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Volume 73, Issue 1

sp. nov., isolated from island soil No Access

Abstract

A Gram-positive, non-motile, pale yellow coloured actinobacterial strain designated MMS17-SY077 was isolated from island soil, and its taxonomic position was investigated using a polyphasic approach. Strain MMS17-SY077 grew optimally at 30 °C, at pH 7 and in the absence of NaCl on Reasoner's 2A agar. Based on the 16S rRNA gene sequence analysis, the strain was assigned to the genus of the family , and the most related species were DSM 16388 (98.8 % sequence similarity), UMS-62 (98.1 %) and DS-10 (97.8 %). Strain MMS17-SY077 formed a distinct cluster within the clade in the phylogenetic tree. Genome-based comparative analyses confirmed a clear distinction between the strain and neighbouring species, as the highest orthologous average nucleotide identity and digital DNA–DNA hybridization values with other related species were 77.2 and 21.4% respectively, which were far below the cutoffs for species distinction. The diagnostic polar lipids of MMS17-SY077 were diphosphatidylglycerol and phosphatidylglycerol, and unidentified glycolipids and an unidentified aminolipid were also present. The main isoprenoid quinones were menaquinones with 11 and 12 isoprene units (MK-11 and MK-12), and main fatty acids were anteiso-C (34.4 %) and iso-C (33.2 %). The whole-cell hydrolysates contained rhamnose, ribose and galactose as diagnostic sugars, and -2,4-diaminobutyric acid as the major diamino acid. The DNA G+C content was 72.1 mol %. Based on phenotypic, chemotaxnomic and phylogenetic characterization, strain MMS17-SY077 should be classified as representing a new species of the genus , for which the name sp. nov. is proposed (type strain MMS17-SY077=KCTC 49423=LMG 31762).

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  • Accepted:
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Keyword(s): Actinomycetota , Agromyces seonyuensis , island soil and Microbacteriaceae
Funding
This study was supported by the:
  • National Institute of Biological Resources
    • Principle Award Recipient: SeungBum Kim
  • National Research Foundation of Korea
    • Principle Award Recipient: SeungBum Kim
© 2023 The Authors
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References

  1. Gledhill WE, Casida LE. Predominant catalase-negative soil bacteria. III. Agromyces, gen. n., microorganisms intermediary to Actinomyces and Nocardia. Appl Microbiol 1969; 18:340–349
     [Google Scholar]
  2. Zgurskaya HI, Evtushenko LI, Akimov VN, Voyevoda HV, Dobrovolskaya TG et al. Emended description of the genus Agromyces and description of Agromyces cerinus subsp. cerinus sp. nov., subsp. nov., Agromyces cerinus subsp. nitratus sp. nov., subsp. nov., Agromyces fucosus subsp. fucosus sp. nov., subsp. nov., and Agromyces fucosus subsp. hippuratus sp. nov., subsp. nov. Int J Syst Bacteriol 1992; 42:635–641
     [Google Scholar]
  3. Euzeby JP. List of Prokaryotic Names with Standing in Nomenclature; 2007 www.bacterio.net
  4. Akimov VN, Evtushenko L et al. Genus IV. Agromyces. In Goodfellow M, Kämpfer P, Busse HJ, Trujillo ME, Suzuki K. eds Bergey’s Manual of Systematic Bacteriology, 2nd edn. New York: Springer; 2012 pp 862–876
     [Google Scholar]
  5. Jurado V, Groth I, Gonzalez JM, Laiz L, Schuetze B et al. Agromyces italicus sp. nov., Agromyces humatus sp. nov. and Agromyces lapidis sp. nov., isolated from Roman catacombs. Int J Syst Evol Microbiol 2005; 55:871–875
     [Google Scholar]
  6. Chen Z, Guan Y, Wang J, Li J. Agromyces binzhouensis sp. nov., an actinobacterium isolated from a coastal wetland of the Yellow River Delta. Int J Syst Evol Microbiol 2016; 66:2278–2283 [View Article] [PubMed]
     [Google Scholar]
  7. Huang J-R, Ming H, Li S, Meng X-L, Zhang J-X et al. Agromyces insulae sp. nov., an actinobacterium isolated from a soil sample. Int J Syst Evol Microbiol 2016; 66:2002–2007 [View Article] [PubMed]
     [Google Scholar]
  8. Dorofeeva LV, Krausova VI, Evtushenko LI, Tiedje JM. Agromyces albus sp. nov., isolated from a plant (Androsace sp.). Int J Syst Evol Microbiol 2003; 53:1435–1438 [View Article] [PubMed]
     [Google Scholar]
  9. Hamada M, Shibata C, Tamura T, Suzuki K. Agromyces marinus sp. nov., a novel actinobacterium isolated from sea sediment. J Antibiot 2014; 67:703–706 [View Article]
     [Google Scholar]
  10. Park E-J, Kim M-S, Jung M-J, Roh SW, Chang H-W et al. Agromyces atrinae sp. nov., isolated from fermented seafood. Int J Syst Evol Microbiol 2010; 60:1056–1059 [View Article] [PubMed]
     [Google Scholar]
  11. Jung SY, Lee SY, Oh TK, Yoon JH. Agromyces allii sp. nov., isolated from the rhizosphere of Allium victorialis var. platyphyllum. Int J Syst Evol Microbiol 2007; 57:588–593 [View Article] [PubMed]
     [Google Scholar]
  12. Corretto E, Antonielli L, Sessitsch A, Compant S, Gorfer M et al. Agromyces aureus sp. nov., isolated from the rhizosphere of Salix caprea L. grown in a heavy-metal-contaminated soil. Int J Syst Evol Microbiol 2016; 66:3749–3754 [View Article] [PubMed]
     [Google Scholar]
  13. Zhao H-M, Du H, Lin J, Chen X-B, Li Y-W et al. Complete degradation of the endocrine disruptor di-(2-ethylhexyl) phthalate by a novel Agromyces sp. MT-O strain and its application to bioremediation of contaminated soil. Sci Total Environ 2016; 562:170–178 [View Article] [PubMed]
     [Google Scholar]
  14. Xue F, Liu ZQ, Wan NW, Zheng YG. Purification, gene cloning, and characterization of a novel halohydrin dehalogenase from Agromyces mediolanus ZJB120203. Appl Biochem Biotechnol 2014; 174:352–364 [View Article] [PubMed]
     [Google Scholar]
  15. Parab V, Phadke M. Co-biodegradation studies of naphthalene and phenanthrene using bacterial consortium. J Environ Sci Health A Tox Hazard Subst Environ Eng 2020; 55:912–924 [View Article] [PubMed]
     [Google Scholar]
  16. Gtari M, Ghodhbane-Gtari F, Nouioui I, Beauchemin N, Tisa LS. Phylogenetic perspectives of nitrogen-fixing actinobacteria. Arch Microbiol 2012; 194:3–11 [View Article] [PubMed]
     [Google Scholar]
  17. Sridhar S, Wang AYM, Chan JFW, Yip CCY, Lau SKP et al. First report of human infection by Agromyces mediolanus, a Gram-positive organism found in soil. J Clin Microbiol 2015; 53:3377–3379 [View Article]
     [Google Scholar]
  18. Kovacs N. Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 1956; 178:703 [View Article] [PubMed]
     [Google Scholar]
  19. Park J, Kim YR, Kim M-K, Jo JH, Im W-T et al. Humibacter soli sp. nov., isolated from soil. Int J Syst Evol Microbiol 2016; 66:2509–2514 [View Article] [PubMed]
     [Google Scholar]
  20. Kim YS, Roh SG, Kim SB. Gordonia insulae sp. nov., isolated from an island soil. Int J Syst Evol Microbiol 2020; 70:2079–2083 [View Article] [PubMed]
     [Google Scholar]
  21. 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]
  22. Jeon Y-S, Lee K, Park S-C, Kim B-S, Cho Y-J et al. EzEditor: a versatile sequence alignment editor for both rRNA- and protein-coding genes. Int J Syst Evol Microbiol 2014; 64:689–691 [View Article] [PubMed]
     [Google Scholar]
  23. Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article] [PubMed]
     [Google Scholar]
  24. 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]
  25. Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S et al. RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep 2015; 5:8365 [View Article] [PubMed]
     [Google Scholar]
  26. Lee I, Ouk Kim Y, Park S-C, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article] [PubMed]
     [Google Scholar]
  27. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:1–4 [View Article] [PubMed]
     [Google Scholar]
  28. Blin K, Wolf T, Chevrette MG, Lu X, Schwalen CJ et al. antiSMASH 4.0-improvements in chemistry prediction and gene cluster boundary identification. Nucleic Acids Res 2017; 45:W36–W41 [View Article] [PubMed]
     [Google Scholar]
  29. Yoon JH, Schumann P, Kang SJ, Park S, Oh TK. Agromyces terreus sp. nov., isolated from soil. Int J Syst Evol Microbiol 2008; 58:1308–1312 [View Article] [PubMed]
     [Google Scholar]
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Agromyces seonyuensis sp. nov., isolated from island soil
Int J Syst Evol Microbiol 73, 005689 (2023); https://doi.org/10.1099/ijsem.0.005689
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