Characterization of the Coffea arabica microbiome: a comparative study of soil and fruit microbial communities under different managements

This document is a master's thesis that characterizes the microbiome of Coffea arabica by comparing soil and fruit microbial communities under two fertilization management systems: conventional (chemical) and organic. In the chapter on the fruit, amplicon analysis showed that organic fertilization reduces dependence on chemical inputs, promotes the development of beneficial microbial communities, and improves plant health, also contributing to the consistency of the beverage's quality and sensory attributes. In the chapter on the soil, a metagenomic analysis showed that soils managed with organic fertilization exhibit greater functional diversity of microorganisms, which play essential roles in nutrient cycling, pathogen suppression, and mitigating the effects of climate change (greater carbon sequestration and lower emissions). The study is presented as pioneering by investigating in situ the functional dynamics of the microbiome in coffee plantations under different fertilization regimes, highlighting that sustainable practices, combined with a better understanding of the microbiome, are key to ensuring productivity, quality and sustainability in coffee farming.