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Abstract

A Gram-stain-negative, aerobic, rod-shaped bacterium (D1M17) was isolated from the seawater surrounding scleractinian coral in Daya Bay, Shenzhen, PR China. Strain D1M17 grew with 0–10 % (w/v) NaCl (optimum, 3–4 %), at 15–37 °C (optimum, 28 °C) and at pH 4.5–8.5 (optimum, pH 7.0–7.5). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain D1M17 formed a lineage within the genus , family , and it was distinct from the most closely related species LMG 25375, JCM 17453 and KCTC 22663 with 16S rRNA gene sequence similarities of 97.2, 97.2 and 97.1 %, respectively. The major respiratory quinone was MK-6. The predominant fatty acids (more than 10 %) were iso-C (28.8 %), iso-C 3-OH (21.5 %) and iso-C G (13.1 %). The DNA G+C content of D1M17 was 34.4 mol%. The polar lipids in D1M17 comprised one phospholipid and five unknown polar lipids. Phenotypic characteristics (physiological, biochemical and chemotaxonomic) also supported the taxonomic novelty of this isolate. Thus, strain D1M17 is considered to represent a novel species within the genus , for which the name sp. nov. is proposed. The type strain is D1M17 (=KCTC 92172= MCCC 1K07224).

Funding
This study was supported by the:
  • Guangdong Key Area R & D Program Project (Award 2020B1111030002)
    • Principle Award Recipient: BaohuaXiao
  • Shenzhen Science and Technology R&D Fund (Award KCXFZ20211020165547011)
    • Principle Award Recipient: BaohuaXiao
  • Shenzhen Science and Technology R&D Fund (Award JCYJ20200109144803833)
    • Principle Award Recipient: BaohuaXiao
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2022-10-11
2024-05-18
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References

  1. Nedashkovskaya OI, Kim SB, Lysenko AM, Frolova GM, Mikhailov VV et al. Description of Aquimarina muelleri gen. nov., sp. nov., and proposal of the reclassification of [Cytophaga] latercula Lewin 1969 as Stanierella latercula gen. nov., comb. nov. Int J Syst Evol Microbiol 2005; 55:225–229 [View Article]
    [Google Scholar]
  2. Chen WM, Sheu FS, Sheu SY. Aquimarina salinaria sp. nov., a novel algicidal bacterium isolated from a saltpan. Arch Microbiol 2012; 194:103–112 [View Article] [PubMed]
    [Google Scholar]
  3. Park SC, Choe HN, Baik KS, Seong CN. Aquimarina gracilis sp. nov., isolated from the gut microflora of a mussel, Mytilus coruscus, and emended description of Aquimarina spongiae. Int J Syst Evol Microbiol 2013; 63:1782–1787 [View Article] [PubMed]
    [Google Scholar]
  4. Yoon BJ, You HS, Lee DH, Oh DC. Aquimarina spongiae sp. nov., isolated from marine sponge Halichondria oshoro. Int J Syst Evol Microbiol 2011; 61:417–421 [View Article] [PubMed]
    [Google Scholar]
  5. Wang YS, Lou ZP, Sun CC, Sun S. Ecological environment changes in Daya Bay, China, from 1982 to 2004. Mar Pollut Bull 2008; 56:1871–1879 [View Article] [PubMed]
    [Google Scholar]
  6. Zhang L, Xiong L, Li J, Huang X. Long-term changes of nutrients and biocenoses indicating the anthropogenic influences on ecosystem in Jiaozhou Bay and Daya Bay, China. Mar Pollut Bull 2021; 168:112406 [View Article] [PubMed]
    [Google Scholar]
  7. Yang X, Tan Y, Li K, Zhang H, Liu J et al. Long-term changes in summer phytoplankton communities and their influencing factors in Daya Bay, China (1991-2017). Mar Pollut Bull 2020; 161:111694 [View Article] [PubMed]
    [Google Scholar]
  8. Ausubel F, Brent R, Kingston RE, Moore DD, Seidman JG. eds Short Protocols in Molecular Biology: A Compendium of Methods from Current Protocols in Molecular Biology New York: Wiley; 1985
    [Google Scholar]
  9. Sun H, Hu Y, Zhou S, Zheng Y, Zhang XH. Glycocaulis profundi sp. nov., a marine bacterium isolated from seawater of the Mariana Trench. Int J Syst Evol Microbiol 2020; 70:814–819 [View Article] [PubMed]
    [Google Scholar]
  10. 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]
    [Google Scholar]
  11. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23:2947–2948 [View Article]
    [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. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [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. 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]
  16. 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]
  17. Wang X, Guo F, Tian P, Yu S, Xue C-X et al. Flammeovirga agarivorans sp. nov., an agar-digesting marine bacterium isolated from surface seawater. Int J Syst Evol Microbiol 2020; 70:6060–6066 [View Article] [PubMed]
    [Google Scholar]
  18. Beveridge TJ, Lawrence JR, Murray RG. Sampling and staining for light microscopy. In Methods for General and Molecular Microbiology, 3rd edn. American Society of Microbiology; 2007 pp 19–33
    [Google Scholar]
  19. Bernardet J-F, 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]
    [Google Scholar]
  20. Tindall BJ, Sikorski J, Smibert RA, Krieg NR. Phenotypic characterization and the principles of comparative systematics. In Methods for General and Molecular Microbiology, 3rd edn. American Society of Microbiology; 2007 pp 330–393
    [Google Scholar]
  21. Yoon J-H, Lee K-C, Kho YH, Kang KH, Kim C-J 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]
  22. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 101. Newark DE: MIDI Inc; 1990
  23. 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]
  24. 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 Meth 1984; 2:233–241 [View Article]
    [Google Scholar]
  25. Collins MD, Shah HN. Fatty acid, menaquinone and polar lipid composition of Rothia dentocariosa. Arch Microbiol 1984; 137:247–249 [View Article]
    [Google Scholar]
  26. Komagata K, Suzuki K-I. 4 Lipid and cell-wall analysis in bacterial systematics. In Methods in Microbiology Amsterdam: Elsevier; 1988 pp 161–207
    [Google Scholar]
  27. Moore E, Arnscheidt A, Krüger A, Strömpl C, Mau M. Simplified protocols for the preparation of genomic DNA from bacterial cultures. MMEM 1999; 1:1–15
    [Google Scholar]
  28. 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 [View Article] [PubMed]
    [Google Scholar]
  29. Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 2007; 23:673–679 [View Article] [PubMed]
    [Google Scholar]
  30. Lagesen K, Hallin P, Rødland EA, Staerfeldt H-H, Rognes T et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100–3108 [View Article] [PubMed]
    [Google Scholar]
  31. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997; 25:955–964 [View Article] [PubMed]
    [Google Scholar]
  32. Gardner PP, Daub J, Tate JG, Nawrocki EP, Kolbe DL et al. Rfam: updates to the RNA families database. Nucleic Acids Res 2009; 37:D136–40 [View Article]
    [Google Scholar]
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