Deminuibacter soli gen. nov., sp. nov., isolated from forest soil, and reclassification of Filimonas aurantiibacter as Arvibacter aurantiibacter comb. nov. Free

Abstract

A novel strain, designated K23C18032701, was isolated from a sample of forest soil collected from Dinghushan Biosphere Reserve, Guangdong Province, PR China. The strain was Gram-stain-negative, aerobic, motile and showed a shape change from a filamentous cell to coccobacilli. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the novel strain belongs to the family Chitinophagaceae , and showed the highest similarities to Arvibacter flaviflagrans JCM 31293 (95.0 %) and Filimonas aurantiibacter LMG 29039 (94.4 %). The major cellular fatty acids included iso-C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 1 G. The predominant polar lipid was phosphatidylethanolamine (PE). The predominant respiratory quinone was menaquinone-7. The major polyamine was sym-homospermidine. The draft genome size of strain K23C18032701 was 5.84 Mb with a DNA G+C content of 47.2 mol%. Based on phenotypic, genotypic and phylogenetic analysis, strain K23C18032701 represents a novel species of a new genus in the family Chitinophagaceae , for which the name Deminuibacter soli is proposed. The type strain is K23C18032701 (=GDMCC 1.1403=KCTC 62913). We also propose the reclassification of Filimonas aurantiibacter as Arvibacter aurantiibacter comb. nov. (type strain 1458=NRRL B-65305=LMG 29039).

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2019-04-01
2024-03-29
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References

  1. 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]
  2. Kämpfer P, Young CC, 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]
  3. Lv YY, Gao ZH, Xia F, Chen MH, Qiu LH. 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]
  4. Siddiqi MZ, Muhammad Shafi S, Choi KD, Im WT. Compostibacter hankyongensis gen. nov., sp nov., isolated from compost. Int J Syst Evol Microbiol 2016; 66:3681–3687 [View Article][PubMed]
    [Google Scholar]
  5. Gao JL, Sun P, Wang XM, Qiu TL, Lv FY, Fy L et al. Filimonas zeae sp. nov., an endophytic bacterium isolated from maize root. Int J Syst Evol Microbiol 2016; 66:2730–2734 [View Article][PubMed]
    [Google Scholar]
  6. Reichenbach H, Dworkin M. The myxobacteria. In Balows A, Trüper HG, Dworkin M, Harder W, Schleifer KH et al. (editors) The Prokaryotes New York: Springer; 1992 pp. 3416–3487
    [Google Scholar]
  7. Shimkets LJ, Dworkin M, Reichenbach H. The myxobacteria. In Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E et al. (editors) In the Prokaryotes New York: Springer; 2006 pp. 31–115
    [Google Scholar]
  8. Chen D-H, Ronald PC. A rapid DNA minipreparation method suitable for AFLP and other PCR applications. Plant Mol Biol Report 1999; 17:53–57 [View Article]
    [Google Scholar]
  9. Lane DJ. 16S/23S rDNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics Chichester: Wiley; 1991 pp. 115–175
    [Google Scholar]
  10. Kim OS, Cho YJ, Lee K, Yoon SH, 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]
  11. 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]
  12. 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]
  13. Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 2003; 52:696–704 [View Article][PubMed]
    [Google Scholar]
  14. 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]
  15. 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]
  16. Coil D, Jospin G, Darling AE. A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data. Bioinformatics 2015; 31:587–589 [View Article][PubMed]
    [Google Scholar]
  17. Lv YY, Wang J, You J, Qiu LH. Chitinophaga dinghuensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 2015; 65:4816–4822 [View Article][PubMed]
    [Google Scholar]
  18. Lv YY, Wang J, Chen MH, You J, Qiu LH. Dinghuibacter silviterrae gen. nov., sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2016; 66:1785–1791 [View Article][PubMed]
    [Google Scholar]
  19. Albert RA, Waas NE, Pavlons SC, Pearson JL, Roecker J et al. Filimonas aurantiibacter sp. nov., an orange-pigmented bacterium isolated from lake water and emended description of the genus Filimonas . Int J Syst Evol Microbiol 2016; 66:4027–4032 [View Article][PubMed]
    [Google Scholar]
  20. Brown AE. Benson′s Microbiological Applications: Laboratory Manual in General Microbiology, 4th ed. New York: McGraw-Hill; 1985
    [Google Scholar]
  21. 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]
  22. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  23. 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]
  24. Tindall BJ, Sikorski J, Smibert RA, Krieg NR. Phenotypic characterization and the principles of comparative systematics. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf G, Schmidt TM et al. (editors) Methods for General and Molecular Microbiology vol. 365 Washington, DC: American Society for Microbiology; 2007 pp. 384–385
    [Google Scholar]
  25. Busse J, Auling G. Polyamine pattern as a chemotaxonomic marker within the Proteobacteria . Syst Appl Microbiol 1988; 11:1–8 [View Article]
    [Google Scholar]
  26. Scherer P, Kneifel H. Distribution of polyamines in methanogenic bacteria. J Bacteriol 1983; 154:1315–1322[PubMed]
    [Google Scholar]
  27. Feng GD, Yang SZ, Xiong X, Li HP, Zhu HH. Sphingomonas spermidinifaciens sp. nov., a novel bacterium containing spermidine as the major polyamine, isolated from an abandoned lead-zinc mine and emended descriptions of the genus Sphingomonas and the species Sphingomonas yantingensis and Sphingomonas japonica. Int J Syst Evol Microbiol 2017; 67:2160–2165 [View Article][PubMed]
    [Google Scholar]
  28. Han JH, Kim TS, Joung Y, Kim SB. Filimonas endophytica sp. nov., isolated from surface-sterilized root of Cosmos bipinnatus. Int J Syst Evol Microbiol 2015; 65:4863–4867 [View Article][PubMed]
    [Google Scholar]
  29. Lin SY, Hameed A, Hsu YH, Liu YC, Lai WA et al. Filimonas aquilariae sp. nov., isolated from agarwood chips. Int J Syst Evol Microbiol 2017; 67:3219–3225 [View Article][PubMed]
    [Google Scholar]
  30. Chaudhary DK, Kim J. Arvibacter flaviflagrans gen. nov., sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2016; 66:4347–4354 [View Article][PubMed]
    [Google Scholar]
  31. Shiratori H, Tagami Y, Morishita T, Kamihara Y, Beppu T et al. Filimonas lacunae gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from fresh water. Int J Syst Evol Microbiol 2009; 59:1137–1142 [View Article][PubMed]
    [Google Scholar]
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