1887

International Journal of Systematic and Evolutionary Microbiology

sp. nov., a starch-degrading bacterium isolated from marine sediment No Access

Abstract

A novel bacterium, designated strain PS13, was isolated from marine sediment collected from the coast of Jeju Island. Strain PS13 was a Gram stain-negative, catalase- and oxidase-positive, aerobic, yellow-pigmented, motile by gliding, and rod-shaped bacterium. Strain PS13 grew optimally at 25 °C and pH 8.0 and in the presence of 3 % (w/v) NaCl. Results of phylogenetic analysis based on 16S rRNA gene sequences showed that strain PS13 belonged to the genus and was closely related to KMM3553 (98.3 % sequence similarity). The DNA–DNA relatedness (17.3–21.8 %) and average nucleotide identity (83.6–84.6 %) values clearly indicated that strain PS13 represents a distinct species of the genus . The major fatty acids were C iso, C 6/C 7 and C iso G. The genomic DNA G+C content of the strain PS13 was 32.2 mol%. On the basis of polyphasic characteristics, it is suggested that strain PS13 be assigned to the genus as the type strain of a novel species, for which the name PS13 (=KCCM 43301=CECT 9918) sp. nov. is proposed.

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Keyword(s): Formosa , polyphasic , genome and marine sediment
© 2020 The Authors
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/content/journal/ijsem/10.1099/ijsem.0.004012
2020-01-28
2020-02-28
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References

  1. Ivanova EP, Alexeeva YV, Flavier S, Wright JP, Zhukova NV et al. Formosa algae gen. nov., sp. nov., a novel member of the family Flavobacteriaceae. Int J Syst Evol Microbiol 2004;54: 705– 711 [CrossRef]
    [Google Scholar]
  2. Nedashkovskaya OI, Kim SB, Vancanneyt M, Snauwaert C, Lysenko AM et al. Formosa agariphila sp. nov., a budding bacterium of the family Flavobacteriaceae isolated from marine environments, and emended description of the genus Formosa. Int J Syst Evol Microbiol 2006;56: 161– 167 [CrossRef]
    [Google Scholar]
  3. Yoon B-J, Oh D-C. Formosa spongicola sp. nov., isolated from the marine sponge Hymeniacidon flavia. Int J Syst Evol Microbiol 2011;61: 330– 333 [CrossRef]
    [Google Scholar]
  4. Park S, Lee J-S, Lee K-C, Yoon J-H. Formosa undariae sp. nov., isolated from a reservoir containing the brown algae Undaria pinnatifida. Int J Syst Evol Microbiol 2013;63: 4130– 4135 [CrossRef]
    [Google Scholar]
  5. Kwon T, Baek K, Lee K, Kang I, Cho J-C. Formosa arctica sp. nov., isolated from Arctic seawater. Int J Syst Evol Microbiol 2014;64: 78– 82 [CrossRef]
    [Google Scholar]
  6. Tanaka R, Vandamme P, Cleenwerck I, Mori T, Ueda M et al. Formosa haliotis sp. nov., a brown-alga-degrading bacterium isolated from the gut of the abalone Haliotis gigantea. Int J Syst Evol Microbiol 2015;65: 4388– 4393 [CrossRef]
    [Google Scholar]
  7. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991;173: 697– 703 [CrossRef]
    [Google Scholar]
  8. Koh H-W, Rani S, Kim S-J, Moon E, Nam SW et al. Halomonas aestuarii sp. nov., a moderately halophilic bacterium isolated from a tidal flat. Int J Syst Evol Microbiol 2017;67: 4298– 4303 [CrossRef]
    [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 [CrossRef]
    [Google Scholar]
  10. Thompson J, 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 [CrossRef]
    [Google Scholar]
  11. Kimura M. The neutral theory of molecular evolution and the world view of the neutralists. Genome 1989;31: 24– 31 [CrossRef]
    [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
    [Google Scholar]
  13. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol 1971;20: 406– 416 [CrossRef]
    [Google Scholar]
  14. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981;17: 368– 376 [CrossRef]
    [Google Scholar]
  15. 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]
    [Google Scholar]
  16. 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]
    [Google Scholar]
  17. Ezaki T, Adnan S, Miyake M. [Quantitative microdilution plate hybridization to determine genetic relatedness among bacterial strains]. Nihon Saikingaku Zasshi 1990;45: 851– 857 [CrossRef]
    [Google Scholar]
  18. Wayne LG, Moore WEC, Stackebrandt E, Kandler O, Colwell RR et al. Report of the AD hoc Committee on reconciliation of approaches to bacterial Systematics. Int J Syst Evol Microbiol 1987;37: 463– 464 [CrossRef]
    [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 [CrossRef]
    [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 [CrossRef]
    [Google Scholar]
  21. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. Ncbi prokaryotic genome annotation pipeline. Nucleic Acids Res 2016;44: 6614– 6624 [CrossRef]
    [Google Scholar]
  22. Blin K, Shaw S, Steinke K, Villebro R, Ziemert N et al. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res 2019;47: W81– W87 [CrossRef]
    [Google Scholar]
  23. Xu L, Dong Z, Fang L, Luo Y, Wei Z et al. OrthoVenn2: a web server for whole-genome comparison and annotation of orthologous clusters across multiple species. Nucleic Acids Res 2019;47: W52– W58 [CrossRef]
    [Google Scholar]
  24. Bowman JP. Description of Cellulophaga algicola sp. nov., isolated from the surfaces of Antarctic algae, and reclassification of Cytophaga uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Cellulophaga uliginosa comb. nov. Int J Syst Evol Microbiol 2000;50: 1861– 1868 [CrossRef]
    [Google Scholar]
  25. Reichenbach H. The order Cytophagales The prokaryotes: Springer; 1992; pp 3631– 3675
    [Google Scholar]
  26. Smibert RM, Krieg NR. Phenotypic characterization In Gerhardt P, Murray RGE. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994; pp 607– 654
    [Google Scholar]
  27. Hu HY, Fujie K, Urano K. Development of a novel solid phase extraction method for the analysis of bacterial quinones in activated sludge with a higher reliability. J Biosci Bioeng 1999;87: 378– 382 [CrossRef]
    [Google Scholar]
  28. Koh H-W, Hong H, Min U-G, Kang M-S, Kim S-G et al. Rhodanobacter aciditrophus sp. nov., an acidophilic bacterium isolated from mine wastewater. Int J Syst Evol Microbiol 2015;65: 4574– 4579 [CrossRef]
    [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 [CrossRef]
    [Google Scholar]
  30. Minnikin DE, Patel PV, Alshamaony L, Goodfellow M. Polar lipid composition in the classification of Nocardia and related bacteria. Int J Syst Bacteriol 1977;27: 104– 117 [CrossRef]
    [Google Scholar]
  31. Komagata K, Suzuki K-I. 4 Lipid and cell-wall analysis in bacterial systematics Methods in Microbiology Elsevier; 1988; pp 161– 207
    [Google Scholar]
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Formosa sediminum sp. nov., a starch-degrading bacterium isolated from marine sediment
Microbiology Society , ijsem004012; https://doi.org/10.1099/ijsem.0.004012
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