Causes and consequences of bacterial local adaptation via MGEs in the plant microbiome

Adaptations that enable plant-associated bacteria to fill disparate niches comprise a critical component of microbial diversity. Genes that confer locally adaptive bacterial traits, ranging from heavy metal resistance to pathogen or symbiont infectivity, often reside within mobile genetic elements (MGEs) that can move between genomes. While MGEs may speed microbial adaptation, they also have selfish fitness interests and potentially separate evolutionary trajectories from their host genome. MGEs can also impose physiological burdens and be limited in the transmissibility of function across hosts, which likely constrains bacterial local adaptation. Given these constraints, the prevalence of adaptive loci on potentially exploitative MGEs poses a dilemma: how do fitness conflicts and alignments between MGEs and the main replicon shape bacterial local adaptation and impact plant hosts? We synthesize research on ways MGEs confer rapid, niche-specific fitness advantages to bacteria, identify factors that promote or constrain bacterial adaptation, and highlight MGE impacts on plants. We focus on large, self-transmissible MGEs (islands, plasmids, and prophages; though we expect relevance to other MGEs as well) to better understand how MGEs bolster yet constrain bacterial local adaptation. We specifically explore the role of MGEs in shaping bacteria that themselves play a role in expanding or contracting the plant niche.