biostudies-literatureLuo RJing-Jin-Ji Regional Integrated Environmental Improvement-National Science and Technology Major Project of Ministry of Ecology and Environment of China327https://www.ebi.ac.uk/biostudies/studies/S-EPMC12937692biostudies-literatureUnknown15(4)Riverine ecosystems represent critical nodes in the global carbon cycle, where the mechanistic role of viruses in modulating eukaryotic carbon cycling remains underexplored, particularly across heterogeneous landscapes. Here, we applied metatranscriptomics to dissect how multi-scale environmental factors and viral gene activity jointly regulate the spatial transcription of carbon cycling genes in riverine eukaryotic communities along the Yongding River, China. Our analyses reveal pronounced spatial heterogeneity in both viral gene expression-notably major capsid proteins of large eukaryotic DNA viruses-and carbon fixation, conversion, and metabolism pathways, peaking in agriculturally impacted plain regions. Multivariate statistics and network analyses demonstrate that land use enhances viBiologySynergistic Effects of Viruses and Environmental Gradients on Carbon Cycling in a River Ecosystem.PMC12937692No. 2025ZD1200800,2025ZD1200803Lin SWang SBo JLuo RDeng HKong WfalseSynergistic Effects of Viruses and Environmental Gradients on Carbon Cycling in a River Ecosystem.Riverine ecosystems represent critical nodes in the global carbon cycle, where the mechanistic role of viruses in modulating eukaryotic carbon cycling remains underexplored, particularly across heterogeneous landscapes. Here, we applied metatranscriptomics to dissect how multi-scale environmental factors and viral gene activity jointly regulate the spatial transcription of carbon cycling genes in riverine eukaryotic communities along the Yongding River, China. Our analyses reveal pronounced spatial heterogeneity in both viral gene expression-notably major capsid proteins of large eukaryotic DNA viruses-and carbon fixation, conversion, and metabolism pathways, peaking in agriculturally impacted plain regions. Multivariate statistics and network analyses demonstrate that land use enhances vi2026-01-01T00:00:00Z2026 Feb2026-07-11T03:16:51.185Z2026-07-11T03:09:22.236ZS-EPMC129376924174463610.3390/biology15040327