Usability of the isoproturon-degrading pdm genes as bioindicators and their horizontal transfer among variable catabolic plasmids. soil

Biobeds have been developed to minimize pesticide point source contamination. Their depuration efficacy relies on the catabolic activities of the microbial community they support. Despite that, we have just started getting insights on the diversity and functional attributes of the microbial community of biobeds. In a series of microcosm studies in a biobed packing material collected from an operative biobed we aimed to explore (a) the role of the pdmA gene on the mineralization of isoproturon (IPU) via q-PCR and RT-q-PCR, (b) the effect of IPU on the diversity of the total (DNA) bacterial community and its active (RNA) fraction through amplicon sequencing and (c) the localization and dispersal mechanisms of pdmA using functional metagenomics. In this frame the abundance of the pdmA gene and of the plasmid pSH (harboring the pdmA gene) of an IPU-degrading Sphingomonas sp. SH strain was quantified along IPU mineralization. pdmA abundance and expression concomitantly increased with IPU mineralization verifying its major role in the transformation of IPU in the biobed packing material. Despite that, amplicon sequencing analysis failed to identify significant effects, positive or negative, on the total bacterial diversity. The pdmA-harboring plasmid pSH showed consistently lower abundance than pdmA suggesting its localization in plasmids or genomic parts other than pSH. Functional metagenomic analysis showed that in three of the fosmids sequenced pdmAB were organized in a well-conserved transposon carried by sphingomonads plasmids with low syntheny to pSH. The fourth fosmid contained a genomic fragment of a Rhodanobacter with an incomplete pdmAB cassette. This study shed light on the interactions of IPU with the bacterial community in biobeds and provided novel insights on the evolution and dispersal of pesticide-degrading traits in the bacterial community of biobed systems.