Anaerobic Fermentation for Production of Carboxylic Acids as Bulk Chemicals from Renewable Biomass

Bacteriophage Challenges in Industrial Processes: A Historical Unveiling and Future Outlook

Humans have used fermentation processes since the Neolithic period, mainly to produce beverages. The turning point occurred in the 1850s, when Louis Pasteur discovered that fermentation resulted from the metabolism of living microorganisms. This discovery led to the fast development of fermented food production. The importance of industrial processes based on fermentation significantly increased. Many branches of industry rely on the metabolisms of bacteria, for example, the dairy industry (cheese, milk, yogurts), pharmaceutical processes (insulin, vaccines, antibiotics), or the production of chemicals (acetone, butanol, acetic acid). These are the mass production processes involving a large financial outlay. That is why it is essential to minimize threats to production. One major threat affecting bacteria-based processes is bacteriophage infections, causing substantial economic losses. The first reported phage infections appeared in the 1930s, and companies still struggle to fight against phages. This review shows the cases of phage infections in industry and the most common methods used to prevent phage infections.

Screening non-conventional yeasts for acid tolerance and engineering Pichia occidentalis for production of muconic acid

Saccharomyces cerevisiae is a workhorse of industrial biotechnology owing to the organism's prominence in alcohol fermentation and the suite of sophisticated genetic tools available to manipulate its metabolism. However, S. cerevisiae is not suited to overproduce many bulk bioproducts, as toxicity constrains production at high titers. Here, we employ a high-throughput assay to screen 108 publicly accessible yeast strains for tolerance to 20 g L-1 adipic acid (AA), a nylon precursor. We identify 15 tolerant yeasts and select Pichia occidentalis for production of cis,cis-muconic acid (CCM), the precursor to AA. By developing a genome editing toolkit for P. occidentalis, we demonstrate fed-batch production of CCM with a maximum titer (38.8 g L-1), yield (0.134 g g-1 glucose) and productivity (0.511 g L-1 h-1) that surpasses all metrics achieved using S. cerevisiae. This work brings us closer to the industrial bioproduction of AA and underscores the importance of host selection in bioprocessing.

Butyric acid: fermentation production using organic waste as low-cost feedstocks

Butyric acid is an important chemical which has many applications in the chemical, food, and pharmaceutical industries. Butyraldehyde, which is derived from propylene, is now converted into butyrate by petrochemical processes known as oxo synthesis. Because of its poor productivity and low butyrate concentration in the fermentation broth, biotechnological production of butyric acid is not economically viable. Typically, a sizable amount of the overall production expenses goes toward the cost of the fermentation substrate. If the fermentation process can use minimal biomass as the feedstock, a cost-competitive production of butyric acid from the fermentation technique would be generated with a strong market prospect. Organic wastes are recommended as a source of butyric acid fermentation feedstock because they are inexpensive, can be generated in huge numbers, and are biodegradable. With a focus on the low-cost feedstock, the many uses of butyric acid are discussed, with its present production status. As a result, this paper explores several butyric acid fermentation-related problems and offers ideas for potential solutions.

Hydrogenosome, Pairing Anaerobic Fungi and H2-Utilizing Microorganisms Based on Metabolic Ties to Facilitate Biomass Utilization

Anaerobic fungi, though low in abundance in rumen, play an important role in the degradation of forage for herbivores. When only anaerobic fungi exist in the fermentation system, the continuous accumulation of metabolites (e.g., hydrogen (H2) and formate) generated from their special metabolic organelles-the hydrogenosome-inhibits the enzymatic reactions in the hydrogenosome and reduces the activity of the anaerobic fungi. However, due to interspecific H2 transfer, H2 produced by the hydrogenosome can be used by other microorganisms to form valued bioproducts. This symbiotic interaction between anaerobic fungi and other microorganisms can be used to improve the nutritional value of animal feeds and produce value-added products that are normally in low concentrations in the fermentation system. Because of the important role in the generation and further utilization of H2, the study of the hydrogensome is increasingly becoming an important part of the development of anaerobic fungi as model organisms that can effectively improve the utilization value of roughage. Here, we summarize and discuss the classification and the process of biomass degradation of anaerobic fungi and the metabolism and function of anaerobic fungal hydrogensome, with a focus on the potential role of the hydrogensome in the efficient utilization of biomass.

Removal of Acetic Acid from Bacterial Culture Media by Adsorption onto a Two-Component Composite Polymer Gel

Organic acids, including acetic acid, are the metabolic products of many microorganisms. Acetic acid is a target product useful in the fermentation process. However, acetic acid has an inhibitory effect on microorganisms and limits fermentation. Thus, it would be beneficial to recover the acid from the culture medium. However, conventional recovery processes are expensive and environmentally unfriendly. Here, we report the use of a two-component hydrogel to adsorb dissociated and undissociated acetic acid from the culture medium. The Langmuir model revealed the maximum adsorption amount to be 44.8 mg acetic acid/g of dry gel at neutral pH value. The adsorption capacity was similar to that of an ion-exchange resin. In addition, the hydrogel maintained its adsorption capability in a culture medium comprising complex components, whereas the ion-exchange did not adsorb in this medium. The adsorbed acetic acid was readily desorbed using a solution containing a high salt concentration. Thus, the recovered acetic acid can be utilized for subsequent processes, and the gel-treated fermentation broth can be reused for the next round of fermentation. Use of this hydrogel may prove to be a more sustainable downstream process to recover biosynthesized acetic acid.

Metabolomics reveals the mechanism of Antarctic yeast Rhodotorula mucliaginosa AN5 to cope with cadmium stress

Heavy metal pollution in Antarctica has far exceeded expectations. Antarctic yeast is widely present in polar marine environment. The mechanisms of metabolomics effect of heavy metal on polar yeast have not been reported previously. In this study, gas chromatography-mass spectrometry (GC-MS) wascarried out to performed the metabolite profiling analysis of Antarctic sea-ice yeast Rhodotorula mucilaginosa AN5 exposed to different cadmium (Cd) stresses of 5 mM (HM5), 10 mM (HM10) and 20 mM (HM20), respectively. Metabolic profile analysis showed that the composition and contents of cellular metabolites have been altered by cadmium. 93 different metabolites were identified altogether, among which 23, 58 and 81 different metabolites were found in HM5, HM10 and HM20 group respectively. MetaboAnalyst analysis showed that in HM5, HM10 and HM20 groups, 12, 24 and 31 metabolic pathways were involved in the stress of cadmium to R. mucilaginosa, respectively. By contrasting with Kyoto Encyclopedia of Genes and Genomes database, we discovered that exposure of yeast AN5 to Cd stress resulted in profound biochemical changes including amino acids, organic acids and saccharides. These results will supply a nonnegligible basis of studying the adaptive resistance mechanism of Antarctic yeast Rhodotorula mucilaginosa to heavy metal.

Current Progress in Production of Building-Block Organic Acids by Consolidated Bioprocessing of Lignocellulose

Several organic acids have been indicated among the top value chemicals from biomass. Lignocellulose is among the most attractive feedstocks for biorefining processes owing to its high abundance and low cost. However, its highly complex nature and recalcitrance to biodegradation hinder development of cost-competitive fermentation processes. Here, current progress in development of single-pot fermentation (i.e., consolidated bioprocessing, CBP) of lignocellulosic biomass to high value organic acids will be examined, based on the potential of this approach to dramatically reduce process costs. Different strategies for CBP development will be considered such as: (i) design of microbial consortia consisting of (hemi)cellulolytic and valuable-compound producing strains; (ii) engineering of microorganisms that combine biomass-degrading and high-value compound-producing properties in a single strain. The present review will mainly focus on production of organic acids with application as building block chemicals (e.g., adipic, cis,cis-muconic, fumaric, itaconic, lactic, malic, and succinic acid) since polymer synthesis constitutes the largest sector in the chemical industry. Current research advances will be illustrated together with challenges and perspectives for future investigations. In addition, attention will be dedicated to development of acid tolerant microorganisms, an essential feature for improving titer and productivity of fermentative production of acids.

A New Pathway for Forming Acetate and Synthesizing ATP during Fermentation in Bacteria

Many bacteria and other organisms carry out fermentations forming acetate. These fermentations have broad importance for foods, agriculture, and industry. They also are important for bacteria themselves because they often generate ATP. Here, we found a biochemical pathway for forming acetate and synthesizing ATP that was unknown in fermentative bacteria. We found that the bacterium Cutibacterium granulosum formed acetate during fermentation of glucose. It did not use phosphotransacetylase or acetate kinase, enzymes found in nearly all acetate-forming bacteria. Instead, it used a pathway involving two different enzymes. The first enzyme, succinyl coenzyme A (succinyl-CoA):acetate CoA-transferase (SCACT), forms acetate from acetyl-CoA. The second enzyme, succinyl-CoA synthetase (SCS), synthesizes ATP. We identified the genes encoding these enzymes, and they were homologs of SCACT and SCS genes found in other bacteria. The pathway resembles one described in eukaryotes, but it uses bacterial, not eukaryotic, gene homologs. To find other instances of the pathway, we analyzed sequences of all biochemically characterized homologs of SCACT and SCS (103 enzymes from 64 publications). Homologs with similar enzymatic activity had similar sequences, enabling a large-scale search for them in genomes. We searched nearly 600 genomes of bacteria known to form acetate, and we found that 6% encoded homologs with SCACT and SCS activity. This included >30 species belonging to 5 different phyla, showing that a diverse range of bacteria encode the SCACT/SCS pathway. This work suggests the SCACT/SCS pathway is important for acetate formation in many branches of the tree of life. IMPORTANCE Pathways for forming acetate during fermentation have been studied for over 80 years. In that time, several pathways in a range of organisms, from bacteria to animals, have been described. However, one pathway (involving succinyl-CoA:acetate CoA-transferase and succinyl-CoA synthetase) has not been reported in prokaryotes. Here, we discovered enzymes for this pathway in the fermentative bacterium Cutibacterium granulosum. We also found >30 other fermentative bacteria that encode this pathway, demonstrating that it could be common. This pathway represents a new way for bacteria to form acetate from acetyl-CoA and synthesize ATP via substrate-level phosphorylation. It could be a target for controlling yield of acetate during fermentation, with relevance for foods, agriculture, and industry.

Metabolic energy conservation for fermentative product formation

Microbial production of bulk chemicals and biofuels from carbohydrates competes with low-cost fossil-based production. To limit production costs, high titres, productivities and especially high yields are required. This necessitates metabolic networks involved in product formation to be redox-neutral and conserve metabolic energy to sustain growth and maintenance. Here, we review the mechanisms available to conserve energy and to prevent unnecessary energy expenditure. First, an overview of ATP production in existing sugar-based fermentation processes is presented. Substrate-level phosphorylation (SLP) and the involved kinase reactions are described. Based on the thermodynamics of these reactions, we explore whether other kinase-catalysed reactions can be applied for SLP. Generation of ion-motive force is another means to conserve metabolic energy. We provide examples how its generation is supported by carbon-carbon double bond reduction, decarboxylation and electron transfer between redox cofactors. In a wider perspective, the relationship between redox potential and energy conservation is discussed. We describe how the energy input required for coenzyme A (CoA) and CO2 binding can be reduced by applying CoA-transferases and transcarboxylases. The transport of sugars and fermentation products may require metabolic energy input, but alternative transport systems can be used to minimize this. Finally, we show that energy contained in glycosidic bonds and the phosphate-phosphate bond of pyrophosphate can be conserved. This review can be used as a reference to design energetically efficient microbial cell factories and enhance product yield.

Correlation between bacterial community succession and propionic acid during gray sufu fermentation

In order to explore the correlation between the production of propionic acid (PA) and the succession of bacterial community during the fermentation of gray sufu, high-throughput sequencing and HPLC (High Performance Liquid Chromatography) were used to monitor the changes of bacterial community and metabolite content. The abundance and metabolite concentration of Propionibacterium increased rapidly in the early stage of fermentation. In the middle stage, the abundance of Lactobacillus began to increase, while the pH decreased rapidly. In the late stage, the concentration of PA began to decrease, but it remained at a high level at the end of fermentation. Correlation analysis showed that Lactobacillus and Bacillus had a strong negative correlation with PA and its precursor. The results showed that Fusobacterium, Providencia, Lactobacillus and Bacillus could be the key factors to reduce the PA content. This study provides a new idea for the quality control of traditional fermented food.

Expanding the Knowledge on the Skillful Yeast Cyberlindnera jadinii

Cyberlindnera jadinii is widely used as a source of single-cell protein and is known for its ability to synthesize a great variety of valuable compounds for the food and pharmaceutical industries. Its capacity to produce compounds such as food additives, supplements, and organic acids, among other fine chemicals, has turned it into an attractive microorganism in the biotechnology field. In this review, we performed a robust phylogenetic analysis using the core proteome of C. jadinii and other fungal species, from Asco- to Basidiomycota, to elucidate the evolutionary roots of this species. In addition, we report the evolution of this species nomenclature over-time and the existence of a teleomorph (C. jadinii) and anamorph state (Candida utilis) and summarize the current nomenclature of most common strains. Finally, we highlight relevant traits of its physiology, the solute membrane transporters so far characterized, as well as the molecular tools currently available for its genomic manipulation. The emerging applications of this yeast reinforce its potential in the white biotechnology sector. Nonetheless, it is necessary to expand the knowledge on its metabolism, regulatory networks, and transport mechanisms, as well as to develop more robust genetic manipulation systems and synthetic biology tools to promote the full exploitation of C. jadinii.

Organic acids as antimicrobial food agents: applications and microbial productions

Food safety is a global health and socioeconomic concern since many people still suffer from various acute and life-long diseases, which are caused by consumption of unsafe food. Therefore, ensuring safety of the food is one of the most essential issues in the food industry, which needs to be considered during not only food composition formulation but also handling and storage. For safety purpose, various chemical preservatives have been used so far in the foods. Recently, there has been renewed interest in replacing chemically originated food safety compounds with natural ones in the industry, which can also serve as antimicrobial agents. Among these natural compounds, organic acids possess the major portion. Therefore, in this paper, it is aimed to review and compile the applications, effectiveness, and microbial productions of various widely used organic acids as antimicrobial agents in the food industry.

Evolutionary engineering of Escherichia coli for improved anaerobic growth in minimal medium accelerated lactate production

Anaerobic fermentation is a favorable process for microbial production of bulk chemicals like ethanol and organic acids. Low productivity is the bottleneck of several anaerobic processes which has significant impact on the technique competitiveness of production strain. Improving growth rate of production strain can speed up the total production cycle and may finally increase productivity of anaerobic processes. In this work, evolutionary engineering of wild-type strain Escherichia coli W3110 was adopted to improve anaerobic growth in mineral medium. Significant increases in exponential growth rate and stationary cell density were achieved in evolved strain WE269, and a 96.5% increase in lactate productivity has also been observed in batch fermentation of this strain with M9 minimal medium. Then, an engineered strain for lactate production (BW100) was constructed by using WE269 as a platform and 98.3 g/L lactate (with an optical purity of D-lactate above 95%) was produced in a 5-L bioreactor after 48 h with a productivity of 2.05 g/(L·h). Finally, preliminary investigation demonstrated that mutation in sucD (sucD M245I) (encoding succinyl-CoA synthetase); ilvG (ilvG Δ1bp) (encoding acetolactate synthase 2 catalytic subunit), and rpoB (rpoB T1037P) (encoding RNA polymerase β subunit) significantly improved anaerobic growth of E. coli. Double-gene mutation in ilvG and sucD resumed most of the growth potential of evolved strain WE269. This work suggested that improving anaerobic growth of production host can increase productivity of organic acids like lactate, and specific mutation-enabled improved growth may also be applied to metabolic engineering for production of other bulk chemicals.

Biosynthesis of butyric acid by Clostridium tyrobutyricum

Butyric acid (C₃H₇COOH) is an important chemical that is widely used in foodstuffs along with in the chemical and pharmaceutical industries. The bioproduction of butyric acid through large-scale fermentation has the potential to be more economical and efficient than petrochemical synthesis. In this paper, the metabolic pathways involved in the production of butyric acid from Clostridium tyrobutyricum using hexose and pentose as substrates are investigated, and approaches to enhance butyric acid production through genetic modification are discussed. Finally, bioreactor modifications (including fibrous bed bioreactor, inner disk-shaped matrix bioreactor, fibrous matrix packed in porous levitated sphere carriers), low-cost feedstocks, and special treatments (including continuous fermentation with cell recycling, extractive fermentation with solvent, using different artificial electron carriers) intended to improve the feasibility of commercial butyric acid bioproduction are summarized.

Adipic acid tolerance screening for potential adipic acid production hosts

BACKGROUND

Biobased processes for the production of adipic acid are of great interest to replace the current environmentally detrimental petrochemical production route. No efficient natural producer of adipic acid has yet been identified, but several approaches for pathway engineering have been established. Research has demonstrated that the microbial production of adipic acid is possible, but the yields and titres achieved so far are inadequate for commercialisation. A plausible explanation may be intolerance to adipic acid. Therefore, in this study, selected microorganisms, including yeasts, filamentous fungi and bacteria, typically used in microbial cell factories were considered to evaluate their tolerance to adipic acid.

RESULTS

Screening of yeasts and bacteria for tolerance to adipic acid was performed in microtitre plates, and in agar plates for A. niger in the presence of adipic acid over a broad range of concentration (0-684 mM). As the different dissociation state(s) of adipic acid may influence cells differently, cultivations were performed with at least two pH values. Yeasts and A. niger were found to tolerate substantially higher concentrations of adipic acid than bacteria, and were less affected by the undissociated form of adipic acid than bacteria. The yeast exhibiting the highest tolerance to adipic acid was Candida viswanathii, showing a reduction in maximum specific growth rate of no more than 10-15% at the highest concentration of adipic acid tested and the tolerance was not dependent on the dissociation state of the adipic acid.

CONCLUSIONS

Tolerance to adipic acid was found to be substantially higher among yeasts and A. niger than bacteria. The explanation of the differences in adipic acid tolerance between the microorganisms investigated are likely related to fundamental differences in their physiology and metabolism. Among the yeasts investigated, C. viswanathii showed the highest tolerance and could be a potential host for a future microbial cell factory for adipic acid.