Coffee, microbial diversity and agroecology: a path towards sustainable production

Abstract Crop management practices impact soil and coffee fruit microbial communities. The objective of this study was to compare the profile of bacterial and fungal communities from soil and fruits of Coffea arabica L. cultivated under conventional and agroforestry management systems in southern Minas Gerais, Brazil, using three biological replicates per system. Soil chemical properties were measured by routine chemical analyses, whereas microbial communities were determined by high-throughput sequencing from soil and fruit samples. Arbuscular mycorrhizal fungi (AMF) were also evaluated by means of spore counts and root colonization. Canonical correlation analysis indicated that the pH, calcium (Ca), organic matter, magnesium (Mg), and available phosphorus had higher influence on bacteria and fungus diversity in the agroforestry management than conventional system. Beta diversity of bacterial and fungal communities in soil and coffee fruits showed significant variations among the different management systems analyzed. However, there were no significant differences in the alpha diversity indices between them. Fifty-two Amplicon Sequence Variants (ASVs) of AMFs were identified in the soil samples. Only a small proportion (8%) of ASVs were shared between the two management systems. However, agroforestry system also showed greater mycorrhizal colonization and a higher number of spores than conventional system. Our results highlight the importance of microbial biodiversity for the long-term sustainability of agroecosystems, but further studies are needed to investigate functional microbial activities and their effects on coffee quality.