Light-driven diel oscillations in microbial metabolism underpin estuarine biogeochemical resilience

Abstract Diel light cycles profoundly influence estuarine biogeochemical processes, yet the mechanistic responses of planktonic prokaryotic communities to these rhythmic cues remain incompletely understood. This study employed an integrative multi-omics approach—combining high-frequency sampling, 16S rRNA gene sequencing, metagenomics, and metatranscriptomics—to elucidate diel dynamics in microbial diversity, interaction networks, and metabolic functions in the Pearl River Estuary. The results revealed significant temporal partitioning in microbial organization: nocturnal communities exhibited higher α-diversity and formed more densely connected co-occurrence networks, indicative of enhanced heterotrophic processes, whereas daytime assemblages were dominated by Cyanobacteria (particularly Synechococcales) with enriched pathways for photoautotrophic carbon fixation and nitrogen assimilation. Metabolic profiling further demonstrated distinct diel oscillations in key biogeochemical processes, including daytime enhancement of Calvin cycle-mediated CO2 fixation and nocturnal upregulation of dissimilatory sulfate reduction. Network topology analysis showed that nighttime communities displayed increased clustering coefficients and reduced path lengths, suggesting more efficient resource utilization under dark conditions. Through reconstruction of 786 metagenome-assembled genomes, we identified Cyanobiaceae as key mediators of diel carbon and nitrogen transformations, while diverse heterotrophic taxa facilitated nighttime nutrient remineralization. This study provides mechanistic insights into how light-driven diel oscillations shape microbial metabolic partitioning and ecological interactions, advancing our understanding of the temporal dynamics that underpin biogeochemical resilience in estuarine ecosystems.