The Regeneration Loop: A Microbial Design Framework for Regenerative Aquaculture

Aquaculture intensification has increased nutrient loading, disease pressure and ecological instability. Microbial interventions probiotics, biofloc systems, bacteriophages and microbial metabolites are widely used to address these problems. However, they are usually evaluated as isolated products rather than as parts of a single ecological system. This review synthesises evidence across these intervention classes and organises it into a Regeneration Loop Framework. The framework links four layers: microbial design inputs, habitat scaffolding, functional microbial processes, and governed ecosystem or host services. Layer 4 outcomes feed back to Layers 1 and 2, so the loop is closed rather than linear. Two patterns emerge from the synthesised evidence. First, interventions that modify habitat conditions carbon-to-nitrogen balancing, biofilm substrates and humic conditioning produce more persistent benefits than single-strain additions. Second, effectiveness depends on how far the culture environment can be physically controlled: habitat engineering dominates in closed and semi-closed systems, whereas feed-mediated interventions are the practical lever in open cages. On this basis, the review proposes a bundled metric set combining microbial, ecosystem and production indicators, and outlines a research agenda for precision microbial management and real-time monitoring in next-generation aquaculture systems.