Anti-Contamination Strategies for Yeast Fermentations

A transcriptomic atlas of acute stress response to low pH in multiple Issatchenkia orientalis strains

IMPORTANCE

Issatchenkia orientalis is a promising industrial chassis to produce biofuels and bioproducts due to its high tolerance to multiple environmental stresses such as low pH, heat, and other chemicals otherwise toxic for the most widely used microbes. Yet, little is known about specific mechanisms of such tolerance in this organism, hindering our ability to engineer this species to produce valuable biochemicals. Here, we report a comprehensive study of the mechanisms of acidic tolerance in this species via transcriptome profiling across variable pH for 12 different strains with different phenotypes. We found multiple regulatory mechanisms involved in tolerance to low pH in different strains of I. orientalis, marking potential targets for future gene editing and perturbation experiments.

Physicochemical and Functional Properties of Yeast-Fermented Cabbage

Microbial fermentation is often used to improve the functionality of plant-based food materials. Herein, we investigated changes in the physicochemical and functional properties of cabbage during yeast fermentation to develop new products using fermented cabbage. Among the 8 types of food-grade yeast, both Saccharomyces cerevisiae and Saccharomyces boulardii fermented 10% cabbage powder solution (w/w) the most effectively, leaving no soluble sugars after 12 h of fermentation. In addition, the yeast fermentation of cabbage resulted in functionally positive outcomes in terms of sulforaphane content, antioxidant properties, and anti-inflammatory activity. Specifically, the yeast-fermented cabbages contained about 500% more sulforaphane. The soluble fraction (5 μg/ml) of yeast-fermented cabbage had no cytotoxicity in murine RAW 264.7 cells, and the radical-scavenging capacity was equivalent to 1 μg/ml of ascorbic acid. Moreover, cabbage fermented with S. boulardii significantly suppressed both lipopolysaccharides (LPS)-induced nitric oxide production and LPS-induced reactive oxygen species production in RAW 264.7 cells, suggesting a potential anti-inflammatory effect. These results support the idea that yeast fermentation is promising for developing functionally improved cabbage products.

Regulatory Small RNAs for a Sustained Eco-Agriculture

Small RNA (sRNA) has become an alternate biotechnology tool for sustaining eco-agriculture by enhancing plant solidity and managing environmental hazards over traditional methods. Plants synthesize a variety of sRNA to silence the crucial genes of pests or plant immune inhibitory proteins and counter adverse environmental conditions. These sRNAs can be cultivated using biotechnological methods to apply directly or through bacterial systems to counter the biotic stress. On the other hand, through synthesizing sRNAs, microbial networks indicate toxic elements in the environment, which can be used effectively in environmental monitoring and management. Moreover, microbes possess sRNAs that enhance the degradation of xenobiotics and maintain bio-geo-cycles locally. Selective bacterial and plant sRNA systems can work symbiotically to establish a sustained eco-agriculture system. An sRNA-mediated approach is becoming a greener tool to replace xenobiotic pesticides, fertilizers, and other chemical remediation elements. The review focused on the applications of sRNA in both sustained agriculture and bioremediation. It also discusses limitations and recommends various approaches toward future improvements for a sustained eco-agriculture system.

Study of the Effect of Antibiotics in Drinking Water on the Content of Antioxidant Compounds in Red Wines

The presence of antibiotic residues in drinking water may be a source of contamination, which could affect the diffusion of polyphenols into the wine must during the traditional fermentation process. Antibiotic residues such as ivermectin, hydroxychloroquine, ciprofloxacin, and azithromycin on the diffusion of polyphenols and anthocyanins during wine fermentation were studied. Different samples were taken at different periods (0, 48, 96, and 168 h) to analyse the total polyphenols, anthocyanin content, and antioxidant capacity, which were correlated with Peleg's equation to establish the diffusion kinetics of these compounds. The results indicated that the presence of antibiotics reduced between 40 and 50% the diffusion of the total polyphenols and monomeric anthocyanins in red wine. The use of ivermectin showed the highest kinetic parameter k₁ compared with the use of other antibiotics. This suggested that the chemical structure and molecular weight of the antibiotics could play an important role in inhibiting the metabolism of yeasts affecting the ethanol and CO₂ production. Consequently, cell membranes would be impermeable and would not allow the release of polyphenols and anthocyanins. Therefore, it is necessary to establish strategies that allow future water quality control in wine production companies.

Continuous biomanufacturing with microbes - upstream progresses and challenges

Current biomanufacturing facilities are mainly built for batch or fed-batch operations, which are subject to low productivities and do not achieve the great bioconversion potential of the rewired cells generated via modern biotechnology. Continuous biomanufacturing should be the future directions for high-yield and low-cost manufacturing of various fermentation products. This review discusses the major challenges and the strategies for continuous biomanufacturing with microbes, which include minimizing contamination risk, enhancing genetic stability over a long-term continuous operation, achieving high product titer, rate, and yield simultaneously by decoupling cell growth from product formation, and using modeling approach to accelerate research and development of continuous biomanufacturing. New strain designs and process engineering strategies, including integration with artificial intelligence, are also discussed for intelligent and the next generation of continuous biomanufacturing.

Ozone in wineries and wine processing: A review of the benefits, application, and perspectives

Ozone (O₃ ) is an emerging eco-friendly technology that has been widely used in the beverage industry due to its broad spectrum of usages, such as fermentation, microbial inactivation, Clean-in-Place (CIP) systems, and postharvest treatment. Wine is among the most financially profitable sectors of the beverage industry. Ozone technology as an alternative approach to conventional methods to inhibit microbes in wine processing and wineries has attracted researchers' attention as this emerging technology will probably play important roles in wineries in the future. This review discusses the prospective applications of ozone in winemaking and wineries and elaborates on ozone's antimicrobial effects on the control of the broad spectrum of microorganisms during wine processing. Also, this paper provides discussions on its effects of O₃  on wine quality and the benefits this emerging technology can bring to wineries. Ozone treatments can improve yeast fermentation by impacting the yeast ecology of postharvested wine grapes, mainly by affecting apiculate yeasts and adjusting the population of undesirable yeasts, such as Brettanomyces spp., during the fermentation process. Furthermore, ozone treatment may enhance wine's anthocyanin concentration, physicochemical properties, color, pH, oxidative stability, and concentration of pleasant volatile compounds and esters. This article presents important information to have a better understanding of the impact of ozone treatment on different stages of wine preparation.

Evaluation of the Biocontrol Potential of a Commercial Yeast Starter against Fuel-Ethanol Fermentation Contaminants

Lactic acid bacteria (LAB) and Brettanomyces bruxellensis are the main contaminants of bioethanol fermentations. Those contaminations affect Saccharomyces cerevisiae performance and reduce ethanol yields and productivity, leading to important economic losses. Currently, chemical treatments such as acid washing and/or antibiotics are used to control those contaminants. However, these control measures carry environmental risks, and more environmentally friendly methods are required. Several S. cerevisiae wine strains were found to secrete antimicrobial peptides (AMPs) during alcoholic fermentation that are active against LAB and B. bruxellensis strains. Thus, in the present study, we investigated if the fuel-ethanol commercial starter S. cerevisiae Ethanol Red (ER) also secretes those AMPs and evaluated its biocontrol potential by performing alcoholic fermentations with mixed-cultures of ER and B. bruxellensis strains and growth assays of LAB in ER pre-fermented supernatants. Results showed that all B. bruxellensis strains were significantly inhibited by the presence of ER, although LAB strains were less sensitive to ER fermentation metabolites. Peptides secreted by ER during alcoholic fermentation were purified by gel-filtration chromatography, and a bioactive fraction was analyzed by ELISA and mass spectrometry. Results confirmed that ER secretes the AMPs previously identified. That bioactive fraction was used to determine minimal inhibitory concentrations (MICs) against several LAB and B. bruxellensis strains. MICs of 1–2 mg/mL were found for B. bruxellensis strains and above 2 mg/mL for LAB. Our study demonstrates that the AMPs secreted by ER can be used as a natural preservative in fuel-ethanol fermentations.

Advances in the Development of Microbial Double-Stranded RNA Production Systems for Application of RNA Interference in Agricultural Pest Control

RNA interference (RNAi) is a valuable and revolutionary technology that has been widely applied in medicine and agriculture. The application of RNAi in various industries requires large amounts of low-cost double-stranded RNA (dsRNA). Chemical synthesis can only produce short dsRNAs; long dsRNAs need to be synthesized biologically. Several microbial chassis cells, such as Escherichia coli, Saccharomyces cerevisiae, and Bacillus species, have been used for dsRNA synthesis. However, the titer, rate of production, and yield of dsRNA obtained by these microorganism-based strategies is still low. In this review, we summarize advances in microbial dsRNA production, and analyze the merits and faults of different microbial dsRNA production systems. This review provides a guide for dsRNA production system selection. Future development of efficient microbial dsRNA production systems is also discussed.

The Role of Yeasts in Fermentation Processes

In recent years, vessels have been discovered that contain the remains of wine with an age close to 7000 years. It is unclear whether, in ancient times, humans accidentally stumbled across fermented beverages like wine or beer, or was it a product intended as such. What is a fact is that since then, alcoholic beverages have been part of the diet and culture of many of the civilizations that have preceded us. The typical examples of beer and wine are an example of many other drinks resulting from the action of yeasts. In addition to these two beverages, various companies have developed other types of fermented foods and non-alcoholic beverages prepared in a traditional or commercial manner. The climatic conditions, the availability of raw material and the preferences of each region have conditioned and favored the maintenance of some of these products. In addition to the aforementioned traditional alcoholic beverages produced from fruits, berries, or grains, humans use yeast in the production of chemical precursors, global food processing such as coffee and chocolate, or even wastewater processing. Yeast fermentation is not only useful in food manufacturing. Its uses extend to other products of high interest such as the generation of fuel from vegetable sources.

Consolidated bioprocessing of raw starch to ethanol by Saccharomyces cerevisiae: Achievements and challenges

Recent advances in amylolytic strain engineering for starch-to-ethanol conversion have provided a platform for the development of raw starch consolidated bioprocessing (CBP) technologies. Several proof-of-concept studies identified improved enzyme combinations, alternative feedstocks and novel host strains for evaluation and application under fermentation conditions. However, further research efforts are required before this technology can be scaled up to an industrial level. In this review, different CBP approaches are defined and discussed, also highlighting the role of auxiliary enzymes for a supplemented CBP process. Various achievements in the development of amylolytic Saccharomyces cerevisiae strains for CBP of raw starch and the remaining challenges that need to be tackled/pursued to bring yeast raw starch CBP to industrial realization, are described. Looking towards the future, it provides potential solutions to develop more cost-effective processes that include cheaper substrates, integration of the 1G and 2G economies and implementing a biorefinery concept where high-value products are also derived from starchy substrates.