Cultivation System Dominates Cucumber Performance and Root-Zone Microbiomes Across Biochar Particle Sizes

Hydroponic (HP) and aquaponic (AQ) systems are widely known in greenhouse production; however, the combined effects of nutrient delivery system and substrate physical structure on crop performance and root-zone microbiomes remain insufficiently understood. Substrate physical properties influence water retention and aeration, which can affect root-associated microorganisms, plant growth, and yield. This study evaluated cucumber (Cucumis sativus L.) growth, yield, nutrient dynamics, physiological stress responses, and bacterial community composition under HP and AQ systems using bamboo-derived biochar substrates and coconut coir as a control. Vegetative growth was enhanced under AQ, with the greatest plant elongation (1102 ± 40.1 cm) and stem diameter (15.1 ± 1.0 mm) observed in biochar-grown plants. Total yield was consistently higher under AQ than HP, with the highest yield recorded in the coarse biochar treatment (28.6 kg m^-2). Aquaponic systems were associated with greater nutrient availability under the conditions evaluated during mid to late season production, including nitrate concentrations of up to 226 mg L^-1. Physiological stress monitoring indicated lower stress exposure under aquaponic conditions in plants grown in medium and coarse biochar substrates across both systems, with 78 to 81% of the growing season classified within low to balanced stress conditions. Bacterial community composition was primarily shaped by cultivation system, which explained 19.3% of the observed variation, whereas substrate treatment did not significantly alter overall bacterial community structure. Overall, cultivation system was the dominant factor associated with variation in cucumber performance and root-zone bacterial communities, while biochar substrates supported improved plant growth, yield, and reduced physiological stress.