Bacterial community succession and functional gene dynamics of nitrogen and phosphorus cycling in recirculating aquaculture systems of shrimp

Abstract Recirculating aquaculture systems (RAS) rely heavily on microbial processes to remove harmful nitrogenous compounds such as ammonia and nitrite. Microbial assemblages within these systems also contribute substantially to broader biogeochemical cycling. Gaining a detailed understanding of the functional potential and abundance of microorganisms responsible for nitrogen (N) and phosphorus (P) transformations is therefore crucial for evaluating nutrient remediation efficiency. In this study, we integrated high-throughput 16S rRNA sequencing with a GeoChip functional gene array to investigate how microbial community dynamics correspond to nutrient fluctuations in full-scale RAS. A suite of multivariate statistical approaches, including ordination and network-based analyses, was applied to characterize shifts in both taxonomic structure and functional gene profiles across operational phases. Our results revealed clear temporal patterns in functional gene abundance. Denitrification-related genes (nosZ, napA, nirK/S) became more prominent toward the later stages of operation, while nitrification genes (amoA/B) were most abundant early in the cycle and declined thereafter. Genes involved in ammonification (ureC) and several P-cycling genes (phnK, phoD, phoX) also increased notably during the final phase. These trends underscore the close relationship between bacterial community succession, species turnover, and nutrient cycling capacity. Overall, the study enhances current understanding of functional microbial dynamics in RAS and provides insights that could guide the development of improved nutrient management and bioremediation strategies for aquaculture systems.