Plant-mediated niche differentiation promotes comammox-dominated nitrification in aquaponic rhizospheres

Sustainable aquaculture requires efficient nitrogen management and reduced N₂O emissions. Integrating plants into these systems (aquaponics) represents a promising strategy to achieve these goals. In this study, a tilapia-chive aquaponics model was used to investigated the mechanisms by which plant root exudates regulate rhizosphere nitrifier microbial communities, with a focus on complete ammonia oxidizers (comammox). Over 70 days, we probed how aquaponics and hydroponic conditions reshape the rhizosphere microbiome using qPCR, qFISH, and selective inhibitor assays to quantify the functional contributions of comammox, AOA, and AOB to nitrification and N₂O production. Results showed that the aquaponics system enhanced root exudation, increasing rhizosphere total organic carbon and creating a mildly acidic micro-environment that selectively enriched comammox. Comammox ultimately dominated the ammonia-oxidizing community (99% in abundance) and activity (98% of nitrification capacity) by the end of the experiment. Consequently, the aquaponics system achieved a sustained reduction in the N₂O conversion rate compared to the hydroponic controls, exceeding 50% in all sampling stages after day 7. This mitigation is attributed to minimized nitrite (NO₂^--N) accumulation and the inherently low N₂O-yielding potential of comammox. These findings reveal a plant-driven mechanism that selects for comammox-dominated nitrification, effectively curbing N₂O emissions while maintaining efficient N conversion. The results offer a potential strategy for improving nitrogen use efficiency and emission control in integrated aquaculture systems.