1887

Abstract

A Gram-stain-negative, strictly aerobic, non-motile, orange-coloured bacterium, designated YR1-1, was isolated from a soil sample collected from the Yellow River Delta wetlands (PR China). Growth was observed at a salinity of 1.0–15.0 % NaCl, 4–45 °C and pH 6.0–9.0. The results of phylogenetic analysis based on the 16S rRNA gene sequences indicated that YR1-1 represented a member of the genus , with the highest sequence similarity to YIM-C238 (97.9 %), followed by (97.1 %) and (96.4 %). The average nucleotide identity and digital DNA–DNA hybridization values between YR1-1 and other closely related type strains of species of the genus were 68.7–86.3% and 17.8–30.9 %. The genome of the strain was 2 899 374 bp in length with 39.8 % DNA G+C content. The predominant fatty acids (>10 %) were iso-C and anteiso-C. The major respiratory quinone was menaquinone-6 (MK-6) and the major polar lipids were phosphatidylethanolamine, phospholipid, diphosphatidylglycerol, two unidentified aminolipids and four unidentified lipids. The combined genotypic and phenotypic data indicate that YR1-1 represents a novel species within the genus , for which the name sp. nov., is proposed. The type strain is YR1-1 (=KCTC 72794=CGMCC 1.17458).

Funding
This study was supported by the:
  • National Natural Science Foundation of China (Award 32070030)
    • Principle Award Recipient: Yue-zhong Li
  • the National Key Research and Development Programs of China (Award 2018YFA0900400 and No. 2018YFA0901704)
    • Principle Award Recipient: Yue-zhong Li
  • the Key Program of Shandong Natural Science Foundation (Award ZR2016QZ002)
    • Principle Award Recipient: Yue-zhong Li
  • the National Natural Science Foundation of China (Award 31670076 and 31471183)
    • Principle Award Recipient: Yue-zhong Li
  • the special national project on investigation of basic resources of China (Award 2019FY100700)
    • Principle Award Recipient: Duo hong Sheng
  • Special investigation on scientific and technological basic resources (Award 2017FY100302)
    • Principle Award Recipient: Yue-zhong Li
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2020-10-29
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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; 14:1601–1609 [View Article][PubMed]
    [Google Scholar]
  2. 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][PubMed]
    [Google Scholar]
  3. 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][PubMed]
    [Google Scholar]
  4. 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]
  5. Zhong YL, Zhang R, Zhang XY, Yu LX, Zhao MF et al. Psychroflexus maritimus sp. nov., isolated from coastal sediment. Arch Microbiol 2020; 202:2127–2133 [View Article][PubMed]
    [Google Scholar]
  6. 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][PubMed]
    [Google Scholar]
  7. Zhong ZP, Liu Y, Wang F, Zhou YG, Liu HC 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]
  8. Chen YG, Cui XL, Wang YX, Tang SK, Zhang YQ 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]
  9. 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][PubMed]
    [Google Scholar]
  10. 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]
  11. 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]
  12. 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][PubMed]
    [Google Scholar]
  13. Feng S, Powell SM, Wilson R, Bowman JP. Proteomic insight into functional changes of proteorhodopsin-containing bacterial species Psychroflexus torquis under different illumination and salinity levels. J Proteome Res 2015; 14:3848–3858 [View Article][PubMed]
    [Google Scholar]
  14. Dong XZ, Cai MY. Chapter 14. Determination of biochemical characteristics. Manual for the Systematic Identification of General Bacteria Beijing: Science Press (in Chinese); 2001 pp 370–398
    [Google Scholar]
  15. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173:697–703 [View Article][PubMed]
    [Google Scholar]
  16. 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]
  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. 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]
  19. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
    [Google Scholar]
  20. 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]
  21. Kim M, Oh HS, Park SC, 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]
  22. Luo R, Liu B, Xie Y, Li Z, Huang W et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 2012; 1:18 [View Article][PubMed]
    [Google Scholar]
  23. Segata N, Börnigen D, Morgan XC, Huttenhower C. PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes. Nat Commun 2013; 4:4–2304 [View Article][PubMed]
    [Google Scholar]
  24. Stothard P, Wishart DS. Circular genome visualization and exploration using CGView. Bioinformatics 2005; 21:537–539 [View Article][PubMed]
    [Google Scholar]
  25. 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]
  26. 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]
  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][PubMed]
    [Google Scholar]
  28. Lee I, Ouk KY, Park SC, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article][PubMed]
    [Google Scholar]
  29. Richter M, Rosselló-Móra R, Michael R, Ramon RM. 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]
  30. Rodriguez-R LM, Konstantinidis KT. Bypassing cultivation to identify bacterial species. Microbe Magazine 2014; 9:111–118 [View Article]
    [Google Scholar]
  31. Burr DJ, Martin A, Maas EW, Ryan KG. In situ light responses of the proteorhodopsin-bearing Antarctic sea-ice bacterium, Psychroflexus torques . ISME J 2017; 11:2155–2158 [View Article][PubMed]
    [Google Scholar]
  32. Liu C, Zhao X, Wang X. Identification and characterization of the psychrophilic bacterium CidnaK gene in the Antarctic Chlamydomoas sp. ICE-L under freezing conditions. J Appl Phycol 2018; 30:3519–3528 [View Article]
    [Google Scholar]
  33. Schmitz-Esser S, Dzieciol M, Nischler E, Schornsteiner E, Bereuter O et al. Abundance and potential contribution of Gram-negative cheese rind bacteria from Austrian artisanal hard cheeses. Int J Food Microbiol 2018; 266:95–103 [View Article][PubMed]
    [Google Scholar]
  34. Claus D. A standardized Gram staining procedure. World J Microbiol Biotechnol 1992; 8:451–452 [View Article][PubMed]
    [Google Scholar]
  35. Zhang R, Zhang XY, Sun XK, Mu DS, Du ZJ et al. Flavobacterium cerinum sp. nov., isolated from Arctic tundra soil. Int J Syst Evol Microbiol 2019; 69:3745–3750 [View Article][PubMed]
    [Google Scholar]
  36. Bernardet JF, Nakagawa Y, Holmes B. Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 2002; 52:1049–1070 [View Article][PubMed]
    [Google Scholar]
  37. Yan L, Wang J, Chen Z, Guan Y, Li J. Microbacterium nanhaiense sp. nov., an actinobacterium isolated from sea sediment. Int J Syst Evol Microbiol 2015; 65:3697–3702 [View Article][PubMed]
    [Google Scholar]
  38. Cowan ST, Steel KJ. Manual for the Identification of Medical Bacteria. Proceedings of the royal society of medicine; 1965; 59468
  39. Du ZJ, Wang ZJ, Zhao JX, Chen GJ. Woeseia oceani gen. nov., sp. nov., a chemoheterotrophic member of the order Chromatiales, and proposal of Woeseiaceae fam. nov. Int J Syst Evol Microbiol 2016; 66:107–112 [View Article][PubMed]
    [Google Scholar]
  40. Kroppenstedt RM. Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 1982; 5:2359–2367 [View Article]
    [Google Scholar]
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