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Background The bioethanol production system used in Brazil is based on the fermentation of sucrose from sugarcane feedstock by highly adapted strains of the yeast Saccharomyces cerevisiae. Bacterial contaminants present in the distillery environment often produce yeast-bacteria cellular co-aggregation particles that resemble yeast-yeast cell adhesion (flocculation). The formation of such particles is undesirable because it slows the fermentation kinetics and reduces the overall bioethanol yield. Results In this study, we investigated the molecular physiology of one of the main S. cerevisiae strains used in Brazilian bioethanol production, PE-2, under two contrasting conditions: typical fermentation, when most yeast cells are in suspension, and co-aggregated fermentation. The transcriptional profile of PE-2 was assessed by RNA-seq during industrial scale fed-batch fermentation. Comparative analysis between the two conditions revealed transcriptional profiles that were differentiated primarily by a deep gene repression in the co-aggregated samples. The data also indicated that Lactobacillus fermentum was likely the main bacterial species responsible for cellular co-aggregation and for the high levels of organic acids detected in the samples. Conclusions Here, we report the high-resolution gene expression profiling of strain PE-2 during industrial-scale fermentations and the transcriptional reprograming observed under co-aggregation conditions. This dataset constitutes an important resource that can provide support for further development of this key yeast biocatalyst. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0196-6) contains supplementary material, which is available to authorized users.

The last century was the scene of an extraordinary social and economic development of mankind. This development had the fossil energy as one of its pillars. The discovery of petrol led the society to shape a development model highly dependent on this source of energy, which has finite resources and also promotes a big increase on the greenhouse gases, with unforeseeable consequences for the human beings as well as the entire life. It is imperative that we change the pillars of energy from fossil to renewables that will be more sustainable and less aggressive to the environment. One of the sources of this new energy platform, probably the best, is biomass. Fibrous plants bring several advantages and fit well within the requirements deemed important to be elected as producers of biomass. Among these characteristics we have the high processing capacity of solar energy into biomass, fast growth, long-term canopy, possibility of large-scale production. Despite of that this plants are adapted to suboptimal environments that allows its production not compete with food production because it requires less energy input, bringing marginal lands into production with its all social-benefit consequences. Among the fibrous plants, SUGAR CANE or, better, ENERGY CANE has one of the biggest potential for biomass productions. Results from several breeding programs has showing the high biomass potential of energy cane over other biomass crops like sorghum, elephant grass and eucalyptus.