Environmental drivers of microbial community dynamics in a cool-water aquaponics system

Aquaponic systems represent an integrated water-efficient approach to food production by combining recirculating aquaculture with hydroponic plant cultivation. Performance and stability of these systems depend not only on fish and plant interactions but also on the structure and function of associated microbial communities, which regulate nutrient cycling and water quality. Microbial communities play a central role in the stability and performance of aquaponic systems, yet the relative importance of temporal dynamics, spatial heterogeneity, and environmental drivers remains poorly understood. In this study, we evaluated microbial consortia and production characteristics in six replicate aquaponic systems with cool/cold water fishes, including rainbow trout ( Oncorhynchus mykiss ) and yellow perch ( Perca flavescens , all female) to cultivate lettuce ( Lactuca sativa ) and kale ( Brassica oleracea ), and investigated microbial community structure across production cycles and system compartments using high-throughput sequencing of 16S rRNA gene and multivariate ecological analyses. DNA samples were collected from fish tank water during the initial control cycle and from key aquaponic compartments, including circulating water, rhizosphere, biodeposits, and biofilters, during three subsequent harvesting cycles. Across all four cycles, a core microbiome was observed, with 136 shared taxa. Microbial communities were consistently structured at the system level where each system supported a distinct microbial assemblage. Permutational multivariate analysis of variance revealed that microbial community composition was significantly influenced by both production cycle and compartment with temporal effects emerging as a dominant driver of variation. Observed shifts in microbial communities were closely associated with temperature and pH gradients. Significant but comparatively weaker differences were observed among individual AP systems, fish species, and plant species. These results indicate that microbial community structure was shaped primarily by temporal succession across production cycles, with additional contributions from spatial structuring and biotic factors. These findings provide insight into ecological processes governing aquaponic microbiomes and highlight the importance of managing environmental conditions to promote system stability and performance.