(R,S)-dichlorprop herbicide in agricultural soil induces proliferation and expression of multiple dioxygenase-encoding genes in the indigenous microbial community.

We investigated the effect of (R,S)-dichlorprop herbicide addition to soil microcosms on the degrading indigenous microbial community by targeting multiple α-ketoglutarate-dependent (α-KG) dioxygenase-encoding genes (rdpA, sdpA and tfdA group I) at both gene and transcript level. The soil microbial community responded with high growth of potential degraders as measured by the abundance of dioxygenase-encoding genes using quantitative real-time PCR (qPCR). rdpA DNA was not detectable in unamended soil but reached over 10⁶ copies g⁻¹ soil after amendment. sdpA and tfdA were both present prior to amendment at levels of ~5 × 10⁴ and ~ 10² copies g⁻¹ soil, respectively, and both reached over 10⁵copies g⁻¹ soil. While expression of all three target genes was detected during two cycles of herbicide degradation, a time-shift occurred between maximum expression of each gene. Gene diversity by denaturing gradient gel electrophoresis (DGGE) uncovered a diversity of sdpA and tfdA genes at the DNA level while rdpA remained highly conserved. However, mRNA profiles indicated that all transcribed tfdA sequences were class III genes while rdpA transcripts shared 100% identity to rdpA of Delftia acidovorans MC1 and sdpA transcripts shared 100% identity to sdpA from Sphingomonas herbicidovorans MH. This is the first report to describe expression dynamics of multiple α-KG dioxygenase-encoding genes in the indigenous microbial community as related to degradation of a phenoxypropionate herbicide in soil.