Horizontal Gene Transfer and Genome Rearrangements Shape Bacterial Adaptation for Bioremediation

Bacterial bioremediation involves bacterial strains and communities and their complex interactions with the environment, aiming to restore ecological balance by degrading contaminants in natural systems (soil, water, air). These processes rely on coordinated gene clusters encoding catabolic pathways. Many xenobiotic-catabolic gene clusters (XGCs) reside on mobile genetic elements (MGE), enabling horizontal gene transfer (HGT) and genome rearrangements that drive rapid microbial adaptation to anthropogenic contaminants. Here we review the evolutionary and ecological roles of HGT and genome restructuring in assembling and optimising biodegradative functions. We introduce the concept of metabolic HGT hubs-microbial taxa, mobile elements, and ecological features that serve as central nodes for gene exchange-facilitating metabolic innovation and cooperation within microbial consortia. These processes enhance ecosystem resilience and pollutant degradation efficiency by promoting functional redundancy and metabolic division of labour. Understanding these dynamics informs strategies for engineering microbial communities and genetic bioaugmentation to improve bioremediation outcomes. Our perspective highlights bioremediation as an extension of metabolic network evolution under anthropogenic selection, emphasising both its potential and the need to consider ecological and biosafety implications.