1887

Abstract

A taxonomic study was carried out on strain SHC163, which was isolated from the gut of . The bacterium was Gram-stain-negative, oxidase-positive, catalase-negative and rod-shaped. Growth was observed at salinities of 0–4.0 % NaCl and at temperatures of 15–35 °C. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SHC163 belonged to the genus , with the highest sequence similarity to CL-SP26 (97.9%), followed by DSM 100420 (97.8 %), CECT 5088 (97.5%) and eight species of the genus (94.7−97.1 %). The average amino acid identity, average nucleotide identity and the digital DNA–DNA hybridization estimate values between strain SHC163 and the type strains of the genus were 64.33−79.78 %, 71.0−78.4 % and 19.2−21.0%, respectively. The principal fatty acids (>5 %) were summed feature 8 (C 7/C 6, 56.5 %), C 7 11-methyl (23.1 %), C (8.7 %). The G+C content of the chromosomal DNA was 67.8 mol%. The respiratory quinone was determined to be Q-10 (100 %). The polar lipids were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, an unidentified phospholipid, an unidentified aminolipid and aminophospholipid. The combined genotypic and phenotypic data show that strain SHC163 represents a novel species within the genus , for which the name sp. nov. is proposed, with the type strain SHC163 (=MCCC 1K04032=KCTC 72524).

Funding
This study was supported by the:
  • the Natural Science Foundation of SZU (Award 201427)
    • Principle Award Recipient: SiChen
  • the Natural Science Foundation of SZU (Award 2019078)
    • Principle Award Recipient: ChenjingShang
  • the Graduate Education Innovation Project (Award 2020JGXM094)
    • Principle Award Recipient: ChenjingShang
  • State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences (Award No. LTO1909)
    • Principle Award Recipient: ChenjingShang
  • the Natural Science Foundation of Guangdong Province, (Award 2017A030310332)
    • Principle Award Recipient: ChenjingShang
  • the Natural Science Foundation of Guangdong Province (Award 2019A1515012047)
    • Principle Award Recipient: SiChen
  • the Scientific and Technical Innovation Council of Shenzhen (Award KQJSCX20170727101743831)
    • Principle Award Recipient: XuYing
  • the National Natural Science Foundation of China (Award 41406095)
    • Principle Award Recipient: SiChen
  • Innovative Research Group Project of the National Natural Science Foundation of China (CN) (Award 41706137)
    • Principle Award Recipient: ChenjingShang
  • the National Key R&D Program of China (Award 2018YFA0902500)
    • Principle Award Recipient: ChenjingShang
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004756
2021-03-16
2022-05-22
Loading full text...

Full text loading...

References

  1. Wagner-Döbler I, Rheims H, Felske A, Pukall R, Tindall BJ. Jannaschia helgolandensis gen. nov., sp. nov., a novel abundant member of the marine Roseobacter clade from the North sea. Int J Syst Evol Microbiol 2003; 53:731–738 [View Article][PubMed]
    [Google Scholar]
  2. Adachi M, Kanno T, Okamoto R, Shinozaki A, Fujikawa-Adachi K et al. Jannaschia cystaugens sp. nov., an Alexandrium (Dinophyceae) cyst formation-promoting bacterium from Hiroshima Bay, Japan. Int J Syst Evol Microbiol 2004; 54:1687–1692 [View Article][PubMed]
    [Google Scholar]
  3. Macián MC, Arahal DR, Garay E, Ludwig W, Schleifer KH et al. Jannaschia rubra sp. nov., a red-pigmented bacterium isolated from sea water. Int J Syst Evol Microbiol 2005; 55:649–653 [View Article][PubMed]
    [Google Scholar]
  4. Choi DH, Yi H, Chun J, Cho BC. Jannaschia seosinensis sp. nov., isolated from hypersaline water of a solar saltern in Korea. Int J Syst Evol Microbiol 2006; 56:45–49 [View Article][PubMed]
    [Google Scholar]
  5. Yoon J-H, Kang S-J, Park S, Oh T-K. Jannaschia donghaensis sp. nov., isolated from seawater of the East Sea, Korea. Int J Syst Evol Microbiol 2007; 57:2132–2136 [View Article][PubMed]
    [Google Scholar]
  6. Kim B-Y, Yoo S-H, Weon H-Y, Jeon Y-A, Hong S-B et al. Jannaschia pohangensis sp. nov., isolated from seashore sand in Korea. Int J Syst Evol Microbiol 2008; 58:496–499 [View Article][PubMed]
    [Google Scholar]
  7. Yoon J-H, Kang S-J, Park S, Oh K-H, Oh T-K, TK O. Jannaschia seohaensis sp. nov., isolated from a tidal flat sediment. Int J Syst Evol Microbiol 2010; 60:191–195 [View Article][PubMed]
    [Google Scholar]
  8. Park S, Yoon J-H. Jannaschia aquimarina sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2012; 62:2631–2636 [View Article][PubMed]
    [Google Scholar]
  9. Jung Y-T, Yoon J-H. Jannaschia faecimaris sp. nov., isolated from a tidal flat sediment. Int J Syst Evol Microbiol 2014; 64:945–951 [View Article][PubMed]
    [Google Scholar]
  10. Park S, Choi SJ, Won S-M, Yoon J-H. Jannaschia confluentis sp. nov., isolated from the junction between the ocean and a freshwater spring. Int J Syst Evol Microbiol 2018; 68:669–674 [View Article][PubMed]
    [Google Scholar]
  11. Zhang R, Wang C, Wang X-T, Mu D-S, Du Z-J, ZJ D. Jannaschia formosa sp. nov., isolated from marine saltern sediment. Int J Syst Evol Microbiol 2019; 69:2037–2042 [View Article][PubMed]
    [Google Scholar]
  12. Liu C, Shao Z. Alcanivorax dieselolei sp. nov., a novel alkane-degrading bacterium isolated from sea water and deep-sea sediment. Int J Syst Evol Microbiol 2005; 55:1181–1186 [View Article][PubMed]
    [Google Scholar]
  13. 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 [View Article][PubMed]
    [Google Scholar]
  14. 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]
  15. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  16. 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]
  17. Rzhetsky A, Nei M. Statistical properties of the ordinary least-squares, generalized least-squares, and minimum-evolution methods of phylogenetic inference. J Mol Evol 1992; 35:367–375 [View Article][PubMed]
    [Google Scholar]
  18. 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]
  19. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article][PubMed]
    [Google Scholar]
  20. Rodriguez-R LM, Konstantinidis KT. Bypassing cultivation to identify bacterial species. Microbe 2014; 9:111–118 [View Article]
    [Google Scholar]
  21. 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 [View Article][PubMed]
    [Google Scholar]
  22. 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]
  23. Auch AF, Klenk H-P, Göker M. Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs. Stand Genomic Sci 2010; 2:142–148 [View Article][PubMed]
    [Google Scholar]
  24. 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 [View Article][PubMed]
    [Google Scholar]
  25. Konstantinidis KT, Tiedje JM. Towards a genome-based taxonomy for prokaryotes. J Bacteriol 2005; 187:6258–6264 [View Article][PubMed]
    [Google Scholar]
  26. 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]
  27. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O. Report of the ad hoc Committee on reconciliation of approaches to bacterial Systematics. International journal of systematic bacteriology 1987; 37:463–464
    [Google Scholar]
  28. Na S-I, Kim YO, Yoon S-H, Ha S-M, Baek I, SI N et al. UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:1–6 [View Article][PubMed]
    [Google Scholar]
  29. Skerman VBD. A Guide to the Identification of the Genera of Bacteria, 2nd ed. Baltimore: Williams & Wilkins; 1967
    [Google Scholar]
  30. Liu X, Lai Q, Du Y, Zhang X, Zhong H et al. Sinomicrobium soli sp. nov., isolated from Arctic soil. Int J Syst Evol Microbiol 2019; 69:1070–1074 [View Article][PubMed]
    [Google Scholar]
  31. Dong X-Z, Cai M-Y. Determinative Manual for Routine Bacteriology Beijing: Scientific Press (English translation); 2001
    [Google Scholar]
  32. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI; 1990
    [Google Scholar]
  33. Tindall BJ. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990; 13:128–130 [View Article]
    [Google Scholar]
  34. Tindall BJ. Lipid composition of Halobacterium lacusprofundi . FEMS Microbiol Lett 1990; 66:199–202 [View Article]
    [Google Scholar]
  35. Kates M. Lipid extraction procedures. Techniques of lipidology Amsterdam: Elsevier; 1986 pp 100–111
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004756
Loading
/content/journal/ijsem/10.1099/ijsem.0.004756
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