sp. nov., isolated from greenhouse soil No Access

Abstract

A Gram-stain-negative, aerobic, non-motile, rod-shaped or occasionally filamentous-shaped bacterial strain, designated 5GH13-10, was isolated from greenhouse soil sampled in Yeoju-si, Republic of Korea. Colonies were milky-coloured, round and convex, and catalase- and oxidase-positive. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 5GH13-10 was related to the genus and had highest 16S rRNA gene sequence identity with Vu-144 (98.4 %). The major cellular fatty acids were iso-C, iso-C G, iso-C 3-OH and summed feature 3 (C 6 and/or C 7). The predominant quinone was menaquinone MK-7, and the polar lipids were composed of phosphatidylethanolamine, one unidentified aminolipid, three unidentified aminophospholipids, one unidentified phospholipid and five unidentified lipids. The genomic DNA G+C content of strain 5GH13-10 was 43.8 mol%. The average nucleotide identity values between strain 5GH13-10 and the closely related species Gsoil 809, Vu-144 and KIS59-12 were 74.86, 74.74 and 69.52 %, and the digital DNA-DNA hybridization values were 20.0, 19.8 and 18.6 %, respectively. Combined phenotypic, phylogenetic and genomic data demonstrated that strain 5GH13-10 is representative of a novel species of the genus , for which we propose the name sp. nov. (type strain 5GH13-10=KACC 18014=NBRC 113162).

Funding
This study was supported by the:
  • National Institute of Agricultural Sciences, Rural Development Administration (Award PJ013549)
    • Principle Award Recipient: Soon-WoKwon
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2022-05-27
2024-03-29
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References

  1. Won M, Weon HY, Hong SB, Han BH, Kwon SW. Arachidicoccus terrestris sp. nov., isolated from greenhouse soil Figshare 2022 DOI: 10.6084/m9.figshare.19227885
    [Google Scholar]
  2. Madhaiyan M, Poonguzhali S, Senthilkumar M, Pragatheswari D, Lee J-S et al. Arachidicoccus rhizosphaerae gen. nov., sp. nov., a plant-growth-promoting bacterium in the family Chitinophagaceae isolated from rhizosphere soil. Int J Syst Evol Microbiol 2015; 65:578–586 [View Article]
    [Google Scholar]
  3. 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]
    [Google Scholar]
  4. Siddiqi MZ, Aslam Z, Im WT. Arachidicoccus ginsenosidivorans sp. nov., with ginsenoside-converting activity isolated from ginseng cultivating soil. Int J Syst Evol Microbiol 2017; 67:1005–1010 [View Article] [PubMed]
    [Google Scholar]
  5. Lee SA, Kim T-W, Sang M-K, Song J, Kwon S-W et al. Arachidicoccus soli sp. nov., a bacterium isolated from soil. Int J Syst Evol Microbiol 2021; 71:004566 [View Article]
    [Google Scholar]
  6. Siddiqi MZ, Shafi SM, Im WT. Complete genome sequencing of Arachidicoccus ginsenosidimutans sp. nov., and its application for production of minor ginsenosides by finding a novel ginsenoside-transforming β-glucosidase. RSC Adv 2017; 7:46745–46759 [View Article]
    [Google Scholar]
  7. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. eds Nucleic Acid Techniques in Bacterial Systematics New York, FL: John Wiley and Sons; 1991 pp 115–175
    [Google Scholar]
  8. 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]
  9. 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]
  10. 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]
  11. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Systematic Zoology 1971; 20:406 [View Article]
    [Google Scholar]
  12. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  13. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article] [PubMed]
    [Google Scholar]
  14. Tamura K. Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G+C-content biases. Mol Biol Evol 1992; 9:678–687 [View Article] [PubMed]
    [Google Scholar]
  15. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
    [Google Scholar]
  16. 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]
  17. Auch AF, von Jan M, Klenk H-P, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010; 2:117–134 [View Article] [PubMed]
    [Google Scholar]
  18. 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]
  19. 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]
  20. Konstantinidis KT, Tiedje JM. Towards a genome-based taxonomy for prokaryotes. J Bacteriol 2005; 187:6258–6264 [View Article] [PubMed]
    [Google Scholar]
  21. 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:D206–14 [View Article] [PubMed]
    [Google Scholar]
  22. Katoh A, Uenohara K, Akita M, Hashimoto T. Early steps in the biosynthesis of NAD in Arabidopsis start with aspartate and occur in the plastid. Plant Physiol 2006; 141:851–857 [View Article] [PubMed]
    [Google Scholar]
  23. Zhu F, Peña M, Bennett GN. Metabolic engineering of Escherichia coli for quinolinic acid production by assembling L-aspartate oxidase and quinolinate synthase as an enzyme complex. Metab Eng 2021; 67:164–172 [View Article] [PubMed]
    [Google Scholar]
  24. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray R, W W, Krieg N. eds Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp 607–654
    [Google Scholar]
  25. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. Newark, DE, USA: Microbial ID Inc; 1990
  26. 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]
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