Transcriptional profile of a bioethanol production contaminant Candida tropicalis

Abstract

The fermentation process is widely used in the industry for bioethanol production. Even though it is widely used, microbial contamination is unpredictable and difficult to control. The problem of reduced productivity is directly linked to competition for nutrients during contamination. Yeasts representing the Candida species are frequently isolated contaminants. Elucidating the behavior of a contaminant during the fermentation cycle is essential for combatting the contamination. Consequently, the aim of the current study was to better understand the functional and transcriptional behavior of a contaminating yeast Candida tropicalis. We used a global RNA sequencing approach (RNA-seq/MiSeq) to analyze gene expression. Genes with significantly repressed or induced expression, and related to the fermentations process, such as sugar transport, pyruvate decarboxylase, amino acid metabolism, membrane, tolerance to high concentrations of ethanol and temperatures, nutrient suppression), and transcription-linked processes, were identified. The expression pattern suggested that the functional and transcriptional behavior of the contaminating yeast during fermentation for bioethanol production is similar to that of the standard yeast Saccharomyces cerevisiae. In addition, the analysis confirmed that C. tropicalis is an important contaminant of the alcoholic fermentation process, generating bioethanol and viability through its tolerance to all the adversities of a fermentation process essential for the production of bioethanol. According on the gene expression profile, many of these mechanisms are similar to those of S. cerevisiae strains currently used for bioethanol production. These mechanisms can inform studies on antimicrobials, to combat yeast contamination during industrial bioethanol production.

Keywords: Alcoholic fermentation; Bioethanol; Candida tropicalis; Contaminant; RNA-seq.

Fig. 1

Heatmap of the top 30 differently expressed genes of contaminant yeast, C. tropicalis at 0 h and 8 h in the fermentation alcoholic cycle. a Down-regulated genes at 8 h (C8 and P8) in contrast to 0 h (C0 and P0); b up-regulated genes at 8 h (C8 and P8) in contrast to 0 h (C0 and P0). Genes with log2 Fold Change > 1 or < − 1 and FDR < 0.01 with statistical significance. Heatmap values are rlog-normalized and scale by z-score. Color scale ate top right represent lowest to highest change in expression (blue and red)

Fig. 2

Biological process quantification for up-regulated and down-regulated genes of contaminant yeast, C. tropicalis at 0 h and 8 h in the fermentation alcoholic cycle. a Biological process represent among down-regulated genes at time 8 h (C8 and P8), represent per the bars in red color in contrast at time 0 h (C0 and P0); b biological process represent among up-regulated genes at time 8 h (C8 and P8), represent per the bars in green color in contrast at time 0 h (C0 and P0)