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Abstract

A novel Gram-stain-negative, light pink-coloured, short rod-shaped, designated strain W17, was isolated from a meadow soil sample collected from Xinjiang, PR China. The 16S rRNA gene sequence analysis indicated that strain W17 was related most closely to M1 (98.72 %) and 8-14-6 (98.44 %). However, strain W17 showed a low level of DNA–DNA relatedness to M1 (32.4±2.6 %) and 8-14-6 (33.5±0.1 %). The genome size of the novel strain was 5.87 Mb and the genomic DNA G+C content was 67.27 mol%. The only respiratory quinone of strain W17 was Q-10. Diphosphatidylglycerol, phosphatidylglycerol. phosphatidylethanolamine and phosphatidylcholine were the major polar lipids. The predominant cellular fatty acids were Cω6 and/or Cω7 (48.53 %), C (20.88 %) and C (14.92 %). The phylogenetic, phenotypic and chemotaxonomic data showed that strain W17 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is W17 (=GDMCC 1.1392=KCTC 62434).

Funding
This study was supported by the:
  • Ministry of Science and Technology of China (Award 2015CB755701)
  • Xinjiang Academy of Agricultural Sciences (Award xjnkq-2019019)
  • National Natural Science Foundation of China, http://dx.doi.org/10.13039/501100001809 (Award 31570080)
  • Ministry of Agriculture of China (Award 2016ZX08009003-002)
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2020-01-06
2024-03-28
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References

  1. Lindsay I, Sly ES. Description of Skermanella parooensis gen. nov., sp. nov. to accommodate Conglomeromonas largomobilis subsp. parooensis following the transfer of Conglomeromonas largomobilis subsp. largomobilis to the genus Azospirillum . Int J Syst Bacteriol 1999; 49:541–544
    [Google Scholar]
  2. Parte AC. LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. Int J Syst Evol Microbiol 2018; 68:1825–1829 [View Article]
    [Google Scholar]
  3. Weon H-Y, Kim B-Y, Hong S-B, Joa J-H, Nam S-S et al. Skermanella aerolata sp. nov., isolated from air, and emended description of the genus Skermanella . Int J Syst Evol Microbiol 2007; 57:1539–1542 [View Article]
    [Google Scholar]
  4. An H, Zhang L, Tang Y, Luo X, Sun T et al. Skermanella xinjiangensis sp. nov., isolated from the desert of Xinjiang, China. Int J Syst Evol Microbiol 2009; 59:1531–1534 [View Article]
    [Google Scholar]
  5. Zhang Z-Y, Gao X-H, Zhang Y-J, Jia M, Lu X-J et al. Skermanella rubra sp. nov., a bacterium isolated from the desert of Xinjiang, China. Antonie van Leeuwenhoek 2015; 108:627–632 [View Article]
    [Google Scholar]
  6. Luo G, Shi Z, Wang H, Wang G. Skermanella stibiiresistens sp. nov., a highly antimony-resistant bacterium isolated from coal-mining soil, and emended description of the genus Skermanella . Int J Syst Evol Microbiol 2012; 62:1271–1276 [View Article]
    [Google Scholar]
  7. Subhash Y, Lee S-S. Skermanella rosea sp. nov., isolated from hydrocarbon-contaminated desert sands. Int J Syst Evol Microbiol 2016; 66:3951–3956 [View Article]
    [Google Scholar]
  8. Lee SS. Skermanella mucosa sp. nov., isolated from crude oil contaminated soil. Antonie van Leeuwenhoek 2017; 110:1053–1060
    [Google Scholar]
  9. Lane DJ. 16S/23S rRNA sequencing. Nucleic Acid Techniques in Bacterial Systematics 1991125–175
    [Google Scholar]
  10. 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]
    [Google Scholar]
  11. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article]
    [Google Scholar]
  12. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article]
    [Google Scholar]
  13. 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]
  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]
    [Google Scholar]
  15. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article]
    [Google Scholar]
  16. LJ D, Cattoir H, Reynaerts A. The quantitative measurement of DNA hybridization from renaturation rates. Febs Journal 1970; 12:133–142
    [Google Scholar]
  17. Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with glimmer. Bioinformatics 2007; 23:673–679 [View Article]
    [Google Scholar]
  18. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997; 25:955–964 [View Article]
    [Google Scholar]
  19. 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]
    [Google Scholar]
  20. 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]
    [Google Scholar]
  21. Xu P, Li W-J, Tang S-K, Zhang Y-Q, Chen G-Z et al. Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family 'Oxalobacteraceae' isolated from China. Int J Syst Evol Microbiol 2005; 55:1149–1153 [View Article]
    [Google Scholar]
  22. Dong XZ, Cai MY. Determinative Manual for Routine Bacteriology Beijing: Scientific Press; 2001
    [Google Scholar]
  23. Park M, Ryu SH, Vu T-HT, Ro H-S, Yun P-Y et al. Flavobacterium defluvii sp. nov., isolated from activated sludge. Int J Syst Evol Microbiol 2007; 57:233–237 [View Article]
    [Google Scholar]
  24. Collins MD. Isoprenoid quinone analyses in bacterial classification and identification. Society for Applied Bacteriology Technical 1985
    [Google Scholar]
  25. 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]
  26. Kämpfer P, Kroppenstedt RM. Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 1996; 42:989–1005 [View Article]
    [Google Scholar]
  27. Wayne LG. International Committee on systematic bacteriology: announcement of the report of the ad hoc Committee on reconciliation of approaches to bacterial Systematics. Zentralbl Bakteriol Mikrobiol Hyg A 1988; 268:433–434 [View Article]
    [Google Scholar]
  28. 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]
    [Google Scholar]
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