Soil fungal communities differ between shaded and sun-intensive coffee plantations in El Salvador

We collected soil samples from a sun coffee system, shade coffee system, and nearby forest from Izalco, Sonsonate, El Salvador. At each coffee system, we collected soil samples from the surface (upper) and 10 cm below the surface (lower), and from the coffee plant drip line (drip line) and the walkway between two plants (walkway). Forest samples were collected from the soil surface only. We used high-throughput ITS meta-barcode sequencing to characterize soil fungal communities and assigned fungal taxa to functional guilds using FUNGuild. Dataset includes R code for main analyses (coffee_R.R). Main files to bring in for that code are the feature table (ASV x sample matrix) = "table-with-taxonomy2.biom", metadata file = "sample_metadata_coffee_final2.txt", tree file = "tree.nwk". Second R file is for the analyses after funguild categories were assigned (coffee_R_funguild.R). The same files are brought in except the taxonomy file to use is "coffee_taxonomy_funguild.csv" which has the funguild assignments.