Facility‐specific ‘house’ microbiome ensures the maintenance of functional microbial communities into coffee beans fermentation: implications for source tracking

Abstract

This work aimed at studying the unconfirmed hypothesis predicting the existence of a connection between coffee farm microbiome and the resulting spontaneous fermentation process. Using Illuminabased amplicon sequencing, 360 prokaryotes and 397 eukaryotes were identified from coffee fruits and leaves, over-ripe fruits, water used for coffee de-pulping, depulped coffee beans, soil, and temporal fermentation samples at an experimental farm in Honduras. Coffee fruits and leaves were mainly associated with high incidence of Enterobacteriaceae, Pseudomonas, Colletotrichum, and Cladosporium. The proportion of Enterobacteriaceae was increased when leaves and fruits were collected on the ground compared to those from the coffee tree. Coffee farm soil showed the richest microbial diversity with marked presence of Bacillus. Following the fermentation process, microorganisms present in depulped coffee beans (Leuconostoc, Gluconobater, Pichia, Hanseniaspora, and Candida) represented more than 90% of the total microbial community, which produced lactic acid, ethanol, and several volatile compounds. The community ecology connections described in this study showed that coffee fruit provides beneficial microorganisms for the fermentation process. Enterobacteria, Colletotrichum, and other microbial groups present in leaves, fruit surface, over-ripe fruits, and soil may transfer unwanted aromas to coffee beans, so they should be avoided from having access to the fermentation tank.

Influence of Environmental Microbiota on the Activity and Metabolism of Starter Cultures Used in Coffee Beans Fermentation

“…The coffee farm soil showed a rich and complex microbial diversity, with 214 bacterial groups (Table S1). The high diversity found in the soil was also observed in other coffeeproducing regions, such as China, Ecuador, Mexico, Brazil, and Honduras [9,10,[28][29][30]. However, most of the bacterial groups that have been identified in coffee farm soils (e.g., Amycolatopsis, Bacillus, Bradyrhizobium, Pseudolabrys, Rhodoplanes, and Sphingomonas) are not associated with the fermentation process, so it should be avoided from having access to the fermentation tank.…”

“…On the other hand, the marked presence of filamentous fungi, such as Cladosporium, Colletotrichum, Fusarium and Mycosphaerellaceae are undesirable in the fermentation process and control measures should be adopted to reduce the contact of soil, leaves, fruits collected from the ground and over-ripe fruits with the fermentation tank. Interestingly, the genera Cladosporium and Fusarium were also observed at high frequency in soil from a Honduran coffee farm [10]. S1).…”

“…Interestingly, the genera Cladosporium and Fusarium were also observed at high frequency in soil from a Honduran coffee farm [10].…”

“…Samples were sequenced in the MiSeq platform using the 500 V2 kits, following standard Illumina protocols. Bioinformatics analyses were performed according to Vale et al [10].…”

“…1 High incidence of Enterobacteriaceae has already been reported in grape and coffee plantations [9,10,24]. In vineyards, this family is considered beneficial because they produce proteases, chitinases and glucanases, which make them excellent antagonistic microorganisms [25].…”