1887

Abstract

A non-motile, rod-shaped, pink-pigmented bacterium NAR14 was isolated from coral from Daya Bay, Shenzhen, PR China. Cells were Gram-stain-negative, aerobic, catalase-positive and oxidase-negative. NAR14 grew with 0–6 % (w/v) NaCl (optimum, 2–4 %), at 10–41 °C (optimum, 28 °C) and at pH 4.0–9.5 (optimum, 5.0). The major respiratory quinone was Q-10. The predominant fatty acids (more than 10%) were summed feature 8 (65.6 %) and C (17.6%). The DNA G+C content of NAR14 was 73.6 %. The polar lipids of NAR14 comprised one diphosphatidylglycerol, one phosphatidylethanolamine, one phosphatidylglycerol, one phosphatidylcholine, one aminolipid and three unknown polar lipids. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that NAR14 formed a lineage within the genus of the family , and it was distinct from the most closely related species JCM 19527 and JCM 17520 with the 16S rRNA gene sequence similarities of 94.61 and 93.98 %, respectively. Phenotypic characteristics (physiological, biochemical and chemotaxonomic) also supported the taxonomic novelty of this isolate. Thus, NAR14 is considered to represent a novel species within the genus , for which the name sp. nov. is proposed. The type strain is NAR14 (=KCTC 92174 = MCCC 1K07275).

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
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005745
2023-02-23
2024-05-19
Loading full text...

Full text loading...

References

  1. Rihs JD, Brenner DJ, Weaver RE, Steigerwalt AG, Hollis DG et al. Roseomonas, a new genus associated with bacteremia and other human infections. J Clin Microbiol 1993; 31:3275–3283 [View Article] [PubMed]
    [Google Scholar]
  2. Lee JH, Kim MS, Baik KS, Kim HM, Lee KH et al. Roseomonas wooponensis sp. nov., isolated from wetland freshwater. Int J Syst Evol Microbiol 2015; 65:4049–4054 [View Article] [PubMed]
    [Google Scholar]
  3. Baik KS, Park SC, Choe HN, Kim SN, Moon J-H et al. Roseomonas riguiloci sp. nov., isolated from wetland freshwater. Int J Syst Evol Microbiol 2012; 62:3024–3029 [View Article] [PubMed]
    [Google Scholar]
  4. 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]
  5. 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]
    [Google Scholar]
  6. 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]
    [Google Scholar]
  7. Ausubel F, Brent R, Kingston RE, Moore DD, Seidman JG et al. Short protocols in molecular biology. In A Compendium of Methodsfrom Current Protocols in Molecular Biology, 3rd. edn New York: John Wiley and Sons; 1995
    [Google Scholar]
  8. 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]
  9. 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]
  10. 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] [PubMed]
    [Google Scholar]
  11. 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]
  12. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  13. Fitch WM. Toward Defining the Course of Evolution: Minimum Change for a Specific Tree Topology. Systematic Zoology 1971; 20:406 [View Article]
    [Google Scholar]
  14. 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]
    [Google Scholar]
  15. 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]
  16. 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]
  17. Beveridge TJ, Lawrence JR, Murray RG. Sampling and staining for light microscopy. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM et al. eds Methods for General and Molecular Microbiology, Third Edition. Washington, DC: American Society of Microbiology; 2007 pp 19–33 [View Article]
    [Google Scholar]
  18. 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]
  19. Tindall BJ, Sikorski J, Smibert RA, Krieg NR. Phenotypic characterization and the principles of comparative systematics. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM et al. eds In Methods for General and Molecular Microbiology, Third Edition. American Society of Microbiology; 2007 pp 330–393
    [Google Scholar]
  20. 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]
  21. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids; 1990
  22. 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]
    [Google Scholar]
  23. 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]
  24. Collins MD, Shah HN. Fatty acid, menaquinone and polar lipid composition of Rothia dentocariosa. Arch Microbiol 1984; 137:247–249 [View Article]
    [Google Scholar]
  25. Komagata K, Suzuki K-I. Lipid and cell-wall analysis in bacterial systematics. Methods in Microbiology 1988; 19:161–207 [View Article]
    [Google Scholar]
  26. Moore E, Arnscheidt A, Krüger A, Strömpl C, Mau M. Simplified protocols for the preparation of genomic DNA from bacterial cultures. In Akkermans ADL, van Elsas JD, de Bruin FJ. eds Molecular Microbial Ecology Manual. Vol. 1.6.1, 1st. edn Dordrecht: Kluwer; 1999 pp 1–15
    [Google Scholar]
  27. 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]
    [Google Scholar]
  28. 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]
  29. 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]
  30. 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]
  31. 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] [PubMed]
    [Google Scholar]
  32. Li F, Huang Y, Hu W, Li Z, Wang Q et al. Roseomonas coralli sp. nov., a heavy metal resistant bacterium isolated from coral. Int J Syst Evol Microbiol 2021; 71: [View Article]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005745
Loading
/content/journal/ijsem/10.1099/ijsem.0.005745
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error