Data from: Contrasting patterns of functional diversity in coffee root fungal communities associated with organic and conventionally-managed fields

The structure and function of fungal communities in the coffee rhizosphere
is shaped by crop environment. Because coffee can be grown along a
management continuum from conventional application of pesticides and
fertilizers in full sun to organic management in a shaded understory, we
used coffee fields to hold host constant while comparing rhizosphere
fungal communities in markedly different environmental conditions with
regard to shade and inputs. We characterized the shade and soil
environment in 25 fields under conventional, organic or transitional
management in two regions of Costa Rica. We amplified the ITS2 region of
fungal DNA from coffee roots in these fields and characterized the
rhizosphere fungal community via high-throughput sequencing. Sequences
were assigned to guilds to determine differences in functional diversity
and trophic structure among coffee field environments. Organic fields had
more shade, a greater richness of shade tree species, more leaf litter,
and were less acidic, with lower soil nitrate availability and higher soil
copper, calcium, and magnesium than conventionally-managed fields,
although differences between organic and conventionally-managed fields in
shade, calcium and magnesium depended on region. Differences in richness
and community composition of rhizosphere fungi between organic and
conventionally-managed fields were also correlated with shade, soil
acidity, nitrate, and copper. Trophic structure differed with coffee field
management. Saprotrophs, plant pathogens, and mycoparasites were more
diverse and plant pathogens were more abundant in organic than in
conventionally-managed fields, while saprotroph-plant pathogens were more
abundant in conventionally-managed fields. These differences reflected
environmental differences and depended on region. IMPORTANCE Rhizosphere
fungi play key roles in ecosystems, as nutrient cyclers, pathogens, and
mutualists, yet little is currently known about which environmental
factors and how agricultural management shape rhizosphere fungal
communities and their functional diversity. This field study of the coffee
agroecosystem suggests that organic management not only fosters a greater
overall diversity of fungi, but also maintains a greater richness of
saprotrophic, plant pathogenic and mycoparasitic fungi that has
implications for efficiency of nutrient cycling and regulation of plant
pathogen populations in agricultural systems. As well as influencing
community composition and richness of rhizosphere fungi, shade management
and use of fungicides and synthetic fertilizers altered the trophic
structure of the coffee agroecosystem.