Soil amelioration impacts viral ecology in saline-alkali lands.

The continuous expansion of saline-alkali lands under climate change threatens food security and reduces soil carbon stocks. A common mitigation strategy is soil amelioration, which converts degraded soils back into an arable state. Microbes play critical roles in soil health and recovery. However, the viruses that infect these microbial communities, and their potential impacts during saline-alkali soil restoration, remain largely unknown. Here, we combined total soil metagenomics and viromics to investigate host-linked viral ecology across four major saline-alkali regions in China, each encompassing two soil amelioration statuses: saline-alkali and reclaimed. We found that viral community structure was shaped by both geography and soil amelioration status, with salinity and alkalinity emerging as key environmental factors. Viral populations were sensitive to soil restoration, showing strong amelioration-status endemism with functional adaptations. Virus-host dynamics ranged from reduced temperate viruses to abundance mismatches in those infecting key carbon-cycling microorganisms, including carbohydrate degraders. 13C-cellulose DNA-SIP experiments provided further support for this mismatch by tracing assimilated carbon transfer between active host and virus populations. Compared with saline-alkali soils, the relative abundance of hosts in restored soils increased from 39.0% to 61.0%, whereas the linked viruses decreased from 60.6% to 39.4%. Together, these findings reveal an underappreciated role of viruses in shaping saline-alkali soil amelioration trajectories, and could improve management strategies for degraded land recovery and carbon storage.