Public Goods Supply Structure Shapes Microbial Network Organization during Full-Scale Anammox Reactor Start-Up

Abstract Key public goods (KPGs) are metabolites or functions produced at a metabolic cost by microbial populations but potentially benefiting the community. In engineered anammox systems, such functions may underpin interdependencies between anaerobic ammonium-oxidizing bacteria (AnAOB) and associated microorganisms, yet their supply-side organization and temporal dynamics remain poorly understood. We integrated genome-resolved metagenomics and metatranscriptomics to quantify relative transcriptional contributions to 33 KPG biosynthesis pathways during start-up of a full-scale anammox reactor. Across 42 high-quality metagenome-assembled genomes (MAGs), these transcriptional contributions were used to infer supply structure and temporal evolution. Inferred KPG supply structures were highly uneven across stages (Gini = 0.74–0.98), with the top 20% of populations accounting for up to 98.7% of total transcriptional contribution. Three resource-specific trajectories emerged: progressively concentrated, persistently concentrated, and dynamically fluctuating supply. AnAOB dominated contributions associated with low-cost amino acids, acetate, nicotinamide adenine dinucleotide, coenzyme A, oxidative-stress defense, and extracellular polymeric substance export potential, but showed apparent dependence on non-AnAOB populations for vitamins, cofactors, and high-cost amino acids. Restructuring was driven mainly by redistribution among retained populations rather than supplier turnover, with the strongest reorganization occurring during early start-up. These findings reveal a structured, resource-dependent, and dynamically reorganized KPG landscape during reactor establishment.