Unravelling the microbiome of industrial sugarcane biorefineries

Research output: Book/ReportPh.D. thesis

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Microbial communities are ubiquitous and play critical roles in several natural processes, from biogeochemical cycles to the regulation of the human health. But we still need to better understand how the interactions between the members of these communities affects its functionality.Synthetic microbial communities are tools that enable to interrogate these questions, by the direct manipulation of such communities. Industrial ethanol fermentations are, by far, the most studied bioprocess, and should be considered an ideal model for this application for several reasons: virtually all its organisms are prone to cultivation; most species are amenable to genetic manipulation; these communities are easily reproducible, and have quantifiable parameters.

Here we present the first metagenomics analysis of actual Brazilian industrial sugarcane ethanol fermentations. Longitudinal sampling and strain level resolution have revealed that different biorefineries share similar microbiome composition and dynamics. We have also observed that strain level variations in the population of Lactobacillus fermentum, driven by the temperature of fermentations, is the responsible for reductions in industrial performance. Further experiments corroborated this observation. Selectively removing such strains could result in a yearly economic gain of ca. 700 million dollars for this industry. Likewise, the improvement in process performance could reduce CO2 emissions by more than 2 x 106 tons/year, due to the replacement of gasoline for this extra ethanol produced. We have also developed an optimized medium, which faithfully simulates the sugarcane molasses broth, allowing for systematic investigation of the microbial interactions within this community. By deconstructing this community in every possible composition we found that higher-order interactions are crucial for its functionality. In addition, a key contaminant species, Lactobacillus amylovorus, is beneficial for the fermentation, due to its metabolic interactions with Saccharomyces cerevisiae. Enriching this particular species during the fermentation seems to be a viable strategy to further improve the performance of this industry.
Original languageEnglish
Number of pages183
Publication statusPublished - 2019

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