1887

Abstract

Gram-negative, aerobic, motile by means of two or more polar or subpolar flagella, rod-shaped strain NS12-5 and Gram-negative, facultatively anaerobic, yellow-coloured, rod-shaped strain RP8 were isolated from rice rhizosphere soil and fermented fruits of in the Republic of Korea, respectively. The result of phylogenetic analyses based on 16S rRNA gene sequences showed that strain NS12-5 was most closely related to 4Y11 with 99.79 % sequence similarity. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between strain NS12-5 and species of the genus were 75.6–91.7 % and 20.3–43.9 %, respectively. Growth occurred at 15–40 °C and pH 5–11, and NaCl was not needed for growth. The major fatty acids of strain NS12-5 were summed feature 3 (comprising C7 and/or C6) and C, and the major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The DNA G+C content of strain NS12-5 was 69.03 mol%. The result of phylogenetic analyses based on 16S rRNA gene sequences revealed that strain RP8 was most closely related to BT328 with 96.01 % sequence similarity. The ANI and dDDH values between strain RP8 and reference strains of the genus were 72.9–76.4 % and 18.6–20.0 %, respectively. Growth occurred at 15–37 °C and pH 5–11, and NaCl was not needed for growth. The major fatty acids of strain RP8 were summed feature 3 (comprising C7 and/or C6), C5 and iso-C. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The DNA G+C contents of strain RP8 were 54.9 mol%. Based on phenotypic, genomic and phylogenetic results, strains NS12-5 and RP8 represent novel species in the genus and , respectively, and the names sp. nov. and sp. nov. are proposed. The type strain of sp. nov. is NS12-5 (=KACC 22691=TBRC 16346) and the type strain of is RP8 (=KACC 22688=TBRC 16345).

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2023-07-05
2024-07-25
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References

  1. Malmqvist Å, Welander T, Moore E, Ternström A, Molin G et al. Ideonella dechloratans gen.nov., sp.nov., a new bacterium capable of growing anaerobically with chlorate as an electron acceptor. Syst Appl Microbiol 1994; 17:58–64 [View Article]
    [Google Scholar]
  2. Sheu SY, Chen ZH, Young CC, Chen WM. Ideonella paludis sp. nov., isolated from a marsh. Int J Syst Evol Microbiol 2016; 66:1052–1057 [View Article]
    [Google Scholar]
  3. Noar JD, Buckley DH. Ideonella azotifigens sp. nov., an aerobic diazotroph of the Betaproteobacteria isolated from grass rhizosphere soil, and emended description of the genus Ideonella. Int J Syst Evol Microbiol 2009; 59:1941–1946 [View Article] [PubMed]
    [Google Scholar]
  4. Chen WM, Chen LC, Sheu DS, Tsai JM, Sheu SY. Ideonella livida sp. nov., isolated from a freshwater lake. Int J Syst Evol Microbiol 2020; 70:4942–4950 [View Article] [PubMed]
    [Google Scholar]
  5. Du J, Liu Y, Pei T, Zhu H. Ideonella alba sp. nov. and Ideonella aquatica sp. nov. isolated from an aquaculture farm. Int J Syst Evol Microbiol 2022; 72: [View Article] [PubMed]
    [Google Scholar]
  6. Bedics A, Táncsics A, Tóth E, Banerjee S, Harkai P et al. Microaerobic enrichment of benzene-degrading bacteria and description of Ideonella benzenivorans sp. nov., capable of degrading benzene, toluene and ethylbenzene under microaerobic conditions. Antonie van Leeuwenhoek 2022; 115:1113–1128 [View Article]
    [Google Scholar]
  7. Chhetri G, Kim I, Kang M, Kim J, So Y et al. Devosia rhizoryzae sp. nov., and Devosia oryziradicis sp. nov., novel plant growth promoting members of the genus Devosia, isolated from the rhizosphere of rice plants. J Microbiol 2022; 60:1–10 [View Article] [PubMed]
    [Google Scholar]
  8. Thorell HD, Stenklo K, Karlsson J, Nilsson T. A gene cluster for chlorate metabolism in Ideonella dechloratans. Appl Environ Microbiol 2003; 69:5585–5592 [View Article]
    [Google Scholar]
  9. Larkin JM, Borrall R. Spirosomaceae, a new family to contain the genera Spirosoma Migula 1894, Flectobacillus Larkin et al. 1977, and Runella Larkin and Williams 1978. Int J Syst Bacteriol 1978; 28:595–596 [View Article]
    [Google Scholar]
  10. Won M, Hong SB, Han BH, Kwon SW. Spirosoma rhododendri sp. nov., isolated from a flower of royal azalea (Rhododendron schlippenbachii). Int J Syst Evol Microbiol 2022; 72: [View Article] [PubMed]
    [Google Scholar]
  11. Rojas J, Ambika Manirajan B, Ratering S, Suarez C, Geissler-Plaum R et al. Spirosoma endbachense sp. nov., isolated from a natural salt meadow. Int J Syst Evol Microbiol 2021; 71:1–7 [View Article] [PubMed]
    [Google Scholar]
  12. Lee JH, Jung J-H, Kim M-K, Choe HN, Seong CN et al. Spirosoma taeanense sp. nov., a radiation resistant bacterium isolated from a coastal sand dune. Antonie van Leeuwenhoek 2021; 114:151–159 [View Article] [PubMed]
    [Google Scholar]
  13. Tahon G, Lebbe L, Willems A. Spirosoma utsteinense sp. nov. isolated from Antarctic ice-free soils from the Utsteinen region, East Antarctica. Int J Syst Evol Microbiol 2019; 71: [View Article] [PubMed]
    [Google Scholar]
  14. Kang H, Cha I, Kim H, Joh K. Spirosoma telluris sp. nov. and Spirosoma arboris sp. nov. isolated from soil and tree bark, respectively. Int J Syst Evol Microbiol 2020; 70:5355–5362 [View Article] [PubMed]
    [Google Scholar]
  15. Ten LN, Okiria J, Lee JJ, Lee SY, Park S et al. Spirosoma terrae sp. nov., isolated from soil from Jeju Island, Korea. Curr Microbiol 2018; 75: [View Article] [PubMed]
    [Google Scholar]
  16. Chung I-M, Hemapriya V, Kim S-H, Ponnusamy K, Arunadevi N et al. Liriope platyphylla extract as a green inhibitor for mild steel corrosion in sulfuric acid medium. Chem Eng Commun 2021; 208:72–88 [View Article]
    [Google Scholar]
  17. Lee J-J, Lee Y-H, Park S-J, Lee S-Y, Kim B-O et al. Spirosoma knui sp. nov., a radiation-resistant bacterium isolated from the Han River. Int J Syst Evol Microbiol 2017; 67:1359–1365 [View Article]
    [Google Scholar]
  18. Lee J-J, Srinivasan S, Lim S, Joe M, Im S et al. Spirosoma radiotolerans sp. nov., a gamma-radiation-resistant bacterium isolated from gamma ray-irradiated soil. Curr Microbiol 2014; 69:286–291 [View Article]
    [Google Scholar]
  19. Lee J-J, Kang M-S, Joo ES, Kim MK, Im W-T et al. Spirosoma montaniterrae sp. nov., an ultraviolet and gamma radiation-resistant bacterium isolated from mountain soil. J Microbiol 2015; 53:429–434 [View Article] [PubMed]
    [Google Scholar]
  20. Slabova OI, Nikitin DI. Influence of the incubation temperature on the reaction of oligotrophic bacteria to stress. Mikrobiologiia 2004; 73:758–762 [PubMed]
    [Google Scholar]
  21. Sheu SY, Chen ZH, Young CC, Chen WM. Ideonella paludis sp. nov., isolated from a marsh. Int J Syst Evol Microbiol 2016; 66:1052–1057 [View Article]
    [Google Scholar]
  22. Chhetri G, Seo T. Pontibacter aquaedesilientis sp. nov., isolated from Jeongbang Waterfall, Jeju Island. Int J Syst Evol Microbiol 2021; 71: [View Article] [PubMed]
    [Google Scholar]
  23. Kim I, Kim J, Chhetri G, Seo T. Flavobacterium humi sp. nov., a flexirubin-type pigment producing bacterium, isolated from soil. J Microbiol 2019; 57:1079–1085 [View Article]
    [Google Scholar]
  24. Kim O-S, Cho Y-J, Lee K, Yoon S-H, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012; 62:716–721 [View Article] [PubMed]
    [Google Scholar]
  25. Kumar S, Stecher G, Li M, Knyaz C, Tamura K et al. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article]
    [Google Scholar]
  26. Kim I, Chhetri G, Kim J, Kang M, So Y et al. Nocardioides donggukensis sp. nov. and Hyunsoonleella aquatilis sp. nov., isolated from Jeongbang Waterfall on Jeju Island. Int J Syst Evol Microbiol 2021; 71: [View Article] [PubMed]
    [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. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  29. 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]
  30. Kang M, Chhetri G, Kim J, Kim I, Seo T. Pontibacter cellulosilyticus sp. nov., a carboxymethyl cellulose-hydrolysing bacterium isolated from coastal water. Int J Syst Evol Microbiol 2021; 71: [View Article] [PubMed]
    [Google Scholar]
  31. Chhetri G, Kim J, Kim I, Kang M, Seo T. Chryseobacterium caseinilyticum sp. nov., a casein hydrolyzing bacterium isolated from rice plant and emended description of Chryseobacterium piscicola. Int J Syst Evol Microbiol 2021; 71: [View Article] [PubMed]
    [Google Scholar]
  32. Blin K, Shaw S, Steinke K, Villebro R, Ziemert N et al. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res 2019; 47:W81–W87 [View Article] [PubMed]
    [Google Scholar]
  33. 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]
  34. Na S-I, Kim YO, Yoon S-H, Ha S-M, Baek I et al. UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285 [View Article] [PubMed]
    [Google Scholar]
  35. Ayoub AT, Elrefaiy MA, Arakawa K. Computational prediction of the mode of binding of antitumor lankacidin c to tubulin. ACS Omega 2019; 4:4461–4471 [View Article] [PubMed]
    [Google Scholar]
  36. Fan H, Ru J, Zhang Y, Wang Q, Li Y. Fengycin produced by Bacillus subtilis 9407 plays a major role in the biocontrol of apple ring rot disease. Microbiol Res 2017; 199:89–97 [View Article] [PubMed]
    [Google Scholar]
  37. 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]
  38. Kim J, Chhetri G, Kim I, Lee B, Jang W et al. Methylobacterium terricola sp. nov., a gamma radiation-resistant bacterium isolated from gamma ray-irradiated soil. Int J Syst Evol Microbiol 2020; 70:2449–2456 [View Article]
    [Google Scholar]
  39. Reddy CA, Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM et al. Phenotypic Characterization and the Principles of Comparative Systematics Washington, DC: Wiley; 2007 [View Article]
    [Google Scholar]
  40. Buck JD. Nonstaining (KOH) method for determination of gram reactions of marine bacteria. Appl Environ Microbiol 1982; 44:992–993 [View Article]
    [Google Scholar]
  41. Smibert RM, Kreig NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Kreig NR. eds Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp 607–654
    [Google Scholar]
  42. Kuykendall LD, Roy MA, O’neill JJ, Devine TE. Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum. Int J Syst Bacteriol 1988; 38:358–361 [View Article]
    [Google Scholar]
  43. Kim J, Lee B, Chhetri G, Kim I, So Y et al. Identification of Mucilaginibacter conchicola sp. nov., Mucilaginibacter achroorhodeus sp. nov. and Mucilaginibacter pallidiroseus sp. nov. and emended description of the genus Mucilaginibacter. Int J Syst Evol Microbiol 2022; 72: [View Article] [PubMed]
    [Google Scholar]
  44. Minnikin DE, Patel PV, Alshamaony L, Goodfellow M. Polar lipid composition in the classification of Nocardia and related bacteria. Int J Syst Bacteriol 1977; 27:104–117 [View Article]
    [Google Scholar]
  45. Chhetri G, Kim J, Kim H, Kim I, Seo T. Pontibacter oryzae sp. nov., a carotenoid-producing species isolated from a rice paddy field. Antonie van Leeuwenhoek 2019; 112:1705–1713 [View Article] [PubMed]
    [Google Scholar]
  46. Lin SY, Hameed A, Tsai CF, Hung MH, Young CC. Agrilactobacillus fermenti sp. nov. isolated from fermented vegetable residue. Int J Syst Evol Microbiol 2022; 72: [View Article] [PubMed]
    [Google Scholar]
  47. Li W, Lee S-Y, Kang I-K, Ten LN, Jung H-Y. Spirosoma agri sp. nov., isolated from apple orchard soil. Curr Microbiol 2018; 75:694–700 [View Article] [PubMed]
    [Google Scholar]
  48. Maeng S, Park Y, Han JH, Lee SE, Zhang J et al. Spirosoma aureum sp. nov., and Hymenobacter russus sp. nov., radiation-resistant bacteria in Cytophagales order isolated from soil. Antonie van Leeuwenhoek 2020; 113:2201–2212 [View Article] [PubMed]
    [Google Scholar]
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