Wickerhamomyces pijperi: An Up-And-Coming Yeast with Pectinolytic Activity Suitable for Cocoa Bean Fermentation

During cocoa bean fermentation, yeasts, particularly those with pectinolytic activity, contribute to pulp degradation, facilitating and accelerating fermentation. This study aimed to identify and evaluate pectinolytic yeast strains for their suitability as starter cultures in cocoa bean fermentation. A high-throughput screening of 1139 yeasts previously isolated from cocoa bean fermentations identified three strains of Wickerhamomyces pijperi with strong pectinolytic activity. These strains also reduced the viscosity of a pectin-enriched cocoa pulp simulation medium (mCPSMpc) from 23.06 ± 0.11 mPa·s (uninoculated sample) to 4.40 ± 0.14 mPa·s, 4.22 ± 0.13 mPa·s, and 4.77 ± 0.17 mPa·s after 24 h for samples inoculated with strains H312, H403, and H404, respectively. W. pijperi H403 and H404, applied in co-culture with Limosilactobacillus fermentum 223 and Saccharomyces cerevisiae H290 in 1 kg lab-scale fermentations, significantly enhanced pulp degradation, with runoff after 23.8 h reaching 12.6–13.3%, compared to 4.7% in uninoculated controls. In 20 kg fermentations in Costa Rica, the effect was less pronounced, likely due to lower inoculation rates and environmental factors. Quantitative PCR confirmed the persistence of W. pijperi H403 in fermentations. Additionally, trial cultivations in 15 L stirred-tank bioreactors successfully demonstrated the ability to produce larger biomass quantities for upscaled applications. These findings highlight W. pijperi H403 as a promising candidate for controlled cocoa fermentation, potentially accelerating biochemical changes and improving process stability.