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The conversion of native forests to coffee plantations in the Atlantic Forest biome has altered soil organic matter (SOM) dynamics, particularly carbon (C) and nitrogen (N) stocks. This study evaluated SOM fractions, molecular composition, and microbial diversity in coffee plantations under conventional (CC), natural (NC), and organic (OC) management, compared with natural vegetation (NV), across three farms in Araponga, Minas Gerais, Brazil. Soil samples were collected under the canopy and between planting rows, at depths of 0.0 to 1.0 m, using a 4 x 2 factorial design with four replicates. Total C and N stocks ranged from 164.28 to 248.66 Mg C ha-1 and from 9.89 to 16.01 Mg N ha-1, respectively, with reductions of 25-34% in cultivated systems relative to NV. More than 65% of soil C was stored below 0.15 m, highlighting the importance of subsoil layers for long-term stabilization. The OC system showed greater litter biomass, root density, and allocation of C and N to mineral-associated organic matter (MAOM) and particulate organic matter (POM), where over 84% of SOM was stabilized. In contrast, NC exhibited higher N mineralization rates (254.1 kg N ha-1), associated with legume presence. Thermochemolysis (TMAH) indicated a predominance of lipids and long-chain alkanes (14-26), particularly at depth, indicating greater molecular recalcitrance. Microbial communities varied among systems, with higher fungal abundance in NC and dominance of Gram-negative bacteria across all systems. Overall, organic management enhanced C sequestration following conversion from CC, underscoring its potential for climate change mitigation in tropical agroecosystems.
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