1887

Abstract

A Gram-stain-negative, aerobic, motile, yellow-pigmented, rod-shaped with a single polar flagellum bacterial strain, designated strain DHG54, was isolated from a forest soil sample of Dinghushan Biosphere Reserve, Guangdong Province, China. Strain DHG54 grew at 12–37 °C (optimum, 28 °C), pH 4.5–8.0 (optimum, pH 6.0–7.0) and in the presence of 0–3.0 % (w/v) NaCl (optimum, 0–1.5 %, w/v). Based on 16S rRNA gene sequence analysis, strain DHG54 formed a clade with the members of the genus and showed highest sequence similarities of 98.2 % to DSM 16301 and KACC 12748. This was also supported by phylogenetic analysis based on the concatenated partial , and housekeeping gene sequences. DNA–DNA hybridization results between strain DHG54 and closely related species were all lower than 70 %. Ubiquinone-8 was the only respiratory quinone, and iso-C, iso-C and iso-C 9 were major fatty acids. The DNA G+C content of strain DHG54 was 65.4 mol%. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. On the basis of the polyphasic characterization results presented here, strain DHG54 represents a novel species of the genus , for which the name sp. nov. (type strain DHG54=GDMCC 1.1187 = LMG 30091) is proposed.

Keyword(s): Dyella , genome , phylogeny , solisilvae and taxonomy
Funding
This study was supported by the:
  • National Natural Science Foundation of China (Award Project no. J1310025)
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003218
2019-01-04
2021-05-17
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/69/4/937.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.003218&mimeType=html&fmt=ahah

References

  1. Xie CH, Yokota A. Dyella japonica gen. nov., sp. nov., a γ-proteobacterium isolated from soil. Int J Syst Evol Microbiol 2005; 55:753–756 [CrossRef][PubMed]
    [Google Scholar]
  2. Naushad S, Adeolu M, Wong S, Sohail M, Schellhorn HE et al. A phylogenomic and molecular marker based taxonomic framework for the order Xanthomonadales: proposal to transfer the families Algiphilaceae and Solimonadaceae to the order Nevskiales ord. nov. and to create a new family within the order Xanthomonadales, the family Rhodanobacteraceae fam. nov., containing the genus Rhodanobacter and its closest relatives. Antonie van Leeuwenhoek 2015; 107:467–485 [CrossRef][PubMed]
    [Google Scholar]
  3. Chen MH, Lv YY, Wang J, Tang L, Qiu LH. Dyella humi sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2016; 66:4372–4376 [CrossRef][PubMed]
    [Google Scholar]
  4. Chen MH, Xia F, Lv YY, Zhou XY, Qiu LH. 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 [CrossRef][PubMed]
    [Google Scholar]
  5. Tang L, Chen MH, Nie XC, Mr MA, Qiu LH et al. a lipolytic bacterium isolated from lower subtropical forest soil. Int J Syst Evol Microbiol 2017; 67:1235–1240
    [Google Scholar]
  6. Xia F, Chen MH, Lv YY, Zhang HY, Qiu LH. 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 [CrossRef][PubMed]
    [Google Scholar]
  7. Cai YM, Gao ZH, Chen MH, Huang YX, Qiu LH. Dyella halodurans sp. nov., isolated from lower subtropical forest soil. Int J Syst Evol Microbiol 2018; 68:3237–3242 [CrossRef][PubMed]
    [Google Scholar]
  8. Gerhardt P, Murray RGE, Wood WA, Krieg NR. Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994
    [Google Scholar]
  9. Harley JP, Prescott LM. Laboratory Exercises in Microbiology, 5th ed. New York: McGraw-Hill; 2002
    [Google Scholar]
  10. Brown AE. Bensons Microbiological Applications: Laboratory Manual in General Microbiology , 4th ed. New York: McGraw-Hill; 1985
    [Google Scholar]
  11. Bauer AW, Kirby WM, Sherris JC, Turck M. Antibiotic susceptibility testing by a standardized single disk method. Am J Clin Pathol 1966; 36:49
    [Google Scholar]
  12. Delong EF. Archaea in coastal marine environments. Proc Natl Acad Sci USA 1992; 89:5685–5689 [CrossRef][PubMed]
    [Google Scholar]
  13. 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 [CrossRef][PubMed]
    [Google Scholar]
  14. 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 [CrossRef][PubMed]
    [Google Scholar]
  15. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [CrossRef][PubMed]
    [Google Scholar]
  16. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  17. Tamura K, Peterson D, Peterson N, Stecher G, Nei M et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011; 28:2731–2739 [CrossRef][PubMed]
    [Google Scholar]
  18. 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 [CrossRef][PubMed]
    [Google Scholar]
  19. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [CrossRef][PubMed]
    [Google Scholar]
  20. Chun J, Rainey FA. Integrating genomics into the taxonomy and systematics of the bacteria and archaea. Int J Syst Evol Microbiol 2014; 64:316–324 [CrossRef][PubMed]
    [Google Scholar]
  21. 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 [CrossRef][PubMed]
    [Google Scholar]
  22. Ezaki T, Hashimoto Y, Yabuuchi E. Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 1989; 39:224–229 [CrossRef]
    [Google Scholar]
  23. Chang HW, Nam YD, Jung MY, Kim KH, Roh SW et al. Statistical superiority of genome-probing microarrays as genomic DNA-DNA hybridization in revealing the bacterial phylogenetic relationship compared to conventional methods. J Microbiol Methods 2008; 75:523–530 [CrossRef][PubMed]
    [Google Scholar]
  24. 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 [CrossRef][PubMed]
    [Google Scholar]
  25. Wayne LG, Moore WEC, Stackebrandt E, Kandler O, Colwell RR et al. Report of the Ad Hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 1987; 37:463–464 [CrossRef]
    [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 [CrossRef][PubMed]
    [Google Scholar]
  27. 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[PubMed]
    [Google Scholar]
  28. 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 [CrossRef]
    [Google Scholar]
  29. 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 [CrossRef]
    [Google Scholar]
  30. 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 [CrossRef]
    [Google Scholar]
  31. Weon HY, Anandham R, Kim BY, Hong SB, Jeon YA et al. Dyella soli sp. nov. and Dyella terrae sp. nov., isolated from soil. Int J Syst Evol Microbiol 2009; 59:1685–1690 [CrossRef][PubMed]
    [Google Scholar]
  32. Zhao F, Guo XQ, Wang P, He LY, 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 [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003218
Loading
/content/journal/ijsem/10.1099/ijsem.0.003218
Loading

Data & Media loading...

Supplements

Supplementary File 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