Effects of replacing chemical fertilizer with organic fertilizer on organic carbon mineralization and carbon cycle functional genes in yellow soil

Fertilization-mediated soil organic carbon (SOC) mineralization is a key process in agroecosystem carbon cycling, yet the microbial mechanisms involved under different fertilization regimes remain unclear. This study, based on a three-year field experiment in acidic yellow soil (Ultisol) in Guizhou, integrated SOC mineralization incubation and metagenomic sequencing to compare SOC mineralization and functional gene profiles under no fertilization (CK), chemical fertilizer alone (NP), and replacing chemical fertilizer with 50% or 100% organic fertilizer (1/2NPM and M). Fertilization significantly increased cumulative mineralized SOC (C t ) ( p < 0.05); NP showed high mineralization, whereas organic-fertilizer replacement reduced the cumulative mineralization ratio (C t /SOC). Metagenomic analysis indicated NP did not substantially alter carbon-cycling genes but lowered the C/N ratio, increasing microbial diversity and driving “carbon-compensation” mineralization. Conversely, 1/2NPM and M improved soil pH, available phosphorus (AP), and nitrate nitrogen (NO₃ − -N), reshaped microbial community structure, up-regulated carbon-fixation genes ( korA , facA , coxS ), and suppressed carbon-degradation genes ( pel , chi ), enhancing carbon sequestration capacity. Partial least squares path modeling confirmed a “stoichiometry-community diversity” cascade significantly regulated SOC mineralization ( p < 0.01), with organic-fertilizer replacement shifting functional profiles from carbon degradation to carbon fixation.