The physiology and biotechnology of dark fermentative biohydrogen production

Review of cathodic electroactive bacteria: Species, properties, applications and electron transfer mechanisms

Cathodic electroactive bacteria (C-EAB) which are capable of accepting electrons from solid electrodes provide fresh avenues for pollutant removal, biosensor design, and electrosynthesis. This review systematically summarized the burgeoning applications of the C-EAB over the past decade, including 1) removal of nitrate, aromatic derivatives, and metal ions; 2) biosensing based on biocathode; 3) electrosynthesis of CH4, H2, organic carbon, NH3, and protein. In addition, the mechanisms of electron transfer by the C-EAB are also classified and summarized. Extracellular electron transfer and interspecies electron transfer have been introduced, and the electron transport mechanism of typical C-EAB, such as Shewanella oneidensis MR-1, has been combed in detail. By bringing to light this cutting-edge area of the C-EAB, this review aims to stimulate more interest and research on not only exploring great potential applications of these electron-accepting bacteria, but also developing steady and scalable processes harnessing biocathodes.

Formate-driven H2 production by whole cells of Thermoanaerobacter kivui

Background

In times of global warming there is an urgent need to replace fossil fuel-based energy vectors by less carbon dioxide (CO2)-emitting alternatives. One attractive option is the use of molecular hydrogen (H2) since its combustion emits water (H2O) and not CO2. Therefore, H2 is regarded as a non-polluting fuel. The ways to produce H2 can be diverse, but steam reformation of conventional fossil fuel sources is still the main producer of H2 gas up to date. Biohydrogen production via microbes could be an alternative, environmentally friendly and renewable way of future H2 production, especially when the flexible and inexpensive C1 compound formate is used as substrate.

Results

In this study, the versatile compound formate was used as substrate to drive H2 production by whole cells of the thermophilic acetogenic bacterium Thermoanaerobacter kivui which harbors a highly active hydrogen-dependent CO2 reductase (HDCR) to oxidize formate to H2 and CO2 and vice versa. Under optimized reaction conditions, T. kivui cells demonstrated the highest H2 production rates (qH2 = 685 mmol g−1 h−1) which were so far reported in the literature for wild-type organisms. Additionally, high yields (Y(H2/formate)) of 0.86 mol mol−1 and a hydrogen evolution rate (HER) of 999 mmol L−1 h−1 were observed. Finally, stirred-tank bioreactor experiments demonstrated the upscaling feasibility of the applied whole cell system and indicated the importance of pH control for the reaction of formate-driven H2 production.

Conclusions

The thermophilic acetogenic bacterium T. kivui is an efficient biocatalyst for the oxidation of formate to H2 (and CO2). The existing genetic tool box of acetogenic bacteria bears further potential to optimize biohydrogen production in future and to contribute to a future sustainable formate/H2 bio-economy.

Novel strategies towards efficient molecular biohydrogen production by dark fermentative mechanism: present progress and future perspective

In the scenario of alarming increase in greenhouse and toxic gas emissions from the burning of conventional fuels, it is high time that the population drifts towards alternative fuel usage to obviate pollution. Hydrogen is an environment-friendly biofuel with high energy content. Several production methods exist to produce hydrogen, but the least energy intensive processes are the fermentative biohydrogen techniques. Dark fermentative biohydrogen production (DFBHP) is a value-added, less energy-consuming process to generate biohydrogen. In this process, biohydrogen can be produced from sugars as well as complex substrates that are generally considered as organic waste. Yet, the process is constrained by many factors such as low hydrogen yield, incomplete conversion of substrates, accumulation of volatile fatty acids which lead to the drop of the system pH resulting in hindered growth and hydrogen production by the bacteria. To circumvent these drawbacks, researchers have come up with several strategies that improve the yield of DFBHP process. These strategies can be classified as preliminary methodologies concerned with the process optimization and the latter that deals with pretreatment of substrate and seed sludge, bioaugmentation, co-culture of bacteria, supplementation of additives, bioreactor design considerations, metabolic engineering, nanotechnology, immobilization of bacteria, etc. This review sums up some of the improvement techniques that profoundly enhance the biohydrogen productivity in a DFBHP process.

Promotion of biological H2 (Bio-H2) production by the nitrogen-fixing anaerobic microbial consortia using humin, a solid-phase humic substance

Dark fermentative biological hydrogen (Bio-H₂) production is expected to be a clean and sustainable H₂ production technology, and the technologies have been studied to increase in the product yield as index. This study achieved high product yields of Bio-H₂ using nitrogen-fixing consortia under nitrogen-deficient conditions with glucose or mannitol as substrate and humin as the extracellular electron mediator: 4.12 mol-H₂/mol-glucose and 3.12 mol-H₂/mol-mannitol. The high Bio-H₂ production was observed under the conditions where both nitrogenase and hydrogenase were active in the presence of humin. Nitrogenase activity was confirmed by acetylene reduction activity and hydrogenase activity by Bio-H₂ production under nitrogenase-inhibiting conditions with NH₄NO₃. [Fe-Fe] hydrogenase detected by a specific PCR and acetate, butyrate, formate, lactate, and pyruvate produced as by-products suggested the involvement of both pyruvate-ferredoxin-oxidoreductase and pyruvate formate lyase pathways in Bio-H₂ production. Humin promoted the Bio-H₂ production beyond the capacity of the consortium, which had reached saturation with the optimum concentrations of glucose and mannitol. Carbon balance suggested the concurrent H₂ consumption by hydrogenotrophic methanogenesis and acetogenesis. Bio-H₂ production of the washed and starved consortium with reduced humin under conditions with or without NH₄NO₃ suggests that humin promoted hydrogenase and nitrogenase activity by donating extracellular electrons. Clostridium and Ruminococcus in the consortia were considered major hydrogen producers. Thus, this study demonstrated the outstanding potential of nitrogen-fixing consortia under nitrogen-deficient conditions with humin as an extracellular electron mediator for dark fermentative Bio-H₂ production with high yields.

The Historical Development of Cultivation Techniques for Methanogens and Other Strict Anaerobes and Their Application in Modern Microbiology

The cultivation and investigation of strictly anaerobic microorganisms belong to the fields of anaerobic microbial physiology, microbiology, and biotechnology. Anaerobic cultivation methods differ from classic microbiological techniques in several aspects. The requirement for special instruments, which are designed to prevent the contact of the specimen with air/molecular oxygen by different means of manipulation, makes this field more challenging for general research compared to working with aerobic microorganisms. Anaerobic microbiological methods are required for many purposes, such as for the isolation and characterization of new species and their physiological examination, as well as for anaerobic biotechnological applications or medical indications. This review presents the historical development of methods for the cultivation of strictly anaerobic microorganisms focusing on methanogenic archaea, anaerobic cultivation methods that are still widely used today, novel methods for anaerobic cultivation, and almost forgotten, but still relevant, techniques.

Progress in microbial biomass conversion into green energy

The increase in global population size over the past 100 decades has doubled the requirements for energy resources. To mitigate the limited fossil fuel available, new clean energy sources being environmental sustainable for replacement of traditional energy sources are explored to supplement the current scarcity. Biomass containing lignin and cellulose is the main raw material to replace fossil energy given its abundance and lower emission of greenhouse gases and NOx when transformed into energy. Bacteria, fungi and algae decompose lignocellulose leading to generation of hydrogen, methane, bioethanol and biodiesel being the clean energy used for heating, power generation and the automobile industry. Microbial Fuel Cell (MFC) uses microorganisms to decompose biomass in wastewater to generate electricity and remove heavy metals in wastewater. Biomass contains cellulose, hemicellulose, lignin and other biomacromolecules which need hydrolyzation for conversion into small molecules by corresponding enzymes in order to be utilized by microorganisms. This paper discusses microbial decomposition of biomass into clean energy and the five major ways of clean energy production, and its economic benefits for future renewable energy security.

Resource recovery from sugarcane vinasse by anaerobic digestion - A review

The increase in biofuel production by 2030, driven by the targets set at the 21st United Nations Framework Convention on Climate Change (COP21), will promote an increase in ethanol production, and consequently more vinasse generation. Sugarcane vinasse, despite having a high polluting potential due to its high concentration of organic matter and nutrients, has the potential to produce value-added resources such as volatile fatty acids (VFA), biohydrogen (bioH₂) and biomethane (bioCH₄) from anaerobic digestion. The objective of this paper is to present a critical review on the vinasse treatment by anaerobic digestion focusing on the final products. Effects of operational parameters on production and recovery of these resources, such as pH, temperature, retention time and type of inoculum were addressed. Given the importance of treating sugarcane vinasse due to its complex composition and high volume generated in the ethanol production process, this is the first review that evaluates the production of VFAs, bioH₂ and bioCH₄ in the treatment of this organic residue. Also, the challenges of the simultaneous production of VFA, bioH₂ and bioCH₄ and resources recovery in the wastewater streams generated in flex-fuel plants, using sugarcane and corn as raw material in ethanol production, are presented. The installation of flex-fuel plants was briefly discussed, with the main impacts on the treatment process of these effluents either jointly or simultaneously, depending on the harvest season.

Design and engineering of artificial microbial consortia for biohydrogen production

In natural microbial ecosystems the metabolic diversity of the organisms enables interaction among the community members and allows them to engage in syntrophic interactions. With regard to biotechnology, artificial microbial consortium engineering is used to improve productivities and yields of bioprocesses. However, to achieve supreme productivity or efficiency at industrial scale, defined ecosystems must be physiologically well-selected to meet eco-biotechnological demands. Here, we present an artificial microbial consortia design and engineering pipeline for developing dark fermentative biohydrogen production processes. The proposed pipeline might be considered as a blue-print for enhancing other bioprocesses that fundamentally face metabolic restrictions or kinetic limitations.

Renewable biohydrogen production from lignocellulosic biomass using fermentation and integration of systems with other energy generation technologies

Biohydrogen is a clean and renewable source of energy. It can be produced by using technologies such as thermochemical, electrolysis, photoelectrochemical and biological, etc. Among these technologies, the biological method (dark fermentation) is considered more sustainable and ecofriendly. Dark fermentation involves anaerobic microbes which degrade carbohydrate rich substrate and produce hydrogen. Lignocellulosic biomass is an abundantly available raw material and can be utilized as an economic and renewable substrate for biohydrogen production. Although there are many hurdles, continuous advancements in lignocellulosic biomass pretreatment technology, microbial fermentation (mixed substrate and co-culture fermentation), the involvement of molecular biology techniques, and understanding of various factors (pH, T, addition of nanomaterials) effect on biohydrogen productivity and yield render this technology efficient and capable to meet future energy demands. Further integration of biohydrogen production technology with other products such as bio-alcohol, volatile fatty acids (VFAs), and methane have the potential to improve the efficiency and economics of the overall process. In this article, various methods used for lignocellulosic biomass pretreatment, technologies in trends to produce and improve biohydrogen production, a coproduction of other energy resources, and techno-economic analysis of biohydrogen production from lignocellulosic biomass are reviewed.

Intestinal Microbiota and Perspectives of the Use of Meta-Analysis for Comparison of Ulcerative Colitis Studies

Meta-analysis is a statistical process summarizing comparable data from a number of scientific papers. The use of meta-analysis in microbiology allows decision-making that has an impact on public health policy. It can happen that the primary researches come to different conclusions, although these are targeted with the same research question. It is, therefore, inevitable to have the means to systematically evaluate information and compare research results. Ulcerative colitis together with Crohn's disease are among the two main inflammatory bowel diseases. This chronic disease of the gastrointestinal tract, with an as yet unclear etiology, is presented by an uncontrolled inflammatory immune response in genetically predisposed individuals to as yet undefined environmental factors in interaction with the intestinal microbiota itself. In patients with ulcerative colitis (UC), changes in the composition and relative abundance of microorganisms could be observed. Sulfate-reducing bacteria (SRB), which commonly occur in the large intestine as part of the commensal microbiota of animals and humans involved in the pathogenesis of the disease, have been shown to occur. SRB are anaerobic organisms affecting short-chain fatty acid metabolism. This work outlines the perspectives of the use of meta-analysis for UC and changes in the representation of intestinal organisms in these patients.

Archaea Biotechnology

Archaea are a domain of prokaryotic organisms with intriguing physiological characteristics and ecological importance. In Microbial Biotechnology, archaea are historically overshadowed by bacteria and eukaryotes in terms of public awareness, industrial application, and scientific studies, although their biochemical and physiological properties show a vast potential for a wide range of biotechnological applications. Today, the majority of microbial cell factories utilized for the production of value-added and high value compounds on an industrial scale are bacterial, fungal or algae based. Nevertheless, archaea are becoming ever more relevant for biotechnology as their cultivation and genetic systems improve. Some of the main advantages of archaeal cell factories are the ability to cultivate many of these often extremophilic organisms under non-sterile conditions, and to utilize inexpensive feedstocks often toxic to other microorganisms, thus drastically reducing cultivation costs. Currently, the only commercially available products of archaeal cell factories are bacterioruberin, squalene, bacteriorhodopsin and diether-/tetraether-lipids, all of which are produced utilizing halophiles. Other archaeal products, such as carotenoids and biohydrogen, as well as polyhydroxyalkanoates and methane are in early to advanced development stages, respectively. The aim of this review is to provide an overview of the current state of Archaea Biotechnology by describing the actual state of research and development as well as the industrial utilization of archaeal cell factories, their role and their potential in the future of sustainable bioprocessing, and to illustrate their physiological and biotechnological potential.

Bacteria coated cathodes as an in-situ hydrogen evolving platform for microbial electrosynthesis

Hydrogen is a key intermediate element in microbial electrosynthesis as a mediator of the reduction of carbon dioxide (CO₂) into added value compounds. In the present work we aimed at studying the biological production of hydrogen in biocathodes operated at − 1.0 V vs. Ag/AgCl, using a highly comparable technology and CO₂ as carbon feedstock. Ten bacterial strains were chosen from genera Rhodobacter, Rhodopseudomonas, Rhodocyclus, Desulfovibrio and Sporomusa, all described as hydrogen producing candidates. Monospecific biofilms were formed on carbon cloth cathodes and hydrogen evolution was constantly monitored using a microsensor. Eight over ten bacteria strains showed electroactivity and H₂ production rates increased significantly (two to eightfold) compared to abiotic conditions for two of them (Desulfovibrio paquesii and Desulfovibrio desulfuricans). D. paquesii DSM 16681 exhibited the highest production rate (45.6 ± 18.8 µM min⁻¹) compared to abiotic conditions (5.5 ± 0.6 µM min⁻¹), although specific production rates (per 16S rRNA copy) were similar to those obtained for other strains. This study demonstrated that many microorganisms are suspected to participate in net hydrogen production but inherent differences among strains do occur, which are relevant for future developments of resilient biofilm coated cathodes as a stable hydrogen production platform in microbial electrosynthesis.

Biohydrogen production beyond the Thauer limit by precision design of artificial microbial consortia

Dark fermentative biohydrogen (H₂) production could become a key technology for providing renewable energy. Until now, the H₂ yield is restricted to 4 moles of H₂ per mole of glucose, referred to as the "Thauer limit". Here we show, that precision design of artificial microbial consortia increased the H₂ yield to 5.6 mol mol^-1 glucose, 40% higher than the Thauer limit. In addition, the volumetric H₂ production rates of our defined artificial consortia are superior compared to any mono-, co- or multi-culture system reported to date. We hope this study to be a major leap forward in the engineering of artificial microbial consortia through precision design and provide a breakthrough in energy science, biotechnology and ecology. Constructing artificial consortia with this drawing-board approach could in future increase volumetric production rates and yields of other bioprocesses. Our artificial consortia engineering blueprint might pave the way for the development of a H₂ production bioindustry.

Formate Utilization by the Crenarchaeon Desulfurococcus amylolyticus

Formate is one of the key compounds of the microbial carbon and/or energy metabolism. It owes a significant contribution to various anaerobic syntrophic associations, and may become one of the energy storage compounds of modern energy biotechnology. Microbial growth on formate was demonstrated for different bacteria and archaea, but not yet for species of the archaeal phylum Crenarchaeota. Here, we show that Desulfurococcus amylolyticus DSM 16532, an anaerobic and hyperthermophilic Crenarchaeon, metabolises formate without the production of molecular hydrogen. Growth, substrate uptake, and production kinetics on formate, glucose, and glucose/formate mixtures exhibited similar specific growth rates and similar final cell densities. A whole cell conversion experiment on formate revealed that D. amylolyticus converts formate into carbon dioxide, acetate, citrate, and ethanol. Using bioinformatic analysis, we examined whether one of the currently known and postulated formate utilisation pathways could be operative in D. amylolyticus. This analysis indicated the possibility that D. amylolyticus uses formaldehyde producing enzymes for the assimilation of formate. Therefore, we propose that formate might be assimilated into biomass through formaldehyde dehydrogenase and the oxidative pentose phosphate pathway. These findings shed new light on the metabolic versatility of the archaeal phylum Crenarchaeota.

O2 sensitivity and H2 production activity of hydrogenases-A review

Hydrogenases are metalloproteins capable of catalyzing the interconversion between molecular hydrogen and protons and electrons. The iron-sulfur clusters within the enzyme enable rapid relay of electrons which are either consumed or generated at the active site. Their unparalleled catalytic efficiency has attracted attention, especially for potential use in H₂ production and/or fuel cell technologies. However, there are limitations to using hydrogenases, especially due to their high O₂ sensitivity. The subclass, called [FeFe] hydrogenases, are particularly more vulnerable to O₂ but proficient in H₂ production. In this review, we provide an overview of mechanistic and protein engineering studies focused on understanding and enhancing O₂ tolerance of the enzyme. The emphasis is on ongoing studies that attempt to overcome O₂ sensitivity of the enzyme while it catalyzes H₂ production in an aerobic environment. We also discuss pioneering attempts to utilize the enzyme in biological H₂ production and other industrial processes, as well as our own perspective on future applications.

Methods for quantification of growth and productivity in anaerobic microbiology and biotechnology

Anaerobic microorganisms (anaerobes) possess a fascinating metabolic versatility. This characteristic makes anaerobes interesting candidates for physiological studies and utilizable as microbial cell factories. To investigate the physiological characteristics of an anaerobic microbial population, yield, productivity, specific growth rate, biomass production, substrate uptake, and product formation are regarded as essential variables. The determination of those variables in distinct cultivation systems may be achieved by using different techniques for sampling, measuring of growth, substrate uptake, and product formation kinetics. In this review, a comprehensive overview of methods is presented, and the applicability is discussed in the frame of anaerobic microbiology and biotechnology.

A Review of the Enhancement of Bio-Hydrogen Generation by Chemicals Addition

Bio-hydrogen production (BHP) produced from renewable bio-resources is an attractive route for green energy production, due to its compelling advantages of relative high efficiency, cost-effectiveness, and lower ecological impact. This study reviewed different BHP pathways, and the most important enzymes involved in these pathways, to identify technological gaps and effective approaches for process intensification in industrial applications. Among the various approaches reviewed in this study, a particular focus was set on the latest methods of chemicals/metal addition for improving hydrogen generation during dark fermentation (DF) processes; the up-to-date findings of different chemicals/metal addition methods have been quantitatively evaluated and thoroughly compared in this paper. A new efficiency evaluation criterion is also proposed, allowing different BHP processes to be compared with greater simplicity and validity.

Elimination of the flavodiiron electron sink facilitates long-term H2 photoproduction in green algae

BACKGROUND

The development of renewable and sustainable biofuels to cover the future energy demand is one of the most challenging issues of our time. Biohydrogen, produced by photosynthetic microorganisms, has the potential to become a green biofuel and energy carrier for the future sustainable world, since it provides energy without CO₂ emission. The recent development of two alternative protocols to induce hydrogen photoproduction in green algae enables the function of the O₂-sensitive [FeFe]-hydrogenases, located at the acceptor side of photosystem I, to produce H₂ for several days. These protocols prevent carbon fixation and redirect electrons toward H₂ production. In the present work, we employed these protocols to a knockout Chlamydomonas reinhardtii mutant lacking flavodiiron proteins (FDPs), thus removing another possible electron competitor with H₂ production.

RESULTS

The deletion of the FDP electron sink resulted in the enhancement of H₂ photoproduction relative to wild-type C. reinhardtii. Additionally, the lack of FDPs leads to a more effective obstruction of carbon fixation even under elongated light pulses.

CONCLUSIONS

We demonstrated that the rather simple adjustment of cultivation conditions together with genetic manipulation of alternative electron pathways of photosynthesis results in efficient re-routing of electrons toward H₂ photoproduction. Furthermore, the introduction of a short recovery phase by regular switching from H₂ photoproduction to biomass accumulation phase allows to maintain cell fitness and use photosynthetic cells as long-term H₂-producing biocatalysts.

Biohydrogen production of obligate anaerobic archaeon Thermococcus onnurineus NA1 under oxic conditions via overexpression of frhAGB-encoding hydrogenase genes

BACKGROUND

The production of biohydrogen (H₂) as a promising future fuel in anaerobic hyperthermophiles has attracted great attention because H₂ formation is more thermodynamically feasible at elevated temperatures and fewer undesired side products are produced. However, these microbes require anoxic culture conditions for growth and H₂ production, thereby necessitating costly and time-consuming physical or chemical methods to remove molecular oxygen (O₂). Therefore, the development of an O₂-tolerant strain would be useful for industrial applications.

RESULTS

In this study, we found that the overexpression of frhAGB-encoding hydrogenase genes in Thermococcus onnurineus NA1, an obligate anaerobic archaeon and robust H₂ producer, enhanced O₂ tolerance. When the recombinant FO strain was exposed to levels of O₂ up to 20% in the headspace of a sealed bottle, it showed significant growth. Whole transcriptome analysis of the FO strain revealed that several genes involved in the stress response such as chaperonin β subunit, universal stress protein, peroxiredoxin, and alkyl hydroperoxide reductase subunit C, were significantly up-regulated. The O₂ tolerance of the FO strain enabled it to grow on formate and produce H₂ under oxic conditions, where prior O₂-removing steps were omitted, such as the addition of reducing agent Na₂S, autoclaving, and inert gas purging.

CONCLUSIONS

Via the overexpression of frhAGB genes, the obligate anaerobic archaeon T. onnurineus NA1 gained the ability to overcome the inhibitory effect of O₂. This O₂-tolerant property of the strain may provide another advantage to this hyperthermophilic archaeon as a platform for biofuel H₂ production.