1887

Abstract

A Gram-stain-negative, ovoid-shaped, motile and strictly aerobic bacterium, designated ZQ172, was isolated from marine sediment sampled on Zhoushan Island located in the East China Sea. Strain ZQ172 grew optimally at temperatures of 25–30 °C, at NaCl concentration of 2.0 % (w/v) and at pH 7.0–8.5. Catalase and oxidase activities, urease, and nitrate reduction were positive. Indole production, methyl red reaction, HS production and hydrolysis of gelatin, starch, casein and Tweens 20, 40, 60 and 80 were negative. The major cellular fatty acid was summed feature 8 (C 7 and/or C 6). The only respiratory quinone was ubiquinone-10. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and phosphatidylcholine. Comparative analysis of the 16S rRNA gene sequence showed highest similarities to JC2049 (97.5 %), JAMH 043 (97.5 %) and CECT 7735 (97.3 %). Phylogenetic analyses indicated that strain ZQ172 clustered with the genus and was closely related to CECT 7735. The average nucleotide identity and digital DNA–DNA hybridization values between strain ZQ172 and related species of the genus were well below the threshold limit for prokaryotic species delineation. The DNA G+C content was 59.6 mol%. Based on its phenotypic, chemotaxonomic and genotypic data, strain ZQ172 is considered to be a representative of a novel species in the genus , for which the name sp. nov. is proposed. The type strain is ZQ172 (=KCTC 62578=MCCC 1K03531).

Funding
This study was supported by the:
  • Natural Science Foundation of Zhejiang Province (Award LH19H300001)
    • Principle Award Recipient: WeiyanZhang
  • National Natural Science Foundation of China (Award 41776168)
    • Principle Award Recipient: ShanHe
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004782
2021-04-22
2021-05-15
Loading full text...

Full text loading...

References

  1. Choi DH, Cho BC. Shimia marina gen. nov., sp. nov., a novel bacterium of the Roseobacter clade isolated from biofilm in a coastal fish farm. Int J Syst Evol Microbiol 2006; 56:1869–1873 [CrossRef][PubMed]
    [Google Scholar]
  2. Arahal DR, La Mura A, Lucena T, Rodrigo-Torres L, Aznar R et al. Shimia thalassica sp. nov., and reclassification of Pseudopelagicola gijangensis as Shimia gijangensis comb. nov., and Thalassobius activus as Cognatishimia activa comb. nov. Int J Syst Evol Microbiol 2019; 69:3405–3413 [CrossRef][PubMed]
    [Google Scholar]
  3. Oren A, Garrity GM. Notification that new names of prokaryotes, new combinations, and new taxonomic opinions have appeared in volume 68, part 7, of the IJSEM. Int J Syst Evol Microbiol 2018; 68:3077–3079 [CrossRef][PubMed]
    [Google Scholar]
  4. Hameed A, Shahina M, Lin S-Y, Lai W-A, Hsu Y-H et al. Shimia biformata sp. nov., isolated from surface seawater, and emended description of the genus Shimia Choi and Cho 2006. Int J Syst Evol Microbiol 2013; 63:4533–4539 [CrossRef][PubMed]
    [Google Scholar]
  5. Park S, Jung Y-T, Won S-M, Park J-M, Yoon J-H. Thalassobius aquaeponti sp. nov., an alphaproteobacterium isolated from seawater. Antonie Van Leeuwenhoek 2014; 106:535–542 [CrossRef][PubMed]
    [Google Scholar]
  6. Yi H, Chun J. Thalassobius aestuarii sp. nov., isolated from tidal flat sediment. J Microbiol 2006; 44:171–176[PubMed]
    [Google Scholar]
  7. Nogi Y, Mori K, Uchida H, Hatada Y. Shimia sagamensis sp. nov., a marine bacterium isolated from cold-seep sediment. Int J Syst Evol Microbiol 2015; 65:2786–2790 [CrossRef][PubMed]
    [Google Scholar]
  8. Nogi Y, Mori K, Makita H, Hatada Y. Thalassobius abyssi sp. nov., a marine bacterium isolated from cold-seep sediment. Int J Syst Evol Microbiol 2016; 66:574–579 [CrossRef][PubMed]
    [Google Scholar]
  9. Chen M-H, Sheu S-Y, Chen CA, Wang J-T, Chen W-M. Shimia isoporae sp. nov., isolated from the reef-building coral Isopora palifera . Int J Syst Evol Microbiol 2011; 61:823–827 [CrossRef][PubMed]
    [Google Scholar]
  10. Hyun D-W, Kim M-S, Shin N-R, Kim JY, Kim PS et al. Shimia haliotis sp. nov., a bacterium isolated from the gut of an abalone, Haliotis discus hannai . Int J Syst Evol Microbiol 2013; 63:4248–4253 [CrossRef][PubMed]
    [Google Scholar]
  11. Kim Y-O, Park S, Nam B-H, Kim D-G, Yoon J-H. Pseudopelagicola gijangensis gen. nov., sp. nov., isolated from the sea squirt Halocynthia roretzi . Int J Syst Evol Microbiol 2014; 64:3447–3452 [CrossRef][PubMed]
    [Google Scholar]
  12. Dong XZ, Cai MY. Determinative Manual for Routine Bacteriology, 1st ed. Beijing: Scientific Press; 2001 pp 353–364
    [Google Scholar]
  13. Zhu XF. Modern Experimental Technique of Microbiology Hangzhou English translation: Zhejiang University Press; 2011
    [Google Scholar]
  14. Zhang W, Zhu S, Cheng Y, Ding L, Li S et al. Rheinheimera mangrovi sp. nov., a bacterium isolated from mangrove sediment. Int J Syst Evol Microbiol 2020; 70:6188–6194 [CrossRef][PubMed]
    [Google Scholar]
  15. 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]
  16. Kates M. Techniques of Lipidology. Isolation, Analysis and Identification of Lipids, 2nd ed. Amsterdam: Elsevier; 1986
    [Google Scholar]
  17. Zhang X-Q, Sun C, Wang C-S, Zhang X, Zhou X et al. Sinimarinibacterium flocculans gen. nov., sp. nov., a gammaproteobacterium from offshore surface seawater. Int J Syst Evol Microbiol 2015; 65:3541–3546 [CrossRef][PubMed]
    [Google Scholar]
  18. Sun C, Wu C, Su Y, Wang R-J, Fu G-Y et al. Hyphococcus flavus gen. nov., sp. nov., a novel alphaproteobacterium isolated from deep seawater. Int J Syst Evol Microbiol 2017; 67:4024–4031 [CrossRef][PubMed]
    [Google Scholar]
  19. 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][PubMed]
    [Google Scholar]
  20. 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][PubMed]
    [Google Scholar]
  21. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [CrossRef][PubMed]
    [Google Scholar]
  22. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [CrossRef]
    [Google Scholar]
  23. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  24. 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 [CrossRef][PubMed]
    [Google Scholar]
  25. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:2182 [CrossRef][PubMed]
    [Google Scholar]
  26. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008; 24:713–714 [CrossRef][PubMed]
    [Google Scholar]
  27. 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][PubMed]
    [Google Scholar]
  28. 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][PubMed]
    [Google Scholar]
  29. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [CrossRef][PubMed]
    [Google Scholar]
  30. 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]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004782
Loading
/content/journal/ijsem/10.1099/ijsem.0.004782
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