1887

Abstract

Four Gram-stain-negative, catalase- and oxidase-positive, rod-shaped and non-motile strains (CAK1W, CAK8W, CAK57W and CCL10W) were isolated from salt lakes in China. Comparisons based on the 16S rRNA gene sequences showed that the four strains show less than 98.9% similarity to species of the genus . The phylogenetic tree reconstructed based on 16S rRNA gene sequences also showed that species are the most closely related neighbours of the four strains. The sequenced draft genome sizes of strains CAK1W, CAK8W, CAK57W and CCL10W were 3.01, 2.95, 3.01 and 3.04 Mbp with G+C contents of 37.3, 35.8, 37.5 and 36.6 %, respectively. The phylogenomic trees reconstructed based on the UBCG and GET_PHYLOMARKERS pipelines all demonstrated that the four strains belong to the genus . The calculated pairwise orthologous average nucleotide identity based on usearch, digital DNA–DNA hybridization and average amino acid sequence identity values among strains CAK1W, CAK8W, CAK57W, CCL10W and other species of the genus were equal or lower than 91.1, 43.5 and 92.2%; the values between strains CAK1W and CAK57W were 98.8, 90.2 and 99.0 %, respectively. The respiratory quinone of the four strains was MK-6. Their major fatty acids were iso-C, C 10, iso-C and anteiso-C. The major polar lipids of the four strains included phosphatidylethanolamine, an unidentified aminolipid and two kinds of unidentified lipids, and only strain CCL10W contained diphosphatidylglycerol. Based on the above descriptions, strains CAK1W, CAK8W, CAK57W and CCL10W should belong to the genus and represent three independent novel species, for which the names sp. nov. (type strain CAK1W=GDMCC 1.2644=KCTC 82857), sp. nov. (type strain CAK8W=GDMCC 1.2646=KCTC 82859) and sp. nov. (type strain CCL10W=GDMCC 1.2631=KCTC 82860) are proposed.

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2022-10-21
2024-11-11
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References

  1. Bowman JP, McCammon SA, Lewis T, Skerratt JH, Brown JL et al. Psychroflexus torquis gen. nov., sp. nov., a psychrophilic species from Antarctic sea ice, and reclassification of Flavobacterium gondwanense (Dobson et al. 1993) as Psychroflexus gondwanense gen. nov., comb. nov. Microbiology 1998; 144 (Pt 6):1601–1609 [View Article]
    [Google Scholar]
  2. Donachie SP, Bowman JP, Alam M. Psychroflexus tropicus sp. nov., an obligately halophilic Cytophaga-Flavobacterium-Bacteroides group bacterium from an Hawaiian hypersaline lake. Int J Syst Evol Microbiol 2004; 54:935–940 [View Article]
    [Google Scholar]
  3. Chen Y-G, Cui X-L, Wang Y-X, Tang S-K, Zhang Y-Q et al. Psychroflexus sediminis sp. nov., a mesophilic bacterium isolated from salt lake sediment in China. Int J Syst Evol Microbiol 2009; 59:569–573 [View Article] [PubMed]
    [Google Scholar]
  4. Yoon JH, Kang SJ, Jung YT, Oh TK. Psychroflexus salinarum sp. nov., isolated from a marine solar saltern. Int J Syst Evol Microbiol 2009; 59:2404–2407 [View Article] [PubMed]
    [Google Scholar]
  5. Zhang H, Hosoi-Tanabe S, Nagata S, Ban S, Imura S. Psychroflexus lacisalsi sp. nov., a moderate halophilic bacterium isolated from a hypersaline lake (Hunazoko-Ike) in Antarctica. J Microbiol 2010; 48:160–164 [View Article] [PubMed]
    [Google Scholar]
  6. Seiler H, Bleicher A, Busse HJ, Hüfner J, Scherer S. Psychroflexus halocasei sp. nov., isolated from a microbial consortium on a cheese. Int J Syst Evol Microbiol 2012; 62:1850–1856 [View Article]
    [Google Scholar]
  7. Chun J, Kang JY, Jahng KY. Psychroflexus salarius sp. nov., isolated from Gomso salt pan. Int J Syst Evol Microbiol 2014; 64:3467–3472 [View Article]
    [Google Scholar]
  8. Zhong Z-P, Liu Y, Wang F, Zhou Y-G, Liu H-C et al. Psychroflexus salis sp. nov. and Psychroflexus planctonicus sp. nov., isolated from a salt lake. Int J Syst Evol Microbiol 2016; 66:125–131 [View Article] [PubMed]
    [Google Scholar]
  9. Jin S, Xia J, Dunlap CA, Rooney AP, Du ZJ. Psychroflexus saliphilus sp. nov., isolated from a marine solar saltern. Int J Syst Evol Microbiol 2016; 66:5124–5128 [View Article]
    [Google Scholar]
  10. Park S, Jung YT, Park JM, Kim SG, Yoon JH. Psychroflexus aestuariivivens sp. nov., isolated from a tidal flat. Int J Syst Evol Microbiol 2016; 66:2146–2151 [View Article] [PubMed]
    [Google Scholar]
  11. Wu S-G, Wang J-J, Wang J-N, Chen Q, Sheng D-H et al. Psychroflexus aurantiacus sp. nov., isolated from soil in the Yellow River Delta wetlands. Int J Syst Evol Microbiol 2020; 70:6284–6293 [View Article] [PubMed]
    [Google Scholar]
  12. Zhong Y-L, Zhang R, Zhang X-Y, Yu L-X, Zhao M-F et al. Psychroflexus maritimus sp. nov., isolated from coastal sediment. Arch Microbiol 2020; 202:2127–2133 [View Article]
    [Google Scholar]
  13. Lu HB, Gao PX, Phurbu D, Wu QL, Xing P. Salegentibacter lacus sp. nov. and Salegentibacter tibetensis sp. nov., isolated from hypersaline lakes on the Tibetan Plateau. Int J Syst Evol Microbiol 2022; 72: [View Article] [PubMed]
    [Google Scholar]
  14. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. eds Nucleic Acid Sequencing Techniques in Bacterial Systematics New York, USA: Wiley; 1991 pp 115–175
    [Google Scholar]
  15. 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]
  16. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic Local Alignment Search Tool. J Mol Biol 1990; 215:403–410 [View Article] [PubMed]
    [Google Scholar]
  17. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 25:4876–4882 [View Article] [PubMed]
    [Google Scholar]
  18. Kimura M. The neutral theory of molecular evolution. Sci Am 1979; 241:98–100 [View Article]
    [Google Scholar]
  19. 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]
  20. Kluge AG, Farris JS. Quantitative phyletics and the evolution of anurans. Syst Zool 1969; 18:1 [View Article]
    [Google Scholar]
  21. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  22. 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]
  23. 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]
  24. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article] [PubMed]
    [Google Scholar]
  25. 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]
  26. Kim D, Park S, Chun J. Introducing EzAAI: a pipeline for high throughput calculations of prokaryotic average amino acid identity. J Microbiol 2021; 59:476–480 [View Article] [PubMed]
    [Google Scholar]
  27. 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]
    [Google Scholar]
  28. Na S-I, Kim YO, Yoon S-H, Ha S-M, Baek I et al. UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285 [View Article] [PubMed]
    [Google Scholar]
  29. Contreras-Moreira B, Vinuesa P. GET_HOMOLOGUES, a versatile software package for scalable and robust microbial pangenome analysis. Appl Environ Microbiol 2013; 79:7696–7701 [View Article] [PubMed]
    [Google Scholar]
  30. Vinuesa P, Ochoa-Sánchez LE, Contreras-Moreira B. GET_PHYLOMARKERS, a software package to select optimal orthologous clusters for phylogenomics and inferring pan-genome phylogenies, used for a critical geno-taxonomic revision of the genus Stenotrophomonas. Front Microbiol 2018; 9:771 [View Article]
    [Google Scholar]
  31. Kanehisa M, Sato Y, Furumichi M, Morishima K, Tanabe M. New approach for understanding genome variations in KEGG. Nucleic Acids Res 2019; 47:D590–D595 [View Article] [PubMed]
    [Google Scholar]
  32. Medema MH, Blin K, Cimermancic P, de Jager V, Zakrzewski P et al. antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Res 2011; 39:W339–W346 [View Article]
    [Google Scholar]
  33. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article] [PubMed]
    [Google Scholar]
  34. 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]
    [Google Scholar]
  35. Moore WEC, Stackebrandt E, Kandler O, Colwell RR, Krichevsky MI et al. Report of the ad hoc Committee on Reconciliation of Approaches to Bacterial Systematics. Int J Syst Bacteriol 1987; 37:463–464 [View Article]
    [Google Scholar]
  36. Konstantinidis KT, Tiedje JM. Towards a genome-based taxonomy for prokaryotes. J Bacteriol 2005; 187:6258–6264 [View Article] [PubMed]
    [Google Scholar]
  37. Ito M, Guffanti AA, Oudega B, Krulwich TA. Mrp, a multigene, multifunctional locus in Bacillus subtilis with roles in resistance to cholate and to Na+ and in pH homeostasis. J Bacteriol 1999; 181:2394–2402 [View Article]
    [Google Scholar]
  38. Kuypers MMM, Marchant HK, Kartal B. The microbial nitrogen-cycling network. Nat Rev Microbiol 2018; 16:263–276 [View Article] [PubMed]
    [Google Scholar]
  39. Biebl H, Pukall R, Lünsdorf H, Schulz S, Allgaier M et al. Description of Labrenzia alexandrii gen. nov., sp. nov., a novel alphaproteobacterium containing bacteriochlorophyll a, and a proposal for reclassification of Stappia aggregata as Labrenzia aggregata comb. nov., of Stappia marina as Labrenzia marina comb. nov. and of Stappia alba as Labrenzia alba comb. nov., and emended descriptions of the genera Pannonibacter, Stappia and Roseibium, and of the species Roseibium denhamense and Roseibium hamelinense. Int J Syst Evol Microbiol 2007; 57:1095–1107 [View Article]
    [Google Scholar]
  40. Reichenbach H, Kohl W, Bottger-Vetter A, Achenbach H. Flexirubin-type pigments in Flavobacterium. Arch Microbiol 1980; 126:291–293 [View Article]
    [Google Scholar]
  41. Zhu XF. Modern Experimental Technique of Microbiology Hangzhou, China: Zhejiang University Press; 2011
    [Google Scholar]
  42. Lu HB, Xing P, Phurbu D, Tang Q, Wu QL. Pelagibacterium montanilacus sp. nov., an alkaliphilic bacterium isolated from Lake Cuochuolong on the Tibetan Plateau. Int J Syst Evol Microbiol 2018; 68:2220–2225 [View Article] [PubMed]
    [Google Scholar]
  43. Ventosa A, Quesada E, Rodriguez-Valera F, Ruiz-Berraquero F, Ramos-Cormenzana A. Numerical taxonomy of moderately halophilic Gram-negative rods. Microbiology 1982; 128:1959–1968 [View Article]
    [Google Scholar]
  44. Kuykendall LD, Roy MA, O’neill JJ, Devine TE. Fatty Acids, Antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum. Int J Syst Bacteriol 1988; 38:358–361 [View Article]
    [Google Scholar]
  45. Sasser M. Identification of bacteria through fatty acid analysis. In Klement Z, Rudolph K, Sands DC. eds Methods in Phytobacteriology Budapest, Hungary: Akademiai Kaido; 1990 pp 199–204
    [Google Scholar]
  46. 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]
  47. Tindall BJ. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 1990; 66:199–202
    [Google Scholar]
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