The pQBR mercury resistance plasmids: a model set of sympatric environmental mobile genetic elements

Plasmids are extrachromosomal mobile genetic elements that can facilitate rapid bacterial adaptation by transferring genes between individuals. Whilst plasmids are known to exist in diverse habitats and encode a range of traits, most of our knowledge about plasmids comes from clinically associated antimicrobial resistance (AMR) plasmids that have already been recruited as vectors of drug resistance and have likely been shaped by strong selection for plasmid-encoded antibiotic resistance. Here, we investigated 26 plasmids from the pQBR collection - a set of large, co-existing mercury resistance environmental plasmids isolated in Pseudomonas spp. from a field in Oxfordshire in the 1990s - and explored the ability of pQBR plasmids to transfer novel chromosomally encoded traits. New whole-genome sequences for 25 plasmids confirmed that these soil-isolated plasmids are generally very large (140-588 kb), constitute at least six distinct genetic groups and have relatives in various other Pseudomonas species and habitats. Despite significant nucleotide-level divergence, Groups I (pQBR103-like, ~406 kb) and IV (pQBR57-like, ~328 kb) showed remarkable ancient similarities in synteny and gene content both with one another and with the PInc-2/IncP-2 family of plasmids known to transfer clinically significant drug resistance between Pseudomonas aeruginosa hosts. None of the pQBR plasmids sequenced to date harboured known AMR determinants, but putative phage defence systems and metal resistances were evident. Transposable elements, including the Tn5042 mercury resistance transposon, were responsible for significant structural variation within plasmid groups, consistent with a predominant role of transposons in rapidly remodelling plasmids. To experimentally test the ability of pQBR plasmids to spread new traits, we developed a novel transposon transfer assay which showed that certain Group IV pQBR plasmids were especially effective at acquiring the chromosomally encoded transposon Tn6291 and that this ability to transfer transposons was likely due to specific plasmid factors rather than generic conjugation rate. Our work presents a tractable set of sequenced plasmids suitable for exploring the evolution and dynamics of gene acquisition by pre-AMR plasmids and provides a key case study highlighting the pervasive interplay between plasmids and transposable elements that can drive microbial genome evolution.