The over-estimation of long-term mineral fertilizer on CO2 release from soil carbonates

Soil inorganic carbon (SIC) contributes up to half to the soil carbon (C) stock globally and is especially crucial in arid and semi-arid zones. Widespread soil acidification due to fertilization neutralize carbonates getting an irrecoverable net source of CO2 out of SIC. Nevertheless, SIC is generally neglected as a CO2 source and disregarded in the C balance between soil and atmosphere. A 40-year fertilization field experiment provides an excellent option to investigate the influences of mineral and organic fertilizers on carbonate-derived CO2 efflux by partitioning CO2 sources using the δ13C signature. Although 40 years of mineral fertilizers caused soil acidification and SIC neutralization, SIC-derived CO2 was comparable with that from the control soils. This could be explained by that mineral fertilizer decreased soil-derived CO2 production and the partial pressure of soil CO2, which led to the weak reduction of SIC dissolution in the long term. Thus, the annual contribution of SIC-derived CO2 to total CO2 under long-term mineral fertilization may look as of minor importance. Organic fertilizers (manure, straw) reduced the proportional contribution of SIC-derived CO₂ by 16–42 % relative to controls, despite elevating total CO₂ emissions by 5.4–9.1 Mg C ha⁻¹ yr⁻¹. This divergence stems from Ca²⁺ inputs during organic matter decomposition, which catalyzed CO₂ reprecipitation as pedogenic carbonates, decoupling dissolution from atmospheric release. Crucially, manure amendments achieved net soil C sequestration (0.47 Mg C ha⁻¹ yr⁻¹). In contrast, straw-induced SIC losses (2.0 Mg C ha⁻¹ over 40 years) negated 52 % of SOC gains, yielding marginal net sequestration (2.4 ± 1.7 Mg C ha⁻¹). These results underscore the imperative to evaluate SIC-SOC interactions when assessing the climate efficiency of organic management. SIC-derived CO₂ efflux fluctuated seasonally, peaking during the flowering phase (19–35 % of total emissions), then declining by 5.0–9.7 %. This temporal decoupling highlights rhizosphere activity as a key regulator of SIC. Ignoring SIC contributions led to a 35 % overestimation of heterotrophic respiration in total CO₂ efflux, illustrating systemic biases in current C models. Our findings advocate for manure-based management to maximize C sequestration not as SOC but as SIC and to minimize CO2 emissions from SIC, a dual strategy to reconcile agricultural productivity with climate resilience in semi-arid regions.