Biofloc acts as a microbial reservoir buffering salinity-induced community turnover in shrimp aquaculture: Insights from quantitative and functional microbiome analysis

Salinity drives critical trade-offs between shrimp survival and growth, especially in shrimp biofloc culture systems, yet how it mechanistically influences absolute bacterial abundance and quantitative functional dynamics remains poorly understood. Using quantitative bacterial amplicon sequencing and functional gene profiling across salinity gradients (0, 15‰, and 30‰) in shrimp ( Penaeus vannamei ) culture systems, we show that biofloc aggregates buffer the loss of bacterial diversity observed under salt stress. Taxonomically, osmotic stress drives a deterministic turnover from freshwater-associated Chloroflexota and Flavobacteriaceae toward osmotolerant Roseobacteraceae and Demequinaceae. Crucially, quantitative PCR (qPCR) identifies biofloc as the primary functional reservoir, enriched with absolute abundances of nitrogen ( amoA , nirS , nxrB ) and phosphorus ( pit ) cycling functional genes. Community assembly was governed by both deterministic and stochastic processes, with drift increasing under 30‰ salinity. Partial least squares path modeling (PLS-PM) confirmed the contrasting effects of salinity regulation on the reduction of community diversity in water bacteria, while promoting the structural stability of the biofloc bacterial community. These bacterial shifts influenced water quality, with functional adaptations mitigating biogeochemical risks such as nitrite accumulation. The mechanistic link between salinity-driven bacterial community succession and ecosystem function offers actionable strategies for sustainable shrimp aquaculture under fluctuating salinity regimes.