Divergent Responses of Bacterial Communities to Permafrost Degradation and Their Associations With Carbon Across Vertical Profiles

ABSTRACT Permafrost degradation poses a significant threat to the organic carbon (C) pool primarily through regulating microorganisms. However, microbial responses and their associations with C loss across vertical profiles remain unclear. Here, we use metagenomic sequencing to investigate bacterial communities in 125 samples from five 15 m‐depth permafrost cores, spanning from the active layer to the permafrost layer along a degradation gradient on the Qinghai‐Tibet Plateau. We find that α ‐diversity decreases, while stochastic processes and community stability increase from the active layer to the permafrost layer. Along permafrost degradation, these community attributes follow similar variations within the active layer but remain constant within the permafrost layer. The relative abundance and interaction of core taxa play important roles in maintaining community stability in the active and permafrost layers, respectively. As permafrost degrades, the negative relationships between community stability and C storage become more intense, especially in the active layer. These findings demonstrate that degradation induces microbial responses that potentially amplify C release, supporting a positive feedback loop to climate warming. Our work provides novel insights into the vertical heterogeneity of this mechanism and is crucial for modeling future permafrost C dynamics.