Abstract: 

Nucleocytoviricota (NCLDV) infecting eukaryotic protists and algae are abundant and diverse in aquatic ecosystems, where they significantly influence microbial carbon cycling through phytoplankton manipulation. Despite extensive research on bacteriophages, the mechanisms underlying NCLDV infection of protist hosts remain largely unexplored. Estuaries, as transitional zones between terrestrial and marine ecosystems, offer unique environmental gradients ideal for investigating microbial community responses to various factors. This study focuses on giant viruses in the subtropical Pearl River Estuary (PRE), a region characterized by significant freshwater input and anthropogenic influence. Utilizing combined short-read and long-read sequencing, we generated high-quality Metagenome-Assembled Genomes (MAGs) to identify genomic adaptations. Diel-resolved metatranscriptomic profiling was conducted at three representative stations along an environmental gradient (two nearshore diatom-dominated sites and one offshore green algae-dominated site) to understand how viral infection strategies vary with host community composition. Our findings reveal that Nucleocytoplasmic Large DNA Viruses (NCLDVs) temporally regulate infection dynamics, thereby synchronizing host metabolism with biogeochemical processes within subtropical estuaries, highlighting their crucial role in driving diurnal microbial community rhythms.