Nitrogen Metabolism and Pathogen Feedback in Intensive Aquaculture: Reframing Ammonia Nitrogen as a Reactive Node

Feeds rich in protein are the dominant nitrogen input in intensive aquaculture, yet only part of dietary nitrogen is retained as animal biomass; the remainder enters water and sediment through uneaten feed, feces, dissolved wastes, mucus, sloughed tissue, and branchial ammonia excretion. This review aims to integrate nutritional, physiological, microbial, and disease-related evidence into an evidence-graded framework that positions ammonia nitrogen as a reactive node linking feed, host, water, sediment, and pathogen risk. To assemble this evidence, we conducted a structured narrative search of Web of Science and PubMed for records in English or Chinese published from 2006 to July 2026, with no restriction on publication type, and classified evidence as direct, indirect, or conceptual. The strongest evidence shows that dietary protein supply, amino acid balance, digestibility, and feeding regime regulate nitrogen retention and ammonia output, while microbial ammonification, nitrification, denitrification, dissimilatory nitrate reduction to ammonium, anammox, and assimilation determine whether reactive nitrogen is regenerated, retained, or removed. Experimental studies further show that ammonia impairs oxidative balance, mucosal barriers, immunity, and disease resistance. In contrast, evidence that pathogen infection quantitatively alters nitrogen retention, ammonia excretion, organic nitrogen release, and sedimentary ammonium regeneration remains limited and largely indirect. Accordingly, ammonia nitrogen is framed as a measurable reactive node rather than a unique source or a universally validated causal loop. Practical management should combine precision nutrition with water, biofloc, sediment, and disease surveillance, while future factorial studies and isotope tracer studies should quantify the complete nitrogen budget under pathogen challenge.