Longitudinal transcriptomic insights into microbial aggregation, trophic cooperation, and genomic adaptation during...

Microbial aggregates such as algal-bacterial granular sludge (ABGS) rely on tightly coordinated microbial interactions to maintain structural stability and functional performance. Despite the significance of co-assembly of phototrophs and heterotrophs in ABGS systems, the ecological and genomic succession during their formation remains poorly understood. Here, time-series multi-omics analysis was conducted to track the dynamic shifts in microbial interactions during ABGS maturation. The granulation process entailed the establishment of extensive cross-phylum nutrient exchange networks between Cyanobacteria and core heterotrophs (e.g., Pseudomonadota and Bacteroidota). Concurrently, metatranscriptomic profiling revealed a significant upregulation of genes associated with biofilm formation (e.g., rpoS, glgC, and cysE) and quorum sensing processes (e.g., yidC and secG) in Cyanobacteria as ABGS stabilized. Furthermore, the spatial densification and metabolic stabilization were accompanied by distinct shifts in community evolutionary strategies: the enrichment of energetically costly antiviral defense systems (R² = 0.65, P < 0.05) but decreased frequency of horizontal gene transfer (HGT). Additionally, analyses of public datasets confirmed that these structural, metabolic, and genomic patterns were conserved across diverse structured algal-bacterial communities. Collectively, our findings demonstrate how physical aggregation, trophic cooperation, and genomic adaptation co-evolve during ABGS formation, providing new insights into the ecological principles governing engineered ecosystems.