Quorum sensing mediates spatiotemporal microbial community dynamics and nitrogen metabolism in biofloc-based Litopenaeus vannamei aquaculture systems.

Biofloc technology (BFT) enables sustainable aquaculture by leveraging microbial communities to enhance water quality and nutrient cycling. However, the role of quorum sensing (QS) in regulating microbial dynamics and metabolic functions within BFT systems remains poorly understood. This study examined how QS spatiotemporally regulates microbial succession and nutrient metabolism in a biofloc-based Litopenaeus vannamei aquaculture system over 82 days culture. Ammonia and nitrite concentrations shifted through four phases: initial (IP), rising (RP), declining (DP), and stabilization (SP). Notably, nitrite levels decreased rapidly from 1.21 mg/L to 0.03 mg/L during DP. Metagenomic analysis revealed Pseudomonadota, Actinomycetota, and Bacteroidota as the consistently dominant phyla, while dominant genera shifted over time. QS pathways displayed temporal heterogeneity: acyl-homoserine lactones (AHLs) and autoinducer-2 (AI-2) predominated during IP, whereas aromatic hydrocarbon kinases (AHKs) and cyclic dimeric guanosine monophosphate (c-di-GMP) were more enriched during SP. KEGG analysis indicated that nitrogen metabolism genes were more abundant in bioflocs than in the water. Genes associated with dissimilatory nitrate reduction and denitrification were significantly more abundant than those involved in other nitrogen metabolic processes (p < 0.05). Furthermore, QS signaling coordinated the complex interaction networks among 30 dominant bacterial genera (e.g., Amaricoccus and Ruegeria) involved in carbon, nitrogen, and sulfur metabolism, which is crucial for maintaining the stability and functionality of the biofloc system. This study elucidates the mechanisms through which microbial signaling orchestrates efficient nitrogen removal and sustains system stability, thereby providing a foundation for developing targeted bioaugmentation strategies to enhance sustainable aquaculture practices.