Betaproteobacteria dominance and diversity shifts in the bacterial community of a PAH-contaminated soil exposed to phenanthrene

Environmental Pollution

Volumn 162, Issue , 2012, Pages 345-353

  Martin, Florence ^a,b   Torelli, Stéphane ^a,b   Le Paslier, Denis ^c,d,e   Barbance, Agns ^c,d,e   Martin Laurent, Fabrice ^f   Bru, David ^f   Geremia, Roberto ^g   Blake, Gérard ^h   Jouanneau, Yves ^a,b  

^a CEA GRENOBLE   (France)

^b VERIMAG   (France)

^c DIF   (France)

^d CNRS   (France)

^e UNIVERSITÉ D EVRY VAL D ESSONNE   (France)

^f UNIVERSITÉ DE BOURGOGNE   (France)

^g UNIVERSITÉ JOSEPH FOURIER   (France)

^h UNIVERSITÉ DE SAVOIE   (France)

Author keywords

16S rRNA sequences; Betaproteobacteria; PAH degradation; Phenanthrene; Stable isotope probing

Indexed keywords

16S RRNA SEQUENCES; BACTERIAL COMMUNITY; BACTERIAL DIVERSITY; BETAPROTEOBACTERIA; BIODEGRADATION IN SOIL; CONSTRUCTED WETLANDS; PAH DEGRADERS; PHENANTHRENE; PHENANTHRENE MINERALIZATION; QUANTITATIVE PCR; ROAD RUNOFF; STABLE-ISOTOPE PROBING;

BACTERIA; BIODEGRADATION; DEGRADATION; DNA SEQUENCES; ISOTOPES; POLYMERASE CHAIN REACTION; RNA; SOIL POLLUTION; SOILS; WETLANDS;

ANTHRACENE;

PHENANTHRENE; RNA 16S; RUNOFF;

BACTERIUM; BIODEGRADATION; DNA; MICROCOSM; MINERALIZATION; PAH; PHENANTHRENE; RNA; SOIL POLLUTION; STABLE ISOTOPE;

ACIDOVORAX; ARTICLE; BETAPROTEOBACTERIA; BIODEGRADATION; CONTROLLED STUDY; ENVIRONMENTAL EXPOSURE; HYDROGENOPHAGA; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; MICROCOSM; MINERALIZATION; NONHUMAN; NUCLEOTIDE SEQUENCE; POLLUTION MONITORING; PREVALENCE; REAL TIME POLYMERASE CHAIN REACTION; RHODOCYCLACEAE; RHODOFERAX; RNA SEQUENCE; SEQUENCE ANALYSIS; SOIL POLLUTION; SPECIES DOMINANCE; UNINDEXED SEQUENCE; WETLAND;

BETAPROTEOBACTERIA; BIODEGRADATION, ENVIRONMENTAL; BIODIVERSITY; MOLECULAR SEQUENCE DATA; PHENANTHRENES; PHYLOGENY; POLYCYCLIC HYDROCARBONS, AROMATIC; SOIL MICROBIOLOGY; SOIL POLLUTANTS;

ACIDOVORAX; BACTERIA (MICROORGANISMS); BETAPROTEOBACTERIA; HYDROGENOPHAGA; RHODOCYCLACEAE; RHODOFERAX; UNIDENTIFIED BACTERIUM;

EID: 83755188011     PISSN: 02697491     EISSN: 18736424     Source Type: Journal    
DOI: 10.1016/j.envpol.2011.11.032     Document Type: Article

References (37)

1. J. Alonso-Gutierrez, A. Figueras, J. Albaiges, N. Jimenez, M. Vinas, A.M. Solanas, and B. Novoa Bacterial communities from shoreline environments (Costa da Morte, Northwestern Spain) affected by the Prestige oil spill Appl. Environ. Microbiol. 75 2009 3407 3418
2. F.M. Ausubel, R. Brent, R. Kingston, D.D. Moore, J.G. Seidman, J.A. Smith, and K. Struhl Short Protocols in Molecular Biology 1999 Academic press
3. A.A. Bodour, J.-M. Wang, M.L. Brusseau, and R.M. Maier Temporal change in culturable phenanthrene degraders in response to long-term exposure to phenanthrene in a soil column system Environ. Microbiol. 5 2003 888 895 (Pubitemid 37181559)
4. A. Cebron, B. Louvel, P. Faure, C. France-Lanord, Y. Chen, J.C. Murrell, and C. Leyval Root exudates modify bacterial diversity of phenanthrene degraders in PAH-polluted soil but not phenanthrene degradation rates Environ. Microbiol. 13 2011 722 736
5. J.R. Cole, K. Konstantinidis, R.J. Farris, and J.M. Tiedje Microbial diversity and phylogeny: extending from rRNAs to genomes W.T. Liu, J.K. Jansson, Environmental Molecular Microbiology 2010 Caister Academic Press 1 19
6. J.R. Cole, Q. Wang, E. Cardenas, J. Fish, B. Chai, R.J. Farris, A.S. Kulam-Syed-Mohideen, D.M. McGarrell, T. Marsh, G.M. Garrity, and J.M. Tiedje The ribosomal database project: improved alignments and new tools for rRNA analysis Nucleic Acids Res. 37 2009 D141 D145
7. S. Demaneche, C. Meyer, J. Micoud, M. Louwagie, J.C. Willison, and Y. Jouanneau Identification and functional analysis of two aromatic-ring- hydroxylating dioxygenases from a Sphingomonas strain that degrades various polycyclic aromatic hydrocarbons Appl. Environ. Microbiol. 70 2004 6714 6725 (Pubitemid 39518583)
8. E. Doyle, L. Muckian, A.M. Hickey, and N. Clipson Microbial PAH degradation Adv. Appl. Microbiol. 65 2008 27 66
9. M.G. Dumont, and J.C. Murrell Stable isotope probing - linking microbial identity to function Nat. Rev. Microbiol. 3 2005 499 504 (Pubitemid 40716176)
10. W.E. Huang, A. Ferguson, A.C. Singer, K. Lawson, I.P. Thompson, R.M. Kalin, M.J. Larkin, M.J. Bailey, and A.S. Whiteley Resolving genetic functions within microbial populations: In situ analyses using rRNA and mRNA stable isotope probing coupled with single-cell Raman-fluorescence in situ hybridization Appl. Environ. Microbiol. 75 2009 234 241
11. C.O. Jeon, W. Park, P. Padmanabhan, C.J. DeRito, R. Snape, and E.L. Madsen Discovery of a bacterium, with distinctive dioxygenase, that is responsible for in situ biodegradation in contaminated sediment Proc. Natl. Acad. Sci. USA 100 2003 13591 13596 (Pubitemid 37444785)
12. A.R. Johnsen, L.Y. Wick, and H. Harms Principles of microbial PAH-degradation in soil Environ. Pollut. 133 2005 71 84 (Pubitemid 41569171)
13. M.D. Jones, D.R. Singleton, W. Sun, and M.D. Aitken Multiple DNA extractions coupled with stable-isotope probing of anthracene-degrading bacteria in contaminated soil Appl. Environ. Microbiol. 77 2011 2984 2991
14. S. Krivobok, S. Kuony, C. Meyer, M. Louwagie, J.C. Willison, and Y. Jouanneau Identification of pyrene-induced proteins in Mycobacterium sp. strain 6PY1: evidence for two ring-hydroxylating dioxygenases J. Bacteriol. 185 2003 3828 3841 (Pubitemid 36735934)
15. N.M. Leys, A. Ryngaert, L. Bastiaens, P. Wattiau, E.M. Top, W. Verstraete, and D. Springael Occurrence and community composition of fast-growing Mycobacterium in soils contaminated with polycyclic aromatic hydrocarbons FEMS Microbiol. Ecol. 51 2005 375 388 (Pubitemid 40128207)
16. N.M.E.J. Leys, A. Ryngaert, L. Bastiaens, W. Verstraete, E.M. Top, and D. Springael Occurrence and phylogenetic diversity of Sphingomonas strains in soils contaminated with polycyclic aromatic hydrocarbons Appl. Environ. Microbiol. 70 2004 1944 1955 (Pubitemid 38500491)
17. T. Lueders, M. Manefield, and M.W. Friedrich Enhanced sensitivity of DNA- and rRNA-based stable isotope probing by fractionation and quantitative analysis of isopycnic centrifugation gradients Environ. Microbiol. 6 2004 73 78 (Pubitemid 38162029)
18. M. Manefield, A.S. Whiteley, R.I. Griffiths, and M.J. Bailey RNA stable isotope probing, a novel means of linking microbial community function to Phylogeny Appl. Environ. Microbiol. 68 2002 5367 5373 (Pubitemid 35265669)
19. C. Martineau, L.G. Whyte, and C.W. Greer Development of a SYBR safe (TM) technique for the sensitive detection of DNA in cesium chloride density gradients for stable isotope probing assays J. Microbiol. Methods 73 2008 199 202
20. J. Oksanen, F. Guillaume Blanchet, R. Kindt, P. Legendre, R.B. O'Hara, G.L. Simpson, P. Solymos, M. Henry, H. Stevens, and H. Wagner Vegan: Community Ecology Package. R Package Version 1.17-6 2011 http://CRAN.R-project.org/ package=vegan
21. R.H. Peng, A.S. Xiong, Y. Xue, X.Y. Fu, F. Gao, W. Zhao, Y.S. Tian, and Q.H. Yao Microbial biodegradation of polyaromatic hydrocarbons FEMS Microbiol. Rev. 32 2008 927 955
22. L. Philippot, D. Tscherko, D. Bru, and E. Kandeler Distribution of high bacterial taxa across the chronosequence of two alpine glacier forelands Microb. Ecol. 61 2010 303 312
23. O. Pinyakong, H. Habe, and T. Omori The unique aromatic catabolic genes in sphingomonads degrading polycyclic aromatic hydrocarbons (PAHs) J. Gen. Appl. Microbiol. 49 2003 1 19 (Pubitemid 36527148)
24. G.M. Pumphrey, and E.L. Madsen Field-based stable isotope probing reveals the identities of benzoic acid-metabolizing microorganisms and their in situ growth in agricultural soil Appl. Environ. Microbiol. 74 2008 4111 4118 (Pubitemid 351962437)
25. R Development Core Team R: A language and environent for statistical computing R. F. f. S Computing 2009 Vienna, Austria
26. R. Rabus, and F. Widdel Anaerobic degradation of ethylbenzene and other aromatic-hydrocarbons by new denitrifying bacteria Arch. Microbiol. 163 1995 96 103
27. S. Radajewski, P. Ineson, N.R. Parekh, and J.C. Murrell Stable-isotope probing as a tool in microbial ecology Nature 403 2000 646 649 (Pubitemid 30104002)
28. L.F.W. Roesch, R.R. Fulthorpe, A. Riva, G. Casella, A.K.M. Hadwin, A.D. Kent, S.H. Daroub, F.A.O. Camargo, W.G. Farmerie, and E.W. Triplett Pyrosequencing enumerates and contrasts soil microbial diversity ISME J. 1 2007 283 290 (Pubitemid 47227850)
29. A.-E. Rotaru, C. Probian, H. Wilkes, and J. Harder Highly enriched Betaproteobacteria growing anaerobically with p-xylene and nitrate FEMS Microbiol. Ecol. 71 2010 460 468
30. P.D. Schloss, S.L. Westcott, T. Ryabin, J.R. Hall, M. Hartmann, E.B. Hollister, R.A. Lesniewski, B.B. Oakley, D.H. Parks, C.J. Robinson, J.W. Sahl, B. Stres, G.G. Thallinger, D.J. Van Horn, and C.F. Weber Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities Appl. Environ. Microbiol. 75 2009 7537 7541
31. D.R. Singleton, S.N. Powell, R. Sangaiah, A. Gold, L.M. Ball, and M.D. Aitken Stable-isotope probing of bacteria capable of degrading salicylate, naphthalene, or phenanthrene in a bioreactor treating contaminated soil Appl. Environ. Microbiol. 71 2005 1202 1209 (Pubitemid 40396656)
32. D.R. Singleton, L.G. Ramirez, and M.D. Aitken Characterization of a polycyclic aromatic hydrocarbon degradation gene cluster in a phenanthrene-degrading Acidovorax strain Appl. Environ. Microbiol. 75 2009 2613 2620
33. D.R. Singleton, R. Sangaiah, A. Gold, L.M. Ball, and M.D. Aitken Identification and quantification of uncultivated Proteobacteria associated with pyrene degradation in a bioreactor treating PAH-contaminated soil Environ. Microbiol. 8 2006 1736 1745 (Pubitemid 44326465)
34. K. Sueoka, H. Satoh, M. Onuki, and T. Mino Microorganisms involved in anaerobic phenol degradation in the treatment of synthetic coke-oven wastewater detected by RNA stable-isotope probing FEMS Microbiol. Lett. 291 2009 169 174
35. L.P. Wackett Stable isotope probing in biodegradation research Trends Biotechnol. 22 2004 153 154 (Pubitemid 38368169)
36. J.C. Willison Isolation and characterization of a novel sphingomonad capable of growth with chrysene as sole carbon and energy source FEMS Microbiol. Lett. 241 2004 143 150 (Pubitemid 39642988)
37. L. Zinger, J. Gury, F. Giraud, S. Krivobok, L. Gielly, P. Taberlet, and R.A. Geremia Improvements of polymerase chain reaction and capillary electrophoresis single-strand conformation polymorphism methods in microbial ecology: toward a high-throughput method for microbial diversity studies in soil Microb. Ecol. 54 2007 203 216 (Pubitemid 47197895)