1887

Abstract

Cells of bacterial strains G9 and 7MK23, isolated from forest soil samples collected from the Dinghushan Biosphere Reserve, Guangdong Province, PR China, were Gram-stain-negative, aerobic and rod-shaped. Strain G9 was motile with single polar flagellum and grew at 12–37 °C (optimum, 28 °C), pH 4.5–8.0 (optimum, pH 6.0–7.5) and in the presence of 0–3.5 % NaCl (optimum, 1.5%, w/v); while strain 7MK23 was non-motile and grew at 12–42 °C (optimum, 28–33 °C), pH 2.5–8.5 (optimum, pH 4.5–6.5) and NaCl levels of 0–1.0 % (optimum, 0–0.5 %, w/v). Phylogenetic analysis based on 16S rRNA gene sequences revealed that both isolates fell within the cluster of the genus . The closely related species (with a 16S rRNA gene sequence similarity >98.65%) of strain G9 were JS14-6 (99.0 %), . THG-B117 (98.8 %) and . DHC06 (98.7 %) while that of strain 7MK23 were . DHON07 (99.2 %) and . DHOC52 (99.1 %), but the average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between strains G9, 7MK23 and the closely related species listed above were in the ranges of 77.5–83.8 % and 22.0–27.0 %, much lower than the species demarcation lines of 95.5 and 70 %, respectively. Phylogenomic analyses using UBCG and Phylophlan also supported that these two strains represent two novel species of . The major fatty acids of strain G9 were iso-C, iso-C 9 and iso-C while that of strain 7MK23 were iso-C and anteiso-C. Ubiquinone-8 was the only respiratory quinone detected in both strains. The polar lipids of strain G9 consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, and several unknown phospholipids, aminophospholipids, aminolipids and lipid while strain 7MK23 contained phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine and several unknown phospholipids and aminophospholipids. The DNA G+C contents of strains G9 and 7MK23 were 64.7 and 63.4 mol%, respectively. On the basis of 16S rRNA gene sequence phylogenetic and phylogenomic analyses as well as phenotypic data obtained, we propose that strains G9 and 7MK23 represent two novel species of the genus , for which the names sp. nov. (type strain G9=KACC 21725=GDMCC 1.2132) and sp. nov. (type strain 7MK23=KCTC 62739=GDMCC 1.1446) are proposed.

Keyword(s): acidiphila , Dyella , phylogeny and telluris
Funding
This study was supported by the:
  • Guangdong province science and technology innovation strategy special fund (Award 2018B020205003)
    • Principle Award Recipient: QiuLi-hong
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2021-09-07
2024-10-14
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References

  1. Xie C-H, Yokota A. Dyella japonica gen. nov., sp. nov., a gamma-proteobacterium isolated from soil. Int J Syst Evol Microbiol 2005; 55:753–756 [View Article]
    [Google Scholar]
  2. Chen M-H, Lv Y-Y, Wang J, Tang L, Qiu L-H. Dyella humi sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2016; 66:4372–4376 [View Article]
    [Google Scholar]
  3. Xia F, Chen M-H, Lv Y-Y, Zhang H-Y, Qiu L-H. Dyella caseinilytica sp. nov., Dyella flava sp. nov. and Dyella mobilis sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2017; 67:3237–3245 [View Article]
    [Google Scholar]
  4. Tang L, Chen M-H, Nie X-C, Ma M-R, Qiu L-H. Dyella lipolytica sp. nov., a lipolytic bacterium isolated from lower subtropical forest soil. Int J Syst Evol Microbiol 2017; 67:1235–1240 [View Article]
    [Google Scholar]
  5. Chen M-H, Xia F, Lv Y-Y, Zhou X-Y, Qiu L-H. Dyella acidisoli sp. nov., D. flagellata sp. nov. and D. nitratireducens sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2017; 67:736–743 [View Article]
    [Google Scholar]
  6. Cai Y-M, Gao Z-H, Chen M-H, Huang Y-X, Qiu L-H. Dyella halodurans sp. nov., isolated from lower subtropical forest soil. Int J Syst Evol Microbiol 2018; 68:3237–3242 [View Article]
    [Google Scholar]
  7. Ou F-H, Gao Z-H, Chen M-H, Bi J-Y, Qiu L-H. Dyella dinghuensis sp. nov. and Dyella choica sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2019; 69:1496–1503 [View Article]
    [Google Scholar]
  8. Zhou X-Y, Gao Z-H, Chen M-H, Jian M-Q, Qiu L-H. Dyella monticola sp. nov. and Dyella psychrodurans sp. nov., isolated from monsoon evergreen broad-leaved forest soil of Dinghu Mountain, China. Int J Syst Evol Microbiol 2019; 69:1016–1023 [View Article]
    [Google Scholar]
  9. Gao Z-H, Yang Z, Chen M-H, Huang Z-J, Qiu L-H. Dyella solisilvae sp. nov., isolated from mixed pine and broad-leaved forest soil. Int J Syst Evol Microbiol 2019; 69:937–943 [View Article]
    [Google Scholar]
  10. Fu J-C, Gao Z-H, Wu T-T, Chen M-H, Qiu L-H. Dyella amyloliquefaciens sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2019; 69:3560–3566 [View Article]
    [Google Scholar]
  11. Anandham R, Kwon S-W, Indira Gandhi P, Kim S-J, Weon H-Y et al. Dyella thiooxydans sp. nov., a facultatively chemolithotrophic, thiosulfate-oxidizing bacterium isolated from rhizosphere soil of sunflower (Helianthus annuus L. Int J Syst Evol Microbiol 2011; 61:392–398 [View Article]
    [Google Scholar]
  12. Zhao F, Guo X-Q, Wang P, He L-Y, Huang Z et al. Dyella jiangningensis sp. nov., a γ-proteobacterium isolated from the surface of potassium-bearing rock. Int J Syst Evol Microbiol 2013; 63:3154–3157 [View Article]
    [Google Scholar]
  13. Bao Y, Kwok AH, He L, Jiang J, Huang Z et al. Complete genome sequence of Dyella jiangningensis Strain SBZ3-12, Isolated from the Surfaces of Weathered Rock. Genome Announc 2014; 2: [View Article]
    [Google Scholar]
  14. Li A, Qu Y, Zhou J, Ma F. Characterization of a newly isolated biphenyl-degrading bacterium, Dyella ginsengisoli LA-4. Appl Biochem Biotechnol 2009; 159:687–695 [View Article]
    [Google Scholar]
  15. DeLong EF. Archaea in coastal marine environments. Proc Natl Acad Sci U S A 1992; 89:5685–5689 [View Article]
    [Google Scholar]
  16. 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]
  17. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22:4673–4680 [View Article]
    [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]
    [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]
    [Google Scholar]
  20. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article]
    [Google Scholar]
  21. 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]
    [Google Scholar]
  22. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article]
    [Google Scholar]
  23. Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008; 18:821–829 [View Article]
    [Google Scholar]
  24. Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH et al. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res 2017; 27:722–736 [View Article]
    [Google Scholar]
  25. Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 2017; 13:e1005595 [View Article]
    [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]
    [Google Scholar]
  27. 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]
    [Google Scholar]
  28. Eddy SR. A new generation of homology search tools based on probabilistic inference. Genome Inform 2009; 23:205–211 [View Article]
    [Google Scholar]
  29. Price MN, Dehal PS, Arkin AP. FastTree 2--approximately maximum-likelihood trees for large alignments. PLoS One 2010; 5:e9490 [View Article]
    [Google Scholar]
  30. 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: [View Article]
    [Google Scholar]
  31. 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]
  32. 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]
  33. Wayne L, Brenner D, Colwell R, Grimont P, Kandler O et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 1987; 37:463–464 [View Article]
    [Google Scholar]
  34. Harley JP. Laboratory Exercises in Microbiology, 5th ed. New York: McGraw-Hill;2002;
    [Google Scholar]
  35. Brown AE. Benson’s Microbiological Applications: Laboratory Manual in General Microbiology, 4th ed. New York: McGraw-Hil;1985;
    [Google Scholar]
  36. Bauer AW, Kirby WM, Sherris JC, Turck M. Antibiotic susceptibility testing by a standardized single disk method. Am J Clin Pathol 1966; 45:493–496 [View Article]
    [Google Scholar]
  37. Kuykendall L, Roy M, O’Neill J, Devine T. Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum. Int J Syst Evol Microbiol 1988; 38:358–361 [View Article]
    [Google Scholar]
  38. Miller LT. Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. J Clin Microbiol 1982; 16:584–586 [View Article]
    [Google Scholar]
  39. Minnikin D, O’Donnell A, 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]
  40. Kroppenstedt RM. Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. Journal of Liquid Chromatography 2006; 5:2359–2367 [View Article]
    [Google Scholar]
  41. Weon H-Y, Anandham R, Kim B-Y, Hong S-B, Jeon Y-A et al. Dyella soli sp. nov and Dyella terrae sp nov, isolated from soil. Int J Syst Evol Microbiol 2009; 59:1685–1690 [View Article]
    [Google Scholar]
  42. Son H-M, Yang J-E, Yi E-J, Park Y, Won K-H et al. Dyella kyungheensis sp. nov., isolated from soil of a cornus fruit field. Int J Syst Evol Microbiol 2013; 63:3807–3811 [View Article]
    [Google Scholar]
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