1887

Abstract

A flagella bacterium, designated strain 202IG2-18 was isolated from a marine sponge from Ulleung-do in the Republic of Korea. Cells were Gram-stain-negative, motile, aerobic, rod-shaped and non-pigmented. The strain was able to grow at pH 5.5–9.5 (optimum, pH 7.5), in the presence of 1–5 % (w/v) NaCl (optimum, 3 %, w/v) and at 18–30 °C (optimum, 30 °C). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 202IG2-18 belonged to the family , and was most closely related to [] NRRL B-41466 (97.9 %), followed by KCCM 43304 (97.1 %), KCTC 62318 (96.3 %) and KCTC 22492 (96.2 %). The predominant fatty acids were iso-C (25.7 %), C 8 (13.5 %), summed feature 3 (C 7 and/or C 6, 12.7 %), iso-C (10.4 %) and C (9.6 %). The only detected respiratory quinone was ubiquinone Q-8. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, three unidentified glycolipids, two unidentified aminophospholipids, an unidentified phospholipid and an unidentified aminolipid. The G+C content of the genomic DNA was 39.8 mol%. The average nucleotide identity values compared to all other related species was below 72.8 % and digital DNA–DNA hybridization values were 21.1–22.3 %, all below the threshold for bacterial species delineation. Phenotypic, phylogenetic, genomic and chemotaxonomic characteristics showed that strain 202IG2-18 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is 202IG2-18 (=KACC 22256=LMG 32203).

Funding
This study was supported by the:
  • National Research Foundation of Korea (Award 2021R1I1A3046479)
    • Principle Award Recipient: Jin-SookPark
  • National Marine Biodiversity Institute of Korea (Award 2021M01100)
    • Principle Award Recipient: Jin-SookPark
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2022-03-01
2024-05-01
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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. Xu S, Yu K, Su H, Chen B, Huang W et al. Proposal of Parashewanella gen. nov. to accommodate Parashewanella curva sp. nov. and Parashewanella spongiae comb. nov. in the Shewanellaceae. Int J Syst Evol Microbiol 2019; 69:1259–1264 [View Article]
    [Google Scholar]
  3. Namirimu T, Park MJ, Yang SH, Zo YG, Kwon KK. Parashewanella tropica sp. nov., a mesophilic bacterium isolated from a marine sponge from Chuuk lagoon, Federated States of Micronesia, and emended description of the genus Parashewanella. Int J Syst Evol Microbiol 2019; 69:3256–3261 [View Article] [PubMed]
    [Google Scholar]
  4. Rameshkumar N. The status of the species Shewanella irciniae Lee et al. 2006. Request for an opinion. Int J Syst Evol Microbiol 2015; 65:2774 [View Article]
    [Google Scholar]
  5. Atlas RM. Handbook of Microbiological Media Boca Raton, Florida, USA: CRC Press; 1993
    [Google Scholar]
  6. Cowan ST, Steel KJ. Manual for the Identification of Medical Bacteria Cambridge: Cambridge University Press; 1974
    [Google Scholar]
  7. Cappuccino JG, Sherman N. Microbiology: A Laboratory Manual, 6th edn. California: Pearson Education Inc; 2002
    [Google Scholar]
  8. Buck JD. Nonstaining (KOH) method for determination of gram reactions of marine bacteria. Appl Environ Microbiol 1982; 44:992–993 [View Article] [PubMed]
    [Google Scholar]
  9. Perry LB. Gliding motility in some non-spreading flexibacteria. J Appl Bacteriol 1973; 36:227–232 [View Article] [PubMed]
    [Google Scholar]
  10. Weon H-Y, Kim B-Y, Joa J-H, Son J-A, Song M-H et al. Methylobacterium iners sp. nov. and Methylobacterium aerolatum sp. nov., isolated from air samples in Korea. Int J Syst Evol Microbiol 2008; 58:93–96 [View Article] [PubMed]
    [Google Scholar]
  11. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. eds Nucleic Acid Techniques in Bacterial Systematics New York: Wiley; 1991
    [Google Scholar]
  12. 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]
  13. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 25:4876–4882 [View Article] [PubMed]
    [Google Scholar]
  14. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucleic Acids Symp Ser 1999; 41:95–98
    [Google Scholar]
  15. 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]
  16. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Systematic Zoology 1971; 20:406 [View Article]
    [Google Scholar]
  17. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  18. 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]
  19. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
    [Google Scholar]
  20. Kimura M. The Neutral Theory of Molecular Evolution Cambridge: Cambridge University Press; 1983 [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. 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]
    [Google Scholar]
  23. Yoon SH, Ha SM, 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. Li FN, Liao SL, Liu SW, Jin T, Sun CH. Aeromicrobium endophyticum sp. nov., an endophytic actinobacterium isolated from reed (Phragmites australis). J Microbiol 2019; 57:725–731 [View Article]
    [Google Scholar]
  25. 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]
  26. Collins MD, Jones D. Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2, 4-diaminobutyric acid. J Appl Bacteriol 1980; 48:459–470 [View Article]
    [Google Scholar]
  27. Hiraishi A, Ueda Y, Ishihara J, Mori T. Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 1996; 42:457–469 [View Article]
    [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. 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]
  30. 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]
  31. Alanjary M, Steinke K, Ziemert N. AutoMLST: an automated web server for generating multi-locus species trees highlighting natural product potential. Nucleic Acids Res 2019; 47:W276–W282 [View Article] [PubMed]
    [Google Scholar]
  32. Lee OO, Lau SCK, Tsoi MMY, Li X, Plakhotnikova I et al. Shewanella irciniae sp. nov., a novel member of the family Shewanellaceae, isolated from the marine sponge Ircinia dendroides in the Bay of Villefranche, Mediterranean Sea. Int J Syst Evol Microbiol 2006; 56:2871–2877 [View Article] [PubMed]
    [Google Scholar]
  33. Yang S-H, Kwon KK, Lee H-S, Kim S-J. Shewanella spongiae sp. nov., isolated from a marine sponge. Int J Syst Evol Microbiol 2006; 56:2879–2882 [View Article] [PubMed]
    [Google Scholar]
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