Nutrient Regime Restructures Root Fungal Communities in Hydroponic and Aquaponic Systems

Background Aquaponics recirculates aquaculture effluent through plant production systems and is widely assumed to provide a more microbially active nutrient environment than conventional hydroponics. Whether this enrichment extends to root-associated fungal communities, or translates into measurable benefits for plant nutrition and yield, has not been established. We tested the hypothesis that aquaculture-derived water enriches root fungal communities independently of nutrient load, and that any such enrichment shapes plant performance. A factorial greenhouse trial compared four contrasting nutrient regimes: source water (negative control), standard coupled-aquaponics, phosphorus- and potassium-supplemented aquaponics, and mineral hydroponics (positive control). These were applied to three tomato cultivars in nutrient film technique gutters supported by coconut coir growbags. Root-associated bacterial (16S rRNA gene) and fungal (ITS) communities were characterized by amplicon sequencing; amplicon-based community inferences were independently verified by ion-chromatography measurement of plant sap nutrients across three canopy levels and four dates, and by per-plant weekly cumulative fruit yields tracked across the full harvest period. Results Hydroponic plants produced the highest cumulative yields and operated at an electrical conductivity approximately four to five times higher than aquaponic treatments (1.78 ± 0.12 vs. 0.37–0.41 mS cm⁻¹). Plant sap nutrient concentrations overlapped across fertilized treatments despite the EC differential, yet only fertilized systems produced commercially viable yields. Fungal alpha and beta diversity restructured across treatments - supplemented aquaponics yielded the lowest fungal richness while standard aquaponics retained the highest. Aquaponic water alone did not generate greater fungal diversity than hydroponics at equivalent nutrient load. Bacterial communities differentiated less among fertilized systems than fungal communities. Conclusions Root-associated fungal assemblages responded more strongly to nutrient origin and supplementation than bacterial communities, but this restructuring did not compensate for yield constraints under low-intensity aquaponic nutrient delivery. Nutrient delivery strategy, rather than biological origin of the water alone, is the primary driver of root microbiome structure in soilless cultivation, with direct implications for nutrient management in aquaponic and hydroponic systems.