title: Biphenyl-metabolizing bacteria in the rhizosphere of horseradish and bulk soil contaminated by polychlorinated biphenyls as revealed by stable isotope probing.
abstract: DNA-based stable isotope probing in combination with terminal restriction fragment length polymorphism was used in order to identify members of the microbial community that metabolize biphenyl in the rhizosphere of horseradish (Armoracia rusticana) cultivated in soil contaminated with polychlorinated biphenyls (PCBs) compared to members of the microbial community in initial, uncultivated bulk soil. On the basis of early and recurrent detection of their 16S rRNA genes in clone libraries constructed from [(13)C]DNA, Hydrogenophaga spp. appeared to dominate biphenyl catabolism in the horseradish rhizosphere soil, whereas Paenibacillus spp. were the predominant biphenyl-utilizing bacteria in the initial bulk soil. Other bacteria found to derive carbon from biphenyl in this nutrient-amended microcosm-based study belonged mostly to the class Betaproteobacteria and were identified as Achromobacter spp., Variovorax spp., Methylovorus spp., or Methylophilus spp. Some bacteria that were unclassified at the genus level were also detected, and these bacteria may be members of undescribed genera. The deduced amino acid sequences of the biphenyl dioxygenase alpha subunits (BphA) from bacteria that incorporated [(13)C]into DNA in 3-day incubations of the soils with [(13)C]biphenyl are almost identical to that of Pseudomonas alcaligenes B-357. This suggests that the spectrum of the PCB congeners that can be degraded by these enzymes may be similar to that of strain B-357. These results demonstrate that altering the soil environment can result in the participation of different bacteria in the metabolism of biphenyl.
authors.affiliation: Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, Institute of Chemical Technology Prague, Technicka 3, 166 28 Prague 6, Czech Republic.
authors.forename: Ondrej
authors.initials: O
authors.lastname: Uhlik
authors.forename: Katerina
authors.initials: K
authors.lastname: Jecna
authors.forename: Martina
authors.initials: M
authors.lastname: Mackova
authors.forename: Cestmir
authors.initials: C
authors.lastname: Vlcek
authors.forename: Miluse
authors.initials: M
authors.lastname: Hroudova
authors.forename: Katerina
authors.initials: K
authors.lastname: Demnerova
authors.forename: Vaclav
authors.initials: V
authors.lastname: Paces
authors.forename: Tomas
authors.initials: T
authors.lastname: Macek
mesh_terms: D031215:Armoracia / Q000382:microbiology*; D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism*; D001483:Base Sequence; D020562:Betaproteobacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism; D001713:Biphenyl Compounds / Q000378:metabolism*; D002247:Carbon Isotopes; D017931:DNA Primers / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics; D005798:Genes, Bacterial; D008969:Molecular Sequence Data; D010802:Phylogeny; D011078:Polychlorinated Biphenyls / Q000378:metabolism*; D012329:RNA, Bacterial / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012988:Soil Microbiology; D012989:Soil Pollutants / Q000378:metabolism*
chemical_list: D001713:Biphenyl Compounds; D002247:Carbon Isotopes; D017931:DNA Primers; D004269:DNA, Bacterial; D011078:Polychlorinated Biphenyls; D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S; D012989:Soil Pollutants; C010574:biphenyl
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