1887

Abstract

A yellow-coloured bacterial strain, designated F-4, was isolated from a farmland soil sample from Qianshan, Anhui province, China. Strain F-4 was Gram-stain-negative, strictly aerobic, oval-shaped, motile (by gliding) and non-spore-forming. Growth occurred at 20–35 °C (optimum, 30 °C), at pH 6.0–8.0 (pH 7.0) and with 0–1.0 % (w/v) NaCl (0 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain F-4 belonged to the genus 16S rRNA gene sequence similarity values between strain F-4 and the type strains of the three recognized species of the genus , KACC 17171, KCTC 42277 and JCM 19637, were 98.1, 96.4 and 95.9 %, respectively. The predominant respiratory quinone was MK-7, with MK-8 as a minor component. The major polar lipids of strain F-4 were three unidentified lipids, two unidentified aminolipids, three unidentified phospholipids, an unidentified aminophospholipid and phosphatidylethanolamine. The major cellular fatty acids were iso-C, iso-C G and iso-C. The G+C content of the genomic DNA based on total genome calculations was 51.3 mol%. The major polyamine of strain F-4 was homospermidine. The average nucleotide identity and the digital DNA–DNA hybridization values for draft genomes between strain F-4 and strain THG-DT86 were 79.8 and 22.6 %, respectively. On the basis of the genotypic and phenotypic data presented here, strain F-4 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is F-4 (=KCTC 62442=CGMCC 1.13562).

Funding
This study was supported by the:
  • Fundamental Research Funds for the Central Universities (Award KYZ201635)
  • National Natural Science Fund of China (Award 41671317)
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2019-02-13
2022-05-27
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References

  1. Zhang L, Wang Y, Wei L, Wang Y, Shen X et al. Taibaiella smilacinae gen. nov., sp. nov., an endophytic member of the family Chitinophagaceae isolated from the stem of Smilacina japonica, and emended description of Flavihumibacter petaseus . Int J Syst Evol Microbiol 2013; 63:3769–3776 [View Article][PubMed]
    [Google Scholar]
  2. Son HM, Kook M, Kim JH, Yi TH. Taibaiella koreensis sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 2014; 64:1018–1023 [View Article][PubMed]
    [Google Scholar]
  3. Kim MK, Kim TS, Joung Y, Han JH, Kim SB et al. Taibaiella soli sp. nov. isolated from pine forest soil. Int J Syst Evol Microbiol 2016; 66:3230–3234
    [Google Scholar]
  4. Tan X, Zhang RG, Meng TY, Liang HZ, Lv J. Taibaiella chishuiensis sp. nov., isolated from freshwater. Int J Syst Evol Microbiol 2014; 64:1795–1801 [View Article][PubMed]
    [Google Scholar]
  5. Szabó I, Szoboszlay S, Táncsics A, Szerdahelyi SG, Szucs Á et al. Taibaiella coffeisoli sp. nov., isolated from the soil of a coffee plantation. Int J Syst Evol Microbiol 2016; 66:1627–1632 [View Article][PubMed]
    [Google Scholar]
  6. Singh H, Du J, Won K, Yang JE, Akter S et al. Taibaiella yonginensis sp. nov., a bacterium isolated from soil of Yongin city. Antonie van Leeuwenhoek 2015; 108:517–524 [View Article][PubMed]
    [Google Scholar]
  7. Fautz E, Reichenbach H. A simple test for flexirubin-type pigments. FEMS Microbiol Lett 1980; 8:87–91 [View Article]
    [Google Scholar]
  8. Bowman JP. Description of Cellulophaga algicola sp. nov., isolated from the surfaces of Antarctic algae, and reclassification of Cytophaga uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Cellulophaga uliginosa comb. nov. Int J Syst Evol Microbiol 2000; 50 Pt 5:1861–1868 [View Article][PubMed]
    [Google Scholar]
  9. Kim MK, Kim TW, Kim TS, Joung Y, Han JH et al. Fluviicoccus keumensis gen. nov., sp. nov., isolated from freshwater. Int J Syst Evol Microbiol 2016; 66:201–205 [View Article][PubMed]
    [Google Scholar]
  10. Yoon J-H, Kim H, Kim S-B, Kim H-J, Kim WY et al. Identification of Saccharomonospora Strains by the Use of Genomic DNA Fragments and rRNA Gene Probes. Int J Syst Bacteriol 1996; 46:502–505 [View Article]
    [Google Scholar]
  11. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics Chichester, UK: Wiley; 1991 pp. 115–175
    [Google Scholar]
  12. Baker GC, Smith JJ, Cowan DA. Review and re-analysis of domain-specific 16S primers. J Microbiol Methods 2003; 55:541–555 [View Article][PubMed]
    [Google Scholar]
  13. Yoon SH, Ha SM, 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]
  14. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 25:4876–4882 [View Article][PubMed]
    [Google Scholar]
  15. 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]
  16. Tamura K, Peterson D, Peterson N, Stecher G, Nei M et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011; 28:2731–2739 [View Article][PubMed]
    [Google Scholar]
  17. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol 2013; 30:2725–2729 [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. 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. Collins MD. Isoprenoid quinone analyses in bacterial classification and identification. In Goodfellow M, Minnikin DE. (editors) Chemical Methods in Bacterial Systematics London: Academic Press; 1985 pp. 267–284
    [Google Scholar]
  21. Nishijima M, Araki-Sakai M, Sano H. Identification of isoprenoid quinones by frit-FAB liquid chromatography–mass spectrometry for the chemotaxonomy of microorganisms. J Microbiol Methods 1997; 28:113–122 [View Article]
    [Google Scholar]
  22. Tindall BJ. Lipid composition of Halobacterium lacusprofundi . FEMS Microbiol Lett 1990; 66:199–202 [View Article]
    [Google Scholar]
  23. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 101 Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  24. Busse H-J, Bunka S, Hensel A, Lubitz W. Discrimination of members of the family Pasteurellaceae based on polyamine patterns. Int J Syst Bacteriol 1997; 47:698–708 [View Article]
    [Google Scholar]
  25. Busse HJ, Kämpfer P, Denner EB. Chemotaxonomic characterisation of Sphingomonas . J Ind Microbiol Biotechnol 1999; 23:242–251 [View Article][PubMed]
    [Google Scholar]
  26. Taibi G, Schiavo MR, Gueli MC, Rindina PC, Muratore R et al. Rapid and simultaneous high-performance liquid chromatography assay of polyamines and monoacetylpolyamines in biological specimens. J Chromatogr B Biomed Sci Appl 2000; 745:431–437 [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; 14:60 [View Article][PubMed]
    [Google Scholar]
  28. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article][PubMed]
    [Google Scholar]
  29. 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]
  30. 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]
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