Nitrogen Transformation Processes in Manure Microbiomes of Earthen Pit and Concrete Storages on Commercial Dairy Farms

Abstract

Abstract Storing manure is an essential aspect of nutrient management on dairy farms, presenting the opportunity to use it effectively as a fertilizer in crop and pasture production. The storage structures are earthen, concrete, or steel-based constructs. However, this practice presents the potential of losing nitrogen (fertilizer value) and emitting greenhouse gases (environmental stressors) to the atmosphere through microbial and physicochemical processes. We have conducted a study to characterize the relevant microbial processes in two manure storage structures, a clay lined earthen pit and an above-ground concrete storage tank, on commercial dairy farms, to inform the development of mitigation practices to preserve the value of manure. First, we analyzed the 16S rRNA-V4 amplicons generated from manure samples collected from several locations and depths (0.3, 1.2 and 2.1–2.75 meters below the surface) of the storages, identifying a set of OTUs and quantifying their abundances. Then, we inferred the respective metabolic capabilities. These results showed that the manure microbiome composition was more complex and exhibited more location-to-location variation in the earthen pit than in the concrete tank. Further, the inlet and a location with hard surface crust in the earthen pit had unique consortia. The microbiomes in both storages had the potential to generate ammonia but lacked the organisms for oxidizing it to gaseous compounds. However, the microbial conversion of nitrate to emittable N2, NO, and N2O via denitrification and to stable ammonia via dissimilatory nitrite reduction seemed possible; minor quantities of nitrate was present in manure, potentially originating from oxidative processes occurring on barn floor. The nitrate-transformation linked OTUs were more prevalent at the near-surface locations and all depths of the inlet. No anammox bacteria and autotrophic nitrifiers, archaeal or bacterial, were detected in both storages. Hydrogenotrophic Methanocorpusculum species were the primary methanogens or methane producers, exhibiting higher abundance in the earthen pit. These findings suggested that microbial activities were not the main drivers for nitrogen loss from manure storage, and commonly reported losses are associated with the physicochemical processes. Finally, the microbiomes of stored manure had the potential to emit greenhouse gases such as NO, N2O, and methane.