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Volume 67, Issue 2

gen. nov., sp. nov., a bacterium within the family , isolated from contaminated soil, capable of degrading aromatic compounds Free

Abstract

A bacterial strain designated Ca6 was isolated from polycyclic aromatic hydrocarbon (PAH)-contaminated soil from the site of a former manufactured gas plant in Charlotte, NC, USA, and linked phylogenetically to the family of the class . Its 16S rRNA gene sequence was highly similar to globally distributed environmental sequences, including those previously designated ‘Pyrene Group 1’ demonstrated to grow on the PAHs phenanthrene and pyrene by stable-isotope probing. The most closely related described relative was strain sk43H (93.6 % 16S rRNA gene sequence identity). In addition to a limited number of organic acids, Ca6 was capable of growth on the monoaromatic compounds benzene and toluene, and the azaarene carbazole, as sole sources of carbon and energy. Growth on the PAHs phenanthrene and pyrene was also confirmed. Optimal growth was observed aerobically under mesophilic temperature, neutral pH and low salinity conditions. Major fatty acids present included summed feature 3 (Cω7 or Cω6) and C. The DNA G+C content of the single chromosome was 55.14  mol% as determined by complete genome sequencing. Due to its distinct genetic and physiological properties, strain Ca6 is proposed as a member of a novel genus and species within the family , for which the name gen. nov., sp. nov. is proposed. The type strain of the species is Ca6 (=ATCC TSD-59=DSM 103039).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): aromatics , biodegradation , polycyclic aromatic hydrocarbons and Rhodocyclaceae
© 2017 IUMS

Erratum

An erratum has been published for this content:
Erratum: gen. nov., sp. nov., a bacterium within the family , isolated from contaminated soil, capable of degrading aromatic compounds
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2017-02-01
2024-04-24
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References

  1. Singleton DR, Sangaiah R, Gold A, Ball LM, Aitken MD. Identification and quantification of uncultivated Proteobacteria associated with pyrene degradation in a bioreactor treating PAH-contaminated soil. Environ Microbiol 2006; 8:1736–1745 [View Article]
     [Google Scholar]
  2. Singleton DR, Hunt M, Powell SN, Frontera-Suau R, Aitken MD. Stable-isotope probing with multiple growth substrates to determine substrate specificity of uncultivated bacteria. J Microbiol Methods 2007; 69:180–187 [View Article][PubMed]
     [Google Scholar]
  3. Singleton DR, Hu J, Aitken MD. Heterologous expression of polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenase genes from a novel pyrene-degrading betaproteobacterium. Appl Environ Microbiol 2012; 78:3552–3559 [View Article][PubMed]
     [Google Scholar]
  4. Martin F, Torelli S, Le Paslier D, Barbance A, Martin-Laurent F et al. Betaproteobacteria dominance and diversity shifts in the bacterial community of a PAH-contaminated soil exposed to phenanthrene. Environ Pollut 2012; 162:345–353 [View Article][PubMed]
     [Google Scholar]
  5. Regonne RK, Martin F, Mbawala A, Ngassoum MB, Jouanneau Y. Identification of soil bacteria able to degrade phenanthrene bound to a hydrophobic sorbent in situ. Environ Pollut 2013; 180:145–151 [View Article][PubMed]
     [Google Scholar]
  6. Humphries JA, Ashe AM, Smiley JA, Johnston CG. Microbial community structure and trichloroethylene degradation in groundwater. Can J Microbiol 2005; 51:433–439 [View Article][PubMed]
     [Google Scholar]
  7. He Z, Xie X, Xiao S, Liu J, Qiu G. Microbial diversity of mine water at Zhong Tiaoshan copper mine, China. J Basic Microbiol 2007; 47:485–495 [View Article][PubMed]
     [Google Scholar]
  8. Kim JS, Crowley DE. Microbial diversity in natural asphalts of the Rancho La Brea Tar Pits. Appl Environ Microbiol 2007; 73:4579–4591 [View Article][PubMed]
     [Google Scholar]
  9. Tang YQ, Li Y, Zhao JY, Chi CQ, Huang LX et al. Microbial communities in long-term, water-flooded petroleum reservoirs with different in situ temperatures in the Huabei Oilfield, China. PLoS One 2012; 7:e33535 [View Article][PubMed]
     [Google Scholar]
  10. Gihring TM, Moser DP, Lin LH, Davidson M, Onstott TC et al. The distribution of microbial taxa in the subsurface water of the Kalahari shield, South Africa. Geomicrobiol J 2006; 23:415–430 [View Article]
     [Google Scholar]
  11. Zhang L, Gao G, Tang X, Shao K. Impacts of different salinities on bacterial biofilm communities in fresh water. Can J Microbiol 2014; 60:319–326 [View Article][PubMed]
     [Google Scholar]
  12. Richardson SD, Lebron BL, Miller CT, Aitken MD. Recovery of phenanthrene-degrading bacteria after simulated in situ persulfate oxidation in contaminated soil. Environ Sci Technol 2011; 45:719–725 [View Article][PubMed]
     [Google Scholar]
  13. Kojima H, Fukui M. Sulfuritalea hydrogenivorans gen. nov., sp. nov., a facultative autotroph isolated from a freshwater lake. Int J Syst Evol Microbiol 2011; 61:1651–1655 [View Article][PubMed]
     [Google Scholar]
  14. Singleton DR, Dickey AN, Scholl EH, Wright FA, Aitken MD. Complete genome sequence of a novel bacterium within the family Rhodocyclaceae that degrades polycyclic aromatic hydrocarbons. Genome Announc 2015; 3:e00251-15 [View Article][PubMed]
     [Google Scholar]
  15. Kasana RC, Salwan R, Dhar H, Dutt S, Gulati A. A rapid and easy method for the detection of microbial cellulases on agar plates using gram's iodine. Curr Microbiol 2008; 57:503–507 [View Article][PubMed]
     [Google Scholar]
  16. Ensley BD, Ratzkin BJ, Osslund TD, Simon MJ, Wackett LP et al. Expression of naphthalene oxidation genes in Escherichia coli results in the biosynthesis of indigo. Science 1983; 222:167–169 [View Article][PubMed]
     [Google Scholar]
  17. Schell MA. Cloning and expression in Escherichia coli of the naphthalene degradation genes from plasmid NAH7. J Bacteriol 1983; 153:822–829[PubMed]
     [Google Scholar]
  18. Singleton DR, Ramirez LG, Aitken MD. Characterization of a polycyclic aromatic hydrocarbon degradation gene cluster in a phenanthrene-degrading Acidovorax strain. Appl Environ Microbiol 2009; 75:2613–2620 [View Article][PubMed]
     [Google Scholar]
  19. Ishii S, Ashida N, Otsuka S, Senoo K. Isolation of oligotrophic denitrifiers carrying previously uncharacterized functional gene sequences. Appl Environ Microbiol 2011; 77:338–342 [View Article][PubMed]
     [Google Scholar]
  20. Weelink SA, van Doesburg W, Saia FT, Rijpstra WI, Röling WF et al. A strictly anaerobic betaproteobacterium Georgfuchsia toluolica gen. nov., sp. nov. degrades aromatic compounds with Fe(III), Mn(IV) or nitrate as an electron acceptor. FEMS Microbiol Ecol 2009; 70:575–585 [View Article][PubMed]
     [Google Scholar]
  21. Kojima H, Fukui M. Sulfurisoma sediminicola gen. nov., sp. nov., a facultative autotroph isolated from a freshwater lake. Int J Syst Evol Microbiol 2014; 64:1587–1592 [View Article][PubMed]
     [Google Scholar]
  22. Fahrbach M, Kuever J, Meinke R, Kämpfer P, Hollender J. Denitratisoma oestradiolicum gen. nov., sp. nov., a 17β-oestradiol-degrading, denitrifying betaproteobacterium. Int J Syst Evol Microbiol 2006; 56:1547–1552 [View Article][PubMed]
     [Google Scholar]
  23. Tarlera S, Denner EB. Sterolibacterium denitrificans gen. nov., sp. nov., a novel cholesterol-oxidizing, denitrifying member of the β-Proteobacteria. Int J Syst Evol Microbiol 2003; 53:1085–1091 [View Article][PubMed]
     [Google Scholar]
  24. 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 [View Article][PubMed]
     [Google Scholar]
  25. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article][PubMed]
     [Google Scholar]
  26. 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][PubMed]
     [Google Scholar]
  27. Cummings MP, Hancock JM, Zvelebil MJ. PAUP* (phylogenetic analysis using parsimony (and other methods). In Dictionary of Bioinformatics and Computational Biology John Wiley & Sons, Ltd; 2004
     [Google Scholar]
  28. Kalyuzhnaya MG, De Marco P, Bowerman S, Pacheco CC, Lara JC et al. Methyloversatilis universalis gen. nov., sp. nov., a novel taxon within the Betaproteobacteria represented by three methylotrophic isolates. Int J Syst Evol Microbiol 2006; 56:2517–2522 [View Article][PubMed]
     [Google Scholar]
  29. Smalley NE, Taipale S, De Marco P, Doronina NV, Kyrpides N et al. Functional and genomic diversity of methylotrophic Rhodocyclaceae: description of Methyloversatilis discipulorum sp. nov. Int J Syst Evol Microbiol 2015; 65:2227–2233 [View Article][PubMed]
     [Google Scholar]
  30. Doronina NV, Kaparullina EN, Trotsenko YA. Methyloversatilis thermotolerans sp. nov., a novel thermotolerant facultative methylotroph isolated from a hot spring. Int J Syst Evol Microbiol 2014; 64:158–164 [View Article][PubMed]
     [Google Scholar]
  31. Hiraishi A, Hoshino Y, Satoh T. Rhodoferax fermentans gen. nov., sp. nov., a phototrophic purple nonsulfur bacterium previously referred to as the 'Rhodocyclus gelatinosus-like' group. Arch Microbiol 1991; 155:330–336 [View Article]
     [Google Scholar]
  32. Pfennig N. Rhodocyclus purpureus gen. nov. and sp. nov., a ring-shaped, vitamin B12-requiring member of the family Rhodospirillaceae. Int J Syst Evol Microbiol 1978; 28:283–288 [View Article]
     [Google Scholar]
  33. Imhoff JF. Genus I. Rhodocyclus Pfennig 1978, 285AL. In Brenner DJ, Staley JT. (editors) Bergey's Manual of Systematic Bacteriology, The Proteobacteria Part B, the Betaproteobacteria vol. 2 New York: Springer; 2005
     [Google Scholar]
  34. Pfennig N. Rhodospirillum tenue sp. n., a new species of the purple nonsulfur bacteria. J Bacteriol 1969; 99:619–620[PubMed]
     [Google Scholar]
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Rugosibacter aromaticivorans gen. nov., sp. nov., a bacterium within the family Rhodocyclaceae, isolated from contaminated soil, capable of degrading aromatic compounds
Int J Syst Evol Microbiol 67, 311 (2017); https://doi.org/10.1099/ijsem.0.001622
/content/journal/ijsem/10.1099/ijsem.0.001622
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