1887

Abstract

Two novel Gram-stain-negative, rod-shaped and non-motile bacterial strains, designated B5-SW-15 and C2-DW-16, were isolated from water collected in mangrove forests in Ranong Province, Thailand. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains B5-SW-15 and C2-DW-16 belonged to the genus and were most closely related to DSM 100212 (98.2 and 98.1 %, respectively) and DSM 29127 (97.7 and 97.6 %, respectively). The average nucleotide identity and digital DNA–DNA hybridization values between strain B5-SW-15, strain C2-DW-16 and related species were 95.8 and 71.6 % (to strain C2-DW-16), 76.8 and 21.3 % (to DSM 100212) and 80.3 and 24.2 % (to DSM 29127), respectively. The predominant cellular fatty acids (>5 %) were summed feature 8 (C and/or C 7), C and C 3-OH. Ubiquinone Q-10 was the sole respiratory quinone. DNA G+C contents of the isolates were 61.0 and 61.2 mol% based on whole genome sequences. Strains B5-SW-15 and C2-DW-16 contained aminolipid, phosphatidylcholine, phosphatidylethanolamine and phosphatidylglycerol as the major polar lipids. On the basis of the results from phenotypic, chemotaxonomic and phylogenetic analyses, strains B5-SW-15 and C2-DW-16 constitute a novel species of the genus in the family for which the name sp. nov. is proposed. The type strain is B5-SW-15 (=BCC 56522=TBRC 9562=KCTC 72743).

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2020-12-01
2024-03-28
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References

  1. Garrity GM, Bell JA, Lilburn T, Garrity GM, Bell JA et al. Family I. Rhodobacteraceae fam. nov. Bergey’s Manual of Systematic Bacteriology. In Brenner DJ, Krieg NR, Staley JT. (editors) The Proteobacteria Part C The Alpha-, Beta-, Delta-, and Epsilonproteobacteria , 2nd ed. New York: Springer; 2005 p 161 [View Article]
    [Google Scholar]
  2. Hördt A, López MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM et al. Analysis of 1000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria . Front Microbiol 2020; 11:468 [View Article][PubMed]
    [Google Scholar]
  3. Oren A, Garrity G. Notification of changes in taxonomic opinion previously published outside the IJSEM. Int J Syst Evol Microbiol 2020; 70:4061–4090 [View Article][PubMed]
    [Google Scholar]
  4. Parte AC. LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. Int J Syst Evol Microbiol 2018; 68:1825–1829 [View Article][PubMed]
    [Google Scholar]
  5. Yoon JH, Kang SJ, Oh TK. Donghicola eburneus gen. nov., sp. nov., isolated from seawater of the East Sea in Korea. Int J Syst Evol Microbiol 2007; 57:73–76 [View Article][PubMed]
    [Google Scholar]
  6. Hameed A, Shahina M, Lin SY, Nakayan P, Liu YC et al. Youngimonas vesicularis gen. nov., sp. nov., of the family Rhodobacteraceae, isolated from surface seawater, reclassification of Donghicola xiamenensis Tan et al. 2009 as Pseudodonghicola xiamenensis gen. nov., comb. nov. and emended description of the genus Donghicola Yoon et al. 2007. Int J Syst Evol Microbiol 2014; 64:2729–2737 [View Article][PubMed]
    [Google Scholar]
  7. Tan T, Wang B, Shao Z. Donghicola xiamenensis sp. nov., a marine bacterium isolated from seawater of the Taiwan Strait in China. Int J Syst Evol Microbiol 2009; 59:1143–1147 [View Article][PubMed]
    [Google Scholar]
  8. Sung HR, Lee JM, Kim M, Yun BR, Shin KS. Donghicola tyrosinivorans sp. nov., a tyrosine-degrading bacterium isolated from seawater. Int J Syst Evol Microbiol 2015; 65:4140–4145 [View Article][PubMed]
    [Google Scholar]
  9. Ezaki T, Yamamoto N, Ninomiya K, Suzuki S, Yabuuchi E. Transfer of Peptococcus indolicus, Peptococcus asaccharolyticus, Peptococcus prevotii, and Peptococcus magnus to the genus Peptostreptococcus and proposal of Peptostreptococcus tetradius sp. nov. Int J Syst Bacteriol 1983; 33:683–698 [View Article]
    [Google Scholar]
  10. Marmur J. A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol 1961; 3:208-IN1 [View Article]
    [Google Scholar]
  11. Saito H, Miura K-I. Preparation of transforming deoxyribonucleic acid by phenol treatment. Biochim Biophys Acta 1963; 72:619–629 [View Article][PubMed]
    [Google Scholar]
  12. Yukphan P, Potacharoen W, Tanasupawat S, Tanticharoen M, Yamada Y. Asaia krungthepensis sp. nov., an acetic acid bacterium in the alpha-Proteobacteria . Int J Syst Evol Microbiol 2004; 54:313–316 [View Article][PubMed]
    [Google Scholar]
  13. Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article][PubMed]
    [Google Scholar]
  14. 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]
  15. Tindall BJ, Rosselló-Móra R, Busse HJ, Ludwig W, Kämpfer P. Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 2010; 60:249–266 [View Article][PubMed]
    [Google Scholar]
  16. 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]
  17. Edgar RC. Muscle: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article][PubMed]
    [Google Scholar]
  18. 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]
  19. 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]
  20. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  21. 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]
  22. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
    [Google Scholar]
  23. 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]
  24. Afgan E, Baker D, van den Beek M, Blankenberg D, Bouvier D et al. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Res 2016; 44:W3–W10 [View Article][PubMed]
    [Google Scholar]
  25. Andrews S. 2010; FastQC: a quality control tool for high throughput sequence data. http://www.bioinformatics.babraham.ac.uk/projects/fastqc
  26. Krueger F. 2015; Trim galore!: a wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files. http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
  27. Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 2017; 13:e1005595 [View Article][PubMed]
    [Google Scholar]
  28. Lee I, Chalita M, Ha SM, Na SI, Yoon S-H et al. ContEst16S: an algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences. Int J Syst Evol Microbiol 2017; 67:2053–2057 [View Article][PubMed]
    [Google Scholar]
  29. 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]
  30. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [View Article][PubMed]
    [Google Scholar]
  31. 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]
  32. 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]
  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. 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]
  35. Hameed A, Shahina M, Lin SY, Cho JC, Lai WA et al. Kordia aquimaris sp. nov., a zeaxanthin-producing member of the family Flavobacteriaceae isolated from surface seawater, and emended description of the genus Kordia . Int J Syst Evol Microbiol 2013; 63:4790–4796 [View Article][PubMed]
    [Google Scholar]
  36. Cowan ST, Steel KJ. Cowan and Steel’s Manual for the Identification of Medical Bacteria . In Barrow GI, Feltham RKA. (editors) Cambridge: Cambridge University Press; 1993
  37. Shin YK, Lee JS, Chun CO, Kim HJ. Isoprenoid quinone profiles of the Leclercia adecarboxylata KCTC 1036T . J Microbiol Biotechnol 1996; 6:68–69
    [Google Scholar]
  38. Collins MD, Jones D. A note on the separation of natural mixtures of bacterial ubiquinones using reverse-phase partition thin-layer chromatography and high performance liquid chromatography. J Appl Bacteriol 1981; 51:129–134 [View Article][PubMed]
    [Google Scholar]
  39. 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]
  40. Minnikin DE, Patel PV, Alshamaony L, Goodfellow M. Polar lipid composition in the classification of Nocardia and related bacteria. Int J Syst Bacteriol 1977; 27:104–117 [View Article]
    [Google Scholar]
  41. Komagata K, Suzuki K-I, Colwell RR, Grigorova R. Lipid and cell-wall analysis in bacterial Systematics. Methods Microbiol. 19: Academic Press 1987161–207
    [Google Scholar]
  42. Sasser M. editor Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids Technical Note # 1012001 Newark: MIDI Inc;
    [Google Scholar]
  43. Matsuda N, Matsuda M, Notake S, Yokokawa H, Kawamura Y et al. Evaluation of a simple protein extraction method for species identification of clinically relevant staphylococci by matrix-assisted laser desorption ionization-time of flight mass spectrometry. J Clin Microbiol 2012; 50:3862–3866 [View Article][PubMed]
    [Google Scholar]
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