For well-over a decade, my laboratory has worked to understand the cellular processes leading to microbial survival, adaptation, and proliferation in fuels. Our research in fuel microbiology and omics has shown that a set of conserved microbial adaptive mechanisms, including biofilm formation, secretion of emulsifiers, stress response and quorum sensing, iron uptake, and activation of efflux pumps serve a critical role in microbial resistance to fuels and toxic organic solvents. In terms of importance, employment of efflux pumps by the microbial cell rises to the top; this system supports homeostasis through the extrusion of fuel hydrocarbons from periplasms and cytosol to maintain a low non-toxic hydrocarbon concentration inside the cell. In this seminar, I will introduce the concept of fuel biodeterioration, its effect on fuel quality and fuel system operation, and how fuel chemical composition and environmental conditions contribute to biocontamination. Furthermore, I will describe our cutting-edge research process that applies functional genomics, transcriptomics, metabolomics, mass spectrometry, and, more recently, nonlinear optics to elucidate the role of efflux pumps in microbial resistance to fuel. The results will highlight how resistance-nodulation-division (RND) efflux pump work in Gram-negative bacteria to provide fuel resistance. Briefly, I will present recent transcriptomics and bioassay results indicating that efflux pumps are a global microbial adaptive mechanism for fuel extending to Gram-positive bacteria and fungi via the action of the major facilitator superfamily (MFS) and ABC-type transporter efflux pump systems. Finally, I will explain how we applied our new understanding on efflux pumps to the development of new fuel biodeterioration detection, prevention and mitigation technology, including a non-toxic biocide that acts as a medicine for the fuel system by blocking efflux pumps in the presence of fuel to render microbes inactive.