Fungal ASVs strongly associated with the coffee bushes in both sun and shade systems and rarely found in the forest samples.

All fungi belong to the Ascomycota phylum. We used NCBI BLASTN 2.9.0+ to present greater taxonomic information, beyond what was assigned using QIIME2 (denoted by *), if greater taxonomic information was available. Four ASVs could be categorized into a trophic mode using FUNguild and our criterion for assignment, two were ‘probable’ pathotrophs (ASV ID underlined) and two were ‘probable’ saprotrophs (ASV ID italicized).