Aquaponic food production combines two well-studied models - recirculating aquaculture systems (RAS) and hydroponics - into a complex multitrophic production system for fish, fruits, and vegetables. Of the three major commodity classes produced in aquaponic systems, fruits and vegetables are implicated in about 11.7% and 34.2% of foodborne illnesses in the US, while fish is only responsible for 2.7%. For this reason, ensuring the safety of the fruit or vegetable crop is a research priority. While provisional good agricultural practices (GAPs) for recirculating (coupled) aquaponic producers have been published by one industry group, universal evidence-based standards for produce safety in aquaponics have not been developed.
The Food Safety Modernization Act's Produce Safety rule regulates microbial water quality in agricultural production, but final agricultural water rules have yet to be published by the Food and Drug Administration. Aquaponic culture water will likely be regulated as either manured water - precluding recirculating aquaponic crop production entirely - or at minimum as surface water, requiring 20 tests for generic E. coli annually as an indicator of microbial water quality. Additionally, one of the provisional GAPs for aquaponics would require growers to design systems that prevent contact between the shared culture water and the edible portion of the crop. However, disinfection of culture water prior to distribution to the plant system could have negative impacts on its microbiome. The inherent pathogen-suppressive effects of the indigenous microbial communities should be preserved if possible. Separation of culture water from the edible portion of the crop also precludes the production of root crops. To evaluate the potential food safety hazards introduced by contact between crop and culture water and inform responsible policy decisions, a thorough investigation of microbial water quality is needed.
Researchers at the University of Hawai'i published the first study of food safety in 11 commercial aquaponics operations in 2012. This survey found very low levels of generic E. coli in culture water—far below the maximum concentration allowed under FSMA—and no E. coli or Salmonella in fish or plants sampled from the systems. Two more recent studies using molecular techniques to characterize bacterial communities have provided some preliminary data. However, both studies were a single, non-replicated snapshot in time. While these previous efforts have focused on bacterial communities, no published work has characterized the rest of the aquatic biome in an aquaponic system, including archaea and eukaryotic organisms. Whole genome sequencing (WGS) offers an opportunity to comprehensively characterize all organisms in the system, which could lead to useful discoveries about microbial ecology and microbe-plant-fish interactions in aquaponics. The present study will employ both WGS and traditional microbiological techniques to investigate aquatic microbial communities in farm-scale replicated research systems as they relate to food safety and human pathogens. Effects of aquaponic unit processes on microbial abundance, community composition, and pathogen presence in culture water will be measured over time. Results to date will be presented.