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The quality of commercial cocoa beans, the principal raw material for chocolate production, relies on the combination of factors that include the type of planting material, the agricultural practices, and the post-harvest processing. Among these, the fermentation of the cocoa beans is still the most relevant since it is the process whereby the precursors of the cocoa flavor arise. The formation of these precursors depends on the activity of different microbial groups on the beans pulp. A comparison of fermentations in different countries showed that a well-defined microbial succession does not always take place and that the role of Bacillus spp. in this process remains unclear. Considering the overriding importance of the fermentation to achieve high quality commercial cocoa beans, we discuss the need of addressing the impact of the farming system, the ripeness state of the pods, and the role of microbial interactions on the fermentation in future research. In addition, the problem of high acidification cocoa beans, aspects dealing with the volatile fraction of the flavor, and the cocoa butter properties, all were identified as critical aspects that need further investigation. The standardization of the microbiological methods and the application of metagenomic approaches would magnify the knowledge in this domain.

In sheltered, eutrophicated estuaries, reduced nitrogen (NH x ), and pH levels in the water layer can be greatly enhanced. In laboratory experiments, we studied the interactive effects of NH x , pH, and shoot density on the physiology and survival of eelgrass (Zostera marina). We tested long-term tolerance to NH x at pH 8 in a 5-week experiment. Short-term tolerance was tested for two shoot densities at both pH 8 and 9 in a 5-day experiment. At pH 8, eelgrass accumulated nitrogen as free amino acids when exposed to high loads of NH x , but showed no signs of necrosis. Low shoot density treatments became necrotic within days when exposed to NH x at pH 9. Increased NH3 intrusion and carbon limitation seemed to be the cause of this, as intracellular NH x could no longer be assimilated. Remarkably, experiments with high shoot densities at pH 9 showed hardly any necrosis, as the plants seemed to be able to alleviate the toxic effects of high NH x loads through joint NH x uptake. Our results suggest that NH x toxicity can be important in worldwide observed seagrass mass mortalities. We argue that the mitigating effect of high seagrass biomass on NH x toxicity is a positive feedback mechanism, potentially leading to alternative stable states in field conditions.

A rationale is given for a modelling approach to identify the mechanisms involved in the functioning and metabolic activity of tissues in the wall of the gastrointestinal tract. Maintenance and productive functions are discussed and related to the distinct compartments of the gastrointestinal tract and the metabolic costs involved. Functions identified are: tissue turnover; tissue proliferation; ion transport; nutrient transport; secretions of digestive enzymes, mucus and immunoglobulins; production of immune cells. The major nutrients involved include glucose, amino acids and volatile fatty acids. In vivo measurements of net portal fluxes of these nutrients in pigs and ruminants are evaluated to illustrate the complexity of physiology and metabolic activity of the gastrointestinal tract. Experimental evidence indicates that high, but variable and specific, nutrient costs are involved in the functioning of the gastrointestinal tract.