1887

Abstract

Two Gram-stain-negative, aerobic, motile, white-pigmented and rod-shaped bacterial strains, 7MH5 and 4 M-K11, were isolated from forest soil of Dinghushan Biosphere Reserve, Guangdong Province, PR China. Strain 7MH5 grew at 4–37 °C (optimum, 28–33 °C), pH 3.5–9.0 (pH 4.0–5.5) and in the presence of 0–3 % (w/v) NaCl (0–1.5 w/v); while strain 4 M-K11 grew at 4–42 °C (20–33 °C), pH 3.5–8.5 (pH 4.5–6.0) and in the presence of 0–2.5 % (w/v) NaCl (0–1.5 w/v). Strains 7MH5 and 4 M-K11 have the highest 16S rRNA gene sequence similarities of 98.6 and 98.7 % to PP52-1, and 98.4 % between themselves. In the 16S rRNA gene sequence phylogram, strains 4 M-K11 and NBRC 106233 formed a clade while 7MH5 were relatively distinct from other species. Based on the UBCG phylogenomic analysis, strains 7MH5 and 4 M-K11 formed a clade with NBRC 105797 and LMG 19450 in the genus of . The DNA G+C contents of strains 7MH5 and 4 M-K11 were 64.2 and 64.3 %, respectively. Digital DNA–DNA hybridization and the average nucleotide identity values of strains 7MH5, 4 M-K11 and closely related strains were in the ranges of 25.2–63.6 % and 81.0–95.5 %, respectively. The two strains had the same major respiratory quinone: ubiquinone-8. Strain 7MH5 had C, Ccyclo, Ccyclo and summed feature 8 (C 7/C 6) as its major fatty acids, while strain 4 M-K11 had major fatty acids of C, Ccyclo and summed feature 2 (iso-C I/C−3OH). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. On the basis of phenotypic and phylogenetic analyses based on both 16S rRNA gene and whole genome sequences, as well as chemotaxonomic data, strains 7MH5 and 4 M-K11 represent two novel species of the genus , for which the names sp. nov. (type strain 7MH5=GDMCC 1.1450=KACC 19962) and sp. nov. (type strain 4 M-K11=GDMCC 1.1284=CGMCC 1.15450=KACC 19961=LMG 29217) are proposed.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003681
2019-12-01
2019-12-15
Loading full text...

Full text loading...

References

  1. Sawana A, Adeolu M, Gupta RS. Molecular signatures and phylogenomic analysis of the genus Burkholderia: proposal for division of this genus into the emended genus Burkholderia containing pathogenic organisms and a new genus Paraburkholderia gen. nov. harboring environmental species. Front Genet 2014;5:429 [CrossRef][PubMed]
    [Google Scholar]
  2. Viallard V, Poirier I, Cournoyer B, Haurat J, Wiebkin S et al. Burkholderia graminis sp. nov., a rhizospheric Burkholderia species, and reassessment of [Pseudomonas] phenazinium, [Pseudomonas] pyrrocinia and [Pseudomonas] glathei as Burkholderia. Int J Syst Bacteriol 1998;48 Pt 2:549–563 [CrossRef][PubMed]
    [Google Scholar]
  3. Yabuuchi E, Kosako Y, Oyaizu H, Yano I, Hotta H et al. Proposal of Burkholderia gen. nov. and transfer of seven species of the genus Pseudomonas homology group II to the new genus, with the type species Burkholderia cepacia (Palleroni and Holmes 1981) comb. nov. Microbiol Immunol 1992;36:1251–1275 [CrossRef][PubMed]
    [Google Scholar]
  4. Dobritsa AP, Samadpour M. Transfer of eleven species of the genus Burkholderia to the genus Paraburkholderia and proposal of Caballeronia gen. nov. to accommodate twelve species of the genera Burkholderia and Paraburkholderia. Int J Syst Evol Microbiol 2016;66:2836–2846 [CrossRef][PubMed]
    [Google Scholar]
  5. Lopes-Santos L, Castro DBA, Ferreira-Tonin M, Corrêa DBA, Weir BS et al. Reassessment of the taxonomic position of Burkholderia andropogonis and description of Robbsia andropogonis gen. nov., comb. nov. Antonie van Leeuwenhoek 2017;110:727–736 [CrossRef][PubMed]
    [Google Scholar]
  6. Estrada-de Los Santos P, Palmer M, Chávez-Ramírez B, Beukes C, Steenkamp ET et al. Whole genome analyses suggests that Burkholderia sensu lato contains two additional novel genera (Mycetohabitans gen. nov., and Trinickia gen. nov.): implications for the evolution of diazotrophy and nodulation in the Burkholderiaceae. Genes 2018;9:389 [CrossRef][PubMed]
    [Google Scholar]
  7. Gerhardt P, Murray RGE, Wood WA, Krieg NR. Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994
    [Google Scholar]
  8. Harley JP, Prescott LM. Laboratory Exercises in Microbiology, 5th ed. New York: McGraw-Hill; 2002
    [Google Scholar]
  9. Brown AE. Bensons Microbiological Applications: Laboratory Manual in General Microbiology , 4th ed. New York: McGraw-Hill; 1985
    [Google Scholar]
  10. Atlas RM. Composition of media. In Parks LC. (editor) Handbook of Microbiology Media, 2nd ed. Boca Raton, FL: CRC Press; 1993; .
    [Google Scholar]
  11. Kim SJ, Ahn JH, Weon HY, Hong SB, Seok SJ et al. Parasegetibacter terrae sp. nov., isolated from paddy soil and emended description of the genus Parasegetibacter. Int J Syst Evol Microbiol 2015;65:113–116 [CrossRef][PubMed]
    [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. Na SI, Kim YO, Yoon SH, Ha SM, Baek I et al. UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018;56:280–285 [CrossRef][PubMed]
    [Google Scholar]
  21. Eddy SR. A new generation of homology search tools based on probabilistic inference. Genome Inform 2009;23:211–215[PubMed]
    [Google Scholar]
  22. Price MN, Dehal PS, Arkin AP. FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS One 2010;5:e9490 [CrossRef][PubMed]
    [Google Scholar]
  23. 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]
  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. 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]
  26. 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]
  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. Sasser M. "Tracking" A Strain Using the Microbial Identification System, MIDI Technical Note.vol. 102 1990
    [Google Scholar]
  32. Weber CF, King GM. Volcanic soils as sources of novel CO-Oxidizing Paraburkholderia and Burkholderia: Paraburkholderia hiiakae sp. nov., Paraburkholderia metrosideri sp. nov., Paraburkholderia paradisi sp. nov., Paraburkholderia peleae sp. nov., and Burkholderia alpina sp. nov. a member of the Burkholderia cepacia complex. Front Microbiol 2017;8:207 [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003681
Loading
/content/journal/ijsem/10.1099/ijsem.0.003681
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most Cited This Month

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