What’s brewing? Impacts of cultivation management on the Coffea arabica soil microbiome

Coffea arabica (coffee) is cultivated on ~28-million acres and is essential to local economies in the tropics. Coffee cultivation, however, is threatened by ongoing climate change as its optimal growth occurs in narrow temperature and precipitation ranges. Areas currently growing coffee might become unsuitable leading to increased deforestation and negative effects on coffee quality. These impacts may be especially strong in coffee cultivated in sun-grown monocultures (~75% of all production) versus shade-grown agroforestry systems given relatively higher temperatures in deforested landscapes. As such, shade-grown coffee systems might be one management strategy used to buffer from future climatic shifts. While shade-grown systems provide many ecosystem benefits, the impact of the cultivation system on soil microbiomes is poorly understood. Soil microorganisms perform vital ecosystem functions including aiding plants in nutrient acquisition, buffering against stress, as well as improving nutrient cycling. This is particularly true in shade-grown coffee systems where soil carbon could be increased through increased microbial biomass and soil nitrogen could be increased through increased plant-association with N-fixing bacteria. Therefore, further understanding of the effects of coffee cultivation methods on soil microbial communities may be key to future coffee productivity and local soil biogeochemical function. To explore these themes, we sampled the soil microbial communities at 30 coffee farms in Colombia, Peru, and El Salvador. These farms varied in cultivation system (sun vs. shade) and flavor profiles that separate specialty grade from conventional quality. Our aim was to explore if soil microbiome diversity and composition differ among the three countries, cultivation systems, and coffee quality. We sequenced the DNA of bacterial (16S) and fungal (ITS) communities in coffee soil on an Illumina MiSeq with analysis completed in QIIME2 to identify microbial taxa and composition. Coffee soil microbiomes had similar relative abundance of phyla and similar number of bacterial and fungal taxa, regardless of country of origin or cultivation system. However, coffee soil microbiomes showed pronounced differences in the microbial community composition among the different countries and cultivation systems. We show that biogeography is an important determinant of coffee soil microbiomes and location-specific impacts need to be considered in future coffee management. Further, our data suggests that sun-grown systems can alter microbial community composition compared to more-sustainable shade-grown systems potentially changing soil functionality. As an example, there were increases in taxa punitively classified as mycorrhizal fungi and N-fixing bacteria in shade-grown coffee systems. Our next steps are to link this microbial data to coffee quality and soil characteristics to uncover potential factors influencing the community structure as well as nutrient cycling rates.