1887

Abstract

A novel bacterium, designated strain SYSU M00256-3, was isolated from a water sample collected from Pearl River Estuary at Guangzhou, PR China. Its taxonomic position was determined by using a polyphasic approach. Cells of the strain were Gram-staining-negative, motile, aerobic and rod-shaped with peritrichous flagella. It could grow at 15–45 °C, pH 4.0–10.0 and in the presence of 0–7.5 % (w/v) NaCl. The chemotaxonomic features of strain SYSU M00256-3 included ubiquinone-10 (Q-10) as the sole respiratory quinone; phosphatidylcholine, phosphatidylmethylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid as major polar lipids; summed feature 8 (C ω and C 6) as the predominant fatty acids (>70 %). On the basis of 16S rRNA gene sequence analysis, strain SYSU M00256-3 was most closely related to the type strains of CGMCC 1.12584 (97.7 %) and CGMCC 1.12426 (97.2 %), KCTC 52373 (96.7 %), CGMCC 1.12583 (96.4 %). The average nucleotide identity (ANI) values between SYSU M00256-3 and CGMCC 1.12584, CGMCC 1.12426, CGMCC 1.12583 and KCTC 52373 were 78.0, 78.2, 77.7 and 78.8, and the dDDH value is 20.0, 20.8, 20.1 and 20.6 correspondingly. Based on the analyses of the phenotypic, genotypic and phylogenetic characteristics, strain SYSU M00256-3 is characterized to represent a novel species of the genus , for which the name sp. nov. is proposed. The type strain is SYSU M00256-3 (=NBRC 112946=CGMCC 1.16156).

Funding
This study was supported by the:
  • Wen-Jun Li , Guangdong Province Science and Technology Innovation Strategy Special Fund , (Award 2018B020206001)
  • Wen-Jun Li , Natural Science Foundation of Guangdong Province , (Award 2016A030312003)
  • Xiaozhen Mou , National Natural Science Foundation of China , (Award 31500004)
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/content/journal/ijsem/10.1099/ijsem.0.004116
2020-03-25
2020-04-01
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References

  1. Suzuki T, Muroga Y, Takahama M, Nishimura Y. Roseigium denhamense gen. nov., sp. nov. and Roseibium hemelinense sp. nov., aerobic bacteriochlorophyll-containing bacteria isolated from the East and West coasts of Australia. Int J Syst Evol Microbiol 2000; 50 Pt 6:2151–2156 [CrossRef][PubMed]
    [Google Scholar]
  2. Biebl H, Pukall R, Lünsdorf H, Schulz S, Allgaier M et al. Description of Labrenzia alexandrii gen. nov., sp. nov., a novel alphaproteobacterium containing bacteriochlorophyll a, and a proposal for reclassification of Stappia aggregata as Labrenzia aggregata comb. nov., of Stappia marina as Labrenzia marina comb. nov. and of Stappia alba as Labrenzia alba comb. nov., and emended descriptions of the genera Pannonibacter, Stappia and Roseibium, and of the species Roseibium denhamense and Roseibium hamelinense. Int J Syst Evol Microbiol 2007; 57:1095–1107 [CrossRef][PubMed]
    [Google Scholar]
  3. Zhong Z-P, Liu Y, Liu H-C, Wang F, Zhou Y-G et al. Roseibium aquae sp. nov., isolated from a saline lake. Int J Syst Evol Microbiol 2014; 64:2812–2818 [CrossRef][PubMed]
    [Google Scholar]
  4. Liu J, Wang Y, Yang X, Sun Z, Ren Q et al. Roseibium sediminis sp. nov., isolated from sea surface sediment. Int J Syst Evol Microbiol 2017; 67:2862–2867 [CrossRef][PubMed]
    [Google Scholar]
  5. Li X, Salam N, Li J-L, Chen Y-M, Yang Z-W et al. Aestuariivirga litoralis gen. nov., sp. nov., a proteobacterium isolated from a water sample, and proposal of Aestuariivirgaceae fam. nov. Int J Syst Evol Microbiol 2019; 69:299–306 [CrossRef][PubMed]
    [Google Scholar]
  6. Ming H, Nie G-X, Jiang H-C, Yu T-T, Zhou E-M et al. Paenibacillus frigoriresistens sp. nov., a novel psychrotroph isolated from a peat bog in Heilongjiang, Northern China. Antonie van Leeuwenhoek 2012; 102:297–305 [CrossRef][PubMed]
    [Google Scholar]
  7. Leifson E. Atlas of bacterial flagellation. Am J Med Sci 1961; 242:267 [CrossRef]
    [Google Scholar]
  8. Nie G-X, Ming H, Li S, Zhou E-M, Cheng J et al. Amycolatopsis dongchuanensis sp. nov., an actinobacterium isolated from soil. Int J Syst Evol Microbiol 2012; 62:2650–2656 [CrossRef][PubMed]
    [Google Scholar]
  9. Kovacs N. Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 1956; 178:703 [CrossRef][PubMed]
    [Google Scholar]
  10. MacFaddin JF, MacFaddin JF. Biochemical Tests for Identification of Medical Bacteria 2000
    [Google Scholar]
  11. Gonzalez C, Gutierrez C, Ramirez C. Halobacterium vallismortis sp. nov. An amylolytic and carbohydrate-metabolizing, extremely halophilic bacterium. Can J Microbiol 1978; 24:710–715 [CrossRef][PubMed]
    [Google Scholar]
  12. Smibert RM, Krieg NR. Phenotypic Characterization 1994
    [Google Scholar]
  13. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [CrossRef][PubMed]
    [Google Scholar]
  14. Tamaoka J. Analysis of bacterial menaquinone mixtures by reverse-phase high-performance liquid chromatography. Methods Enzymol 1986; 123:251–256 [CrossRef][PubMed]
    [Google Scholar]
  15. Collins MD, Jones D. Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2, 4-diaminobutyric acid. J Appl Bacteriol 1980; 48:459–470 [CrossRef]
    [Google Scholar]
  16. Minnikin DE, Collins MD, Goodfellow M. Fatty acid and polar lipid composition in the classification of Cellulomonas, Oerskovia and Related Taxa. J Appl Bacteriol 1979; 47:87–95 [CrossRef]
    [Google Scholar]
  17. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 19901–7
    [Google Scholar]
  18. Li W-J, Xu P, Schumann P, Zhang Y-Q, Pukall R et al. Georgenia ruanii sp. nov., a novel actinobacterium isolated from forest soil in Yunnan (China), and emended description of the genus Georgenia. Int J Syst Evol Microbiol 2007; 57:1424–1428 [CrossRef][PubMed]
    [Google Scholar]
  19. 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 [CrossRef][PubMed]
    [Google Scholar]
  20. 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 [CrossRef][PubMed]
    [Google Scholar]
  21. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [CrossRef][PubMed]
    [Google Scholar]
  22. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  23. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [CrossRef][PubMed]
    [Google Scholar]
  24. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol 1971; 20:406–416 [CrossRef]
    [Google Scholar]
  25. Kimura M. The Neutral Theory of Molecular Evolution Cambridge: Cambridge University Press; 1983
    [Google Scholar]
  26. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [CrossRef][PubMed]
    [Google Scholar]
  27. 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; 14:14 [CrossRef]
    [Google Scholar]
  28. Blin K, Shaw S, Steinke K, Villebro R, Ziemert N et al. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res 2019; 47:W81–W87 [CrossRef]
    [Google Scholar]
  29. 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 [CrossRef][PubMed]
    [Google Scholar]
  30. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [CrossRef][PubMed]
    [Google Scholar]
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