1887

Abstract

A novel bacterial strain, C3212, was isolated from a marine alga collected from the sea shore of Yantai, China. The strain was Gram-stain-negative, rod-shaped, aerobic, non-motile, and oxidase- and catalase-positive. Growth was observed at 8–37 °C (optimum, 28 °C), at pH 6.0–9.0 (optimum, pH 7.0) and in the presence of 1.0–7.0 % (w/v) NaCl (optimum, 4.0 %). The major respiratory quinone was ubiquinone-8 (Q-8). The polar lipids of strain C3212 consisted of diphosphatidylglycerol (cardiolipin), phosphatidylglycerol, phosphatidylethanolamine, an unidentified aminophospholipid, an unidentified phospholipid and an unidentified polar lipid. The major fatty acids were Cω and/or Cω, and Cω and/or Cω. The DNA G+C content of strain C3212 was 44.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that the novel strain was related most closely to XH122, IMCC 9719 and DSM 2157 with similarities of 98.0, 97.5 and 94.3 %, respectively. Estimated DNA–DNA hybridization values were 14.2, 20.7 and 13.9 % between strain C3212 and XH122, IMCC 9719 and DSM 2157, respectively. Phenotypic, phylogenetic and genomic analyses revealed that strain C3212 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is C3212 (=MCCC 1K03600=KCTC 72121).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003694
2019-12-01
2019-12-06
Loading full text...

Full text loading...

References

  1. Öersted AS. De regionibus marinis, elementa topographiae historiconaturalis freti Oeresund. Inaug Diss J C Scharling, Copenhagen 1844
    [Google Scholar]
  2. Boden R, Scott KM. Evaluation of the genus Thiothrix Winogradsky 1888 (Approved Lists 1980) emend. Aruga et al. 2002: reclassification of Thiothrix disciformis to Thiolinea disciformis gen. nov., comb. nov., and of Thiothrix flexilis to Thiofilum flexile gen. nov., comb nov., with emended description of Thiothrix. Int J Syst Evol Microbiol 2018;68:2226–2239 [CrossRef]
    [Google Scholar]
  3. Bland JA, Brock TD. The marine bacterium Leucothrix mucor as an algal epiphyte. Mar Biol 1973;23:283–292 [CrossRef]
    [Google Scholar]
  4. Zhang Z, Gao X, Wang L, Zhang XH. Leucothrix pacifica sp. nov., isolated from seawater of South Pacific Gyre and emended description of the genus. Int J Syst Evol Microbiol 2015;65:2397–2402
    [Google Scholar]
  5. Baek K, Choi A, Lee YM, Lee HK, Cho J-C. Leucothrix arctica sp. nov., isolated from Arctic seawater. Int J Syst Evol Microbiol 2018;68:3851–3855 [CrossRef]
    [Google Scholar]
  6. Wang Y, Zhou C, Ming H, Kang J, Chen H et al. Pseudofulvibacter marinus sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2016;66:1301–1305 [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. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics New York: John Wiley Sons; 1991; pp.115–147
    [Google Scholar]
  9. Yoon SH, Sm H, 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
    [Google Scholar]
  10. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004;32:1792–1797 [CrossRef]
    [Google Scholar]
  11. 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]
  12. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39:783–791 [CrossRef]
    [Google Scholar]
  13. Rosselló-Móra R, Amann R. Past and future species definitions for Bacteria and Archaea. Syst Appl Microbiol 2015;38:209–216 [CrossRef]
    [Google Scholar]
  14. 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 [CrossRef]
    [Google Scholar]
  15. Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 2006;33:152–155
    [Google Scholar]
  16. Luo R, Liu B, Xie Y, Li Z, Huang W et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 2012;1:18 [CrossRef]
    [Google Scholar]
  17. Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 2007;23:673–679 [CrossRef]
    [Google Scholar]
  18. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016;32:929–931 [CrossRef]
    [Google Scholar]
  19. 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]
  20. Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol 2018;36:996–1004 [CrossRef][PubMed]
    [Google Scholar]
  21. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 2018;35:1547–1549 [CrossRef]
    [Google Scholar]
  22. Goris J, Klappenbach JA, Vandamme P, Coenye T, Konstantinidis KT, Konstantinidis KT et al. DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007;57:81–91 [CrossRef]
    [Google Scholar]
  23. Auch AF, von Jan M, Klenk H-P, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010;2:117–134 [CrossRef]
    [Google Scholar]
  24. Michael R, Ramon RM. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009;106:19126–19131
    [Google Scholar]
  25. Rosselló-Mora R, Amann R. The species concept for prokaryotes. FEMS Microbiol Rev 2001;25:39–67 [CrossRef]
    [Google Scholar]
  26. Beveridge TJ, Lawrence JR, Murray RGE. Sampling and staining for light microscopy. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM et al. (editors) Methods for General and Molecular Bacteriology, 3rd ed. Washington, DC: American Society for Microbiology; 2007; pp.19–33
    [Google Scholar]
  27. Lyman J, Fleming RH. Composition of seawater. J Mar Res 1940;3:134–146
    [Google Scholar]
  28. Wang Y, Liu T, Ming H, Sun P, Cao C et al. Thalassotalea atypica sp. nov., isolated from seawater, and emended description of Thalassotalea eurytherma. Int J Syst Evol Microbiol 2018;68:271–276 [CrossRef]
    [Google Scholar]
  29. Breznak JA, Costilow RN. Physicochemical factors in growth. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: ASM Press; 1994; pp.137–154
    [Google Scholar]
  30. Tindall BJ, Sikorski J, Smibert RM, Krieg NR. Phenotypic characterization and the principles of comparative systematics. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf G, Schmidt TM et al. (editors) Methods for General and Molecular Microbiology Washington, DC: ASM Press; 2007; pp.330–393
    [Google Scholar]
  31. Hsu SC, Lockwood JL. Powdered chitin agar as a selective medium for enumeration of actinomycetes in water and soil. Applied Microbiol 1975;29:422–426
    [Google Scholar]
  32. Collins MD. Isoprenoid quinones. In Goodfellow M, O’Donnell AG. (editors) Chemical Methods in Prokaryotic Systematics Chichester: Wiley Press; 1994; pp.265–309
    [Google Scholar]
  33. 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]
  34. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003694
Loading
/content/journal/ijsem/10.1099/ijsem.0.003694
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most Cited This Month

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