Soil pH decline promotes soil organic carbon accumulation by regulating the microbial carbon sequestration pathway

Microbial fixation of carbon dioxide (CO₂) is an important source of soil organic carbon (SOC). However, the factors and mechanisms influencing CO₂ sequestration driven by soil microorganisms remain poorly understood. In this study, farmland soil samples from 15 sites were collected in a typical watershed in Southwest China, and soil and microbial characteristics were comprehensively analyzed to uncover the key factors influencing microbial CO₂ sequestration. The results suggested that changes in soil pH were the main driving factor of SOC storage. Decreasing soil pH significantly increased the abundance of cbbL, pycA, and acsB, which led to CO₂ sequestration. Concurrently, the abundance of other functional genes involved in the Calvin cycle, the Reductive citrate cycle, and the Reductive acetyl–Coenzyme A (CoA) pathway, which was also differentially upregulated. Hyphomicrobiales, Pseudonocardiales, and Corynebacteriales were the core species carrying CO₂ sequestration genes, whose abundance at the order level further supported the hypothesis that changes in pH achieve SOC accumulation by affecting the function of the microbial community. This study uniquely highlights soil pH as a fundamental indicator that may have an important effect on microbial CO₂ sequestration and SOC accumulation through mesoscale sampling and genomic evidence, providing practical insight into the influences on microbial-mediated CO₂ sequestration.