<p><a>Facing challenges for increasing demands for agricultural land, water, and energy, aquaponics has emerged as a sustainable solution that can contribute to global food production while minimizing environmental impacts. In a recirculating aquaponic system, the waste produced by aquatic animals is processed through microbes and breaks down into compounds for plant uptake. By recycling nutrients and water between hydroponics and aquaculture systems, aquaponics can reduce the waste of fish feeds and the use of chemical fertilizers and use 90-99% less water than conventional aquaculture. However, a few studies reported that nutrient use efficiency is still low in aquaponics, and only 10-37% and 20-30% of nitrogen (N) is typically assimilated by plants and fish, respectively. Yield reduction is commonly reported for plants in aquaponics. Due to the unique water physical and chemical environment, the microbiomes are more diverse in aquaponics than in hydroponics. While the most important microbial group is considered nitrifying bacteria, <i>Nitrosomonas</i> spp. and <i>Nitrobacter</i> spp. mediating the N conversion process from ammonia into nitrate,</a> some plant growth-promoting bacteria (PGPB) in soils were found in aquaponics indicating their important function in the system. Meanwhile, the use of aquaculture wastewater can introduce and promote the growth of harmful microbial pathogens, posing a food safety concern. </p> The goal of this research is to investigate the effects of microbiomes in aquaponic systems. A series of studies were conducted to examine the effects of different bacterial groups on food crop yield and quality and investigate the potential risk of contamination with enteric pathogens in aquaponic systems. The specific objectives are: to 1) examine whether enteric pathogens present in aquaponics and hydroponics; 2) investigate the effects of plant age and root damage on internalization of STEC <i>E. coli</i> in leafy vegetables and herbs. 3) examine the effects of pH on the plant yield in aquaponics; and 4) investigate the effects of PGPB on lettuce in aquaponics and hydroponics3. The data obtained from this research will fill the knowledge gap and provide new management strategies for cultivating crops in aquaponics, which will greatly promote the application of aquaponics to provide a solution for the increasing food demands in the future.