1887

Abstract

Strain AH-1, a Gram-negative, aerobic, non-spore-forming, motile, rod-shaped bacterium, was isolated from tetrabromobisphenol A-contaminated soil in China. The taxonomic position was investigated using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain AH-1 was a member of the genus Shinella and showed the highest sequence similarity to Shinella fusca DC-196 (97.7 %), Shinella granuli Ch06 (97.3 %), Shinella daejeonensis MJ02 (97.1 %) and Shinella yambaruensis MS4 (96.8 %), and lower (<96.7 %) sequence similarity to other known Shinella species. Chemotaxonomic analysis revealed that strain AH-1 possessed Q-10 as the major isoprenoid quinone; and summed feature 8 (C18 : 1ω6c/C18 : 1ω7c), C16 : 0, C12 : 0 aldehyde, C18 : 0, C19 : 0 cyclo ω8c and C18 : 0 3-OH were the predominant fatty acids. Strain AH-1 showed low DNA–DNA relatedness to S. fusca DC-196 (28.6±5.7 %), S. granuli Ch06 (43.7±3.8 %) and S. daejeonensis MJ02 (48.1±2.6 %). The DNA G+C content was 68.2 mol%. Based on the phylogenetic and phenotypic characteristics, chemotaxonomic data and DNA–DNA hybridization, strain AH-1 is considered a novel species of the genus Shinella , for which the name Shinella pollutisoli sp. nov. (type strain AH-1=KCTC 52677=CCTCC AB 2017242) is proposed.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.002883
2018-06-27
2024-03-29
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/68/8/2602.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.002883&mimeType=html&fmt=ahah

References

  1. An DS, Im WT, Yang HC, Lee ST. Shinella granuli gen. nov., sp. nov., and proposal of the reclassification of Zoogloea ramigera ATCC 19623 as Shinella zoogloeoides sp. nov. Int J Syst Evol Microbiol 2006; 56:443–448 [View Article][PubMed]
    [Google Scholar]
  2. Lin DX, Wang ET, Tang H, Han TX, He YR et al. Shinella kummerowiae sp. nov., a symbiotic bacterium isolated from root nodules of the herbal legume Kummerowia stipulacea. Int J Syst Evol Microbiol 2008; 58:1409–1413 [View Article][PubMed]
    [Google Scholar]
  3. Matsui T, Shinzato N, Tamaki H, Muramatsu M, Hanada S. Shinella yambaruensis sp. nov., a 3-methyl-sulfolane-assimilating bacterium isolated from soil. Int J Syst Evol Microbiol 2009; 59:536–539 [View Article][PubMed]
    [Google Scholar]
  4. Vaz-Moreira I, Faria C, Lopes AR, Svensson LA, Moore ER et al. Shinella fusca sp. nov., isolated from domestic waste compost. Int J Syst Evol Microbiol 2010; 60:144–148 [View Article][PubMed]
    [Google Scholar]
  5. Lee M, Woo SG, Ten LN. Shinella daejeonensis sp. nov., a nitrate-reducing bacterium isolated from sludge of a leachate treatment plant. Int J Syst Evol Microbiol 2011; 61:2123–2128 [View Article][PubMed]
    [Google Scholar]
  6. Subhash Y, Lee SS. Shinella curvata sp. nov., isolated from hydrocarbon-contaminated desert sands. Int J Syst Evol Microbiol 2016; 66:3929–3934 [View Article][PubMed]
    [Google Scholar]
  7. Li R, Zheng J, Wang R, Song Y, Chen Q et al. Biochemical degradation pathway of dimethoate by Paracoccus sp. Lgjj-3 isolated from treatment wastewater. Int Biodeter Biodegr 2010; 64:51–57 [View Article]
    [Google Scholar]
  8. Buck JD. Nonstaining (KOH) method for determination of gram reactions of marine bacteria. Appl Environ Microbiol 1982; 44:992–993[PubMed]
    [Google Scholar]
  9. Bernardet JF, Nakagawa Y, Holmes B. Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes 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]
  10. McCarthy AJ, Cross T. A taxonomic study of Thermomonospora and other monosporic Actinomycetes. Microbiology 1984; 130:5–25 [View Article]
    [Google Scholar]
  11. Nielsen P, Fritze D, Priest FG. Phenetic diversity of alkaliphilic Bacillus strains: proposal for nine new species. Microbiology 1995; 141:1745–1761 [View Article]
    [Google Scholar]
  12. Lane DL. 16S/23S rRNA sequencing. In Stackebrandt ER, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics Chichester, UK: Wiley; 1991 pp. 115–175
    [Google Scholar]
  13. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012; 62:716–721 [View Article][PubMed]
    [Google Scholar]
  14. 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]
  15. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 1999; 41:95–98
    [Google Scholar]
  16. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article][PubMed]
    [Google Scholar]
  17. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  18. 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 [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. Mandel M, Marmur J. Use of ultraviolet absorbance-temperature profile for determining the guanine plus cytosine content of DNA. Methods Enzymol 1968; 12:195–206
    [Google Scholar]
  21. 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 [View Article]
    [Google Scholar]
  22. Wayne LG. International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 1987; 37:463–464
    [Google Scholar]
  23. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  24. Tindall BJ. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990; 13:128–130 [View Article]
    [Google Scholar]
  25. Tindall BJ. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 1990; 66:199–202 [View Article]
    [Google Scholar]
  26. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in Actinomycetes and Corynebacteria. J Gen Microbiol 1977; 100:221–230 [View Article][PubMed]
    [Google Scholar]
  27. Tamaoka J, Katayama-Fujimura Y, Kuraishi H. Analysis of bacterial menaquinone mixtures by high-performance liquid chromatography. J Appl Bacteriol 1983; 54:31–36 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.002883
Loading
/content/journal/ijsem/10.1099/ijsem.0.002883
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF
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