Abundance and Expression of Enantioselective rdpA and sdpA Dioxygenase Genes during Degradation of the Racemic Herbicide ( R , S )-2-(2,4-Dichlorophenoxy)Propionate in Soil

TherdpA andsdpA genes encode two enantioselective α-ketoglutarate-dependent dioxygenases catalyzing the initial step of microbial degradation of the chiral herbicide (R ,S )-2-(2,4-dichlorophenoxy)propionate (R ,S -dichlorprop). Primers were designed to assess abundance and transcription dynamics ofrdpA andsdpA genes in a natural agricultural soil. No indigenousrdpA genes were detected, butsdpA genes were present at levels of approximately 103 copies g of soil−1 . Cloning and sequencing of partialsdpA genes revealed a high diversity within the naturalsdpA gene pool that could be divided into four clusters by phylogenetic analysis. BLASTp analysis of deduced amino acids revealed that members of cluster I shared 68 to 69% identity, cluster II shared 78 to 85% identity, cluster III shared 58 to 64% identity, and cluster IV shared 55% identity to their closest SdpA relative in GenBank. Expression ofrdpA andsdpA inDelftia acidovorans MC1 inoculated in soil was monitored by reverse transcription quantitative real-time PCR (qPCR) duringin situ degradation of 2 and 50 mg kg−1 of (R ,S )-dichlorprop. (R ,S )-Dichlorprop amendment created a clear upregulation of bothrdpA andsdpA gene expression during the active phase of14 C-labeled (R ,S )-dichlorprop mineralization, particularly following the second dose of 50 mg kg−1 herbicide. Expression of both genes was maintained at a low constitutive level in nonamended soil microcosms. This study is the first to report the presence of indigenoussdpA genes recovered directly from natural soil and also comprises the first investigation into the transcription dynamics of two enantioselective dioxygenase genes during thein situ degradation of the herbicide (R ,S )-dichlorprop in soil.