Abstract

Commercial-scale dairy farms produce large volumes of manure, posing environmental, animal health, and public health risks due to persistent pathogens and the accumulation of organic pollutants. This field-scale study evaluated the effects of covered anaerobic lagoons (CLs) and open facultative lagoons (OLs) on microbial reduction, solids stabilization, and manure biogeochemical characteristics on commercial dairy farms in California’s Central Valley during the summer months. Manure samples collected from lagoon inlets, outlets, and secondary lagoons were analyzed for Escherichia coli, total solids (TS), volatile solids (VS), and genomic DNA degradation. CL systems achieved substantially greater E. coli reductions (98.38%; 1.82 log) than OL systems (54.88%; 0.35 log), indicating enhanced pathogen suppression under anaerobic conditions. Progressive declines in genomic DNA concentrations and electropherogram signal intensities across treatment stages further demonstrated microbial biomass degradation during storage. In the CL system, TS concentrations decreased from approximately 0.985% at the inlet to 0.485% at the outlet, representing a 50.7% reduction, with an additional 56% reduction observed in the secondary lagoon. For moisture content, both CL and OL systems exhibited increases of approximately 0.37–0.5% from their respective inlets to outlets, with only marginal increases observed in the secondary lagoon. Comparable trends were observed in the OL system. Significant differences in TS, VS, moisture content, pH, electrical conductivity, and major cations (Na+, K+, Ca2+) occurred between CL and OL systems and among treatment stages. The secondary lagoon further enhanced microbial and solids reductions in both systems. Overall, the findings show that CL systems provide superior pathogen reduction and support biogas recovery, whereas OL systems demonstrate stronger VS stabilization. These results offer practical, field-based insights to inform improved manure management and pathogen mitigation strategies for commercial dairy operations.

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