Metataxonomic Analysis of Microbial Communities in Aquaponic Systems at Two Facilities in the Midwest United States

Aquaponic production relies on microbial activity to convert fish wastes into nutrients for plants. An aquaponic system contains multiple compartments that each have varying environmental pressures that can impact the types of microbes living in the compartment. Furthermore, differences in fish and plant species, system startup and management, and water source can impact microbial communities that colonize an aquaponic system. In this study, we sampled two aquaponic facilities that each operated six replicate aquaponic systems. Metataxonomic analyses were performed on the samples to compare the microbial communities of aquaponic facilities in Minnesota (MN) and Wisconsin (WI), assess the consistency of the microbial communities across multiple systems within a single facility, and evaluate the abundance and types of microbes present within each compartment of a system. Proteobacteria, Bacteroidetes, and Actinobacteria were common in both facilities, but nitrifying organisms were in greater abundance at the WI facility. Microbial communities were largely consistent among systems within a facility, but microbial communities among different compartments of the systems varied. Nitrifying organisms were primarily associated with the biofilter compartment of the MN systems but were found throughout the WI systems, which do not have a dedicated biofiltration compartment. While nitrifying organisms have an important role in an aquaponic system, they comprise less than 10% of the total microbial community of the aquaponic systems we sampled. Other taxa are likely to have equally important roles in the productivity of an aquaponic system, but those taxa and their functions have not been well characterized, and it is unclear how system startup, management, and other factors impact colonization and maintenance of these taxa.