1887

Abstract

A Gram-stain-negative, aerobic, gliding, reddish-orange-coloured, rod-shaped strain, designated SR4, was isolated from surface seawater sampled at Luhuitou fringing reef (South China Sea). Phylogenetic analyses based on the 16S rRNA gene, phylogenomic analysis of single-copy gene families and whole genome data affiliated it to the genus . It was most closely related to NBRC 100898 (97.99 % 16S rRNA gene similarity). The genome average nucleotide identity and DNA–DNA relatedness values between strain SR4 and its reference strains were less than 74.2 and 16.3 %, respectively. Growth occurred at 20–35 °C (optimum, 28 °C), pH 6.0–9.0 (optimum, pH 7.0) and in the presence of 1–6 % (w/v) NaCl (optimum, 2–4 %). The dominant fatty acids were C, iso-C and C 6,9,12,15. The polar lipid profile of strain SR4 comprised phosphatidylethanolamine, two glycolipids, two aminophospholipids and three unidentified lipids. The major respiratory quinone was MK-7. The DNA G+C content of strain SR4 was 34.20 mol%. On the basis of the polyphasic evidence, strain SR4 is proposed as representing a novel species of the genus , for which the name sp. nov. is proposed. The type strain is SR4 (=KCTC 82075=MCCC 1A17137).

Funding
This study was supported by the:
  • Scientific Research Foundation of Third Institute of Oceanography, MNR (Award 2019003)
    • Principle Award Recipient: Jiaguang Xiao
  • Scientific Research Foundation of Third Institute of Oceanography, MNR (Award 2020005)
    • Principle Award Recipient: Xiaolei Wang
  • National Key Research and Development Program of China (Award 2017YFA0604902)
    • Principle Award Recipient: Wentao Niu
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2020-10-23
2021-10-19
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References

  1. Nedashkovskaya OI, Ludwig W. Phylum XIV. Flammeovirgaceae fam. nov. Bergey’s Manual of Systematics of Archaea and Bacteria 2015 pp 1–6
    [Google Scholar]
  2. Zhang L, Shen X, Liu Y, Li S. Nafulsella turpanensis gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from soil. Int J Syst Evol Microbiol 2013; 63:1639–1645 [View Article][PubMed]
    [Google Scholar]
  3. Tang M, Chen C, Li J, Xiang W, Wu H et al. Fabivirga thermotolerans gen. nov., sp. nov., a novel marine bacterium isolated from culture broth of a marine cyanobacterium. Int J Syst Evol Microbiol 2016; 66:1095–1099 [View Article][PubMed]
    [Google Scholar]
  4. Wang H, Li J, Zheng T, Hill RT, Hu X. Imperialibacter roseus gen. nov., sp. nov., a novel bacterium of the family Flammeovirgaceae isolated from Permian groundwater. Int J Syst Evol Microbiol 2013; 63:4136–4140 [View Article][PubMed]
    [Google Scholar]
  5. Nakagawa Y, Hamana K, Sakane T, Yamasato K. Reclassification of Cytophaga aprica (Lewin 1969) Reichenbach 1989 in Flammeovirga gen. nov. as Flammeovirga aprica comb. nov. and of Cytophaga diffluens (ex Stanier 1940; emend. Lewin 1969) Reichenbach 1989 in Persicobacter gen. nov. as Persicobacter diffluens comb. nov. Int J Syst Bacteriol 1997; 47:220–223 [View Article]
    [Google Scholar]
  6. Takahashi M, Suzuki K-I, Nakagawa Y. Emendation of the genus Flammeovirga and Flammeovirga aprica with the proposal of Flammeovirga arenaria nom. rev., comb. nov. and Flammeovirga yaeyamensis sp. nov. Int J Syst Evol Microbiol 2006; 56:2095–2100 [View Article][PubMed]
    [Google Scholar]
  7. Hosoya S, Yokota A. Flammeovirga kamogawensis sp. nov., isolated from coastal seawater in Japan. Int J Syst Evol Microbiol 2007; 57:1327–1330 [View Article][PubMed]
    [Google Scholar]
  8. Xu H, Fu Y, Yang N, Ding Z, Lai Q et al. Flammeovirga pacifica sp. nov., isolated from deep-sea sediment. Int J Syst Evol Microbiol 2012; 62:937–941 [View Article][PubMed]
    [Google Scholar]
  9. Jeong Y-S, Kang W, Sung H, Lee J-Y, Yun J-H et al. Flammeovirga pectinis sp. nov., isolated from the gut of the Korean scallop, Patinopecten yessoensis . Int J Syst Evol Microbiol 2020; 70:499–504 [View Article][PubMed]
    [Google Scholar]
  10. Angly FE, Heath C, Morgan TC, Tonin H, Rich V et al. Marine microbial communities of the Great Barrier Reef lagoon are influenced by riverine floodwaters and seasonal weather events. PeerJ 2016; 4:e1511 [View Article][PubMed]
    [Google Scholar]
  11. Mhuantong W, Nuryadi H, Trianto A, Sabdono A, Tangphatsornruang S et al. Comparative analysis of bacterial communities associated with healthy and diseased corals in the Indonesian sea. PeerJ 2019; 7:e8137 [View Article][PubMed]
    [Google Scholar]
  12. Zhang YY, Ling J, Yang QS, Wang YS, Sun CC et al. The diversity of coral associated bacteria and the environmental factors affect their community variation. Ecotoxicology 2015; 24:1467–1477 [View Article][PubMed]
    [Google Scholar]
  13. Li J, Chen Q, Long LJ, Dong JD, Yang J et al. Bacterial dynamics within the mucus, tissue and skeleton of the coral Porites lutea during different seasons. Sci Rep 2014; 4:1–8 [View Article][PubMed]
    [Google Scholar]
  14. Li J, Chen Q, Zhang S, Huang H, Yang J et al. Highly heterogeneous bacterial communities associated with the South China Sea reef corals Porites lutea, Galaxea fascicularis and Acropora millepora . PLoS One 2013; 8:e71301 [View Article][PubMed]
    [Google Scholar]
  15. Moore ERB, Arnscheidt A, Krüger A, Strömpl C, Mau M. Simplified protocols for the preparation of genomic DNA from bacterial cultures. Molecular Microbial Ecology Manual 1 1999 pp 1–15
    [Google Scholar]
  16. Luo R, Liu B, Xie Y, Li Z, Huang W et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 2012; 1:18–24 [View Article][PubMed]
    [Google Scholar]
  17. Zhang Z, Yu T, Xu T, Zhang X-H. Aquimarina pacifica sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2014; 64:1991–1997 [View Article][PubMed]
    [Google Scholar]
  18. 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]
  19. 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]
  20. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article][PubMed]
    [Google Scholar]
  21. 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]
  22. Lin H, Yu M, Wang X, Zhang X-H. Comparative genomic analysis reveals the evolution and environmental adaptation strategies of vibrios. BMC Genomics 2018; 19:135 [View Article][PubMed]
    [Google Scholar]
  23. Contreras-Moreira B, Vinuesa P. GET_HOMOLOGUES, a versatile software package for scalable and robust microbial pangenome analysis. Appl Environ Microbiol 2013; 79:7696–7701 [View Article][PubMed]
    [Google Scholar]
  24. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 2013; 30:772–780 [View Article][PubMed]
    [Google Scholar]
  25. Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 2009; 25:1972–1973 [View Article][PubMed]
    [Google Scholar]
  26. Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 2015; 32:268–274 [View Article][PubMed]
    [Google Scholar]
  27. Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods 2017; 14:587–589 [View Article][PubMed]
    [Google Scholar]
  28. Hoang DT, Chernomor O, von Haeseler A, Minh BQ, Vinh LS. UFBoot2: improving the ultrafast bootstrap approximation. Mol Biol Evol 2018; 35:518–522 [View Article][PubMed]
    [Google Scholar]
  29. Guindon S, Dufayard J-F, Lefort V, Anisimova M, Hordijk W et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 2010; 59:307–321 [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]
  31. Wayne LG, Moore WEC, Stackebrandt E, Kandler O, Colwell RR et al. Report of the AD hoc Committee on reconciliation of approaches to bacterial Systematics. Int J Syst Evol Microbiol 1987; 37:463–464 [View Article]
    [Google Scholar]
  32. Beveridge TJ, Lawrence JR, Murray RG. Sampling and staining for light microscopy. In Reddy CA, Beveridge TJ, Breznak TA, Marzluf G, Schmidt TM. (editors) Methods for General and Molecular Microbiology Washington, DC: American Society for Microbiology; 2007 pp 19–33
    [Google Scholar]
  33. Bernardet JF, Nakagawa Y, Holmes B. 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]
    [Google Scholar]
  34. 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]
  35. Yoon JH, Lee KC, Kho YH, Kang KH, Kim CJ et al. Halomonas alimentaria sp. nov., isolated from jeotgal, a traditional Korean fermented seafood. Int J Syst Evol Microbiol 2002; 52:123–130 [View Article][PubMed]
    [Google Scholar]
  36. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. USFCC News Lett 20 1990 pp 1–6
    [Google Scholar]
  37. 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]
  38. Collins MD, Shah HN. Fatty acid, menaquinone and polar lipid composition of Rothia dentocariosa . Arch Microbiol 1984; 137:247–249 [View Article]
    [Google Scholar]
  39. Komagata K, Suzuki KI. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–207
    [Google Scholar]
  40. Xie CH, Yokota A. Phylogenetic analyses of Lampropedia hyalina based on the 16S rRNA gene sequence. J Gen Appl Microbiol 2003; 49:345–349 [View Article][PubMed]
    [Google Scholar]
  41. Li B, Li Y, Liu R, Xue C, Zhu X et al. Vibrio ouci sp. nov. and Vibrio aquaticus sp. nov., two marine bacteria isolated from the East China Sea. Int J Syst Evol Microbiol 2020; 70:172–179 [View Article][PubMed]
    [Google Scholar]
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