Perennial legumes in crop rotations increase soil C sequestration from greater productivity with N2 fixation. Here, we corroborated increases in soil organic carbon (SOC) and harvests modelled in 5 yr wheat–oats–barley–alfalfa/brome–alfalfa/brome (5Y) vs. 2 yr wheat–fallow (WF) rotations with those measured from 1929 to 2018. Harvest and SOC gains of 100–150 g C m−2 yr−1 and 15–25 g C m−2 yr−1 were modelled and measured in 5Y vs. WF rotations with different fertilizer and manure amendments. Modelled gains were closely related to annualized rates of N2 fixation by alfalfa of 8–10 g N m−2 yr−1. However, N2 fixation also drove increases in modelled N2O emissions of ca. 0.06 g N m−2 yr−1, which partially offset gains in SOC. Gains in harvest, SOC, and N2O emissions of 60–90 g C m−2 yr−1, 15 g C m−2 yr−1, and 0.05 g N m−2 yr−1 were modelled and measured in both rotations with amendments of N + P relative to unamended treatments. Harvest and SOC gains were smaller, and leaching and N2O losses larger, with amendments of N without P. After 100 yr of RCP 8.5 climate change, harvests in WF changed little from those in baseline runs, whereas those in 5Y rose with N + P because of increased N2 fixation. SOC declined in WF with all amendments and could only be raised in 5Y with N + P amendments. These model findings indicated the importance of N2 fixation and P amendments in determining responses of agroecosystem productivity and C sequestration to climate change.
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