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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 71, Issue 3

sp. nov., isolated from western Pacific Ocean sediment Free

Abstract

A Gram-stain-negative bacterium, designated strain 40Bstr401, was isolated from a sediment sample collected from the western Pacific Ocean. Analysis of its 16S rRNA gene sequence revealed that strain 40Bstr401 belongs to the genus and is closely related to type strains Ar-22 (98.2 %), 105 (98.2 %) and BB-My12 (97.4 %). The average nucleotide identity values for 40Bstr401 with Ar-22 and 105 are 79.3 % and 78.8 %, respectively. The DNA–DNA hybridization values between strain 40Bstr401 and Ar-22 and 105 are 26.7 and 26.6 %, respectively. The major isoprenoid quinone of 40Bstr401 is MK-6, and iso-C 3-OH and iso-C are the dominant cellular fatty acids. The major polar lipids are phosphatidylethanolamine, four unidentified amino lipids and two unidentified lipids. The G+C content of the genomic DNA is 42.9 mol%. Its phylogenetic distinctiveness and chemotaxonomic differences, together with the phenotypic properties observed in this study, indicate that strain 40Bstr401 can be differentiated from closely related species. Therefore, we propose strain 40Bstr401 represents a novel species in the genus , for which the name sp. nov. is suggested. The type strain is 40Bstr401 (=MCCC 1K04568=KCTC 82139).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Bacteroidetes , Flavobacteriaceae , Flavobacteriales , Flavobacteriia , Muricauda and taxonomy
Funding
This study was supported by the:
  • China Ocean Mineral Resources R & D Association (CPMRA) Foundation (Award DY135-E2-02-07)
    • Principle Award Recipient: NotApplicable
  • Zhejiang Provincial Top Key Discipline of Biological Engineering (Award ZS2018010)
    • Principle Award Recipient: JigangChen
  • Ningbo Public Welfare Technology Application Research Project (CN) (Award 202002N3115)
    • Principle Award Recipient: JigangChen
  • National Program on Global Change and Air-Sea Interaction (Award GASI-04-HYDZ-02)
    • Principle Award Recipient: NotApplicable
© 2021 The Authors
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2021-03-12
2024-04-25
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References

  1. Bruns A, Rohde M, Berthe-Corti L. Muricauda ruestringensis gen. nov., sp. nov., a facultatively anaerobic, appendaged bacterium from German North Sea intertidal sediment. Int J Syst Evol Microbiol 2001; 51:1997–2006 [View Article][PubMed]
     [Google Scholar]
  2. Lee S-Y, Park S, Oh T-K, Yoon J-H. Muricauda beolgyonensis sp. nov., isolated from a tidal flat. Int J Syst Evol Microbiol 2012; 62:1134–1139 [View Article][PubMed]
     [Google Scholar]
  3. Wu Y-H, Yu P-S, Zhou Y-D, Xu L, Wang C-S et al. Muricauda antarctica sp. nov., a marine member of the Flavobacteriaceae isolated from Antarctic seawater. Int J Syst Evol Microbiol 2013; 63:3451–3456 [View Article][PubMed]
     [Google Scholar]
  4. Kim JM, Jin HM, Jeon CO. Muricauda taeanensis sp. nov., isolated from a marine tidal flat. Int J Syst Evol Microbiol 2013; 63:2672–2677 [View Article][PubMed]
     [Google Scholar]
  5. Yoon J-H, Lee M-H, Oh T-K, Park Y-H. Muricauda flavescens sp. nov. and Muricauda aquimarina sp. nov., isolated from a salt lake near Hwajinpo Beach of the East Sea in Korea, and emended description of the genus Muricauda . Int J Syst Evol Microbiol 2005; 55:1015–1019 [View Article][PubMed]
     [Google Scholar]
  6. Yoon J-H, Kang S-J, Jung Y-T, Oh T-K. Muricauda lutimaris sp. nov., isolated from a tidal flat of the Yellow Sea. Int J Syst Evol Microbiol 2008; 58:1603–1607 [View Article][PubMed]
     [Google Scholar]
  7. Zhang X, Liu X, Lai Q, Du Y, Sun F et al. Muricauda indica sp. nov., isolated from deep sea water. Int J Syst Evol Microbiol 2018; 68:881–885 [View Article][PubMed]
     [Google Scholar]
  8. Wang Y, Yang X, Liu J, Wu Y, Zhang X-H. Muricauda lutea sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2017; 67:1064–1069 [View Article][PubMed]
     [Google Scholar]
  9. Yang C, Li Y, Guo Q, Lai Q, Wei J et al. Muricauda zhangzhouensis sp. nov., isolated from mangrove sediment. Int J Syst Evol Microbiol 2013; 63:2320–2325 [View Article][PubMed]
     [Google Scholar]
  10. Zhang Z, Gao X, Qiao Y, Wang Y, Zhang X-H. Muricauda pacifica sp. nov., isolated from seawater of the South Pacific Gyre. Int J Syst Evol Microbiol 2015; 65:4087–4092 [View Article][PubMed]
     [Google Scholar]
  11. Su Y, Yang X, Wang Y, Liu Y, Ren Q et al. Muricauda marina sp. nov., isolated from marine snow of Yellow Sea. Int J Syst Evol Microbiol 2017; 67:2446–2451 [View Article][PubMed]
     [Google Scholar]
  12. Li G, Lai Q, Yan P, Shao Z. Roseovarius amoyensis sp. nov. and Muricauda amoyensis sp. nov., isolated from the Xiamen coast. Int J Syst Evol Microbiol 2019; 69:3100–3108 [View Article][PubMed]
     [Google Scholar]
  13. Parte AC. LPSN - List of prokaryotic names with standing in nomenclature (bacterio.net), 20 years on. Int J Syst Evol Microbiol 2018; 68:1825–1829 [View Article][PubMed]
     [Google Scholar]
  14. Wang X, Lin D, Jing X, Zhu S, Yang J et al. Complete genome sequence of the highly Mn(II) tolerant Staphylococcus sp. AntiMn-1 isolated from deep-sea sediment in the Clarion-Clipperton Zone. J Biotechnol 2018; 266:34–38 [View Article][PubMed]
     [Google Scholar]
  15. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics Chichester, United Kingdom: John Wiley & Sons; 1991 pp 115–175
     [Google Scholar]
  16. 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]
  17. Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article][PubMed]
     [Google Scholar]
  18. 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]
  19. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
     [Google Scholar]
  20. 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]
  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. Nei M, Kumar S. Molecular Evolution and Phylogenetics New York: Oxford University Press; 2000
     [Google Scholar]
  23. 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 [View Article][PubMed]
     [Google Scholar]
  24. 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; 14:60 [View Article][PubMed]
     [Google Scholar]
  25. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article][PubMed]
     [Google Scholar]
  26. Nordberg H, Cantor M, Dusheyko S, Hua S, Poliakov A et al. The genome portal of the Department of energy joint genome Institute: 2014 updates. Nucleic Acids Res 2014; 42:D26–D31 [View Article][PubMed]
     [Google Scholar]
  27. 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 [View Article][PubMed]
     [Google Scholar]
  28. McBride MJ, Xie G, Martens EC, Lapidus A, Henrissat B et al. Novel features of the polysaccharide-digesting gliding bacterium Flavobacterium johnsoniae as revealed by genome sequence analysis. Appl Environ Microbiol 2009; 75:6864–6875 [View Article][PubMed]
     [Google Scholar]
  29. Colston SM, Fullmer MS, Beka L, Lamy B, Gogarten JP et al. Bioinformatic genome comparisons for taxonomic and phylogenetic assignments using Aeromonas as a test case. mBio 2014; 5:e02136–14 [View Article][PubMed]
     [Google Scholar]
  30. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article][PubMed]
     [Google Scholar]
  31. Bernardet JF, 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
     [Google Scholar]
  32. Gosink JJ, Woese CR, Staley JT. Polaribacter gen. nov., with three new species, P. irgensii sp. nov., P. franzmannii sp. nov. and P. filamentus sp. nov., gas vacuolate polar marine bacteria of the Cytophaga-Flavobacterium-Bacteroides group and reclassification of 'Flectobacillus glomeratus' as Polaribacter glomeratus comb. nov. Int J Syst Bacteriol 1998; 8:223–235 [View Article][PubMed]
     [Google Scholar]
  33. Chen Y, Zhu S, Lin D, Wang X, Yang J et al. Devosia naphthalenivorans sp. nov., isolated from East Pacific Ocean sediment. Int J Syst Evol Microbiol 2019; 69:1974–1979 [View Article][PubMed]
     [Google Scholar]
  34. Komagata K, Suzuki K. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–207
     [Google Scholar]
  35. da Costa MS, Albuquerque L, Nobre MF, Wait R. The identification of polar lipids in prokaryotes. Methods Microbiol 2011; 38:165–181
     [Google Scholar]
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Muricauda sediminis sp. nov., isolated from western Pacific Ocean sediment
Int J Syst Evol Microbiol 71, 004757 (2021); https://doi.org/10.1099/ijsem.0.004757
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