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Odor emissions from anaerobic lagoons containing large populations of phototrophic bacteria are usually minimal. This study was conducted to determine whether copper (123 ppm) and zinc (2,310 ppm) in diets fed to weanling pigs for therapeutic purposes affect phototrophic conditions within lagoons. Column reactors containing 47 L of swine lagoon sludge and supernatant were used to represent lagoons. The reactors were placed in an environmental chamber maintained at 24° C. Copper, zinc, and control manure were added to the reactors at a volatile solids loading rate of 128 gvs m–3 da–1 using a hydraulic retention time of 32.5 days. Bacteriochlorophyll a, copper, reduction-oxidation potential, salinity, sulfate, sulfide, and zinc were then measured for at least 99 days. Sulfide, total copper and total zinc were the only parameters to be significantly impacted. The copper and zinc concentrations in the sludge increased but that of supernatant in the individual reactors changed little during the study period. However, the addition of dietary copper significantly increased the concentrations of sulfides in the supernatant, creating a condition that appeared toxic to phototrophic bacteria. In contrast, a decrease in sulfide concentration resulted from the addition of dietary zinc, resulting in an environment that may have been favorable to phototrophic bacteria. Thus, to minimize potential odor concerns, zinc rather than copper may be the best choice as a dietary supplement for weanling pigs.