gen. nov., sp. nov., a novel bacterium of the family isolated from soil of a farming field Free

Abstract

A Gram-stain-negative bacterium, designated strain YJ03, was isolated from a spinach farming field soil at Shinan in Korea. Strain YJ03 was found to be an aerobic, non-motile and non-spore-forming bacterium which can grow at 10–33 °C (optimum, 25–28 °C), at pH 6.6–9.5 (optimum, pH 7.0–7.5) and at salinities of 0–1.0 % (w/v) NaCl (optimum, 0 % NaCl). Sequence similarities of the 16S rRNA gene of strain YJ03 with the closely related relatives were in the range 93.9–92.2 %, and the results of phylogenomic analysis indicated that strain YJ03 was clearly separated from species of the genera in the family , showing average nucleotide identity values of 68.8–64.3 %. The predominant isoprenoid quinone was identified as MK-7 and the major fatty acids were iso-C, iso-C 3-OH and an unidentified fatty acid with an equivalent chain-length of 13.565. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, four unidentified aminolipids and six unidentified lipids. The G+C content of the genome was determined to be 41.8 mol%. On the basis of phenotypic and chemotaxonomic properties and phylogenetic and phylogenomic analyses using 16S rRNA gene sequences and whole-genome sequences in this study, strain YJ03 is considered to represent a novel species of a new genus in the family , for which the name gen. nov., sp. nov., is proposed. The type strain of is YJ03 (=KACC 19548=NBRC 113195).

Funding
This study was supported by the:
  • Strategic Initiative for Microbiomes in Agriculture and Food, Ministry of Agriculture, Food and Rural Affairs, Republic of Korea (Award grant number 918016-4)
    • Principle Award Recipient: Not Applicable
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2020-08-19
2024-03-29
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References

  1. Kämpfer P, Young C-C, Sridhar KR, Arun AB, Lai WA et al. Transfer of [Flexibacter] sancti, [Flexibacter] filiformis, [Flexibacter] japonensis and [Cytophaga] arvensicola to the genus Chitinophaga and description of Chitinophaga skermanii sp. nov. Int J Syst Evol Microbiol 2006; 56:2223–2228 [View Article][PubMed]
    [Google Scholar]
  2. Kämpfer P, Lodders N, Falsen E. Hydrotalea flava gen. nov., sp. nov., a new member of the phylum Bacteroidetes and allocation of the genera Chitinophaga, Sediminibacterium, Lacibacter, Flavihumibacter, Flavisolibacter, Niabella, Niastella, Segetibacter, Parasegetibacter, Terrimonas, Ferruginibacter, Filimonas and Hydrotalea to the family Chitinophagaceae fam. nov. Int J Syst Evol Microbiol 2011; 61:518–523 [View Article][PubMed]
    [Google Scholar]
  3. Kim S-J, Cho H, Ahn J-H, Weon H-Y, Seok S-J et al. Pseudoflavitalea rhizosphaerae gen. nov., sp. nov., isolated from rhizosphere of tomato, and proposal to reclassify Flavitalea soli as Pseudoflavitalea soli comb. nov. Int J Syst Evol Microbiol 2016; 66:4167–4171 [View Article][PubMed]
    [Google Scholar]
  4. Weon HY, Kim BY, Yoo SH, Lee SY, Kwon SW et al. Niastella koreensis gen. nov., sp. nov. and Niastella yeongjuensis sp. nov., novel members of the phylum Bacteroidetes, isolated from soil cultivated with Korean ginseng. Int J Syst Evol Microb 1782; iol 2006:1777
    [Google Scholar]
  5. Zhang K, Tang Y, Zhang L, Dai J, Wang Y et al. Parasegetibacter luojiensis gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from a forest soil. Int J Syst Evol Microbiol 2009; 59:3058–3062 [View Article][PubMed]
    [Google Scholar]
  6. Siddiqi MZ, Im W-T. Pseudobacter ginsenosidimutans gen. nov., sp. nov., isolated from ginseng cultivating soil. Int J Syst Evol Microbiol 2016; 66:3449–3455 [View Article][PubMed]
    [Google Scholar]
  7. Wang Y, Cai F, Tang Y, Dai J, Qi H et al. Flavitalea populi gen. nov., sp. nov., isolated from soil of a Euphrates poplar (Populus euphratica) forest. Int J Syst Evol Microbiol 2011; 61:1554–1560 [View Article][PubMed]
    [Google Scholar]
  8. Lv Y-Y, Gao Z-H, Xia F, Chen M-H, Qiu L-H. Puia dinghuensis gen. nov., sp. nov., isolated from monsoon evergreen broad-leaved forest soil. Int J Syst Evol Microbiol 2017; 67:4639–4645 [View Article][PubMed]
    [Google Scholar]
  9. Zhang X, Song S, Tang L, Wang Y, Zhang X et al. Gynurincola endophyticus gen. nov., sp. nov., a novel bacterium of the family Chitinophagaceae . Int J Syst Evol Microbiol 2019; 69:816–820 [View Article][PubMed]
    [Google Scholar]
  10. An D-S, Lee H-G, Im W-T, Liu Q-M, Lee S-T. Segetibacter koreensis gen. nov., sp. nov., a novel member of the phylum Bacteroidetes, isolated from the soil of a ginseng field in South Korea. Int J Syst Evol Microbiol 2007; 57:1828–1833 [View Article][PubMed]
    [Google Scholar]
  11. DeLong EF. Archaea in coastal marine environments. Proc Natl Acad Sci U S A 1992; 89:5685–5689 [View Article][PubMed]
    [Google Scholar]
  12. 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]
  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. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  15. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [View Article]
    [Google Scholar]
  16. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [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. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
    [Google Scholar]
  19. 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]
  20. Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 2006; 33:152–155
    [Google Scholar]
  21. 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 approches to bacterial Systematics. Int J Syst Bacteriol 1987; 37:463–464
    [Google Scholar]
  22. 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]
  23. Yarza P, Yilmaz P, Pruesse E, Glöckner FO, Ludwig W et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol 2014; 12:635–645 [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. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [View Article][PubMed]
    [Google Scholar]
  26. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ et al. The seed and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 2014; 42:D206–D214 [View Article][PubMed]
    [Google Scholar]
  27. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016; 44:6614–6624 [View Article][PubMed]
    [Google Scholar]
  28. Yoon S-H, Ha S-M, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article][PubMed]
    [Google Scholar]
  29. 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]
  30. 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]
  31. 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]
  32. Farris JS. Estimating phylogenetic trees from distance matrices. Am Nat 1972; 106:645–668 [View Article]
    [Google Scholar]
  33. Rosselló-Móra R, Amann R. Past and future species definitions for bacteria and archaea. Syst Appl Microbiol 2015; 38:209–216 [View Article][PubMed]
    [Google Scholar]
  34. 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]
  35. Qin Q-L, Xie B-B, Zhang X-Y, Chen X-L, Zhou B-C et al. A proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol 2014; 196:2210–2215 [View Article][PubMed]
    [Google Scholar]
  36. 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]
  37. Rodriguez-R LM, Konstantinidis KT. Bypassing cultivation to identify bacterial species. Microbe 2014; 9:111–118 [View Article]
    [Google Scholar]
  38. Murray RGE, Doetsch RN, Robinow F. Determinative and cytological light microscopy. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp 21–41
    [Google Scholar]
  39. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp 607–654
    [Google Scholar]
  40. Leifson E. Determination of carbohydrate metabolism of marine bacteria. J Bacteriol 1963; 85:1183–1184 [View Article][PubMed]
    [Google Scholar]
  41. Bauer AW, Kirby WM, Sherris JC, Turck M. Antibiotic susceptibility testing by a standardized single disk method. Am J Clin Pathol 1966; 45:493–496 [View Article][PubMed]
    [Google Scholar]
  42. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  43. Collins MD, Jones D. Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 1981; 45:316–354 [View Article][PubMed]
    [Google Scholar]
  44. Yabuuchi E, Kosako Y, Naka T, Suzuki S, Yano I. Proposal of Sphingomonas suberifaciens (van Bruggen, Jochimsen and brown 1990) comb. nov., Sphingomonas natatoria (Sly 1985) comb. nov., Sphingomonas ursincola (Yurkov et al. 1997) comb. nov., and emendation of the genus Sphingomonas . Microbiol Immunol 1999; 43:339–349 [View Article][PubMed]
    [Google Scholar]
  45. Yabuuchi E, Yano I, Oyaizu H, Hashimoto Y, Ezaki T et al. Proposals of Sphingomonas paucimobilis gen. nov. and comb. nov., Sphingomonas parapaucimobilis sp. nov., Sphingomonas yanoikuyae sp. nov., Sphingomonas adhaesiva sp. nov., Sphingomonas capsulata comb. nov., and two genospecies of the genus Sphingomonas . Microbiol Immunol 1990; 34:99–119 [View Article][PubMed]
    [Google Scholar]
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