The growing extent of contaminated land and water due to industrialization is a major global concern and the remediation of contaminated sites is a key goal of a sustainable future.  Organophosphate (OP) compounds represent a major environmental contaminant due to their role as a nerve agent and thus widespread application as pesticides.  In addition to acute toxicity to humans, which results in over a million poisonings annually, chronic exposure to these compounds may lead to long term neurological and developmental effects. Microbial bioremediation of toxic compounds often suffers from a lack of understanding of the types and roles of degrading bacteria within the context of the diverse community and ecological drivers present in the system.  New technologies are leading to a more holistic understanding which synthesizes information regarding the organisms present, functional gene abundances and environmental variables.   Here we have used shotgun metagenomics to profile microbial communities from agricultural soils across a gradient of OP insecticide usage and varying in their ability to degrade OP compounds in situ.   We found that the major determinant of both taxonomic composition and genomic functional potential was a site history of insecticide usage.   These shifts were driven by an increase in genes related to phosphorus metabolism, membrane transport, stress response and chemotaxis.  These metabolisms were also found to increase in abundance after the addition of OP insecticide to laboratory samples which previously had low concentrations of these compounds.  By applying network analysis to this dataset, we have built a model that links key  taxa to OP degrading genes within a wider metabolic network  to elucidate the consequences of organophosphate pesticide on microbial community structure and function,  and to predict strategies to encourage the degradation of these compounds in situ leading to bioremediation of contaminated sites.