A major challenge in microbial biofilm control is biocide resistance. Phenotypic adaptations and physical protective effects have been historically thought to be the primary mechanisms for glutaraldehyde resistance in bacterial biofilms. Recent studies indicate the presence of genetic mechanisms for glutaraldehyde resistance, but very little is known about the contributory genetic factors. Here, we demonstrate that efflux pumps contribute to glutaraldehyde resistance in Pseudomonas fluorescens and Pseudomonas aeruginosa biofilms. The RNA-seq data show that efflux pumps and phosphonate degradation, lipid biosynthesis, and polyamine biosynthesis metabolic pathways were induced upon glutaraldehyde exposure. Furthermore, chemical inhibition of efflux pumps potentiates glutaraldehyde activity, suggesting that efflux activity contributes to glutaraldehyde resistance. Additionally, induction of known modulators of biofilm formation, including phosphonate degradation, lipid biosynthesis, and polyamine biosynthesis, may contribute to biofilm resistance and resilience. Fundamental understanding of the genetic mechanism of biocide resistance is critical for the optimization of biocide use and development of novel disinfection strategies. Our results reveal genetic components involved in glutaraldehyde resistance and a potential strategy for improved control of biofilms. P oor control of biofilm growth is a major concern in many industries, including health care, food production, and oil and gas (1-4). For example, medical device-associated biofilms are the source of 60% to 70% of nosocomial infections (5). In the oil and gas industry, biofilms present a serious hazard to infrastructure through corrosion and reduced oil quality (6). Biocides are typically used to control and inactivate the biofilms, but resistance to biocides decreases the efficacy of disinfection. Biocide resistance was historically believed to be rare (7), but numerous reports of microbial biofilms resistant to biocides, including chlorine, quaternary ammonium compounds, and aldehydes (8-12), indicate a more widespread phenomenon. Biofilms are inherently more resistant to biocide treatments (8-12), a feature generally attributed to physical mechanisms, such as limited penetration of biocides through exopolysaccharides, reactivity and absorption of biocides to biofilm matrix, and phenotypic adaptations (13-15). Recent reports suggest that genetic factors may also contribute to biocide resistance; for example, efflux pumps were shown to contribute to biocide resistance, indicating the potential for genetically mediated biocide resistance mechanisms (10, 11). The cross-resistance between biocides and antibiotics provides further evidence that biocide resistance may be mediated by genetic factors (15, 16). The control and design of effective biofilm disinfection strategies require understanding of the mechanisms of action of antimicrobials and biocide resistance of biofilms, specifically, the genetically modulated response of microbial biofilms.Glutaraldehyde...