Beneficial microorganisms play an important role in enhancing plant health, especially by promoting resistance to plant pathogen infection. The purpose of this study was to gain an understanding of such protection by i) examining the responses of fresh produce (lettuce) to beneficial treatments in their transcriptomes, ii) comparing biological (bacteria, fungi, and oomycete) communities and their diversity when treated with Pseudomonas chlororaphis (beneficial bacterium) in windowfarm hydroponic systems, and iii) identifying the microorganisms in root areas and water. P. chlororaphis treatment was for increasing plant growth and fighting for Pythium ultimum infection. In addition, two more treatments were conducted: i) adding supporting media for increasing bacterial colonizing areas around roots and ii) UV irradiation in water for controlling nuisance biofilm buildup. Changes in gene regulation and expression in lettuce in response to these treatments were investigated. Comparisons of microbial profiles among the treatments and microbial identification were conducted using samples of supporting media (around roots) and water. The results demonstrated that i) P. chlororaphis enhanced lettuce growth, ii) P. chlororaphis-treated lettuce showed dominantly expressed genes for membrane, catalytic activity, cellular process, and metabolic process categories, iii) P. chlororaphis treatment induced genes related to growth promotion and defense pathways, and iv) the microbial community of the root area was affected significantly by P. chlororaphis treatment and microbial diversity in water was significantly changed by UV irradiation. This study provided insight into how beneficial treatments affects the fresh produce growth in root areas and water in a vertical hydroponic system.