gen. nov., sp. nov., a bacterium in the family isolated from seawater Free

Abstract

A Gram-stain-negative, yellow-pigmented, non-spore-forming, non-motile, rod-shaped, catalase-positive, strictly aerobic bacterial strain, designated CAU 1491, was isolated from seawater and its taxonomic position was examined using a polyphasic approach. Cells of strain CAU 1491 grew optimally at 30 °C, pH 7.5 and in 2.0 % (w/v) NaCl. Phylogenetic analysis based on the 16S rRNA gene sequence of CAU 1491 showed that it formed a distinct lineage within the family as a separate deep branch, with 97.0 % or lower sequence similarity to representatives of the genera , and . The major cellular fatty acids of strain CAU 1491 were iso-C, iso-C G, iso-C 3-OH and summed feature 3. The polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylserine, phosphatidylethanolamine and an unidentified phospholipid. The strain contained MK-6 as the sole respiratory quinone. Genome sequencing revealed that strain CAU 1491 has a genome size of 3.13 Mbp and a G+C content of 32.4 mol%. On the basis of the phenotypic, chemotaxonomic and genomic data, strain CAU 1491 represents a new genus and species in the family for which the name gen. nov., sp. nov. is proposed. The type strain of is CAU 1491 (=KCTC 72003=NBRC 113695).

Funding
This study was supported by the:
  • Chung-Ang University (Award 2018)
    • Principle Award Recipient: Wonyong Kim
  • National Institute of Biological Resources (Award NIBR201902203)
    • Principle Award Recipient: Wonyong Kim
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004314
2020-07-03
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/8/4562.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004314&mimeType=html&fmt=ahah

References

  1. Bernardet J-F, Nakagawa Y, Holmes B. 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 [View Article][PubMed]
    [Google Scholar]
  2. Nedashkovskaya OI, Vancanneyt M, Kim SB, Hoste B, Bae KS. Algibacter mikhailovii sp. nov., a novel marine bacterium of the family Flavobacteriaceae, and emended description of the genus Algibacter . Int J Syst Evol Microbiol 2007; 57:2147–2150 [View Article][PubMed]
    [Google Scholar]
  3. Bernardet JF, Segers P, Vancanneyt M, Berthe F, Kersters K et al. Cutting a Gordian knot: emended classification and description of the genus Flavobacterium, emended description of the family Flavobacteriaceae, and proposal of Flavobacterium hydatis nom. nov. (basonym, Cytophaga aquatilis Strohl and Tait 1978). Int J Syst Bacteriol 1996; 46:128–148 [View Article]
    [Google Scholar]
  4. Yang S-J, Cho J-C. Gaetbulibacter marinus sp. nov., isolated from coastal seawater, and emended description of the genus Gaetbulibacter . Int J Syst Evol Microbiol 2008; 58:315–318 [View Article][PubMed]
    [Google Scholar]
  5. Nedashkovskaya OI, Kwon KK, Yang S-H, Lee H-S, Chung KH et al. Lacinutrix algicola sp. nov. and Lacinutrix mariniflava sp. nov., two novel marine alga-associated bacteria and emended description of the genus Lacinutrix . Int J Syst Evol Microbiol 2008; 58:2694–2698 [View Article][PubMed]
    [Google Scholar]
  6. 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]
    [Google Scholar]
  7. Zhang D-C, Liu Y-X, Huang H-J, Weber K, Margesin R. Oceanihabitans sediminis gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from the Yellow Sea. Int J Syst Evol Microbiol 2016; 66:3400–3405 [View Article][PubMed]
    [Google Scholar]
  8. McCammon SA, Bowman JP. Taxonomy of Antarctic Flavobacterium species: description of Flavobacterium gillisiae sp. nov., Flavobacterium tegetincola sp. nov., and Flavobacterium xanthum sp. nov., nom. rev. and reclassification of [Flavobacterium] salegens as Salegentibacter salegens gen. nov., comb. nov. Int J Syst Evol Microbiol 2000; 50 Pt 3:1055–1063 [View Article][PubMed]
    [Google Scholar]
  9. Lasa A, Diéguez AL, Romalde JL. Description of Lacinutrix venerupis sp. nov.: a novel bacterium associated with reared clams. Syst Appl Microbiol 2015; 38:115–119 [View Article][PubMed]
    [Google Scholar]
  10. Yoon J-H, Lee S-Y, Oh T-K. Gaetbulibacter lutimaris sp. nov., isolated from a tidal flat sediment. Int J Syst Evol Microbiol 2013; 63:995–1000 [View Article][PubMed]
    [Google Scholar]
  11. Lee YM, Hwang CY, Lee I, Jung Y-J, Cho Y et al. Lacinutrix jangbogonensis sp. nov., a psychrophilic bacterium isolated from Antarctic marine sediment and emended description of the genus Lacinutrix . Antonie van Leeuwenhoek 2014; 106:527–533 [View Article][PubMed]
    [Google Scholar]
  12. Hameed A, Shahina M, Lin S-Y, Lai W-A, Hsu Y-H et al. Aquibacter zeaxanthinifaciens gen. nov., sp. nov., a zeaxanthin-producing bacterium of the family Flavobacteriaceae isolated from surface seawater and emended descriptions of the genera Aestuariibaculum and Gaetbulibacter . Int J Syst Evol Microbiol 2014; 64:138–145 [View Article][PubMed]
    [Google Scholar]
  13. Kim J-H, Kanjanasuntree R, Kim D-H, Lee J-S, Sukhoom A et al. Arenibacillus arenosus gen. nov., sp. nov., a member of the family Rhodobacteraceae isolated from sea sand. Int J Syst Evol Microbiol 2019; 69:153–158 [View Article][PubMed]
    [Google Scholar]
  14. Marmur J. A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol 1961; 3:208–IN1 [View Article]
    [Google Scholar]
  15. Nam S-W, Kim W, Chun J, Goodfellow M. Tsukamurella pseudospumae sp. nov., a novel actinomycete isolated from activated sludge foam. Int J Syst Evol Microbiol 2004; 54:1209–1212 [View Article][PubMed]
    [Google Scholar]
  16. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23:2947–2948 [View Article][PubMed]
    [Google Scholar]
  17. 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]
  18. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  19. 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]
  20. Felsenstein J. PHYLIP – phylogeny inference package (version3.2). Cladistics 1989; 5:164–166
    [Google Scholar]
  21. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
    [Google Scholar]
  22. 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 Pt 5:1861–1868 [View Article][PubMed]
    [Google Scholar]
  23. Nicholson WL, Setlow P. Sporulation, germination and outgrowth. In Harwood CR, Cutting SM. (editors) Molecular Biological Methods for Bacillus Chichester: Wiley; 1990 pp 391–450
    [Google Scholar]
  24. Conn HJ, Bartholomew JW, Jennison MW. Society of American Bacteriologists Staining methods. Manual of Microbial Methods New York: McGraw-Hill; 1957 pp 30–36
    [Google Scholar]
  25. Rodríguez-Valera F, Ruiz-Berraquero F, Ramos-Cormenzana A. Characteristics of the heterotrophic bacterial populations in hypersaline environments of different salt concentrations. Microb Ecol 1981; 7:235–243 [View Article][PubMed]
    [Google Scholar]
  26. Cappuccino JG, Sherman N. Microbiology-A Laboratory Manual, 6th ed. Benjamin Cummings: Pearson Education, Inc; 2002
    [Google Scholar]
  27. Lanyi B. Classical and rapid identification methods for medically important. Method Microbiol 1987; 19:
    [Google Scholar]
  28. Smibert RM. Phenotypic characterization. Methods for general and molecular bacteriology 1994
    [Google Scholar]
  29. Minnikin DE, Hutchinson IG, Caldicott AB, Goodfellow M. Thin-Layer chromatography of methanolysates of mycolic acid-containing bacteria. J Chromatogr A 1980; 188:221–233 [View Article]
    [Google Scholar]
  30. 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]
  31. Komagata K, Suzuki K. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–208
    [Google Scholar]
  32. Lee I, Ouk Kim Y, Park S-C, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article][PubMed]
    [Google Scholar]
  33. 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]
  34. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75–15 [View Article][PubMed]
    [Google Scholar]
  35. 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 [View Article][PubMed]
    [Google Scholar]
  36. Kim M, Oh H-S, Park S-C, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article][PubMed]
    [Google Scholar]
  37. 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]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004314
Loading
/content/journal/ijsem/10.1099/ijsem.0.004314
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed