Comparative genomics unravels mechanisms of genetic adaptation for the catabolism of the phenylurea herbicide linuron in Variovorax

Biodegradation of the phenylurea herbicide linuron appears a specialization within a specific cladeof the Variovoraxgenus. The linuron catabolicability is likely acquired by horizontal gene transferbut the mechanisms involved are not known. The full genome sequences of six linuron degrading Variovoraxstrains isolated from geographically distant locations were analyzed to acquire insight in the mechanisms of genetic adaptation towards linuron metabolism in Variovorax. Whole genome sequenceanalysis confirmed the phylogenetic position of the linuron degraders in a separate cladewithin Variovoraxand indicated their unlikely origin from a common ancestral linuron degrader. The linuron degraders differentiated from non-degraders by the presence of multiple plasmids of 20 to 839 kb, including plasmids of unknown plasmid groups. The linuron catabolicgene clusters showed (i) high conservation and syntenyand (ii) strain-dependent distribution among the different plasmids. All were bordered by IS1071 elements forming composite transposonstructures appointing IS1071 as key for catabolicgene recruitment. Most of the strain carried at least one broad host range plasmid that might have been a second instrument for catabolicgene acquisition. We conclude that clade1Variovorax strains, despite their different geographical origin, made use of a limited genetic repertoire to acquire linuron biodegradation.