Data from: Physical and microbial root-zone factors underlying tomato wilt in long-term biofloc aquaponic systems

Experimental Aquaponics Systems
Twelve independent aquaponics systems were established in a double poly greenhouse located at the EW Shell Fisheries Center in Auburn, AL. Each aquaponics system consisted of a 700L fish tank stocked with 40 tilapia and a 1 m2 grow bed filled with pea gravel substrate. The systems were run for two years which involved tilapia grow out from March to November in 2023 and 2024. Fingerlings were stocked in March (20-50 g) and grown to 400-500 g at which point they were harvested (November). In 2024, a partial harvest was carried out in September to ensure fish mass in the tanks did not exceed 20 kg/ m3 of water. Cherry tomatoes were cultivated in the grow beds with two crops per year (4 crops in total). More specific detail on the operational parameters of these systems can be found in our prior publications:
https://doi.org/10.1016/j.aquaculture.2025.743286
https://doi.org/10.1016/j.biteb.2025.102439
Four experimental conditions were tested with three independent aquaponics system replicates for each condition. These conditions involved testing two factors: allowing natural sunlight penetration into the fish tanks (versus covering them to block light) and running the systems in coupled versus decoupled operation. Coupled operation allows water to recirculate from the fish tank to the grow bed and then back to the fish tank. Decoupled operation allows water to flow from the fish tank to the grow bed and then to a sump. Water is recirculated between the sump and grow bed. When water from the fish tank is used for irrigation, this causes the sump to overflow into a drain. The net effect is one-way flow from fish tank to grow bed. As both factors were tested in a full factorial design, this resulted in the four experimental treatments: Light decoupled, Light coupled, Dark decoupled, and Dark coupled.
An ebb and flow irrigation cycle was achieved using a bell siphon in 2023. This system was prone to clogging and was switched to a timer-controlled flow regime in 2024 (30 minutes on, 30 minutes off). Also, 6 tomato plants per grow bed were used in 2023 while 5 tomato plants per bed were planted in 2024 to provide more space for each plant. The Favorita F1 varietal from Johnny’s Seeds was used in all trials except for Spring of 2023 where the Washington varietal was used. Ripe tomatoes were harvested from each system multiple times per week in response to plant production levels. Fruits were weighed for each system. Cumulative tomato yields were tracked for each system and divided by the number of plants in the system.
In 2023, solids removal between the fish tank and grow bed consisted of a series of foam filter materials (Pentair PF7 and PF17C). In 2024, radial flow separators (RFS) were installed to remove large solid particulates (mostly fecal matter) followed by one layer of foam filter material (Pentair PF7 only). This change was implemented in response to high levels of solids deposition on filter material and in grow beds in the 2023 trial. Sludge removal from the RFS was carried out several times per week. Volumes and total suspended solids (TSS) in removed material were recorded to understand how effectively the RFS was removing solids across the different system types.