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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 70, Issue 5

sp. nov., a marine bacterium isolated from intertidal sand of the Yellow Sea Free

Abstract

A novel rod-shaped and Gram-stain-negative bacterium, designated strain RZ05, was isolated from a sand sample collected from the intertidal zone of the Yellow Sea, PR China. Results of phylogenetic analysis based on 16S rRNA gene sequences revealed that strain RZ05 clusters within the genus , a member of the family , and has the highest sequence similarity to KCTC 22021 (97.8 %), followed by KCTC 52191 (97.2 %). Cells of this strain were observed to be aerobic, oxidase- and catalase-positive, motile by gliding and formed yellow colonies. Growth occurred at 7–40 °C (optimum, 30 °C), at pH 6.5–9.5 (optimum, pH 7.0) and with 0.5–6 % (optimum, 2 %) NaCl. Its polar lipid profile included phosphatidylethanolamine, two unidentified glycolipids, one unidentified aminolipid and four unidentified lipids. The major cellular fatty acids were iso-C, iso-C G, iso-C 3-OH, iso-C 3-OH, iso-C 3-OH, summed feature 9 (10-methyl C/iso-C ω9) and summed feature 3 (iso-C 2-OH/C ω7/C ω6). The only respiratory quinone was menaquinone 6 (MK-6). The genome of strain RZ05 was 4.65 Mbp with a G+C content of 38.9 mol%. The average nucleotide identity and DNA–DNA hybridization values between strain RZ05 and its most closely related type strain KCTC 22021 were 80.3 and 26.3  %, respectively. The results of phylogenetic, phenotypic and chemotaxonomic analyses indicated that strain RZ05 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is RZ05 (=KCTC 62834=MCCC 1K03617).

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  • Accepted:
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  • Published Online:
Keyword(s): bacteroidetes , Flavobacteriaceae , intertidal sand and Maribacter luteus sp. nov.
Funding
This study was supported by the:
  • Natural Science Foundation of Shandong Province (Award ZR2019PC021)
    • Principle Award Recipient: Ang Liu
  • National Natural Science Foundation of China (Award 31300005)
    • Principle Award Recipient: Yan-Jiao Zhang
  • National Natural Science Foundation of China (Award 81801982)
    • Principle Award Recipient: Ang Liu
© 2020 The Authors
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2020-05-07
2024-05-04
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References

  1. Nedashkovskaya OI, Kim SB, Han SK, Lysenko AM, Rohde M et al. Maribacter gen. nov., a new member of the family Flavobacteriaceae, isolated from marine habitats, containing the species Maribacter sedimenticola sp. nov., Maribacter aquivivus sp. nov., Maribacter orientalis sp. nov. and Maribacter ulvicola sp. nov. Int J Syst Evol Microbiol 2004; 54:1017–1023 [View Article][PubMed][PubMed]
     [Google Scholar]
  2. Barbeyron T, Carpentier F, L'haridon S, Schüler M, Michel G et al. Description of Maribacter forsetii sp. nov., a marine Flavobacteriaceae isolated from North Sea water, and emended description of the genus Maribacter . Int J Syst Evol Microbiol 2008; 58:790–797 [View Article][PubMed][PubMed]
     [Google Scholar]
  3. Jung Y-T, Lee J-S, Yoon J-H. Maribacter caenipelagi sp. nov., a member of the Flavobacteriaceae isolated from a tidal flat sediment of the Yellow Sea in Korea. Antonie van Leeuwenhoek 2014; 106:733–742 [View Article][PubMed][PubMed]
     [Google Scholar]
  4. Thongphrom C, Kim J-H, Kim W. Maribacter arenosus sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2016; 66:4826–4831 [View Article][PubMed][PubMed]
     [Google Scholar]
  5. Nedashkovskaya OI, Vancanneyt M, De Vos P, Kim SB, Lee MS et al. Maribacter polysiphoniae sp. nov., isolated from a red alga. Int J Syst Evol Microbiol 2007; 57:2840–2843 [View Article][PubMed][PubMed]
     [Google Scholar]
  6. Weerawongwiwat V, Kang H, Jung MY, Kim W. Maribacter chungangensis sp. nov., isolated from a green seaweed, and emended descriptions of the genus Maribacter and Maribacter arcticus . Int J Syst Evol Microbiol 2013; 63:2553–2558 [View Article][PubMed][PubMed]
     [Google Scholar]
  7. Jackson SA, Kennedy J, Morrissey JP, O'Gara F, Dobson ADW. Maribacter spongiicola sp. nov. and Maribacter vaceletii sp. nov., isolated from marine sponges, and emended description of the genus Maribacter . Int J Syst Evol Microbiol 2015; 65:2097–2103 [View Article][PubMed][PubMed]
     [Google Scholar]
  8. Liu A, Liu H-M, Du F, Wang S, Zhao L-Y et al. Flavivirga rizhaonensis sp. nov., a marine bacterium isolated from intertidal sand. Antonie van Leeuwenhoek 2019; 112:1645–1653 [View Article][PubMed][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][PubMed]
     [Google Scholar]
  10. Edgar RC. Muscle: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 2004; 5:113 [View Article][PubMed][PubMed]
     [Google Scholar]
  11. 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][PubMed]
     [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][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][PubMed]
     [Google Scholar]
  14. Kimura M. The Neutral Theory of Molecular Evolution Cambridge: Cambridge University Press; 1983
     [Google Scholar]
  15. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed][PubMed]
     [Google Scholar]
  16. Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008; 18:821–829 [View Article][PubMed][PubMed]
     [Google Scholar]
  17. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016; 44:6614–6624 [View Article][PubMed][PubMed]
     [Google Scholar]
  18. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [View Article][PubMed][PubMed]
     [Google Scholar]
  19. Na S-I, Kim YO, Yoon S-H, Ha S-M, Baek I et al. UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285 [View Article][PubMed][PubMed]
     [Google Scholar]
  20. Langille MGI, Brinkman FSL. IslandViewer: an integrated interface for computational identification and visualization of genomic islands. Bioinformatics 2009; 25:664–665 [View Article][PubMed][PubMed]
     [Google Scholar]
  21. Loenen WAM, Dryden DTF, Raleigh EA, Wilson GG, Murray NE. Highlights of the DNA cutters: a short history of the restriction enzymes. Nucleic Acids Res 2014; 42:3–19 [View Article][PubMed][PubMed]
     [Google Scholar]
  22. Williams RJ. Restriction endonucleases: classification, properties, and applications. Mol Biotechnol 2003; 23:225–244 [View Article][PubMed][PubMed]
     [Google Scholar]
  23. Marraffini LA. Crispr-Cas immunity in prokaryotes. Nature 2015; 526:55–61 [View Article][PubMed][PubMed]
     [Google Scholar]
  24. Shmakov S, Smargon A, Scott D, Cox D, Pyzocha N et al. Diversity and evolution of class 2 CRISPR-Cas systems. Nat Rev Microbiol 2017; 15:169–182 [View Article][PubMed][PubMed]
     [Google Scholar]
  25. Goldfarb T, Sberro H, Weinstock E, Cohen O, Doron S et al. BREX is a novel phage resistance system widespread in microbial genomes. Embo J 2015; 34:169–183 [View Article][PubMed][PubMed]
     [Google Scholar]
  26. Gordeeva J, Morozova N, Sierro N, Isaev A, Sinkunas T et al. BREX system of Escherichia coli distinguishes self from non-self by methylation of a specific DNA site. Nucleic Acids Res 2019; 47:253–265 [View Article][PubMed][PubMed]
     [Google Scholar]
  27. Couvin D, Bernheim A, Toffano-Nioche C, Touchon M, Michalik J et al. CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins. Nucleic Acids Res 2018; 46:W246–W251 [View Article][PubMed][PubMed]
     [Google Scholar]
  28. 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]
  29. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krige NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp 607–654
     [Google Scholar]
  30. Wu Y-H, Xu L, Zhou P, Wang C-S, Oren A et al. Brevirhabdus pacifica gen. nov., sp. nov., isolated from deep-sea sediment in a hydrothermal vent field. Int J Syst Evol Microbiol 2015; 65:3645–3651 [View Article][PubMed][PubMed]
     [Google Scholar]
  31. Komagata K, Suzuki KI. 4 lipid and cell-wall analysis in bacterial Systematics. Methods in Microbiology 1987; 19:161–207
     [Google Scholar]
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Maribacter luteus sp. nov., a marine bacterium isolated from intertidal sand of the Yellow Sea
Int J Syst Evol Microbiol 70, 3497 (2020); https://doi.org/10.1099/ijsem.0.004206
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