Identifying the Effects of Fish and Rhizosphere on the Structure of the Planktonic Bacterial Communities and Resistome in an Aquaponics Recirculation Loop

ABSTRACT Since they are saving resources, recirculating aquaculture systems (RAS) are perceived as a viable production strategy. Among them, aquaponics combines aquaculture and hydroponic vegetable production. This system entails a closed‐loop water system and continuity between two main “generators of bacterial biodiversity” the plant and the fish, respectively associated with the rhizosphere and the gut microbiome. These ecosystems are powerful bioreactors capable of shaping microbial community structures by mimicking macroscale environmental interactions through selection, competition, and genetic invasion. This work aimed to clarify the respective roles of these bioreactors on planktonic bacteria and antibiotic‐resistant bacteria (ARB) composition and segregation within a commercial aquaponic system composed of four aquaponics units differing by the fish reared. These units were assessed using a high‐throughput qPCR (HT‐qPCR) analysis of 384 antibiotic resistant genes (ARGs) and mobile genetic elements (MGEs) as well as 16S rRNA metabarcoding. The results highlight that the most important driver of bacterial communities and ARG distribution pattern in aquaponics environments appears to be the fish through their associated microbiota. Rhizosphere micro‐environment seems to act as a mitigation factor on the relative abundance of detectable ARGs.