Soil and cherry bacterial communities predict flavor on coffee farms

Coffee (Coffea arabica) is a popular beverage worldwide with increasing value placed on sensory qualities as specialty markets grow. Plant-associated microbiomes have emerged as a potential but poorly understood driver of coffee flavor that may interact with other environmental and farm management factors. To determine if coffee plant-associated bacteria are linked with flavor, we collected 320 soil and 320 coffee cherry samples from 22 farms in Cundinamarca, Colombia that varied in farm management system (shade vs. sun-grown) and in flavor (presence vs. absence of a specialty flavor profile). We found, using amplicon sequencing, that soil and cherry bacterial communities differed between sun and shade farms and between farms that did and did not produce specialty flavored coffee, with shade + flavor farms notably distinct. Flavor presence was predicted by the abundance of multiple bacterial strains in soils and cherries, but correlations with flavor differed between sun and shade systems. These bacterial taxa correlated with coffee flavor may guide future efforts to optimize farms for specialty quality characteristics. Overall, the observed complex relationships between plant-associated bacteria and coffee flavor will likely require that initiatives seeking to optimize microbiomes for quality outcomes be tailored to individual farm systems and local conditions.