The cultivation of crops in the presence of trees (agroforestry) and organic agriculture are management strategies thought to reduce nutrient losses to the environment and increase soil organic matter. Little is known, however, about the differences between organic and conventionally managed agroforests. This research examines how soil nutrient pools and mechanisms for nutrient retention may vary between these two different types of coffee agroforests. We determined variation in soil nutrient pools and nutrient retention capacity among (1) coffee farms in Costa Rica receiving mineral (conventional management) and organic inputs (organic management) and (2) different combinations of shade tree species. Soil nutrient pools and retention capacity were altered by fertilizer management. Soil nitrogen (N) and carbon (C) pools were significantly larger in conventional agroforests, but C:N ratios were similar among agroforests. Soil phosphorus (P) pools were significantly higher in organic agroforests. Overall, C and N concentrations were strongly positively correlated with oxalate-extractable aluminum concentrations. We did not observe many strong species effects; however, soil cation exchange capacity was higher under Coffea–Musa combinations than under Coffea and N-fixing Erythrina combinations. Thus, mechanisms are in place to promote nutrient retention in agroforestry systems, but these mechanisms can be altered by management practices with consequences for long-term nutrient storage.
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