1887

Abstract

Cells of bacterial strains 4 G-K06 and 4MSK11, isolated from soil samples collected from monsoon evergreen broad-leaved forest of the Dinghushan Mountain (112° 31′ E 23° 10′ N), Guangdong Province, PR China, were Gram-stain-negative, aerobic, non-spore-forming, non-motile and rod-shaped. Strain 4 G-K06 grew at 10–37 °C, pH 3.5–7.5 and 0–3.5 % (w/v) NaCl; while 4MSK11 grew at 4–42 °C, pH 3.5–7.5 and 0–2.5 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed strain 4 G-K06 formed a clade with Dyella flagellata 4 M-K16, Dyella acidisoli 4M-Z03, Dyella humi DHG40 and Dyella nitratireducens DHG59, while strain 4MSK11 formed a clade with Dyella caseinilytica DHOB09 and Dyella mobilis DHON07, both within the genus Dyella . The result of the partial atpD, gyrB and lepA gene sequence analysis supported the conclusion based on 16S rRNA gene sequence analysis, which showed that these two strains represent two novel species of Dyella . The average nucleotide identity and digital DNA–DNA hybridization value for the whole genomes were 75.0–79.0 and 20.3–22.6 % between strains 4 G-K06, 4MSK11 and those described Dyella species with genome sequences; while the DNA–DNA hybridization rates between strains 4 G-K06, 4MSK11 and closely related Dyella species (without genome sequence) were 29.5–41.8 %. The major cellular fatty acids of these two strains were iso-C15 : 0, iso-C16 : 0 and iso-C17 : 1 ω9c, while the major polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and several unidentified phospholipids and aminophospholipids. The only ubiquinone of these two strains was ubiquinone-8. The DNA G+C contents of 4 G-K06 and 4MSK11 were 60.4 and 61.3 mol%, respectively. On the basis of the evidence presented here, strains 4 G-K06 and 4MSK11 represent two novel species of the genus Dyella , for which the names Dyella monticola sp. nov. (type strain 4 G-K06=LMG 30268=GDMCC 1.1188) and Dyella psychrodurans sp. nov. (type strain 4MSK11=KCTC 62280=GDMCC 1.1185) are proposed.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003259
2019-01-31
2019-10-21
Loading full text...

Full text loading...

References

  1. 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]
  2. Xie CH, Yokota A. Dyella japonica gen. nov., sp. nov., a gamma-proteobacterium isolated from soil. Int J Syst Evol Microbiol 2005;55:753–756 [CrossRef][PubMed]
    [Google Scholar]
  3. An DS, Im WT, Yang HC, Yang DC, Lee ST. Dyella koreensis sp. nov., a beta-glucosidase-producing bacterium. Int J Syst Evol Microbiol 2005;55:1625–1628 [CrossRef][PubMed]
    [Google Scholar]
  4. Jung HM, Ten LN, Kim KH, An DS, Im WT et al. Dyella ginsengisoli sp. nov., isolated from soil of a ginseng field in South Korea. Int J Syst Evol Microbiol 2009;59:460–465 [CrossRef][PubMed]
    [Google Scholar]
  5. Lee DW, Lee SD. Dyella marensis sp. nov., isolated from cliff soil. Int J Syst Evol Microbiol 2009;59:1397–1400 [CrossRef][PubMed]
    [Google Scholar]
  6. 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]
  7. Anandham R, Kwon SW, Indira Gandhi P, Kim SJ, Weon HY 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 [CrossRef][PubMed]
    [Google Scholar]
  8. Son HM, Yang JE, Yi EJ, Park Y, Won KH et al. Dyella kyungheensis sp. nov., isolated from soil of a cornus fruit field. Int J Syst Evol Microbiol 2013;63:3807–3811 [CrossRef][PubMed]
    [Google Scholar]
  9. 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]
  10. Kim MS, Hyun DW, Kim JY, Kim S, Bae JW et al. Dyella jejuensis sp. nov., isolated from soil of Hallasan Mountain in Jeju Island. J Microbiol 2014;52:373–377 [CrossRef][PubMed]
    [Google Scholar]
  11. 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]
  12. 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]
  13. Tang L, Chen MH, Nie XC, Ma MR, Qiu LH. Dyella lipolytica sp. nov., a lipolytic bacterium isolated from lower subtropical forest soil. Int J Syst Evol Microbiol 2017;67:1235–1240 [CrossRef][PubMed]
    [Google Scholar]
  14. 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]
  15. Chaudhary DK, Kim J. Dyella agri sp. nov., isolated from reclaimed grassland soil. Int J Syst Evol Microbiol 2017;67:4246–4252 [CrossRef][PubMed]
    [Google Scholar]
  16. 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. Accept
    [Google Scholar]
  17. Gerhardt P. Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994
    [Google Scholar]
  18. Benson HJ. Microbiological Applications: A Laboratory Manual in General Microbiology, 4th ed. Dubuque, Iowa: W.C. Brown; 1985; complete version
    [Google Scholar]
  19. Atlas RM. Handbook of Media for Environmental Microbiology, 2nd ed. Boca Raton: Taylor & Francis; 2005
    [Google Scholar]
  20. 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]
  21. Stackebrandt E, Goodfellow M. Nucleic Acid Techniques in Bacterial Systematics Chichester: Wiley; 1991
    [Google Scholar]
  22. 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]
  23. 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]
  24. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981;17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  25. 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]
  26. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39:783–791 [CrossRef][PubMed]
    [Google Scholar]
  27. 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]
  28. 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]
  29. 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]
  30. 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]
  31. 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]
  32. 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]
  33. 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]
  34. 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]
  35. 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]
  36. 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]
  37. 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]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003259
Loading
/content/journal/ijsem/10.1099/ijsem.0.003259
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