Microbial community dynamics and functional shifts in aquaponic systems: Implications for sustainable aquaculture

Aquaponics presents an innovative and sustainable approach to integrated agriculture and aquaculture. However, studies on bacterial communities and their interactions within aquaponics systems, particularly concerning farmed fish, remain limited. This study explores the microbial dynamics within an aquaponics system through 16S rRNA gene amplicon sequencing of the V3-V4 regions over 60-days. We assessed microbial diversity at the genus level across nine samples between control and treatment groups. Both species richness and Shannon index analyses revealed no significant differences in overall microbial diversity between the two groups. However, SIMPER analysis identified 16 genera that contributed to the observed differences between the control and treatment groups, highlighting specific shifts in microbial composition despite the overall similarity in diversity metrics. The Candidatus Planktophila (hgcI clade), which increased after day 30 in the treatment group, is thought to have improved water quality through nutrient cycling and organic carbon degradation, positively impacting both fish and plants Functional analysis also revealed key shifts, including an increase in phototransduction, vascular smooth muscle contraction, and flavonoid biosynthesis. Notably, the increased presence of flavonoid biosynthesis pathways may contribute to immune function and stress reduction in fish, while supporting the development and resilience of plants. These results suggest that aquaponics supports beneficial microorganisms without drastically altering microbial composition, while creating a stable, symbiotic environment that benefits both fish and plants, highlighting it as an environmentally sustainable method for both aquaculture and agriculture. • An aquaponics system was designed to examine microbial communities. • The aquaponics system showed no significant change in overall microbial diversity, but only 16 taxa showed changes. • The flavonol biosynthesis pathway, was significantly enriched in the aquaponics group.