Plant surfaces are host to diverse and distinct arrays of integron gene cassettes

Integrons are microbial gene capture and expression systems that contribute to bacterial adaptation. While integron research has focused heavily on their contribution to the global spread of antimicrobial resistance, their role in bacterial niche adaptation is potentially much broader, as integrons provide their hosts with the capacity to sample from the vast repertoire of functionally diverse genes found within gene cassettes. Integrons and gene cassettes have now been identified within diverse bacterial groups across a wide range of environments, from pristine soils through to human and domestic animal stool samples and polluted river systems. To date, however, there has been little investigation of integrons associated with key crop plants. To investigate whether integrons may contribute to niche adaptive processes in agriculturally important plant microbiomes, we compared the gene cassette and microbial profiles in rhizoplanes of four important crop species grown under controlled glasshouse conditions. We identified 32,584 unique integron gene cassettes, the majority of which were represent genes of unknown function, but also included resistance determinants, toxin-antitoxin gene pairs and others with putative functions associated with plant growth promotion. Although different plant species housed similar rhizoplane bacterial communities, each was associated with complex and distinct suites of gene cassettes, suggesting that they might play a role in plant species-specific interactions. Our findings show that the rhizosphere microbiome carries myriad integron gene cassettes which have the potential to influence the plant-bacterial interactions.