainan Province (Award 821RC643)
    • Principle Award Recipient: Qing-YiXie
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2024-05-16
2024-06-19
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References

  1. Inahashi Y, Matsumoto A, Danbara H, Ōmura S, Takahashi Y. Phytohabitans suffuscus gen. nov., sp. nov., an actinomycete of the family Micromonosporaceae isolated from plant roots. Int J Syst Evol Microbiol 2010; 60:2652–2658 [View Article] [PubMed]
    [Google Scholar]
  2. Inahashi Y, Matsumoto A, Ōmura S, Takahashi Y. Phytohabitans flavus sp. nov., Phytohabitans rumicis sp. nov. and Phytohabitans houttuyneae sp. nov., isolated from plant roots, and emended description of the genus Phytohabitans. Int J Syst Evol Microbiol 2012; 62:2717–2723 [View Article] [PubMed]
    [Google Scholar]
  3. Niemhom N, Chutrakul C, Suriyachadkun C, Thawai C. Phytohabitans kaempferiae sp. nov., an endophytic actinomycete isolated from the leaf of Kaempferia larsenii. Int J Syst Evol Microbiol 2016; 66:2917–2922 [View Article] [PubMed]
    [Google Scholar]
  4. Triningsih DW, Harunari E, Hamada M, Enomoto N, Tamura T et al. Phytohabitans aurantiacus sp. nov., an actinomycete isolated from soil. Int J Syst Evol Microbiol 2023; 73: [View Article] [PubMed]
    [Google Scholar]
  5. Komaki H, Tamura T. Polyketide synthase and nonribosomal peptide synthetase gene clusters in type strains of the genus Phytohabitans. Life 2020; 10:257 [View Article] [PubMed]
    [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. Itoh T, Kudo T, Parenti F, Seino A. Amended description of the genus Kineosporia, based on chemotaxonomic and morphological studies. Int J Syst Bacteriol 1989; 39:168–173 [View Article]
    [Google Scholar]
  8. Raper KB, Fennell DI. The Genus Aspergillus Baltimore: Williams and Wilkins; 1965 p 686
    [Google Scholar]
  9. Castiglione F, Lazzarini A, Carrano L, Corti E, Ciciliato I et al. Determining the structure and mode of action of microbisporicin, a potent lantibiotic active against multiresistant pathogens. Chem Biol 2008; 15:22–31 [View Article]
    [Google Scholar]
  10. 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]
  11. Xie Q, Lin H, Li L, Brown R, Goodfellow M et al. Verrucosispora wenchangensis sp. nov., isolated from mangrove soil. Antonie van Leeuwenhoek 2012; 102:1–7 [View Article] [PubMed]
    [Google Scholar]
  12. Williams ST, Goodfellow M, Alderson G, Wellington EM, Sneath PH et al. Numerical classification of Streptomyces and related genera. J Gen Microbiol 1983; 129:1743–1813 [View Article] [PubMed]
    [Google Scholar]
  13. Williams ST, Cross T. Actinomycetes. In Booth C. ed Methods in Microbiology London: Academic Press; 1971 pp 295–334
    [Google Scholar]
  14. 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]
  15. 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]
  16. Becker B, Lechevalier MP, Lechevalier HA. Chemical composition of cell-wall preparations from strains of various form-genera of aerobic actinomycetes. Appl Microbiol 1965; 13:236–243 [View Article] [PubMed]
    [Google Scholar]
  17. 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]
  18. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. In Technical Note vol 101 Newark, DE: Microbial ID; 1990
    [Google Scholar]
  19. Wang C, Xu X-X, Qu Z, Wang H-L, Lin H-P et al. Micromonospora rhizosphaerae sp. nov., isolated from mangrove rhizosphere soil. Int J Syst Evol Microbiol 2011; 61:320–324 [View Article] [PubMed]
    [Google Scholar]
  20. 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 [View Article] [PubMed]
    [Google Scholar]
  21. 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]
  22. 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]
  23. 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]
  24. 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]
  25. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  26. Kluge AG, Farris JS. Quantitative phyletics and the evolution of Anurans. Syst Zool 1969; 18:1 [View Article]
    [Google Scholar]
  27. 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]
  28. 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]
  29. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
    [Google Scholar]
  30. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008; 24:713–714 [View Article] [PubMed]
    [Google Scholar]
  31. 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]
  32. Rodriguez-R LM, Konstantinidis KT. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. PeerJ Preprints 2016; 4e1900v1 [View Article]
    [Google Scholar]
  33. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 2013; 14:60 [View Article] [PubMed]
    [Google Scholar]
  34. 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] [PubMed]
    [Google Scholar]
  35. Blin K, Shaw S, Augustijn HE, Reitz ZL, Biermann F et al. antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation. Nucleic Acids Res 2023; 51:W46–W50 [View Article] [PubMed]
    [Google Scholar]
  36. 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 [View Article] [PubMed]
    [Google Scholar]
  37. 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 [View Article] [PubMed]
    [Google Scholar]
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