Soil microbial composition varies in response to coffee agroecosystem management

ABSTRACTSoil microbes are essential to the continued productivity of sustainably-managed agroecosystems. In shade coffee plantations, the relationship between soil microbial composition, soil nutrient availability, and coffee productivity have been demonstrated, but the effect of management on the composition of the soil microbial communities remains relatively unexplored. To further understand how management modulates the soil microbiome, we surveyed the soil fungal and bacterial communities, as well as soil chemistry and canopy composition in a Nicaraguan coffee cooperative, across 19 individual farms. Using amplicon sequencing, we found that management (organic or conventional), stand age, and previous land use strongly affected the soil microbiome, albeit in different ways. Bacterial communities were most strongly associated with soil chemistry, while fungal communities were more strongly associated with the composition of the canopy and historical land use of the coffee plantation. Notably, both fungal and bacterial richness decreased with stand age. In addition to revealing the first in-depth characterization of the soil microbiome in coffee plantations in Nicaragua, our results highlight how fungal and bacterial communities are simultaneously modulated by long-term land use legacies (i.e., an agricultural plot’s previous land use) and short-term press disturbance (i.e., farm age).One-sentence-summaryThe composition of soil fungal and bacteria communities in shade coffee plantations depend on the combination of the farm’s management type, its previous land use, and the coffee plants’ stand age, but are differently influenced by each.