Humans have replaced biologically rich mid-elevational forests with coffee (Coffea arabica) throughout the tropics. Coffee, like many crops, is cultivated on farms that fall along a continuum from conventional to organic management. How do differences in management affect mycorrhizal associations? What might be the long-term consequences for rhizosphere fungal diversity? In this two-year study, we sought to address these questions by characterizing differences in fungal community composition (via high throughput sequencing of DNA extracts from coffee roots using fungal ITS2-specific primers) and environmental parameters (including fertilizer and pesticide use, soil nutrients, shade, shade tree richness, leaf litter depth, slope, aspect and elevation) for twenty-five conventional and organic coffee fields in two regions of Costa Rica, Santa Elena de Monteverde and San Vito de Coto Brus.
Four environmental factors consistently differed between conventionally-managed and organic fields: shade, shade tree diversity, leaf litter and available nitrate in the soil. Organic fields had more than twice as many shade tree species, twice as much shade, nearly twice as much leaf litter, and one-third as much soil nitrate as conventional fields. Abundance and richness of AM fungi, ascomycetes and basidiomycetes were positively correlated with aspects of tree cover (shade, leaf litter, tree richness) and negatively correlated with soil nitrate availability. Species richness of AM fungi was higher in organic fields than conventional ones. The AM fungal community was more homogeneous in composition in conventional fields than in organic fields, and only organic fields exhibited differences in community composition between regions. While abundances of most of the 58 AM fungal species detected in this study did not differ between coffee field types, 3 species in the Ambisporaceae and Gigasporaceae were more abundant in conventional coffee and 5 in the Glomeraceae, Acaulosporaceae and Diversisporaceae were more abundant in organic fields. Abundances of almost all AM fungal species were either uncorrelated or negatively correlated with soil nutrient availability and positively correlated with shade, with the exception of Gigaspora margarita. Our results suggest that coffee farms managed for tree species diversity, soil cover, and minimal additions of nitrate will maintain a greater diversity of fungi. Correlating environmental variables with frequency of detection of individual species offers insights into potential drivers for maintenance of species diversity and the role of niche conservatism in determining community composition.