Electron bifurcation mechanism and homoacetogenesis explain products yields in mixed culture anaerobic fermentations

Anaerobic fermentation of organic wastes using microbial mixed cultures is a promising avenue to treat residues and obtain added-value products. However, the process has some important limitations that prevented so far any industrial application. One of the main issues is that we are not able to predict reliably the product spectrum (i.e. the stoichiometry of the process) because the complex microbial community behaviour is not completely understood. To address this issue, in this work we propose a new metabolic network of glucose fermentation by microbial mixed cultures that incorporates electron bifurcation and homoacetogenesis. Our methodology uses NADH balances to analyse published experimental data and evaluate the new stoichiometry proposed. Our results prove for the first time the inclusion of electron bifurcation in the metabolic network as a better description of the experimental results. Homoacetogenesis has been used to explain the discrepancies between observed and theoretically predicted yields of gaseous H2 and CO2 and it appears as the best solution among other options studied. Overall, this work supports the consideration of electron bifurcation as an important biochemical mechanism in microbial mixed cultures fermentations and underlines the importance of considering homoacetogenesis when analysing anaerobic fermentations

Electro-extractive fermentation for efficient biohydrogen production

Electrodialysis, an electrochemical membrane technique, was found to prolong and enhance the production of biohydrogen and purified organic acids via the anaerobic fermentation of glucose by Escherichia coli. Through the design of a model electrodialysis medium using cationic buffer, pH was precisely controlled electrokinetically, i.e. by the regulated extraction of acidic products with coulombic efficiencies of organic acid recovery in the range 50–70% maintained over continuous 30-day experiments. Contrary to\ud previous reports, E. coli produced H2 after aerobic growth in minimal medium without inducers and with a mixture of organic acids dominated by butyrate. The selective separation of organic acids from fermentation provides a potential nitrogen-free carbon source for further biohydrogen production in a parallel photofermentation. A parallel study incorporated this fermentation system into an integrated biohydrogen refinery (IBR) for the conversion of organic waste to hydrogen and energy

Integrating dark and light biohydrogen production strategies: towards the hydrogen economy

Biological methods of hydrogen production are preferable to chemical methods because of the possibility to use sunlight, CO2 and organic wastes as substrates for environmentally benign conversions, under moderate conditions. By combining different microorganisms with different capabilities, the individual strengths of each may be exploited and their weaknesses overcome. Mechanisms of bio-hydrogen production are described and strategies for their integration are discussed. Dual systems can be\ud divided broadly into wholly light-driven systems (with microalgae/cyanobacteria as the 1st stage) and partially light-driven systems (with a dark, fermentative initial reaction). Review and evaluation of published data suggests that the latter type of system holds greater promise for industrial application. This is because the calculated land area required for a wholly light-driven dual system would be too large for either centralised (macro-) or decentralised(micro-) energy generation. The potential contribution to the hydrogen economy of partially light-driven dual systems is overviewed alongside that of other biofuels such as bio-methane and bio-ethanol

Development of a D-xylose fermenting and inhibitor tolerant industrial Saccharomyces cerevisiae strain with high performance in lignocellulose hydrolysates using metabolic and evolutionary engineering

Background: The production of bioethanol from lignocellulose hydrolysates requires a robust, D-xylose-fermenting and inhibitor-tolerant microorganism as catalyst. The purpose of the present work was to develop such a strain from a prime industrial yeast strain, Ethanol Red, used for bioethanol production. Results: An expression cassette containing 13 genes including Clostridium phytofermentans XylA, encoding D-xylose isomerase (XI), and enzymes of the pentose phosphate pathway was inserted in two copies in the genome of Ethanol Red. Subsequent EMS mutagenesis, genome shuffling and selection in D-xylose-enriched lignocellulose hydrolysate, followed by multiple rounds of evolutionary engineering in complex medium with D-xylose, gradually established efficient D-xylose fermentation. The best-performing strain, GS1.11-26, showed a maximum specific D-xylose consumption rate of 1.1 g/g DW/h in synthetic medium, with complete attenuation of 35 g/L D-xylose in about 17 h. In separate hydrolysis and fermentation of lignocellulose hydrolysates of Arundo donax (giant reed), spruce and a wheat straw/hay mixture, the maximum specific D-xylose consumption rate was 0.36, 0.23 and 1.1 g/g DW inoculum/h, and the final ethanol titer was 4.2, 3.9 and 5.8% (v/v), respectively. In simultaneous saccharification and fermentation of Arundo hydrolysate, GS1.11-26 produced 32% more ethanol than the parent strain Ethanol Red, due to efficient D-xylose utilization. The high D-xylose fermentation capacity was stable after extended growth in glucose. Cell extracts of strain GS1.11-26 displayed 17-fold higher XI activity compared to the parent strain, but overexpression of XI alone was not enough to establish D-xylose fermentation. The high D-xylose consumption rate was due to synergistic interaction between the high XI activity and one or more mutations in the genome. The GS1.11-26 had a partial respiratory defect causing a reduced aerobic growth rate. Conclusions: An industrial yeast strain for bioethanol production with lignocellulose hydrolysates has been developed in the genetic background of a strain widely used for commercial bioethanol production. The strain uses glucose and D-xylose with high consumption rates and partial cofermentation in various lignocellulose hydrolysates with very high ethanol yield. The GS1.11-26 strain shows highly promising potential for further development of an all-round robust yeast strain for efficient fermentation of various lignocellulose hydrolysates

A Clostridium group IV species dominates and suppresses a mixed culture fermentation by tolerance to medium chain fatty acids products

A microbial community is engaged in a complex economy of cooperation and competition for carbon and energy. In engineered systems such as anaerobic digestion and fermentation, these relationships are exploited for conversion of a broad range of substrates into products, such as biogas, ethanol, and carboxylic acids. Medium chain fatty acids (MCFAs), for example, hexanoic acid, are valuable, energy dense microbial fermentation products, however, MCFA tend to exhibit microbial toxicity to a broad range of microorganisms at low concentrations. Here, we operated continuous mixed population MCFA fermentations on biorefinery thin stillage to investigate the community response associated with the production and toxicity of MCFA. In this study, an uncultured species from the Clostridium group IV (related to Clostridium sp. BS-1) became enriched in two independent reactors that produced hexanoic acid (up to 8.1 g L−1), octanoic acid (up to 3.2 g L−1), and trace concentrations of decanoic acid. Decanoic acid is reported here for the first time as a possible product of a Clostridium group IV species. Other significant species in the community, Lactobacillus spp. and Acetobacterium sp., generate intermediates in MCFA production, and their collapse in relative abundance resulted in an overall production decrease. A strong correlation was present between the community composition and both the hexanoic acid concentration (p = 0.026) and total volatile fatty acid concentration (p = 0.003). MCFA suppressed species related to Clostridium sp. CPB-6 and Lactobacillus spp. to a greater extent than others. The proportion of the species related to Clostridium sp. BS-1 over Clostridium sp. CPB-6 had a strong correlation with the concentration of octanoic acid (p = 0.003). The dominance of this species and the increase in MCFA resulted in an overall toxic effect on the mixed community, most significantly on the Lactobacillus spp., which resulted in a decrease in total hexanoic acid concentration to 32 ± 2% below the steady-state average. As opposed to the current view of MCFA toxicity broadly leading to production collapse, this study demonstrates that varied tolerance to MCFA within the community can lead to the dominance of some species and the suppression of others, which can result in a decreased productivity of the fermentation

In vitro bioconversion of polyphenols from black tea and red wine/grape juice by human intestinal microbiota displays strong interindividual variability

Dietary polyphenols in tea and wine have been associated with beneficial health effects. After ingestion, most polyphenols are metabolized by the colonic microbiota. The current study aimed at exploring the interindividual variation of gut microbial polyphenol bioconversion from 10 healthy human subjects. In vitro fecal batch fermentations simulating conditions in the distal colon were performed using polyphenols from black tea and a mixture of red wine and grape juice. Microbial bioconversion was monitored by NMR- and GC-MS-based profiling of diverse metabolites and phenolics. The complex polyphenol mixtures were degraded to a limited number of key metabolites. Each subject displayed a specific metabolite profile differing in composition and time courses as well as levels of these metabolites. Moreover, clear differences depending on the polyphenol sources were observed. In conclusion, varying metabolite pathways among individuals result in different metabolome profiles and therefore related health effects are hypothesized to differ between subjects

The future of bioethanol

Yeasts have been domesticated by mankind before horses. After the mastering of alcoholic fermentation for centuries, yeasts have become the protagonist of one of the most important biotechnological industries worldwide: the production of bioethanol. This chapter will initially present some important challenges to be overcome in this industry, both in first and second generation biofuel production. Then, it will briefly revisit some advances obtained in recent years. Finally, it will present and discuss some opportunities, in the scope of metabolic engineering and synthetic biology, that will likely be present in the future of bioethanol

Co-Fermenting Pyrolysis Aqueous Condensate and Pyrolysis Syngas with Anaerobic Microbial Communities Enables L-Malate Production in a Secondary Fermentative Stage

The pyrolytic conversion of lignocellulosic biomass into fuels and chemicals is a promising option for the valorization of agricultural and forestry residues. However, technological developments are still needed to maximize product recovery and carbon fixation of the pyrolysis process. The pyrolysis aqueous condensate (PAC), a pyrolysis by-product, has a high water content and is highly toxic, hampering its use. The anaerobic digestion of PAC from different biomasses has been proven a viable technology for PAC valorization and detoxification, but its toxicity limits the methanogenic potential. Alternatively, methanation or VFA production from syngas by anaerobic mixed cultures are technologies of scientific interest. This study investigates the potential of a two-stage process to convert the carbon and energy in syngas and PAC into L-malate. PAC and syngas were co-fermented by two mixed cultures at 37 and 55 °C, identifying kinetic inhibitions and the effects of increasing PAC concentrations on the product pool. The media from selected mixed culture fermentations were then inoculated with Aspergillus oryzae for L-malate production. The results show that mixed cultures can perform simultaneous syngas fermentation and PAC detoxification. While PAC concentrations above 2% completely inhibited methanogenesis, CO consumption was inhibited at PAC concentrations above 5%, regardless of the temperature. In fermentations where PAC inhibited methanation, the mixed cultures channelled the carbon and electrons from syngas and PAC to volatile fatty acids or acetate/H2 production, depending on the incubation temperature. Substantial detoxification of PAC was observed under PAC concentrations up to 10% independently of the rates of syngas metabolism. PAC detoxification enabled the further valorization of the acetate produced via syngas and PAC fermentations into L-malate, achieving yields up to 0.17 mM/mM. These results are promising for the development of an integrated process that simultaneously detoxifies and recovers value from gaseous and aqueous waste streams originating from pyrolysis

Minimizing acetate formation in E. coli fermentations

Escherichia coli remains the best established production organisms in industrial biotechnology. However, during aerobic fermentation runs at high growth rates, considerable amounts of acetate are accumulated as by-product. This by-product has negative effects on growth and protein production. Over the last 20 years, substantial research efforts have been spent to reduce acetate accumulation during aerobic growth of E. coli on glucose. From the onset it was clear that this quest should not be a simple nor uncomplicated one. Simple deletion of the acetate pathway, reduced the acetate accumulation, but instead other by-products were formed. This minireview gives a clear outline of these research efforts and the outcome of them, including bioprocess level approaches and genetic approaches. Recently, the latter seems to have some promising results

Improvement of Biogas Production by Bioaugmentation

Biogas production technologies commonly involve the use of natural anaerobic consortia of microbes. The objective of this study was to elucidate the importance of hydrogen in this complex microbial food chain. Novel laboratory biogas reactor prototypes were designed and constructed. The fates of pure hydrogen-producing cultures of Caldicellulosiruptor saccharolyticus and Enterobacter cloacae were followed in time in thermophilic and mesophilic natural biogas-producing communities, respectively. Molecular biological techniques were applied to study the altered ecosystems. A systematic study in 5-litre CSTR digesters revealed that a key fermentation parameter in the maintenance of an altered population balance is the loading rate of total organic solids. Intensification of the biogas production was observed and the results corroborate that the enhanced biogas productivity is associated with the increased abundance of the hydrogen producers. Fermentation parameters did not indicate signs of failure in the biogas production process. Rational construction of more efficient and sustainable biogas-producing microbial consortia is proposed