Filamentous fungi diversity in the natural fermentation of Amazonian cocoa beans and the microbial enzyme activities

The purpose of this study was to investigate the diversity of filamentous fungi and the hydrolytic potential of their enzymes for a future understanding of the influence of these factors on the sensory characteristics of the cocoa beans used to obtain chocolate. Filamentous fungi were isolated from the natural cocoa fermentation boxes in the municipality of Tucuman, Pará, Brazil, and evaluated for the potential production of amylases, cellulases, pectinases, and xylanases. The fermentation was monitored by analyzing the pH and temperature. The strains were identified by sequencing the ITS1/ITS4 section of the 5.8S rDNA and partially sequencing the 18S and 28S regions, and the molecular identification was confirmed by phylogenetic reconstruction. The fungi isolated were comprised of three classes from the Ascomycota phylum and one class from the Basidiomycota phylum. There were found 19 different species, of this amount 16 had never been previously reported in cocoa fermentation. This fact characterizes the fermentation occurring in this municipality as having wide fungal diversity. Most of the strains isolated had the ability to secrete enzymes of interest. Cladosporium cladosporioides, Fomitopsis subtropical, Aspergillus versicolor, Penicillium pimiteouiense, Phanerochaete australis, Neonothopanus nambi, and Aspergillus parasiticus were the strains that excelled in the secretion of the following enzymes: amylase, pectinase, cellulase, and xylanase. The presence of 16 species not yet reported in cocoa seed fermentations and their potential hydrolytic activities show a diversity of filamentous fungi in this microbial biome that needs to be better understood.