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Abstract

A Gram-stain-negative, non-spore-forming, aerobic, curved rod-shaped bacterium, designed strain R142, was isolated from a coralline algae sp. in the Beibu Gulf, China. Optimal growth occurred with 0–0.5 % (w/v) NaCl, at 25 °C and at pH 8. Global alignment based on 16S rRNA gene sequences indicated that strain R142 shared 93.8 % similarity with its closest type strain, KU14G. Phylogenetic analyses showed that strain R142 forms a distinct branch alongside KU41E, SW-11, KU14G, MEBiC06469 and SM-6. The major polar lipids of strain R142 were phosphatidylethanolamine and phosphatidylglycerol. The primary cellular fatty acids were C, Cω7, Cω7, C and C. The genome DNA G+C ratio was 56.4 mol%. The only detected respiratory quinone was ubiquinone 8. The low 16S rRNA gene sequence similarity and differences in cellular fatty acids readily distinguished strain R142 from all validly published type strains. Strain R142 is therefore suggested to represent a novel species of a new genus, for which the name gen. nov., sp. nov. is proposed. The type strain of is R142 (=MCCC 1K03816=KCTC 72138).

Funding
This study was supported by the:
  • Innovative Research Group Project of the National Natural Science Foundation of China (CN) (Award 41866004)
    • Principle Award Recipient: Guanghua Wang
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2020-05-04
2025-01-23
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References

  1. Spring S, Scheuner C, Göker M, Klenk H-P. A taxonomic framework for emerging groups of ecologically important marine gammaproteobacteria based on the reconstruction of evolutionary relationships using genome-scale data. Front Microbiol 2015; 6:281 [View Article][PubMed][PubMed]
    [Google Scholar]
  2. Distel DL, Morrill W, MacLaren-Toussaint N, Franks D, Waterbury J. Teredinibacter turnerae gen. nov., sp. nov., a dinitrogen-fixing, cellulolytic, endosymbiotic gamma-proteobacterium isolated from the gills of wood-boring molluscs (Bivalvia: Teredinidae). Int J Syst Evol Microbiol 2002; 52:2261–2269 [View Article][PubMed][PubMed]
    [Google Scholar]
  3. Nishijima M, Adachi K, Sano H, Yamasato K. Marinibactrum halimedae gen. nov., sp. nov., a gammaproteobacterium isolated from a marine macroalga. Int J Syst Evol Microbiol 2015; 65:3866–3871 [View Article][PubMed][PubMed]
    [Google Scholar]
  4. Chen M-H, Sheu S-Y, Arun AB, Young C-C, Chen CA et al. Pseudoteredinibacter isoporae gen. nov., sp. nov., a marine bacterium isolated from the reef-building coral Isopora palifera . Int J Syst Evol Microbiol 2011; 61:1887–1893 [View Article][PubMed][PubMed]
    [Google Scholar]
  5. Miller IJ, Vanee N, Fong SS, Lim-Fong GE, Kwan JC. Lack of overt genome reduction in the bryostatin-producing bryozoan symbiont "Candidatus Endobugula sertula". Appl Environ Microbiol 2016; 82:6573–6583 [View Article][PubMed][PubMed]
    [Google Scholar]
  6. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics Chichester: Wiley; 1991 pp 115–175
    [Google Scholar]
  7. 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][PubMed]
    [Google Scholar]
  8. Pruesse E, Peplies J, Glöckner FO. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 2012; 28:1823–1829 [View Article][PubMed][PubMed]
    [Google Scholar]
  9. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed][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][PubMed]
    [Google Scholar]
  11. Swofford DL. PAUP: Phylogenetic Analysis Using Parsimony, Version 3.1.1 Champaign, IL: Illinois Natural History Survey; 1993
    [Google Scholar]
  12. 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][PubMed]
    [Google Scholar]
  13. 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][PubMed]
    [Google Scholar]
  14. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed][PubMed]
    [Google Scholar]
  15. 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][PubMed]
    [Google Scholar]
  16. Lim HJ, Lee E-H, Yoon Y, Chua B, Son A. Portable lysis apparatus for rapid single-step DNA extraction of Bacillus subtilis . J Appl Microbiol 2016; 120:379–387 [View Article][PubMed][PubMed]
    [Google Scholar]
  17. Li R, Li Y, Kristiansen K, Wang J. Soap: short oligonucleotide alignment program. Bioinformatics 2008; 24:713–714 [View Article][PubMed][PubMed]
    [Google Scholar]
  18. Li R, Zhu H, Ruan J, Qian W, Fang X et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 2010; 20:265–272 [View Article][PubMed][PubMed]
    [Google Scholar]
  19. Li D, Liu C-M, Luo R, Sadakane K, Lam T-W. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 2015; 31:1674–1676 [View Article][PubMed][PubMed]
    [Google Scholar]
  20. Wu Y-W, Simmons BA, Singer SW. MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets. Bioinformatics 2016; 32:605–607 [View Article][PubMed][PubMed]
    [Google Scholar]
  21. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article][PubMed][PubMed]
    [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][PubMed]
    [Google Scholar]
  23. 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][PubMed]
    [Google Scholar]
  24. Bernardet J-F, Nakagawa Y, Holmes B. Subcommittee on the taxonomy of flavobacterium and cytophaga-like bacteria of the international committee on systematics of prokaryotes. Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 2002; 52:1049–1070 [View Article][PubMed][PubMed]
    [Google Scholar]
  25. Gerhardt P, Murray RGE, Wood WA, Krieg NR. Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994
    [Google Scholar]
  26. Dong XZ, Cai MY. Determinative Manual for Routine Bacteriology Beijing: Scientific Press; 2001
    [Google Scholar]
  27. Tindall BJ, Sikorski J, Smibert RM, Krieg NR et al. 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 Washington, DC: American Society for Microbiology; 2007 pp 330–393
    [Google Scholar]
  28. Iwaki H, Fujioka M, Hasegawa Y. Isolation and characterization of marine nonylphenol-degrading bacteria and description of Pseudomaricurvus alkylphenolicus gen. nov., sp. nov. Curr Microbiol 2014; 68:167–173 [View Article][PubMed][PubMed]
    [Google Scholar]
  29. Iwaki H, Takada K, Hasegawa Y. Maricurvus nonylphenolicus gen. nov., sp. nov., a nonylphenol-degrading bacterium isolated from seawater. FEMS Microbiol Lett 2012; 327:142–147 [View Article][PubMed][PubMed]
    [Google Scholar]
  30. Lo N, Kim KH, Baek K, Jia B, Jeon CO. Aestuariicella hydrocarbonica gen. nov., sp. nov., an aliphatic hydrocarbon-degrading bacterium isolated from a sea tidal flat. Int J Syst Evol Microbiol 2015; 65:1935–1940 [View Article][PubMed][PubMed]
    [Google Scholar]
  31. Collins MD. Isoprenoid quinones. In Goodfellow M, O’Donnell AG. (editors) Chemical Methods in Prokaryotic Systematics Chichester: John Wiley & Sons; 1994 pp 345–401
    [Google Scholar]
  32. Komagata K, Suzuki K. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–207
    [Google Scholar]
  33. Kamekura M. Lipids of extreme halophiles. In Vreeland RH, Hochstein LI. (editors) The Biology of Halophilic Bacteria Boca Raton: CRC Press;; 1993 pp 135–161
    [Google Scholar]
  34. Tindall BJ. Lipid composition of Halobacterium lacusprofundi . FEMS Microbiol Lett 1990; 66:199–202 [View Article]
    [Google Scholar]
  35. Seo H-S, Yang S-H, Oh JH, Lee J-H, Kwon KK. Pseudomaricurvus alcaniphilus sp. nov., a marine bacterium isolated from tidal flat sediment and emended descriptions of the genus Pseudomaricurvus, Pseudomaricurvus alkylphenolicus Iwaki et al. 2014 and Maricurvus nonylphenolicus Iwaki et al. 2012. Int J Syst Evol Microbiol 2015; 65:3591–3596 [View Article][PubMed][PubMed]
    [Google Scholar]
  36. Urios L, Intertaglia L, Lesongeur F, Lebaron P. Eionea nigra gen. nov., sp. nov., a gammaproteobacterium from the Mediterranean sea. Int J Syst Evol Microbiol 2011; 61:1677–1681 [View Article][PubMed][PubMed]
    [Google Scholar]
  37. Baek K, Choi A, Cho J-C. Eionea flava sp. nov., isolated from coastal seawater, and emended description of the genus Eionea . Int J Syst Evol Microbiol 2015; 65:2975–2979 [View Article][PubMed][PubMed]
    [Google Scholar]
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