Experimental capture of genomic islands defines a widespread class of genetic element capable of non-autonomous transfer

Bacteria acquire new genes by horizontal gene transfer (HGT). Acquisition is typically mediated by mobile genetic elements (MGEs), however, beyond plasmids, bacteriophages and certain integrative conjugative elements (ICEs), the nature and diversity of MGEs is poorly understood. The bacterium Pseudomonas fluorescens SBW25 was propagated by serial transfer in the presence of filtrate obtained from garden compost communities. Genome sequencing of derived colonies revealed acquisition of three different mobile elements, each integrated immediately downstream of tmRNA . All are flanked by direct repeats and harbour a tyrosine integrase ( intY ), followed by a cargo of accessory genes including putative phage defence systems. Although characteristic of genomic islands, MGE–classifiers showed no matches to mobile elements. Interrogation of DNA sequence databases showed that similar elements are widespread in the genus Pseudomonas and beyond, with Vibrio Pathogenicity Island–1 (VPI–1) from V. cholerae being a notable example. Bioinformatic analyses demonstrate frequent transfer among diverse hosts. With focus on a single 55 kb element (I55) we show that intY is necessary for excision and circularisation, that the element is incapable of autonomous horizontal transfer, but is mobilizable — in the absence of direct cell–cell contact — upon addition of community filtrate. Further analyses demonstrate that I55 enhances host fitness in the presence of community filtrate, which stems in part from ability to defend against phages.