Carbon (C) storage potential was quantified for four tree species which are commonly incorporated into tree-based intercropping (TBI) systems and compared with conventional agricultural systems in southern Ontario, Canada. In the 31-year-old TBI system at the University of Guelph’s Agroforestry Research Station, Norway spruce (<em>Picea abies</em>), white cedar (<em>Thuja occidentalis</em>), black walnut (<em>Juglans nigra</em>) and red oak (<em>Quercus rubra</em>) were planted in tree rows, intercropped with soybean (<em>Glycine max</em>). In the conventional agricultural field, soybean was grown in a monocropping system. Above and belowground tree and crop C content, soil organic C (SOC) and system level C was quantified for each tree species as well as the conventional agricultural system. Red oak TBI systems had the highest SOC followed by black walnut, Norway spruce and white cedar with values of 93.2, 83.9, 78.1, and 72.2 t C ha<sup>-1</sup>, respectively. Red oak TBI systems also had the highest mean tree C content, followed by black walnut, Norway spruce and white cedar, with values of 299.7, 285.8, 255.4 and 70.1 kg C tree<sup>-1</sup>, respectively. Total system level C, which incorporated SOC, tree C content and tree planting densities was 134.8, 126.4, 115.7, 95.6 and 75.6 t C ha<sup>-1</sup> respectively for spruce, oak, walnut and cedar TBI systems and the agricultural field. TBI systems provide higher C sequestration potentials than conventional agricultural fields, and Norway spruce and red oak should be included into TBI systems in southern Ontario to maximize C sequestration benefits.
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