1887

Abstract

A novel Gram-stain-negative, strictly aerobic, rod-shaped motile bacterium with a single flagellum, designated strain WRAS1, was isolated from deep seawater of the Okinawa Trough. Growth occurred in the presence of 0.0–9.0 % NaCl (w/v; optimum, 3.0–4.0 %), at 4–45 °C (optimum, 28–37 °C) and pH 7.0–10.0 (optimum, pH 7.0–8.0). The major fatty acid (>10 % of total fatty acids) was summed feature 8, comprising C 6 and/or C 7. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine and three unidentified lipids. The major respiratory quinone was ubiquinone-10. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain WRAS1 was in the genus and showed the highest 16S rRNA gene sequence similarity of 97.5 % to JCM13833. Genome relatedness between strain WRAS1 and JCM13833 was computed using both average nucleotide identity and DNA–DNA hybridization with values of 74.11 % and 22.70±2.3 %, respectively. The genomic DNA G+C content calculated from the genome sequence of strain WRAS1 was 65.6 %. On the basis of polyphasic analyses, strain WRAS1 is considered to represent a novel species in the genus , for which the name sp. nov. is proposed. The type strain is WRAS1 (=CGMCC 1.16123=MCCC 1K03253 =KCTC 52696).

Funding
This study was supported by the:
  • National Key R and D Program of China (Award 2018YFC0310701)
  • National Natural Science Foundation of China (Award U1706208)
  • Scientific and Technological Innovation Project of Qingdao National Laboratory for Marine Science and Technology (Award 2016ASKJ14)
  • National Natural Science Foundation of China (Award 91751202)
  • Scientific and Technological Innovation Project of Qingdao National Laboratory for Marine Science and Technology (Award 2018SDKJ0406-4)
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003217
2019-01-10
2024-03-29
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/69/4/920.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.003217&mimeType=html&fmt=ahah

References

  1. Lee OO, Tsoi MM, Li X, Wong PK, Qian PY. Thalassococcus halodurans gen. nov., sp. nov., a novel halotolerant member of the Roseobacter clade isolated from the marine sponge Halichondria panicea at Friday Harbor, USA. Int J Syst Evol Microbiol 2007; 57:1919–1924 [View Article][PubMed]
    [Google Scholar]
  2. Park S, Jung YT, Kim SI, Yoon JH. Thalassococcus lentus sp. nov., an alphaproteobacterium isolated from seawater of a seaweed farm. Antonie van Leeuwenhoek 2013; 103:465–473 [View Article][PubMed]
    [Google Scholar]
  3. Steinsbu BO, Thorseth IH, Nakagawa S, Inagaki F, Lever MA et al. Archaeoglobus sulfaticallidus sp. nov., a thermophilic and facultatively lithoautotrophic sulfate-reducer isolated from black rust exposed to hot ridge flank crustal fluids. Int J Syst Evol Microbiol 2010; 60:2745–2752 [View Article][PubMed]
    [Google Scholar]
  4. Balch WE, Fox GE, Magrum LJ, Woese CR, Wolfe RS. Methanogens: reevaluation of a unique biological group. Microbiol Rev 1979; 43:260–296[PubMed]
    [Google Scholar]
  5. Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG et al. Short Protocols in Molecular Biology: A Compendium of Methods from Current Protocols in Molecular Biology, 3rd ed. New York: Wiley; 1995
    [Google Scholar]
  6. Zhang Z, Yu T, Xu T, Zhang XH. Aquimarina pacifica sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2014; 64:1991–1997 [View Article][PubMed]
    [Google Scholar]
  7. Yoon SH, Ha SM, 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]
  8. 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]
  9. 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]
  10. Beveridge TJ, Lawrence JR, Murray RG. Sampling and staining for light microscopy. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf G, Schmidt TM et al. (editors) Methods for General and Molecular Microbiology Washington, DC: American Society for Microbiology; 2007 pp. 19–33
    [Google Scholar]
  11. Tindall BJ, Sikorski J, Smibert RA, Krieg NR. Phenotypic Characterization and the Principles of Comparative Systematics. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM et al. (editors) Methods for General and Molecular Microbiology Washington, DC: American Society of Microbiology; 2007 pp. 330–393
    [Google Scholar]
  12. Hsu SC, Lockwood JL. Powdered chitin agar as a selective medium for enumeration of actinomycetes in water and soil. Appl microbial 1975; 29:422–426
    [Google Scholar]
  13. Bruns A, Rohde M, Berthe-Corti L. Muricauda ruestringensis gen. nov., sp. nov., a facultatively anaerobic, appendaged bacterium from German North Sea intertidal sediment. Int J Syst Evol Microbiol 2001; 51:1997–2006 [View Article][PubMed]
    [Google Scholar]
  14. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  15. Xie CH, Yokota A. Phylogenetic analyses of Lampropedia hyalina based on the 16S rRNA gene sequence. J Gen Appl Microbiol 2003; 49:345–349 [View Article][PubMed]
    [Google Scholar]
  16. 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]
  17. Collins MD, Shah HN. Fatty acid, menaquinone and polar lipid composition of Rothia dentocariosa . Arch Microbiol 1984; 137:247–249 [View Article]
    [Google Scholar]
  18. Komagata K, Suzuki K-I. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1988; 19:161–207
    [Google Scholar]
  19. Moore ERB, Arnscheidt A, Krüger A, Strömpl C, Mau M et al. Simplified protocols for the preparation of genomic DNA from bacterial cultures. Mol Microbial Ecol Manual 1999; 1:1–15
    [Google Scholar]
  20. Tritt A, Eisen JA, Facciotti MT, Darling AE. An integrated pipeline for de novo assembly of microbial genomes. PLoS One 2012; 7:e42304 [View Article][PubMed]
    [Google Scholar]
  21. 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]
  22. 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]
  23. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article][PubMed]
    [Google Scholar]
  24. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003217
Loading
/content/journal/ijsem/10.1099/ijsem.0.003217
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF
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