Soil texture mediates soil organic matter persistence pathways under winter warming and crop diversification in agroecosystems

Soil organic matter (SOM) chemistry in agroecosystems is strongly influenced by land management and climate change, yet it remains unclear how climate-smart practices and warming interact with soil texture to influence SOM transformation and persistence. We applied targeted and non-targeted analyses to investigate the impacts of diverse crop rotations (DCR) and DCR combined with winter warming (DCR + W) on SOM chemistry across two agricultural soils (loamy sand and silt loam). After eight years of treatment, neither DCR nor DCR + W significantly altered total soil carbon (C), despite changes in SOM composition and microbial communities. Across soil types, DCR and DCR + W reduced microbial biomass by 26–34% relative to the conventional treatment and altered microbial community structure. In the silt loam soil, DCR, especially with warming, was associated with greater accumulation of microbial-derived compounds, consistent with potential physicochemical protection in a finer textured soil. Contrastingly, the coarse textured soil showed greater accumulation of plant-derived compounds, although losses of cutin- and suberin-derived biopolymers under DCR indicated treatment-dependent differences in their transformation and retention. Overall, DCR and winter warming altered SOM composition without detectable changes in total soil C, with soil texture heavily influencing molecular responses. These findings demonstrate that soil properties provide important context for how climate-smart practices and a changing climate influence SOM transformation and highlight the value of molecular-level measurements for detecting changes that are not apparent from soil C metrics alone.