Exploring the Impacts of Postharvest Processing on the Microbiota and Metabolite Profiles during Green Coffee Bean Production

Abstract

The postharvest treatment and processing of fresh coffee cherries can impact the quality of the unroasted green coffee beans. In the present case study, freshly harvested Arabica coffee cherries were processed through two different wet and dry methods to monitor differences in the microbial community structure and in substrate and metabolite profiles. The changes were followed throughout the postharvest processing chain, from harvest to drying, by implementing up-to-date techniques, encompassing multiple-step metagenomic DNA extraction, highthroughput sequencing, and multiphasic metabolite target analysis. During wet processing, a cohort of lactic acid bacteria (i.e., Leuconostoc, Lactococcus, and Lactobacillus) was the most commonly identified microbial group, along with enterobacteria and yeasts (Pichia and Starmerella). Several of the metabolites associated with lactic acid bacterial metabolism (e.g., lactic acid, acetic acid, and mannitol) produced in the mucilage were also found in the endosperm. During dry processing, acetic acid bacteria (i.e., Acetobacter and Gluconobacter) were most abundant, along with Pichia and non-Pichia (Candida, Starmerella, and Saccharomycopsis) yeasts. Accumulation of associated metabolites (e.g., gluconic acid and sugar alcohols) took place in the drying outer layers of the coffee cherries. Consequently, both wet and dry processing methods significantly influenced the microbial community structures and hence the composition of the final green coffee beans. This systematic approach to dissecting the coffee ecosystem contributes to a deeper understanding of coffee processing and might constitute a state-of-the-art framework for the further analysis and subsequent control of this complex biotechnological process.IMPORTANCE Coffee production is a long process, starting with the harvest of coffee cherries and the on-farm drying of their beans. In a later stage, the dried green coffee beans are roasted and ground in order to brew a cup of coffee. The on-farm, postharvest processing method applied can impact the quality of the green coffee beans. In the present case study, freshly harvested Arabica coffee cherries were processed through wet and dry processing in four distinct variations. The microorganisms present and the chemical profiles of the coffee beans were analyzed throughout the postharvest processing chain. The up-to-date techniques implemented facilitated the investigation of differences related to the method applied. For instance, different microbial groups were associated with wet and dry processing methods. Additionally, metabolites associated with the respective microorganisms accumulated on the final green coffee beans.

Influence of Solar Radiation and Wet Processing on the Final Quality of Arabica Coffee

“…This fact may have influenced positively the fermentation with water for the experiment located in the South-Southeast and influenced it negatively in the experiment located in the East, confirming the need for greater monitoring during the fermentation stages of Arabica coffee [14].…”

“…For De Bruyn et al [14], further studies should be undertaken to strengthen the understanding of the impact of the microbiota on coffee quality and provide robust data for the development of more controlled fermentation processes.…”

“…The works of Silva et al [8], Silva et al [9], and Pereira et al [10] have discussed the significant effect of yeasts during the fermentation process, and those of Ribeiro et al [11], Evangelista et al [12], Masoud and Jespersen [13], and finally De Bruyn et al [14] discussed the effect of bacteria. These microorganisms were detected in wet fermentation processes of the Arabica coffee, generating significant impacts on coffee quality.…”

Effect of Different Fermentation Methods on Physicochemical Composition and Sensory Quality of Coffee (Coffea arabica)

“…Hence acids generated by the microorganisms during fermentation accumulates in the beans. A report by [6] indicate that microbial metabolites such as acetic acids produced during post-harvest processing accumulate in the coffee beans. The presence of these acids could lower pH levels.…”

“…The better cup quality produced from naturally fermented coffee is mainly attributed to the involvement of microorganisms in the degradation process of mucilage. These microorganisms produce volatile flavoring compounds which can diffuse in to the beans [6]. A literature report by Nigam and Singh [9] noted that free amino acids could be released in the bean following the degradation of proteins during the fermentation process in coffee.…”