title: Alternative primer sets for PCR detection of genotypes involved in bacterial aerobic BTEX degradation: distribution of the genes in BTEX degrading isolates and in subsurface soils of a BTEX contaminated industrial site.
abstract: Eight new primer sets were designed for PCR detection of (i) mono-oxygenase and dioxygenase gene sequences involved in initial attack of bacterial aerobic BTEX degradation and of (ii) catechol 2,3-dioxygenase gene sequences responsible for meta-cleavage of the aromatic ring. The new primer sets allowed detection of the corresponding genotypes in soil with a detection limit of 10(3)-10(4) or 10(5)-10(6) gene copies g(-1) soil, assuming one copy of the gene per cell. The primer sets were used in PCR to assess the distribution of the catabolic genes in BTEX degrading bacterial strains and DNA extracts isolated from soils sampled from different locations and depths (vadose, capillary fringe and saturated zone) within a BTEX contaminated site. In both soil DNA and the isolates, tmoA-, xylM- and xylE1-like genes were the most frequently recovered BTEX catabolic genes. xylM and xylE1 were only recovered from material from the contaminated samples while tmoA was detected in material from both the contaminated and non-contaminated samples. The isolates, mainly obtained from the contaminated locations, belonged to the Actinobacteria or Proteobacteria (mainly Pseudomonas). The ability to degrade benzene was the most common BTEX degradation phenotype among them and its distribution was largely congruent with the distribution of the tmoA-like genotype. The presence of tmoA and xylM genes in phylogenetically distant strains indicated the occurrence of horizontal transfer of BTEX catabolic genes in the aquifer. Overall, these results show spatial variation in the composition of the BTEX degradation genes and hence in the type of BTEX degradation activity and pathway, at the examined site. They indicate that bacteria carrying specific pathways and primarily carrying tmoA/xylM/xylE1 genotypes, are being selected upon BTEX contamination.
authors.affiliation: Environmental and Process Technology (Vito), Flemish Institute for Technological Research, B-2400 Mol, Belgium.
authors.forename: Barbara
authors.initials: B
authors.lastname: Hendrickx
authors.forename: Howard
authors.initials: H
authors.lastname: Junca
authors.forename: Jolana
authors.initials: J
authors.lastname: Vosahlova
authors.forename: Antje
authors.initials: A
authors.lastname: Lindner
authors.forename: Irene
authors.initials: I
authors.lastname: Rüegg
authors.forename: Margarete
authors.initials: M
authors.lastname: Bucheli-Witschel
authors.forename: Folkert
authors.initials: F
authors.lastname: Faber
authors.forename: Thomas
authors.initials: T
authors.lastname: Egli
authors.forename: Margit
authors.initials: M
authors.lastname: Mau
authors.forename: Michael
authors.initials: M
authors.lastname: Schlömann
authors.forename: Maria
authors.initials: M
authors.lastname: Brennerova
authors.forename: Vladimir
authors.initials: V
authors.lastname: Brenner
authors.forename: Dietmar H
authors.initials: DH
authors.lastname: Pieper
authors.forename: Eva M
authors.initials: EM
authors.lastname: Top
authors.forename: Winnie
authors.initials: W
authors.lastname: Dejonghe
authors.forename: Leen
authors.initials: L
authors.lastname: Bastiaens
authors.forename: Dirk
authors.initials: D
authors.lastname: Springael
mesh_terms: D039903:Actinobacteria / Q000235:genetics / Q000378:metabolism; D001420:Bacteria, Aerobic / Q000235:genetics* / Q000378:metabolism; D001426:Bacterial Proteins; D001673:Biodegradation, Environmental; D002238:Carbohydrate Epimerases; D017931:DNA Primers; D004787:Environmental Pollution; D022761:Gene Transfer, Horizontal; D005798:Genes, Bacterial / Q000502:physiology*; D006838:Hydrocarbons / Q000378:metabolism*; D007220:Industrial Waste; D016133:Polymerase Chain Reaction / Q000379:methods*; D020560:Proteobacteria / Q000235:genetics / Q000378:metabolism; D012988:Soil Microbiology; D012989:Soil Pollutants / Q000378:metabolism*; D013045:Species Specificity; D013379:Substrate Specificity
chemical_list: D001426:Bacterial Proteins; D017931:DNA Primers; D006838:Hydrocarbons; D007220:Industrial Waste; D012989:Soil Pollutants; D002238:Carbohydrate Epimerases; C432940:XylM protein, Lactococcus lactis