Role of virus‐mediated lysis in spatiotemporal dynamics of prokaryotic communities in river–estuary–coastal ecosystems

Abstract Viral lysis accounts for approximately 50% of prokaryotic mortality, significantly influencing the diversity, composition, and succession of prokaryotic communities. Despite its importance, the specific influence of viral lysis on seasonal dynamics within aquatic ecosystems remains poorly understood. In this study, we investigated the seasonal dynamics of prokaryotes in the river–estuary–coastal ecosystem surrounding Xiamen Island and explored the environmental factors and virus‐mediated cell lysis driving microbial seasonal successions across spatiotemporal scales. A taxon‐specific cell lysis was applied to evaluate the contribution of viral lysis to seasonal variations in prokaryotes. Our findings revealed distinct spatiotemporal successions within the prokaryotic community structure, where temporal‐related factors, spatial‐related factors, and virus‐mediated cell lysis contribute comparably to the seasonal variation of prokaryotes. The viral lysis controls on prokaryotic structures were determined by a significant negative correlation between the total microbial community and the cell lysis index (CLI) from amplicon sequence variant (ASV) to order levels. Viral lytic shaping on prokaryotic communities was more pronounced in the estuary–coastal compared to the river region, with similar seasonal variations noted. Specific ASVs, such as ASV3 ( Nitrosopumilales ), ASV2 ( Synechococcales ), ASV16 ( Nitrosopumilales ), and ASV17 ( Oceanospirillales ) were significantly correlated with CLI, highlighting the pivotal role of viral lysis in their seasonal succession. This study highlights the intricate interplay between microbial populations and viral lysis across spatiotemporal scales, enhancing our understanding of how top‐down (virus‐mediated cell lysis) and bottom‐up (environmental factors) controls drive the seasonal variations in prokaryotic communities.