Analysis of a Bacterial Community in 3-Chlorobenzoate-Contaminated Soil by PCR-DGGE Targeting the 16S rRNA Gene and Benzoate 1,2-Dioxygenase Gene (benA)

We analyzed the changes that occurred in a bacterial community from forest soil after adding 3-chlorobenzoate (3CB) by two different PCR-denaturing gradient gel electrophoreses (DGGEs), targeting the 16S rRNA gene and benA encoding the benzoate 1,2-dioxygenase large subunit. The concentration of 3CB in the soil had decreased to about 40% of that added (500 ppm) after seven days at 28°C. Total DNA was directly extracted from the soil before and after incubation, and subjected to PCR-DGGE. Four new bands clearly appeared after the incubation with 3CB in the DGGE profiles of both the 16S rRNA gene and benA. The major bands were sequenced and compared with sequences obtained from DNA databases by phylogenetic analysis. All four of the new bands in the profiles of the 16S rRNA gene were most closely related to Burkholderia spp. Moreover, three of the four bands that intensified after the addition of 3CB in the profiles of benA were also most closely related to known benA sequences derived from Burkholderia strains. These results suggest that several Burkholderia-related bacteria played significant roles in the degradation of 3CB in the soil.