Traditional fermentations of the local Ecuadorian cocoa type Nacional, with its fine flavor, are carried out in boxes and on platforms for a short time. A multiphasic approach, encompassing culture-dependent and -independent microbiological analyses of fermenting cocoa pulp-bean samples, metabolite target analyses of both cocoa pulp and beans, and sensory analysis of chocolates produced from the respective fermented dry beans, was applied for the investigation of the influence of these fermentation practices on the yeast and bacterial species diversity and community dynamics during cocoa bean fermentation. A wide microbial species diversity was found during the first 3 days of all fermentations carried out. The prevailing ethanol-producing yeast species were Pichia kudriavzevii and Pichia manshurica, followed by Saccharomyces cerevisiae. Leuconostoc pseudomesenteroides (glucose and fructose fermenting), Fructobacillus tropaeoli-like (fructose fermenting), and Lactobacillus fermentum (citrate converting, mannitol producing) represented the main lactic acid bacterial species in the fermentations studied, resulting in intensive heterolactate metabolism of the pulp substrates. Tatumella saanichensis and Tatumella punctata were among the members of the family Enterobacteriaceae present during the initial phase of the cocoa bean fermentations and could be responsible for the production of gluconic acid in some cases. Also, a potential new yeast species was isolated, namely, Candida sorbosivorans-like. Acetic acid bacteria, whose main representative was Acetobacter pasteurianus, generally appeared later during fermentation and oxidized ethanol to acetic acid. However, acetic acid bacteria were not always present during the main course of the platform fermentations. All of the data taken together indicated that short box and platform fermentation methods caused incomplete fermentation, which had a serious impact on the quality of the fermented dry cocoa beans.

Lab-scale systems modelling the spontaneous cocoa bean fermentation process are useful tools to research the influence of process parameters on the fermentation and the final bean quality. In this study in Honduras, a 1-kg lab-scale fermentation (LS-F) was compared to a 300-kg on-farm fermentation (OF-F) in a multiphasic approach, analysing microbial counts, microbial species diversity, physico-chemical parameters, and final dried bean quality. Yeast and total aerobic counts of up to 8 log CFU/g during the LS-F were comparable to the OF-F, while counts for lactic acid bacteria and acetic acid bacteria were up to 3 log CFU/g lower during the LS-F than during the OF-F. While species of the genera Hansenia, Saccharomyces, and Acetobacter dominated most of the fermentation processes, the genera dominating the drying phases were Pichia, Trichosporon, Pediococcus, and Acetobacter. Dried beans resulting from the LS-F, compared to the OF-F, were similar in contents of acetic acid, 6 times lower in lactic acid, up to 4 times higher in residual sugars, and 3-12 times higher in polyphenols. Dried beans processed at LS showed a similar flavour profile in terms of astringency, bitterness, acidity, and brown, fine, and cocoa flavours, but 2 units higher off-flavours than OF processed beans. With 81%, the share of well-fermented beans from the LS-F complied with industrial standards, whereas 7% over-fermented beans were above the threshold. Conclusively, the 5-day model fermentation and subsequent drying successfully mimicked the on-farm process, providing a high-throughput method to screen microbial strains to be used as starter cultures.

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