Abstract

Aquaponic systems are increasingly recognized as resource-efficient and environmentally sustainable food production models. However, the interactions between aquaponic environments and fish intestinal microbiota remain insufficiently understood. This study investigated a largemouth bass ( Micropterus salmoides )-water celery ( Oenanthe javanica ) aquaponic system, with samples collected at three intervals of six weeks each. At each time point, intestinal samples (three fish per tank pooled as one biological replicate) and corresponding water samples were collected from triplicate tanks. Using 16S rDNA high-throughput sequencing, we analyzed the composition, dynamics, and core microbiota of microbial communities in the fish intestine, aquaponic water, and inlet water compartments. Distinct yet interconnected microbial successions were observed between the fish intestine and aquaponic water, with intestinal communities exhibiting clear stage-dependent shifts during host development. Several shared core microbial taxa were consistently detected in both intestinal and water samples, suggesting the presence of stable resident microbiota within the aquaponic ecosystem. Notably, unlike microbiome patterns commonly reported in conventional non-aquaponic aquaculture systems, aquaponic system exhibited coordinated temporal dynamics between host-associated and environmental microbiota. These findings highlight the structured interactions between host-associated and environmental microbial communities and provide a microbial ecological perspective for optimizing biological disease prevention strategies and sustainable aquaponic management.