1887

Abstract

A Gram-stain-negative, non-pigmented, non-spore-forming, motile, strictly aerobic bacterial strain, designated CAU 1492, was isolated from a coastal sand dune and its taxonomic position was examined using a polyphasic approach. Cells of strain CAU 1492 grew optimally at 30 °C, pH 7.0 and in 3 % (w/v) NaCl. Phylogenetic analysis based on the 16S rRNA gene sequence of CAU 1492 showed that it formed a distinct lineage within the family as a separate deep branch, with 96.8 % or lower sequence similarity values to representatives of the genera , , , , , , and . Strain CAU 1492 was closely related to DPG-138 (96.8 %), SW-277 (96.7 %), SCM-1 (96.7 %), FF3 (96.6 %) and BB-MW15 (96.4 %) based on 16S rRNA gene sequences. The major cellular fatty acids of strain CAU 1492 were cyclo-C 8 and summed feature 8 (C 7/C 6). The polar lipid pattern was composed of phosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid and an unidentified aminolipid. The strain contained Q-10 as the sole respiratory quinone. The draft genome of strain CAU 1492 was 4.63 Mb with a DNA G+C content of 63.1 mol%. The genome includes 4292 protein-coding genes and a five rRNA operons. On the basis of the phenotypic, chemotaxonomic and genomic data, strain CAU 1492 represents a novel genus in the family for which the name gen. nov., sp. nov. is proposed. The type strain of is CAU 1492 (=KCTC 62998=NBRC 113696).

Funding
This study was supported by the:
  • Chung-Ang University (Award 2019)
    • Principle Award Recipient: Baek Jihye
  • National Institute of Biological Resources (Award NIBR201902203)
    • Principle Award Recipient: Wonyong Kim
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004534
2020-10-29
2021-08-02
Loading full text...

Full text loading...

References

  1. Garrity GM, Bell JA, Lilburn T. Class I. Alphaproteobacteria class. nov. In Brenner DJ, Krieg NR, Staley JT, Garrity GM. (editors) Bergey’s Manual of Systematic Bacteriology, 2nd edn, vol. 2 (The Proteobacteria), part C (The Alpha-, Beta-, Delta-, and Epsilonproteobacteria) New York: Springer; 2005 p 1
    [Google Scholar]
  2. Garrity GM, Bell JA, Lilburn T. Order III. Rhodobacterales ord. nov. In Brenner DJ, Krieg NR, Staley JT, Garrity GM. (editors) Bergey’s Manual of Systematic Bacteriology, 2nd edn, vol. 2 (The Proteobacteria), part C (The Alpha-, Beta-, Delta-, and Epsilonproteobacteria) New York: Springer; 2005 p 161
    [Google Scholar]
  3. Yoon JH, Park SY, Jung TJ. Aestuariihabitans beolgyonensis gen. nov., sp. nov., a novel alphaproteobacterium isolated from tidal flat sediment. Antonie van Leeuwenhoek 2013; 104:217–224 [View Article][PubMed]
    [Google Scholar]
  4. Yoon JH, Kang SJ, Oh TK. Donghicola eburneus gen. nov., sp. nov., isolated from seawater of the East Sea in Korea. Int J Syst Evol Microbiol 2007; 57:73–76 [View Article][PubMed]
    [Google Scholar]
  5. Martens T, Heidorn T, Pukall R, Simon M, Tindall BJ et al. Reclassification of Roseobacter gallaeciensis Ruiz-Ponte et al. 1998 as Phaeobacter gallaeciensis gen. nov., comb. nov., description of Phaeobacter inhibens sp. nov., reclassification of Ruegeria algicola (Lafay et al. 1995) Uchino et al. 1999 as Marinovum algicola gen. nov., comb. nov., and emended descriptions of the genera Rosebacter, Ruegeris and Leisingera . Int J Syst Evol Microbiol 2006; 56:1293–1304 [View Article][PubMed]
    [Google Scholar]
  6. Yoon JH, Kang SJ, Lee JK. Marivita geojedonensis sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2013; 63:423–427 [View Article][PubMed]
    [Google Scholar]
  7. Fukui Y, Abe M, Kobayashi M, Shimada Y, Saito H et al. Sulfitobacter porphyrae sp. nov., isolated from the red alga Porphyra yezoensis . Int J Syst Evol Microbiol 2014; 64:438–443 [View Article][PubMed]
    [Google Scholar]
  8. Park S, Park JM, Jung YT, Won SM, Yoon JH. Primorskyibacter insulae sp. nov., isolated from the junction between the ocean and a freshwater spring. Int J Syst Evol Microbiol 2015; 65:3971–3976 [View Article][PubMed]
    [Google Scholar]
  9. Yoon JH, Kang SJ, Oh TK. Roseovarius aestuarii sp. nov., isolated from a tidal flat of the Yellow Sea in Korea. Int J Syst Evol Microbiol 2008; 58:1198–1202 [View Article][PubMed]
    [Google Scholar]
  10. Kim JH, Kanjanasuntree R, Kim DH, Lee JS, Sukhoom A. 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
    [Google Scholar]
  11. Gordon RE, Mihm JM. Identification of Nocardia (Erikson) nov. comb. Ann N Y Acad Sci 1962; 98:628–636 [View Article]
    [Google Scholar]
  12. Marmur J. A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol 1961; 3:208–218 [View Article]
    [Google Scholar]
  13. Lane DJ. 16s/23s rrna sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics London: John Wiley & Sons Ltd; 1991 pp 115–175
    [Google Scholar]
  14. Nam SW, 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]
  15. 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]
  16. Jukes TH, Cantor CR. Evolution of protein molecules. In Munro HH. editor Mammalian Protein Metabolism New York: Academic Press; 1969 pp 21–132
    [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. 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]
  22. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
    [Google Scholar]
  23. Davis JJ, Wattam AR, Aziz RK, Brettin T, Butler R et al. The PATRIC bioinformatics resource center: expanding data and analysis capabilities. Nucleic Acids Res 2020; 48:D606–D612 [View Article][PubMed]
    [Google Scholar]
  24. Yoon S-H, Ha S-M, Lim J, Kwon S, Chun J et al. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article][PubMed]
    [Google Scholar]
  25. 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 [View Article][PubMed]
    [Google Scholar]
  26. 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]
  27. 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]
  28. 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]
  29. 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]
  30. 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]
  31. Conn HJ, Bartholomew JW, Jennison MW. The Society of American Bacteriologists Staining methods. Manual of Microbial Methods New York: McGraw-Hill; 1957 pp 30–36
    [Google Scholar]
  32. 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]
  33. Cappuccino JG, Sherman N. Microbiology: a Laboratory Manual, 6th ed. Menlo Park, CA: Benjamin/Cummings; 2002
    [Google Scholar]
  34. Leifson E. Determination of carbohydrate metabolism of marine bacteria. J Bacteriol 1963; 85:1183–1184 [View Article][PubMed]
    [Google Scholar]
  35. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  36. Komagata K, Suzuki K. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–208
    [Google Scholar]
  37. 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]
  38. Price MN, Dehal PS, Arkin AP. FastTree 2 – approximately maximum-likelihood trees for large alignments. PLoS One 2010; 5:e9490 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004534
Loading
/content/journal/ijsem/10.1099/ijsem.0.004534
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited this month Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error