1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 74, Issue 8

sp. nov., sp. nov. and sp. nov., endophytic actinobacteria isolated from wild orchid ( Roxb) No Access

Abstract

Three novel mycelium-forming actinobacteria, designated OC33-EN06, OC33-EN07, and OC33-EN08, were isolated from wild orchid ( Roxb), collected from a hill evergreen forest in Northern Thailand. Strains OC33-EN06 and OC33-EN07 showed the highest 16S rRNA gene similarity with TT00-04, 99.17 and 99.45%, respectively. Strain OC33-EN08 showed high similarity with four species, namely ‘ Odt1-22’ (99.37%), DSM 45062 (99.02%), 014-5 (99.02%), and SF1 (98.81%). Comparative genome analysis of OC33-EN06, OC33-EN07, and OC33-EN08 with the closely related type strains showed that average nucleotide identity (ANI) based on , ANI based on MUMmer, and average amino acid identity values were less than 95% and the digital DNA–DNA hybridization values were less than 70%, all below the thresholds for species demarcation. The digital G+C content of OC33-EN06, OC33-EN07, and OC33-EN08 were 74.5, 74, and 74 mol%, respectively. These three strains developed bud-like chains of non-motile cylindrical spores with a smooth surface. The cell-wall peptidoglycan contained -diaminopimelic acid. The whole-cell sugars contained ribose, arabinose, and galactose. The predominant menaquinone was MK-8(H). The phospholipid profile included phosphatidylcholine, phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, and phosphatidylinositol. Based on comparative analysis of genotypic, phenotypic and chemotaxonomic data, strains OC33-EN06 (=TBRC 18349=NBRC 116543), OC33-EN07 (=TBRC 18350=NBRC 116544), and OC33-EN08 (=TBRC 18318=NBRC 116542) represent the type strains of three novel species of the genus for which the names sp. nov., sp. nov., and sp. nov., are proposed.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Actinomycetospora aeridis , Actinomycetospora aurantiaca , Actinomycetospora flava , endophyte and orchid
Funding
This study was supported by the:
  • National Science and Technology Development Agency (NSTDA)
    • Principle Award Recipient: ChanwitSuriyachadkun
  • National Center for Genetic Engineering and Biotechnology (BIOTEC)
    • Principle Award Recipient: ChanwitSuriyachadkun
  • National Research Council of Thailand (NRCT)
    • Principle Award Recipient: ChanwitSuriyachadkun
© 2024 The Authors
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2024-09-02
2024-09-19
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References

  1. Alibrandi P, Schnell S, Perotto S, Cardinale M. Diversity and structure of the endophytic bacterial communities associated with three terrestrial orchid species as revealed by 16S rRNA gene metabarcoding. Front Microbiol 2020; 11:604964 [View Article] [PubMed]
     [Google Scholar]
  2. Sakdapetsiri C, Ngaemthao W, Suriyachadkun C, Duangmal K, Kitpreechavanich V. Actinomycetospora endophytica sp. nov., isolated from wild orchid (Podochilus microphyllus Lindl.) in Thailand. Int J Syst Evol Microbiol 2018; 68:3017–3021 [View Article] [PubMed]
     [Google Scholar]
  3. Jiang Y, Wiese J, Tang S-K, Xu L-H, Imhoff JF et al. Actinomycetospora chiangmaiensis gen. nov., sp. nov., a new member of the family Pseudonocardiaceae. Int J Syst Evol Microbiol 2008; 58:408–413 [View Article] [PubMed]
     [Google Scholar]
  4. Tamura T, Ishida Y, Hamada M, Otoguro M, Yamamura H et al. Description of Actinomycetospora chibensis sp. nov., Actinomycetospora chlora sp. nov., Actinomycetospora cinnamomea sp. nov., Actinomycetospora corticicola sp. nov., Actinomycetospora lutea sp. nov., Actinomycetospora straminea sp. nov. and Actinomycetospora succinea sp. nov. and emended description of the genus Actinomycetospora. Int J Syst Evol Microbiol 2011; 61:1275–1280 [View Article] [PubMed]
     [Google Scholar]
  5. Zhang Y, Liu C, Zhang J, Shen Y, Li C et al. Actinomycetospora atypica sp. nov., a novel soil actinomycete and emended description of the genus Actinomycetospora. Antonie van Leeuwenhoek 2014; 105:891–897 [View Article]
     [Google Scholar]
  6. Suriyachadkun C, Chunhametha S, Thawai C, Tamura T, Potacharoen W et al. Planotetraspora thailandica sp. nov., isolated from soil in Thailand. Int J Syst Evol Microbiol 2009; 59:992–997 [View Article] [PubMed]
     [Google Scholar]
  7. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
     [Google Scholar]
  8. Saito H, Miura KI. Preparation of transforming deoxyribonucleic acid by phenol treatment. Biochim Biophys Acta 1963; 72:619–629 [PubMed]
     [Google Scholar]
  9. Pootakham W, Mhuantong W, Yoocha T, Putchim L, Sonthirod C et al. High resolution profiling of coral-associated bacterial communities using full-length 16S rRNA sequence data from PacBio SMRT sequencing system. Sci Rep 2017; 7:2774 [View Article] [PubMed]
     [Google Scholar]
  10. 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]
  11. 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]
  12. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucleic Acids Symp Ser 1999; 41:95–98
     [Google Scholar]
  13. 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]
  14. Felsenstein J. Parsimony in systematics: biological and statistical issues. Annu Rev Ecol Syst 1983; 14:313–333 [View Article]
     [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. 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]
  17. 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]
  18. Nei M, Kumar S. Molecular Evolution and Phylogenetics New York: Oxford University Press; 2000
     [Google Scholar]
  19. 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]
  20. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  21. Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 2018; 34:i884–i890 [View Article] [PubMed]
     [Google Scholar]
  22. Nurk S, Bankevich A, Antipov D, Gurevich AA, Korobeynikov A et al. Assembling single-cell genomes and mini-metagenomes from chimeric MDA products. J Comput Biol 2013; 20:714–737 [View Article] [PubMed]
     [Google Scholar]
  23. 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]
  24. Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 2013; 29:1072–1075 [View Article] [PubMed]
     [Google Scholar]
  25. 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]
  26. Rodriguez-R LM, Konstantinidis KT. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. PeerJ Preprints 2016 [View Article]
     [Google Scholar]
  27. Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Göker M. TYGS and LPSN:a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res 2022; 50:D801–D807 [View Article] [PubMed]
     [Google Scholar]
  28. 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]
  29. Lefort V, Desper R, Gascuel O. FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program. Mol Biol Evol 2015; 32:2798–2800 [View Article] [PubMed]
     [Google Scholar]
  30. Kanehisa M, Sato Y, Morishima K. BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J Mol Biol 2016; 428:726–731 [View Article] [PubMed]
     [Google Scholar]
  31. Blin K, Shaw S, Augustijn HE, Reitz ZL, Biermann F et al. antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structuresand visualisation. Nucleic Acids Res 2023; 51:W46–W50 [View Article] [PubMed]
     [Google Scholar]
  32. Konstantinidis KT, Tiedje JM. Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci USA 2005; 102:2567–2572 [View Article] [PubMed]
     [Google Scholar]
  33. Luo C, Rodriguez-R LM, Konstantinidis KT. MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences. Nucleic Acids Res 2014; 42:e73 [View Article] [PubMed]
     [Google Scholar]
  34. 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]
  35. 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]
  36. Kelly KL. Inter-Society Color Council – National Bureau of Standard Color Name Charts Illustrated with Centroid Colors Washington, DC: US Government Printing Office; 1964
     [Google Scholar]
  37. 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]
  38. Arai T. Culture Media for Actinomycetes Tokyo: The Society for Actinomycetes Japan; 1975
     [Google Scholar]
  39. Williams ST, Cross T. Actinomycetes. Methods Microbiol 1971; 4:295–334 [View Article]
     [Google Scholar]
  40. 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]
  41. Komagata K, Suzuki KI. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–207 [View Article]
     [Google Scholar]
  42. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [View Article] [PubMed]
     [Google Scholar]
  43. Wu C, Lu X, Qin M, Wang Y, Ruan J. Analysis of menaquinone compound in microbial cells by HPLC. Microbiology 1989; 16:176–178
     [Google Scholar]
  44. 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]
  45. Sasser M. Technical Note 101: Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids Newark, DE: MIDI; 2001
     [Google Scholar]
  46. Tomiyasu I. Mycolic acid composition and thermally adaptative changes in Nocardia asteroides. J Bacteriol 1982; 151:828–837 [View Article] [PubMed]
     [Google Scholar]
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Actinomycetospora aeridis sp. nov., Actinomycetospora flava sp. nov. and Actinomycetospora aurantiaca sp. nov., endophytic actinobacteria isolated from wild orchid (Aerides multiflora Roxb)
Int J Syst Evol Microbiol 74, 006505 (2024); https://doi.org/10.1099/ijsem.0.006505
/content/journal/ijsem/10.1099/ijsem.0.006505
/content/journal/ijsem/10.1099/ijsem.0.006505
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