title: Molecular analysis and development of 16S rRNA oligonucleotide probes to characterize a diclofop-methyl-degrading biofilm consortium.
abstract: Genomic DNA from nine individual bacteria, isolated from a diclofop-methyl-degrading biofilm consortium, was extracted for genetic characterization. The degradation of diclofop-methyl produces metabolites that are known intermediates or substrates for bacteria that degrade a variety of chlorinated aromatic compounds. Accordingly, oligonucleotide primers were designed from specific catabolic genes for chlorinated organic degradation pathways, and tested by PCR to determine if these genes are involved in diclofop-methyl degradation. DNA homology between the PCR products and the known catabolic genes investigated by Southern hybridization analysis and by sequencing, suggested that novel catabolic genes are functioning in the isolates. Specific fluorescent oligonucleotides were designed for two of the isolates, following 16S rDNA sequencing and identification of each of the isolates. These probes were successfully used for fluorescent in situ hybridization (FISH) studies of the two isolates in the biofilm consortium.
authors.affiliation: Department of Natural Resource Sciences, McGill University, Ste-Anne-de-Bellevue, QC, Canada.
authors.forename: L
authors.initials: L
authors.lastname: Laramée
authors.forename: J R
authors.initials: JR
authors.lastname: Lawrence
authors.forename: C W
authors.initials: CW
authors.lastname: Greer
mesh_terms: D001419:Bacteria / Q000145:classification* / Q000235:genetics / Q000378:metabolism; D001673:Biodegradation, Environmental; D018441:Biofilms / Q000145:classification*; D015139:Blotting, Southern; D016172:DNA Fingerprinting; D004269:DNA, Bacterial / Q000032:analysis; D005456:Fluorescent Dyes / Q000138:chemical synthesis; D055768:Halogenated Diphenyl Ethers; D006540:Herbicides / Q000378:metabolism*; D017404:In Situ Hybridization, Fluorescence; D015345:Oligonucleotide Probes / Q000138:chemical synthesis; D010647:Phenyl Ethers / Q000378:metabolism*; D016133:Polymerase Chain Reaction; D012336:RNA, Ribosomal, 16S / Q000032:analysis*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
chemical_list: D004269:DNA, Bacterial; D005456:Fluorescent Dyes; D055768:Halogenated Diphenyl Ethers; D006540:Herbicides; D015345:Oligonucleotide Probes; D010647:Phenyl Ethers; D012336:RNA, Ribosomal, 16S; C012891:dichlorfop-methyl