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Cocoa beans fermentation is a spontaneous process, essential for the generation of quality starting material for fine chocolate production. The understanding of this process has been studied by the application of high-throughput sequencing technologies, which grants a better assessment of the different microbial taxa and their genes involved in this microbial succession. The present study used shotgun metagenomics to determine the enzyme-coding genes of the microbiota found in two different groups of cocoa beans varieties during the fermentation process. The statistical evaluation of the most abundant genes in each group and time studied allowed us to identify the potential metabolic pathways involved in the success of the different microorganisms. The results showed that, albeit the distinction between the initial (0 h) microbiota of each varietal group was clear, throughout fermentation (24–144 h) this difference disappeared, indicating the existence of selection pressures. Changes in the microbiota enzyme-coding genes over time pointed to the distinct ordering of fermentation at 24–48 h (T1), 72–96 h (T2), and 120–144 h (T3). At T1, the significantly more abundant enzyme-coding genes were related to threonine metabolism and those genes related to the glycolytic pathway, explained by the abundance of sugars in the medium. At T2, the genes linked to the metabolism of ceramides and hopanoids lipids were clearly dominant, which are associated with the resistance of microbial species to extreme temperatures and pH values. In T3, genes linked to trehalose metabolism, related to the response to heat stress, dominated. The results obtained in this study provided insights into the potential functionality of microbial community succession correlated to gene function, which could improve cocoa processing practices to ensure the production of more stable quality end products.

Ecological communities vary considerably in space and time and understanding such changes has fundamental relevance for ecology and conservation sciences. Mountains provide an excellent scenario for studies addressing spatial and temporal variation, as they vary in conditions and resources in a small geographic region. Here, we aimed to understand the patterns of variation in ant metacommunity composition across time and along an elevational gradient in a tropical mountain, focusing both on the taxonomic and functional facets of diversity. We used a β-diversity metric and broke it into nestedness and turnover to estimate short-term temporal changes in ant metacommunity composition. We tested the following hypotheses: (i) taxonomic and functional temporal β-diversity increase along the elevational gradient and (ii) turnover is the main component driving taxonomic temporal β-diversity and nestedness for functional temporal β-diversity. Rejecting our first hypothesis, we found that both taxonomic and functional temporal β-diversity did not increase with elevation. Yet, the values were always high, indicating that both species and functional traits are highly variable over time. In accordance with our second hypothesis, we found that turnover was the main component of taxonomic β-diversity. Yet adding complexity to our hypothesis, the contribution of nestedness to functional β-diversity decreased with increasing elevation. These results suggest that at low elevations, the turnover in species composition may then cause changes in trait composition because of the loss of some traits, yet preserving the most common functions (nested functional communities), while at high elevations functional capabilities may change over time (turnover of traits). In the context of global warming, where tropical mountain insects are expected to change their distributional range upwards, it is extremely important to consider the importance of the turnover on the temporal variation in functional traits and functions of ant metacommunity at higher elevations.