Résumé
Cocoa fermentation is a spontaneous fermentation that lasts 4 to 8 days. It is mainly based on the succession of three groups of microorganisms: yeasts, lactic acid bacteria and acetic bacteria that carry out respectively the alcoholic, lactic and acetic fermentation. The beans are sterile until the opening of the pod. The inoculation of the beans is usually naturally done using the environment around the pod opening and the fermentation process. Post-harvest treatment processes differ from one country to another and influence the fermentation progress. However, three species of lactic and acetic bacteria (L. plantarum, L. fermentum and A. pasteurianus) dominate the fermentations in all countries. On the other hand, their intraspecific diversity was rarely studied. In this study, we used the metabarcoding method to study the interspecific diversity of bacterial communities associated with the fermentation of cocoa beans in 3 countries: Mexico, Ivory Coast and Guyana. In addition, this method was used to identify the contribution of the surfaces related to the pre- and post-harvest environment of cocoa pods during the fermentation, which was carried out in Mexico. The dominance of the genera Lactobacillus and Acetobacter during fermentation in each country has been confirmed. In addition, the presence of country-specific genera was founded on the first day of fermentation. All the surfaces linked to the fermentation environment participate to the inoculation of the dominant genera. They act as bacterial tanks. A collection of lactic and acetic bacteria strains was produced. L. plantarum and A. pasteurianus were the most isolated species. Intra-specific diversity of A. pasteurianus strain was studied. For this, their genomic polymorphisms were analyzed using PCR amplification on repeated sequences and their biochemical characteristics were compared in a specific medium, simulating the conditions of the cocoa pulp at the 2nd day of fermentation. Our study showed that the strains of A. pasteurianus could be present in the three different countries. Some strains were distinguished for their greater affinity for lactic acid than the others, which is interesting in order to improve the organoleptic quality of the final cocoa. The results on intra-specific diversity allow us to propose potential candidates for the production of culture starters for the fermentation of cocoa beans.