Safe halophilic bioaugmentation in hypersaline aquaculture systems: ecological mechanisms, resistome risks, and design principles

Abstract

Abstract Hypersaline aquaculture systems are increasingly affected by organic enrichment, nutrient accumulation, and microbial instability associated with intensive production. Bioaugmentation has frequently been proposed as an environmentally friendly strategy to enhance biogeochemical transformations and improve water quality in such systems. However, conventional bioaugmentation approaches often show inconsistent performance under high-salinity conditions due to ecological mismatch, limited persistence of introduced strains, and insufficient consideration of biosafety risks. In particular, the environmental dissemination of antimicrobial resistance genes (ARGs) has emerged as a critical concern for microbial interventions in aquatic production environments. In this review, current knowledge on halophilic microbial ecology, resistome dynamics, and hypersaline biogeochemical processes was synthesized to develop a resistome-informed framework one that treats ARG mobility and genetic context as primary design constraints for safe halophilic bioaugmentation. The ecological roles of obligate halophiles are examined as a natural containment mechanism, while the functional importance of biofilms and bacteria–archaea consortia in sustaining carbon, nitrogen, and phosphorus transformations under hypersaline conditions is discussed. At the same time, structured microbial habitats are recognized as potential hotspots for horizontal gene transfer, particularly through plasmids, integrons, and extracellular DNA. To address these challenges, a design-to-govern approach is proposed in which microbial selection, genomic screening of ARG context, and evaluation of transfer potential are integrated into the early stages of bioaugmentation design. In addition, a tiered monitoring framework combining targeted molecular assays and metagenomic analysis is outlined to support risk-informed deployment and adaptive management. By positioning resistome characteristics as a core design constraint rather than a secondary consideration, halophilic bioaugmentation can be advanced toward safer and more scalable applications in hypersaline aquaculture systems.