title: Changes in bacterial populations and in biphenyl dioxygenase gene diversity in a polychlorinated biphenyl-polluted soil after introduction of willow trees for rhizoremediation.
abstract: The aim of this study was to analyze the structural and functional changes occurring in a polychlorinated-biphenyl (PCB)-contaminated soil ecosystem after the introduction of a suitable host plant for rhizoremediation (Salix viminalis). We have studied the populations and phylogenetic distribution of key bacterial groups (Alpha- and Betaproteobacteria, Acidobacteria, and Actinobacteria) and the genes encoding iron-sulfur protein alpha (ISPalpha) subunits of the toluene/biphenyl dioxygenases in soil and rhizosphere by screening gene libraries using temperature gradient gel electrophoresis. The results, based on the analysis of 415 clones grouped into 133 operational taxonomic units that were sequence analyzed (>128 kbp), show that the rhizospheric bacterial community which evolved from the native soil community during the development of the root system was distinct from the soil community for all groups studied except for the Actinobacteria. Proteobacteria were enriched in the rhizosphere and dominated both in rhizosphere and soil. There was a higher than expected abundance of Betaproteobacteria in the native and in the planted PCB-polluted soil. The ISPalpha sequences retrieved indicate a high degree of catabolic and phylogenetic diversity. Many sequences clustered with biphenyl dioxygenase sequences from gram-negative bacteria. A distinct cluster that was composed of sequences from this study, some previously described environmental sequences, and a putative ISPalpha from Sphingomonas wittichii RW1 seems to contain greater diversity than the presently recognized toluene/biphenyl dioxygenase subfamily. Moreover, the rhizosphere selected for two ISPalpha sequences that accounted for almost 60% of the gene library and were very similar to sequences harbored by Pseudomonas species.
authors: Departamento de Biología, c/Darwin 2, Universidad Autónoma de Madrid, 28049 Madrid, Spain.
authors: Daniel Aguirre
authors: DA
authors: de Cárcer
authors: Marta
authors: M
authors: Martín
authors: Ulrich
authors: U
authors: Karlson
authors: Rafael
authors: R
authors: Rivilla
mesh_terms: D001419:Bacteria / Q000235:genetics / Q000254:growth & development*; D001673:Biodegradation, Environmental; D004269:DNA, Bacterial / Q000032:analysis / Q000302:isolation & purification; D049308:Dioxygenases / Q000235:genetics* / Q000378:metabolism; D017753:Ecosystem; D004787:Environmental Pollution; D015723:Gene Library; D005798:Genes, Bacterial; D014644:Genetic Variation; D010802:Phylogeny; D011078:Polychlorinated Biphenyls / Q000378:metabolism*; D032108:Salix; D012988:Soil Microbiology; D012989:Soil Pollutants; D014197:Trees
chemical_list: D004269:DNA, Bacterial; D012989:Soil Pollutants; D011078:Polychlorinated Biphenyls; D049308:Dioxygenases
references: Annu Rev Phytopathol. 2001;39:461-90
references: 11701873
references: Environ Microbiol. 2005 Jan;7(1):140-6
references: 15643944
references: Appl Environ Microbiol. 2004 Sep;70(9):5485-92
references: 15345436
references: Appl Environ Microbiol. 1997 Aug;63(8):3233-41
references: 9251210
references: Anal Biochem. 2002 Jan 1;300(1):101-3
references: 11743698
references: Appl Environ Microbiol. 1998 Mar;64(3):871-9
references: 9501427
references: Environ Microbiol. 2002 Nov;4(11):654-66
references: 12460273
references: Adv Microb Physiol. 1997;38:47-84
references: 8922118
references: Nucleic Acids Res. 2005 Jan 1;33(Database issue):D294-6
references: 15608200
references: Environ Microbiol. 2000 Dec;2(6):644-53
references: 11214797
references: Annu Rev Microbiol. 2002;56:211-36
references: 12142496
references: Appl Environ Microbiol. 2005 Mar;71(3):1501-6
references: 15746353
references: Appl Environ Microbiol. 1998 Jan;64(1):112-8
references: 9435067
references: Appl Environ Microbiol. 2000 May;66(5):1960-9
references: 10788367
references: J Bacteriol. 1991 Jan;173(2):697-703
references: 1987160
references: Appl Environ Microbiol. 2001 Apr;67(4):1874-84
references: 11282645
references: Appl Environ Microbiol. 2002 Aug;68(8):3673-82
references: 12147459
references: Trends Biotechnol. 2003 Mar;21(3):123-30
references: 12628369
references: Environ Microbiol. 1999 Jun;1(3):199-212
references: 11207739
references: FEMS Microbiol Lett. 2002 Oct 29;216(1):61-6
references: 12423753
references: Appl Environ Microbiol. 2006 Mar;72(3):1719-28
references: 16517615
references: ISME J. 2007 Jul;1(3):215-23
references: 18043632
references: J Microbiol Methods. 1999 Jun;36(3):203-13
references: 10379806
references: Appl Environ Microbiol. 1999 Apr;65(4):1721-30
references: 10103273
references: Microb Ecol. 2001 Aug;42(2):136-149
references: 12024277
references: Appl Environ Microbiol. 1999 Apr;65(4):1731-7
references: 10103274
references: Bioinformatics. 2004 Sep 22;20(14):2317-9
references: 15073015
references: Comput Appl Biosci. 1996 Aug;12(4):357-8
references: 8902363
references: FEMS Microbiol Rev. 1997 Nov;21(3):213-29
references: 9451814
references: Mol Plant Microbe Interact. 2004 Jan;17(1):6-15
references: 14714863
references: Microbiol Mol Biol Rev. 1997 Jun;61(2):121-35
references: 9184007
references: Curr Opin Biotechnol. 2000 Jun;11(3):236-43
references: 10851146
references: J Bacteriol. 2005 Apr;187(7):2483-90
references: 15774891
references: Microbiology. 2003 Jun;149(Pt 6):1475-81
references: 12777487
references: Appl Environ Microbiol. 2005 May;71(5):2687-94
references: 15870360
references: J Mol Biol. 2004 Sep 17;342(3):1041-52
references: 15342255
references: Nucleic Acids Res. 1994 Nov 11;22(22):4673-80
references: 7984417
references: Appl Environ Microbiol. 2006 Apr;72(4):2331-42
references: 16597927
references: Appl Environ Microbiol. 2006 May;72(5):3504-14
references: 16672497
references: Appl Environ Microbiol. 1991 Aug;57(8):2351-9
references: 16348543