Microbial dynamics along nutrient flow and removal in an integrated multitrophic aquaculture system

Microbial community assembly in marine integrated multi-trophic aquaculture (IMTA) systems remains poorly understood, particularly across interconnected extractive compartments spanning spatial and temporal scales. Two-step biofilters that incorporate seaweeds and multi-species biofilms (periphyton) are widely used to remove excess nitrogen and phosphorus from aquaculture effluents while simultaneously generating protein-rich, edible biomass. Variations in nutrient composition along these biofilters suggest that microbial diversity and functionality may be differentially shaped within the system. To address this knowledge gap, in this study, using the 16S rRNA gene amplicon sequencing technique, we examined the assembly and potential functions of aquatic microbial communities along the treatment of marine effluent by Ulva fasciata and periphyton, where species selection may occur spatially through microbial colonization of the different plant substrates or through changes in water-nutrient content. At the same time, we assessed temporal dynamics by the weekly changes over 5 weeks. Community structure and functionality demonstrated that environmental heterogeneity primarily determined dissimilarity among microbial communities across the biofilter’s compartments. Microbial beta diversity of periphyton, Ulva thallus, and rearing water was distinct over time. This confirmed the important role of environmental selection despite hydraulic homogeneity caused by the high dispersal rate of running water within the interconnected biofilters. The periphyton microbial community harbored the highest alpha diversity, followed by the water microbiome and Ulva -associated microbiota. In terms of functional potential, nitrogen and sulfur metabolism were generally higher in periphyton than in the water and Ulva assemblies. While nitrate reduction by periphyton is associated with the high prevalence of genes involved in denitrification, the Ulva -microbes interaction benefits the alga through bacterial dissimilatory nitrate reduction to ammonia. Overall, these findings provide novel insights into the spatial and temporal dynamics of microbiomes in integrated culture systems, contribute to optimal IMTA designs and microbial management in holistic mariculture.