1887

Abstract

Two marine bacterial strains, designated S2-4-21 and MT2-5-19, were isolated from two tidal flat sediments of cordgrass and adjacent oyster culture field in Quanzhou bay, China, respectively. Both strains were Gram-staining-negative, rod-shaped, non-flagellated, non-motile, aerobic, had NaCl requirements, and contained carotenoid and flexirubin pigments. The 16S rRNA gene sequence similarity (99.8%), average nucleotide identity value (99.4%) and average amino acid identity (99.3%) between strain S2-4-21 and strain MT2-5-19 strongly supported that they belonged to a single species. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain S2-4-21 and strain MT2-5-19 formed a monophyletic branch affiliated to the family , sharing similarities of 94.6% with CY01 and 7SM30, and of 94.1 and 92.8% with MEBiC 12267 and DSM 19858, respectively. Phylogenomic analysis based on the whole genome sequences supported that the two strains formed a distinct monophyletic clade within members, which was phylogenetically different from the clades of and . The major respiratory quinone was menaquinone MK-6. The major fatty acids (>10%) consisted of C iso, C, summed feature 9 (C iso 9/C 10-methyl) and C iso 3-OH. The polar lipid profiles of strain S2-4-21 and strain MT2-5-19 are identical, including phosphatidylethanolamine, four unidentified aminolipids, and four unidentified lipids. The genomic size was 4.9–5.0 Mb with genomic DNA G+C content of 41.5 mol%. Based on the above characteristics, strains S2-4-21 and MT2-5-19 represented a novel species of a novel genus in the family . Thus, gen. nov. sp. nov. is proposed with type strain S2-4-21 (=MCCC 1K03818=KCTC 72152), and another strain MT2-5-19 (=KCTC 72539=MCCC 1K03874).

Funding
This study was supported by the:
  • ZhaobinHuang , Specialized Research Fund for the Doctoral Program of Higher Education of China , (Award H19005)
  • ZhaobinHuang , National Infrastructure of Microbial Resources of China , (Award NIMR 2020-9)
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004606
2020-12-10
2021-03-01
Loading full text...

Full text loading...

References

  1. McBride MJ. The Family Flavobacteriaceae. The Prokaryotes – Other Major Lineages of Bacteria and the Archaea 2014
    [Google Scholar]
  2. Jung S-Y, Kang S-J, Lee M-H, Lee S-Y, Oh T-K et al. Gaetbulibacter saemankumensis gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from a tidal flat sediment in Korea. Int J Syst Evol Microbiol 2005; 55:1845–1849 [CrossRef][PubMed]
    [Google Scholar]
  3. Choi DH, Cho BC. Lutibacter litoralis gen. nov., sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from tidal flat sediment. Int J Syst Evol Microbiol 2006; 56:771–776 [CrossRef][PubMed]
    [Google Scholar]
  4. Kim K-Y, Park S-J, Hahm Y-T, Cha C-J. Marinitalea sucinacia gen. nov., sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from tidal flat sediment. FEMS Microbiol Lett 2011; 314:89–94 [CrossRef][PubMed]
    [Google Scholar]
  5. Yoon SH, SM H, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically United database of 16S rRNA and whole genome assemblies. Int J Syst Evol Microbiol 2016
    [Google Scholar]
  6. Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T et al. The Silva ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 2013; 41:D590–D596 [CrossRef][PubMed]
    [Google Scholar]
  7. 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]
  8. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [CrossRef][PubMed]
    [Google Scholar]
  9. Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 2013; 29:1072–1075 [CrossRef][PubMed]
    [Google Scholar]
  10. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [CrossRef][PubMed]
    [Google Scholar]
  11. Hyatt D, Chen G-L, Locascio PF, Land ML, Larimer FW et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119 [CrossRef][PubMed]
    [Google Scholar]
  12. Yoon S-H, Ha S-M, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [CrossRef][PubMed]
    [Google Scholar]
  13. Rodriguez-R LM, Konstantinidis KT. Bypassing cultivation to identify bacterial species. Microbe 2014; 9:111–118 [CrossRef]
    [Google Scholar]
  14. Na S-I, Kim YO, Yoon S-H, Ha S-M, Baek I, SI N et al. UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285 [CrossRef][PubMed]
    [Google Scholar]
  15. Bernardet J-F, Nakagawa Y, Holmes B. Subcommittee On The Taxonomy Of Flavobacterium And Cytophaga-Like Bacteria Of The International Committee On Systematics Of Prokaryotes 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 [CrossRef][PubMed]
    [Google Scholar]
  16. Komagata K, Suzuki K. Lipid and cell-wall analysis in bacterial systematics. Methods in Microbiology 1987; 19:161–207
    [Google Scholar]
  17. Huang Z, Dong C, Shao Z. Paraphotobacterium marinum gen. nov., sp. nov., a member of the family Vibrionaceae, isolated from surface seawater. Int J Syst Evol Microbiol 2016; 66:3050–3056 [CrossRef][PubMed]
    [Google Scholar]
  18. Darjany LE, Whitcraft CR, Dillon JG. Lignocellulose-responsive bacteria in a southern California salt marsh identified by stable isotope probing. Front Microbiol 2014; 5:263 [CrossRef][PubMed]
    [Google Scholar]
  19. Lee I, Ouk Kim Y, Park S-C, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [CrossRef][PubMed]
    [Google Scholar]
  20. Luo C, Rodriguez-R LM, Konstantinidis KT. MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences. Nucleic Acids Res 2014; 42:e73 [CrossRef][PubMed]
    [Google Scholar]
  21. Nicholson AC, Gulvik CA, Whitney AM, Humrighouse BW, Bell ME et al. Division of the genus Chryseobacterium: Observation of discontinuities in amino acid identity values, a possible consequence of major extinction events, guides transfer of nine species to the genus Epilithonimonas, eleven species to the genus Kaistella, and three species to the genus Halpernia gen. nov., with description of Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. derived from clinical specimens. Int J Syst Evol Microbiol 2020; 70:4432–4450 [CrossRef][PubMed]
    [Google Scholar]
  22. Zhang Y-J, Zhao J-R, Zhang X-Y, Chen G-Z, Zhou M-Y et al. Euzebyella marina sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2017; 67:920–924 [CrossRef][PubMed]
    [Google Scholar]
  23. Lucena T, Pascual J, Giordano A, Gambacorta A, Garay E et al. Euzebyella saccharophila gen. nov., sp. nov., a marine bacterium of the family Flavobacteriaceae . Int J Syst Evol Microbiol 2010; 60:2871–2876 [CrossRef][PubMed]
    [Google Scholar]
  24. Nedashkovskaya OI, Suzuki M, Lee J-S, Lee KC, Shevchenko LS et al. Pseudozobellia thermophila gen. nov., sp. nov., a bacterium of the family Flavobacteriaceae, isolated from the green alga Ulva fenestrata . Int J Syst Evol Microbiol 2009; 59:806–810 [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004606
Loading
/content/journal/ijsem/10.1099/ijsem.0.004606
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited this month Most Cited RSS feed

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