November 2025 Science Summary

Aloha,

As we head into the season of sweets in the United States (from Halloween to New Year's Eve), I wanted to include a fascinating article (Gopaulchan et al. 2025) on how scientists recently learned a trick to get fancier-tasting chocolate by using the right mix of bacteria and fungi! It's a jam-packed wild read. I've also got two articles on the Pantanal. 

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FIGURING OUT WHAT MAKES CHOCOLATE TASTIER
Gopaulchan et al. 2025 advances the frontier of scientific understanding of flavor development in chocolate. It has a few components. First they measured changes in temperature and pH over a week in fermenting Colombian cacao beans to estimate microbial activity (they correlated with the color changes used to assess fermentation end point). Second they sequenced the genome every 24 hours to watch diversity decline for both bacteria (Fig 1e, Acetobacteraceae dominating over time) and fungi (Fig 1f, Saccharomycetaceae dominating over time). But crucially, they third compared how these shifts happened at three farms w/ similar genetics but different microbial mixes. Look at Fig 2e and 2f!!! The two new farms had diversity increase again eventually, and one farm had significant populations of families that were only present in trace amounts before! OK, stay with me. Fourth, they extracted cocoa liquor and compared their three farms to reference choocolates (Fig 3b). One farm tastes "West African" (roasty, dark wood, tobacco), and two taste more "Malagasy" (one emphasizing light / caramelly / tropical flavors, and the other more fruity and bitter). Fifth they figured out which familiies of microbes were likely most essential for flavor (Fig 4) and sixth put together different incoculant mixes (most had the full diversity of microbes minus a different single strain missing for each mix, plus a random mix). They then (seventh) did controlled cacao bean fermentation w/ each mix plus an uninoculated control (in the lab so it wouldn't have the wild strains), and tasted the results (eighth), finding that the beans inoculated with the full mix of strains had better flavors than those inoculated w/ fewer strains or none at all (Fig 5h). The authors argue that with synthetic starters and controlled fermentation, chocolate flavor could be improved in more industrial-scale chocolate.

PANTANAL:
Fernando et al. 2025 looks at variation in fish biodiversity across the Upper Paraguay River Basin (the Pantanal and its headwaters, see Fig 1). They found the Pantanal floodplain has higher fish species richness than the headwaters, BUT note that the headwaters have: more undescribed species (at least 60), clear threats to the hydrology, likely more endemic species, and headwater threats are likely to impact species in the floodplain as well. Mid-altitudes had high richness in a small area due to overlap in species from below and above. Considering all factors, the authors recommend more conservation focus on the headwaters.

Tomas et al. 2025 recommends eight principles for good conservation policy in the Pantanal: 1) manage the entire Upper Paraguay River Basin; 2&3) use a range of management options for the entire region (not only some habitats); 4) maintain environmental heterogeneity and functionality; 5) Maintain hydrological integrity and connectivity; 6) expand protected areas to represent all ecosystems; 7) incentivize conservation (e.g., via carbon or biodiversity credits, payment for ecosystem services, etc.); and 8) support Indigenous people and their way of living.


REFERENCES:
Fernando, A. M. E., Severo‐Neto, F., Ferreira, F. S., Mateus, L., Tondato‐Carvalho, K. K., Kashiwaqui, E. A. L., Gimenes Junior, H., Domingues, W. M., Pavanelli, C. S., Pinho, H. L. L., Penha, J., & Súarez, Y. R. (2025). Fish distribution across altitudinal gradients in the Upper Paraguay River Basin: Implications for conservation in the Pantanal region. Conservation Science and Practice, 7(7), 1–12. https://doi.org/10.1111/csp2.13290

Gopaulchan, D., Moore, C., Ali, N., Sukha, D., Florez González, S. L., Herrera Rocha, F. E., Yang, N., Lim, M., Dew, T. P., González Barrios, A. F., Umaharan, P., Salt, D. E., & Castrillo, G. (2025). A defined microbial community reproduces attributes of fine flavour chocolate fermentation. Nature Microbiology, 10(9), 2130–2152. https://doi.org/10.1038/s41564-025-02077-6

Tomas, W. M., Andrade, M. H., Berlinck, C. N., Bolzan, F., Camilo, A. R., Catella, A. C., Chiaravalloti, R. M., da Cunha, C. N., Damasceno Junior, G. A., Fernando, A. M. E., Garcia, L. C., Girard, P., Ikeda‐Castrillon, S. K., da Silva, C. J., Laps, R., Mateus, L., Morato, R. G., Mourão, G., Nunes, A. V., … Urbanetz, C. (2025). Eight basic principles for the elaboration of public policies and development projects for the Pantanal. Conservation Science and Practice, 7(7), 1–10. https://doi.org/10.1111/csp2.13207


Sincerely,
 
Jon
 
p.s. The paintings were both made partly by a dog; we put paint on a board, covered it with plastic wrap, and put a "pup cup" on top so as the dog ate the treat it smeared the paint and made art! Here's a pic of the painting on the right before the dog helped, and another of the dog (Jito) in action.