Negative plant-inoculum feedback limits productivity in aquaponics

The demand for food will outpace productivity of conventional agriculture due to projected growth of the human population, concomitant with shrinkage of arable land, increasing scarcity of freshwater, and a rapidly changing climate. Efforts to increase conventional agricultural output come with significant environmental impacts stemming from deforestation and excessive use of chemicals, including soil salinization, erosion, and nutrient runoffs. While aquaponics has potential to sustainably supplement food production with minimal environmental impact, there is a need to better characterize the complex interplay between the various components (fish, plant, microbiome) of these systems to optimize scale up and productivity. Here, we investigated how the practice of continued transfer of microbial communities from pre-existing systems might promote or impede productivity of aquaponics. Specifically, we monitored plant growth phenotypes, water chemistry, and microbiome composition of rhizospheres, biofilters, and fish feces over 61-days of lettuce (Lactuca sativa) growth in aquaponic systems inoculated with bacteria that were either commercially sourced or originating from a pre-existing aquaponic system. Strikingly, L. sativa shoot and root growth were significantly reduced across replicates treated with a pre-existing aquaponic system inoculum, when compared to replicates treated with a commercial inoculum. Reduced plant productivity was associated with enrichment in specific bacterial genera, including Pseudomonas, through inoculum transfer from pre-existing systems - a phenomenon consistent with 'negative feedback' in soil ecology. These findings underscore the need for diagnostic tools to monitor microbiome composition for early detection of potential negative inoculum feedback in aquaponic systems.