Evaluation of Cellular Responses of Heterotrophic Escherichia coli Cultured with Autotrophic Chlamydomonas reinhardtii as a Nutrient Source by Analyses Based on Microbiology and Transcriptome.

Heterotrophic microorganism Escherichia coli LS5218 was cultured with flesh green alga Chlamydomonas reinhardtii C-9: NIES-2235 as a nutrient supplier. In order to evaluate the cell response of Escherichia coli with Chlamydomonas reinhardtii, Escherichia coli was evaluated with microbial methods and comprehensive gene transcriptional analyses. Escherichia coli with Chlamydomonas reinhardtii showed a specific growth rate (µmax) of 1.04 ± 0.27, which was similar to that for cells growing in Luria-Bertani medium (µmax = 1.20 ± 0.40 h-1). Furthermore, comparing the cellular responses of Escherichia coli in a green-algae-containing medium with those in the Luria-Bertani medium, transcriptomic analysis showed that Escherichia coli upregulated gene transcription levels related to glycolysis, 5-phospho-d-ribosyl-1-diphosphate, and lipid synthesis; on the other hand, it decreased the levels related to lipid degradation. In particular, the transcription levels were increased by 103.7 times on pgm (p * < 0.05 (p = 0.015)) in glycolysis, and decreased by 0.247 times on fadE (p * < 0.05 (p = 0.041)) in lipolysis. These genes are unique and could regulate the direction of metabolism; these responses possibly indicate carbon source assimilation as a cellular response in Escherichia coli. This paper is the first report to clarify that Escherichia coli, a substance-producing strain, directly uses Chlamydomonas reinhardtii as a nutrient supplier by evaluation of the cellular responses analyzed with microbial methods and transcriptome analysis.

Evaluation of Cell Responses of Saccharomyces cerevisiae under Cultivation Using Wheat Bran as a Nutrient Resource by Analyses of Growth Activities and Comprehensive Gene Transcription Levels.

Wheat bran has high nutritional values and is also cheaper than yeast nitrogen base as an important component of a medium. Although its use in microbial cultivations is expected, research and development has hardly progressed so far. In this study, with experimental Saccharomyces cerevisiae BY4741, the cell responses to wheat bran as a nutrient were evaluated by analyses of cell growth, ethanol production, and comprehensive gene transcription levels. Comparing wheat bran and yeast nitrogen base, BY4741 showed specific growth rates of 0.277 ± 0.002 and 0.407 ± 0.035 as a significant difference. Additionally, wheat bran could be used as a restricted media component like yeast nitrogen base. However, in 24 h of cultivation with wheat bran and yeast nitrogen base, although conversion ratios of ethanol productions showed no significant difference at 63.0 ± 7.2% and 62.5 ± 8.2%, the ratio of cell production displayed a significant difference at 7.31 ± 0.04% and 4.90 ± 0.16%, indicating a different cell response. In fact, the comprehensive evaluation of transcription levels strongly suggested major changes in glucose metabolism. This study indicated that BY4741 could switch transcription levels efficiently to use wheat bran.

Development of a Prediction Method of Cell Density in Autotrophic/Heterotrophic Microorganism Mixtures by Machine Learning Using Absorbance Spectrum Data.

Microflora is actively used to produce value-added materials in industry, and each cell density should be controlled for stable microflora use. In this study, a simple system evaluating the cell density was constructed with artificial intelligence (AI) using the absorbance spectra data of microflora. To set up the system, the prediction system for cell density based on machine learning was constructed using the spectra data as the feature from the mixture of Saccharomyces cerevisiae and Chlamydomonas reinhardtii. As the results of predicting cell density by extremely randomized trees, when the cell densities of S. cerevisiae and C. reinhardtii were shifted and fixed, the coefficient of determination (R2) was 0.8495; on the other hand, when the cell densities of S. cerevisiae and C. reinhardtii were fixed and shifted, the R2 was 0.9232. To explain the prediction system, the randomized trees regressor of the decision tree-based ensemble learning method as the machine learning algorithm and Shapley additive explanations (SHAPs) as the explainable AI (XAI) to interpret the features contributing to the prediction results were used. As a result of the SHAP analyses, not only the optical density, but also the absorbance of the Soret and Q bands derived from the chloroplasts of C. reinhardtii could contribute to the prediction as the features. The simple cell density evaluating system could have an industrial impact.

Estimation of Carbon Metabolism in Saccharomyces cerevisiae Acclimatized to Glycerol Assimilation with Quantitative PCR.

Saccharomyces cerevisiae has the potential to produce value-added chemicals; however, this strain is restricted by using glycerol as a carbon source. Although acclimatization of S. cerevisiae as a glycerol-assimilating strain was confirmed so far, the reason why S. cerevisiae can be acclimatized was not clear in detail with limited information on the metabolic changes. In this report, glycerol-assimilating strains from S. cerevisiae BY4741 were isolated, and the biomass production, ethanol fermentation, and transcription levels related to glycolysis and the tricarboxylic acid cycle under aerobic and slightly anaerobic conditions were analyzed. As the results show, although µmax was equal to 0.15 h-1 between wildtype and glycerol-assimilating strains in an aerobic culture including glucose, the differences in max biomass production and percentage yields of ethanol and transcription levels between the two strains were shown. In slightly anaerobic culture, the differences in transcription levels downstream of glycolysis were also displayed. In the case of the glycerol-assimilating strain with glycerol under aerobic conditions, although the transcription levels related to ethanol production were sufficient, the ethanol production was not detected. Additionally, the biomass production reached a plateau even in the culture containing sufficient glycerol, indicating that the redox imbalance even in the cells of the glycerol-acclimatized strain could disturb the utilization of glycerol. The obtained knowledge will promote the use of glycerol resources with the glycerol-acclimatized S. cerevisiae in view of carbon recycling.