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Volume 70, Issue 6

sp. nov., isolated from a tidal flat Free

Abstract

A Gram-stain-negative, aerobic, non-spore-forming, motile by single polar flagellum and ovoid or rod-shaped bacterial strain, designated JBTF-M18, was isolated from tidal-flat sediment collected from the Yellow Sea, Republic of Korea. The neighbour-joining phylogenetic tree of 16S rRNA gene sequences showed that strain JBTF-M18 fell within the clade comprising the type strains of species. Strain JBTF-M18 exhibited 16S rRNA gene sequence similarity values of 97.1–98.8 % to the type strains of , , and and of less than 96.9 % to the type strains of the other species. The average nucleotide identity and digital DNA–DNA hybridization values between strain JBTF-M18 and the type strains of and were 72.0 and 89.5% and 18.9 and 38.1 %, respectively. DNA–DNA relatedness values between strain JBTF-M18 and the type strains of and were 14 and 19 %, respectively. The DNA G+C content of strain JBTF-M18 from genomic sequence data was 52.9 %. Strain JBTF-M18contained MK-6 as the predominant menaquinone and Q-7 and Q-8 as the predominant ubiquinones. It had iso-C, summed feature 3 (C ω and/or C ω) and C as the major fatty acids. The major polar lipids of strain JBTF-M18 were phosphatidylethanolamine and phosphatidylglycerol. Distinguished phenotypic properties, along with the phylogenetic and genetic distinctiveness, revealed that strain JBTF-M18 is separated from recognized species. On the basis of the data presented, strain JBTF-M18 is considered to represent a novel species of the genus , for which the name sp. nov. is proposed. The type strain is JBTF-M18 (=KACC 19869=NBRC 113583).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): genome , novel species , polyohasic taxonomy , Shewanella insulae and tidal flat
Funding
This study was supported by the:
  • Rural Development Administration (Award PJ013743)
    • Principle Award Recipient: Jung-Hoon Yoon
  • National Institute of Biological Resources (Award project on survey of indigenous species of Korea)
    • Principle Award Recipient: Jung-Hoon Yoon
© 2020 The Authors
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2020-06-08
2024-05-14
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References

  1. MacDonell MT, Colwell RR. Phylogeny of the Vibrionaceae, and recommendation for two new genera, Listonella and Shewanella . Syst Appl Microbiol 1985; 6:171–182 [View Article]
     [Google Scholar]
  2. MacDonell MT, Colwell RR. Shewanella gen. nov. In Validation of the publication of new names and new combinations previously effectively published outside the IJSB, List No. 20. Int J Syst Bacteriol 1986; 36:354–356
     [Google Scholar]
  3. 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]
  4. Ivanova EP, Nedashkovskaya OI, Zhukova NV, Nicolau DV, Christen R et al. Shewanella waksmanii sp. nov., isolated from a sipuncula (Phascolosoma japonicum). Int J Syst Evol Microbiol 2003; 53:1471–1477 [View Article][PubMed]
     [Google Scholar]
  5. Yoon J-H, Yeo S-H, Kim I-G, Oh T-K. Shewanella marisflavi sp. nov. and Shewanella aquimarina sp. nov., slightly halophilic organisms isolated from sea water of the Yellow Sea in Korea. Int J Syst Evol Microbiol 2004; 54:2347–2352 [View Article][PubMed]
     [Google Scholar]
  6. Gao H, Obraztova A, Stewart N, Popa R, Fredrickson JK et al. Shewanella loihica sp. nov., isolated from iron-rich microbial mats in the Pacific Ocean. Int J Syst Evol Microbiol 2006; 56:1911–1916 [View Article][PubMed]
     [Google Scholar]
  7. Kim J-Y, Yoo H-S, Lee D-H, Park S-H, Kim Y-J et al. Shewanella algicola sp. nov., a marine bacterium isolated from brown algae. Int J Syst Evol Microbiol 2016; 66:2218–2224 [View Article]
     [Google Scholar]
  8. Yun B-R, Park S, Kim M-K, Park J, Kim SB. Shewanella saliphila sp. nov., Shewanella ulleungensis sp. nov. and Shewanella litoralis sp. nov., isolated from coastal seawater. Int J Syst Evol Microbiol 2018; 68:2960–2966 [View Article][PubMed]
     [Google Scholar]
  9. Nozue H, Hayashi T, Hashimoto Y, Ezaki T, Hamasaki K et al. Isolation and characterization of Shewanella alga from human clinical specimens and emendation of the description of S. alga Simidu et al., 1990, 335. Int J Syst Bacteriol 1992; 42:628–634 [View Article][PubMed]
     [Google Scholar]
  10. Venkateswaran K, Dollhopf ME, Aller R, Stackebrandt E, Nealson KH. Shewanella amazonensis sp. nov., a novel metal-reducing facultative anaerobe from Amazonian shelf muds. Int J Syst Bacteriol 1998; 48 Pt 3:965–972 [View Article][PubMed]
     [Google Scholar]
  11. Venkateswaran K, Moser DP, Dollhopf ME, Lies DP, Saffarini DA et al. Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov. Int J Syst Bacteriol 1999; 49 Pt 2:705–724 [View Article][PubMed]
     [Google Scholar]
  12. Xu M, Guo J, Cen Y, Zhong X, Cao W et al. Shewanella decolorationis sp. nov., a dye-decolorizing bacterium isolated from activated sludge of a waste-water treatment plant. Int J Syst Evol Microbiol 2005; 55:363–368 [View Article][PubMed]
     [Google Scholar]
  13. Yoon JH, Lee ST, Kim SB, Kim WY, Goodfellow M et al. Restriction fragment length polymorphism analysis of PCR-amplified 16S ribosomal DNA for rapid identification of Saccharomonospora strains. Int J Syst Bacteriol 1997; 47:111–114 [View Article]
     [Google Scholar]
  14. Yoon J-H, Kim H, Kim I-G, Kang KH, Park Y-H. Erythrobacter flavus sp. nov., a slight halophile from the East Sea in Korea. Int J Syst Evol Microbiol 2003; 53:1169–1174 [View Article][PubMed]
     [Google Scholar]
  15. Stackebrandt E, Goebel BM. Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Evol Microbiol 1994; 44:846–849 [View Article]
     [Google Scholar]
  16. 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]
  17. 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 [View Article][PubMed]
     [Google Scholar]
  18. Lee I, Chalita M, Ha S-M, Na S-I, Yoon S-H et al. ContEst16S: an algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences. Int J Syst Evol Microbiol 2017; 67:2053–2057 [View Article][PubMed]
     [Google Scholar]
  19. 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]
  20. 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]
  21. Ezaki T, Hashimoto Y, Yabuuchi E. Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 1989; 39:224–229 [View Article]
     [Google Scholar]
  22. Park S, Jung Y-T, Choi SJ, Yoon J-H. Erythrobacter aquimixticola sp. nov., isolated from the junction between the ocean and a freshwater spring. Int J Syst Evol Microbiol 2017; 67:2964–2969 [View Article][PubMed]
     [Google Scholar]
  23. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article][PubMed]
     [Google Scholar]
  24. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [View Article][PubMed]
     [Google Scholar]
  25. Konstantinidis KT, Tiedje JM. Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci U S A 2005; 102:2567–2572 [View Article][PubMed]
     [Google Scholar]
  26. Wayne LG, Moore WEC, Stackebrandt E, Kandler O, Colwell RR, Brenner DJ, Grimont PAD et al. Report of the AD hoc Committee on reconciliation of approaches to bacterial Systematics. Int J Syst Evol Microbiol 1987; 37:463–464 [View Article]
     [Google Scholar]
  27. Komagata K, Suzuki K. Lipids and cell-wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–207
     [Google Scholar]
  28. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
     [Google Scholar]
  29. 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]
  30. Embley TM, Wait R. Structural lipids of eubacteria. In Goodfellow M, O’Donnell AG. (editors) Modern Microbial Methods. Chemical Methods in Prokaryotic Systematics Chichester: John Wiley & Sons;; 1994. pp 121–161
     [Google Scholar]
  31. Kim J-Y, Yoo H-S, Lee D-H, Park S-H, Kim Y-J et al. Shewanella algicola sp. nov., a marine bacterium isolated from brown algae. Int J Syst Evol Microbiol 2016; 66:2218–2224 [View Article][PubMed]
     [Google Scholar]
  32. Park S, Won S-M, Kim H, Park D-S, Yoon J-H. Aestuariivita boseongensis gen. nov., sp. nov., isolated from a tidal flat sediment. Int J Syst Evol Microbiol 2014; 64:2969–2974 [View Article][PubMed]
     [Google Scholar]
  33. Lányí B. Classical and rapid identification methods for medically important bacteria. Methods Mocrobiol 1987; 19:1–67
     [Google Scholar]
  34. Bruns A, Rohde M, Berthe-Corti L. Muricauda tuestringensis 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]
  35. Barrow GI, Feltham RKA. Cowan and Steel’s Manual for the Identification of Medical Bacteria, 3rd edn. Cambridge: Cambridge University Press; 1993
     [Google Scholar]
  36. Baumann P, Baumann L. The marine Gram-negative eubacteria: genera Photobacterium, Beneckea, Alteromonas, Pseudomonas, and Alcaligenes . In Starr MP, Stolp H, Trüper HG, Balows A, Schlegel HG. (editors) The Prokaryotes Berlin: Springer;; 1981 pp 1302–1331
     [Google Scholar]
  37. Cohen-Bazire G, Sistrom WR, Stanier RY. Kinetic studies of pigment synthesis by non-sulfur purple bacteria. J Cell Comp Physiol 1957; 49:25–68 [View Article][PubMed]
     [Google Scholar]
  38. Staley JT. Prosthecomicrobium and Ancalomicrobium: new prosthecate freshwater bacteria. J Bacteriol 1968; 95:1921–1942 [View Article][PubMed]
     [Google Scholar]
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Shewanella insulae sp. nov., isolated from a tidal flat
Int J Syst Evol Microbiol 70, 3872 (2020); https://doi.org/10.1099/ijsem.0.004252
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