Microbial dormancy under freeze–thaw cycling regulates alpine soil responses to warming

Abstract Microbial regulation of soil carbon cycling in cold ecosystems remains poorly constrained in Earth system models, largely due to limited observations and unresolved mechanisms. Here, we develop a freeze–thaw-enabled microbial-ecological model (MEND-FT) and integrate it with multi-year whole-soil warming experiments in an alpine meadow on the Qinghai-Tibetan Plateau to investigate warming effects on soil carbon dynamics from microbial physiology to ecosystem processes. This experiment-model framework reveals amplified warming impacts during non-growing seasons, an underexplored period, driven by reduced frozen depths ( − 43 cm), prolonged thaw duration ( + 38 days), and widespread microbial dormancy. MEND-FT reproduces observed minimal enzyme responses and resolves seasonal microbial activity shifts via dormancy regulation, mechanisms absent from previous analyses. We further refine microbial carbon use efficiency estimates to align with ecosystem-level benchmarks, showing slight but persistent declines under warming. Long-term simulations suggest that the modest soil carbon loss ( − 2.2%) co-occurs with increased microbial biomass and enhanced oxidase activity, consistent with freeze-thaw-induced microbial physiological regulation rather than substrate depletion alone. Together, these findings provide compelling evidence that microbial dormancy-resuscitation dynamics govern soil carbon responses to climate and environmental changes, offering a scalable and transferable mechanistic framework for improving predictions of soil carbon persistence and greenhouse gas emissions across diverse biomes.