Enrichment of syngas-converting mixed microbial consortia for ethanol production and thermodynamics-based design of enrichment strategies

Low electric current in a bioelectrochemical system facilitates ethanol production from CO using CO-enriched mixed culture

Fossil resources must be replaced by renewable resources in production systems to mitigate green-house gas emissions and combat climate change. Electro-fermentation utilizes a bioelectrochemical system (BES) to valorize industrial and municipal waste. Current electro-fermentation research is mainly focused on microbial electrosynthesis using CO2 for producing commodity chemicals and replacing petroleum-based infrastructures. However, slow production rates and low titers of metabolites during CO2-based microbial electrosynthesis impede its implementation to the real application in the near future. On the other hand, CO is a highly reactive gas and an abundant feedstock discharged from fossil fuel-based industry. Here, we investigated CO and CO2 electro-fermentation, using a CO-enriched culture. Fresh cow fecal waste was enriched under an atmosphere of 50% CO and 20% CO2 in N2 using serial cultivation. The CO-enriched culture was dominated by Clostridium autoethanogenum (≥89%) and showed electro-activity in a BES reactor with CO2 sparging. When 50% CO was included in the 20% CO2 gas with 10 mA applied current, acetate and ethanol were produced up to 12.9 ± 2.7 mM and 2.7 ± 1.1 mM, respectively. The coulombic efficiency was estimated to 148% ± 8% without an electron mediator. At 25 mA, the culture showed faster initial growth and acetate production but no ethanol production, and only at 86% ± 4% coulombic efficiency. The maximum optical density (OD) of 10 mA and 25 mA reactors were 0.29 ± 0.07 and 0.41 ± 0.03, respectively, whereas it was 0.77 ± 0.19 without electric current. These results show that CO electro-fermentation at low current can be an alternative way of valorizing industrial waste gas using a bioelectrochemical system.

Enrichment of a mixed syngas-converting culture for volatile fatty acids and methane production

The present study evaluated the production potential of CH4, carboxylic acids and alcohols from a mixed culture enriched using synthetic syngas. The influence of syngas concentration on the microbial community and products productivity and selectivity was investigated. The results demonstrated the enrichment of a mesophilic mixed culture capable of converting CO and H2 mainly to CH4 and acetate, along with butyrate. The selectivity values showed that acetate production was enhanced during the first cycle in all conditions tested (up to 20 %), while CH4 was the main product generated during following cycles. Concretely, CH4 selectivity remained unaffected by syngas concentration, reaching a stable value of 41.6 ± 2.0 %. On the other hand, butyrate selectivity was only representative at the highest syngas concentration and lower pH values (26.1 ± 5.8 %), where the H2 consumption was completely inhibited. Thus, pH was identified as a key parameter for both butyrate synthesis and the development of hydrogenotrophic activity.

Optimal preparation of food waste to increase its utility for sophorolipid production by Starmerella bombicola

Secondary feedstocks, such as food waste (FW), have been used for yeasts (e.g. Starmerella bombicola) to produce sophorolipids (SLs), which are commercially available biosurfactants. However, the quality of FW varies by location and season and may contains chemicals that inhibit SLs production. Therefore, it is crucial to identify such inhibitors and, if possible, remove them, to ensure efficient utilization. In this study, large scale FW was first analysed to determine the concentration of potential inhibitors. Lacticacid, acetic acid and ethanol were identified and found to be inhibitors of the growth of S. bombicola and its SLs production. Various methods were then evaluated for their ability to remove these inhibitors. Finally, a simple and effective strategy for removing inhibitors from FW was developed that complied with the 12 principles of green chemistry and could be adopted by industry for high SLs production.

Microbial Enrichment Techniques on Syngas and CO2 Targeting Production of Higher Acids and Alcohols

(1) Background: Microbial conversion of gaseous molecules, such as CO2, CO and H2, to valuable compounds, has come to the forefront since the beginning of the 21st century due to increasing environmental concerns and the necessity to develop alternative technologies that contribute to a fast transition to a more sustainable era. Research efforts so far have focused on C1–C2 molecules, i.e., ethanol and methane, while interest in molecules with higher carbon atoms has also started to emerge. Research efforts have already started to pay off, and industrial installments on ethanol production from steel-mill off-gases as well as methane production from the CO2 generated in biogas plants are a reality. (2) Methodology: The present study addresses C4–C6 acids and butanol as target molecules and responds to how the inherent metabolic potential of mixed microbial consortia could be revealed and exploited based on the application of different enrichment methods (3) Results and Conclusions: In most of the enrichment series, the yield of C4–C6 acids was enhanced with supplementation of acetic acid and ethanol together with the gas substrates, resulting in a maximum of 43 and 68% (e-mol basis) for butyric and caproic acid, respectively. Butanol formation was also enhanced, to a lesser degree though and up to 9% (e-mol basis). Furthermore, the microbial community exhibited significant shifts depending on the enrichment conditions applied, implying that a more profound microbial analysis on the species level taxonomy combined with the development of minimal co-cultures could set the basis for discovering new microbial co-cultures and/or co-culturing schemes.

Syngas Fermentation to Acetate and Ethanol with Adaptative Electroactive Carboxydotrophs in Single Chambered Microbial Electrochemical System

Microbial electrosynthesis system (MES; single-chambered) was fabricated and evaluated with carbon cloth/graphite as a working/counter electrode employing an enriched microbiome. Continuous syngas sparging (at working electrode; WE) enabled the growth of endo electrogenic bacteria by availing the inorganic carbon source. Applied potential (−0.5 V) on the working electrode facilitated the reduction in syngas, leading to the synthesis of fatty acids and alcohols. The higher acetic acid titer of 3.8 g/L and ethanol concentration of 0.2 g/L was observed at an active microbial metabolic state, evidencing the shift in metabolism from acetogenic to solventogenesis. Voltammograms evidenced distinct redox species with low charge transfer resistance (Rct; Nyquist impedance). Reductive catalytic current (−0.02 mA) enabled the charge transfer efficiency of the cathodes favoring syngas conversion to products. The surface morphology of carbon cloth and system-designed conditions favored the growth of electrochemically active consortia. Metagenomic analysis revealed the enrichment of phylum/class with Actinobacteria, Firmicutes/Clostridia and Bacilli, which accounts for the syngas fermentation through suitable gene loci.

Effect of external acetate on lactate-based carboxylate platform: Shifted lactate overloading limit and hydrogen co-production

Chain elongation is an anaerobic biotechnological process that converts short chain carboxylates and an electron donor (e.g. ethanol, lactate) into more valuable medium chain carboxylates. Caproate production in lactate-based chain elongation is gaining popularity, however, the relation between lactate (electron donor) and acetate (electron acceptor) has not yet been fully elucidated. Herein, for the first time, the effect of an external acetate on the lactate-based chain elongation in a continuously-fed bioreactor was tested to verify how the external acetate would affect the product spectrum, gas production, as well as stability and efficiency of carboxylates production. Periodic fluctuations in caproate production were observed in bioreactor continuously fed with lactate as a sole carbon source due to the lack of an electron acceptor (acetate) and low chain elongation performance. The recovery of stable caproate production (68.9 ± 2.2 mmol C/L/d), total lactate consumption, and high hydrogen co-production (748 ± 76 mL_H2/d) was observed as an effect of the addition of an external acetate. The lactate conversion with the external acetate in the second bioreactor ensured stable and dominant caproate production from the beginning of the process. Moreover, despite the continuous lactate overloading in the process with external acetate, stable caproate production was achieved (71.7 ± 2.4 mmol C/L/d) and previously unobserved hydrogen production occurred (213 ± 30 mL_H2/d). Thus, external electron acceptor addition (i.e. acetate) was proposed as an effective method for stable lactate-based caproate production. Microbiological analysis showed the dominance of microbes closely related to Ruminococcaceae bacterium CPB6 and Acinetobacter throughout the process. Co-occurrence networks based on taxon abundances and process parameters revealed microbial sub-networks responding to lactate concentrations.

Biological production of medium-chain carboxylates through chain elongation: An overview

Medium chain carboxylates (MCCs) have wide applications in various industries, but the traditional MCCs production methods are costly and unsustainable. Anaerobic fermentation offers a more scalable, economical and eco-friendly platform for producing MCCs through chain elongation which converts short chain carboxylates and electron donor into more valuable MCCs. However, the underlying microbial pathways are not well understood. In this review, biological production of MCCs through chain elongation is introduced elaborately, including the metabolic pathways, electron donor and substrates, microorganisms and influencing factors. Then, the strategies for enhancing MCCs production are extensively analyzed and summarized, along with the technologies for MCCs separation from the fermentation broth. Finally, challenges and perspectives concerning the large-scale MCCs production are proposed, providing suggestions for the future research. Extensive review demonstrated that anaerobic fermentation has great potential in achieving economical and sustainable MCCs production from complex organic substrates, including organic waste streams, which would significantly broaden the application of MCCs, especially in the renewable energy field. An interdisciplinary approach with knowledge from microbiology and biochemistry to chemical separations and environmental engineering is required to use this promising technology as a valorization method for converting organic biomass or organic wastes into valuable MCCs.

Conversion of Carbon Monoxide to Chemicals Using Microbial Consortia

Syngas, a gaseous mixture of CO, H₂ and CO₂, can be produced by gasification of carbon-containing materials, including organic waste materials or lignocellulosic biomass. The conversion of bio-based syngas to chemicals is foreseen as an important process in circular bioeconomy. Carbon monoxide is also produced as a waste gas in many industrial sectors (e.g., chemical, energy, steel). Often, the purity level of bio-based syngas and waste gases is low and/or the ratios of syngas components are not adequate for chemical conversion (e.g., by Fischer-Tropsch). Microbes are robust catalysts to transform impure syngas into a broad spectrum of products. Fermentation of CO-rich waste gases to ethanol has reached commercial scale (by axenic cultures of Clostridium species), but production of other chemical building blocks is underexplored. Currently, genetic engineering of carboxydotrophic acetogens is applied to increase the portfolio of products from syngas/CO, but the limited energy metabolism of these microbes limits product yields and applications (for example, only products requiring low levels of ATP for synthesis can be produced). An alternative approach is to explore microbial consortia, including open mixed cultures and synthetic co-cultures, to create a metabolic network based on CO conversion that can yield products such as medium-chain carboxylic acids, higher alcohols and other added-value chemicals.

Biofuel and chemical production from carbon one industry flux gas by acetogenic bacteria

Carbon one industry flux gas generated from fossil fuels, various industrial and domestic waste, as well as lignocellulosic biomass provides an innovative raw material to lead the sustainable development. Through the chemical and biological processing, the gas mixture composed of CO, CO₂, and H₂, also termed as syngas, is converted to biofuels and high-value chemicals. Here, the syngas fermentation process is elaborated to provide an overview. Sources of syngas are summarized and the influences of impurities on biological fermentation are exhibited. Acetogens and carboxydotrophs are the two main clusters of syngas utilizing microorganisms, their essential characters are presented, especially the energy metabolic scheme with CO, CO₂, and H₂. Synthetic biology techniques and microcompartment regulation are further discussed and proposed to create a high-efficiency cell factory. Moreover, the influencing factors in fermentation and products in carboxylic acids, alcohols, and others such like polyhydroxyalkanoate and poly-3-hydroxybutyrate are addressed. Biological fermentation from carbon one industry flux gas is a promising alternative, the latest scientific advances are expatiated hoping to inspire more creative transformation.

Bioaugmented Mixed Culture by Clostridium aceticum to Manipulate Volatile Fatty Acids Composition From the Fermentation of Cheese Production Wastewater

Production of targeted volatile fatty acid (VFA) composition by fermentation is a promising approach for upstream and post-stream VFA applications. In the current study, the bioaugmented mixed microbial culture by Clostridium aceticum was used to produce an acetic acid dominant VFA mixture. For this purpose, anaerobic sequencing batch reactors (bioaugmented and control) were operated under pH 10 and fed by cheese processing wastewater. The efficiency and stability of the bioaugmentation strategy were monitored using the production and composition of VFA, the quantity of C. aceticum (by qPCR), and bacterial community profile (16S rRNA Illumina Sequencing). The bioaugmented mixed culture significantly increased acetic acid concentration in the VFA mixture (from 1170 ± 18 to 122 ± 9 mgCOD/L) compared to the control reactor. Furthermore, the total VFA production (from 1254 ± 11 to 5493 ± 36 mgCOD/L) was also enhanced. Nevertheless, the bioaugmentation could not shift the propionic acid dominancy in the VFA mixture. The most significant effect of bioaugmentation on the bacterial community profile was seen in the relative abundance of the Thermoanaerobacterales Family III. Incertae sedis, its relative abundance increased simultaneously with the gene copy number of C. aceticum during bioaugmentation. These results suggest that there might be a syntropy between species of Thermoanaerobacterales Family III. Incertae sedis and C. aceticum. The cycle analysis showed that 6 h (instead of 24 h) was adequate retention time to achieve the same acetic acid and total VFA production efficiency. Biobased acetic acid production is widely applicable and economically competitive with petroleum-based production, and this study has the potential to enable a new approach as produced acetic acid dominant VFA can replace external carbon sources for different processes (such as denitrification) in WWTPs. In this way, the higher treatment efficiency for WWTPs can be obtained by recovered substrate from the waste streams that promote a circular economy approach.

Microbial biofilms in biorefinery - Towards a sustainable production of low-value bulk chemicals and fuels

Harnessing the potential of biocatalytic conversion of renewable biomass into value-added products is still hampered by unfavorable process economics. This has promoted the use of biofilms as an alternative to overcome the limitations of traditional planktonic systems. In this paper, the benefits and challenges of biofilm fermentations are reviewed with a focus on the production of low-value bulk chemicals and fuels from waste biomass. Our study demonstrates that biofilm fermentations can potentially improve productivities and product yields by increasing biomass retention and allowing for continuous operation at high dilution rates. Furthermore, we show that biofilms can tolerate hazardous environments, which improve the conversion of crude biomass under substrate and product inhibitory conditions. Additionally, we present examples for the improved conversion of pure and crude substrates into bulk chemicals by mixed microbial biofilms, which can benefit from microenvironments in biofilms for synergistic multi-species reactions, and improved resistance to contaminants. Finally, we suggest the use of mathematical models as useful tools to supplement experimental insights related to the effects of physico-chemical and biological phenomena on the process. Major challenges for biofilm fermentations arise from inconsistent fermentation performance, slow reactor start-up, biofilm carrier costs and carrier clogging, insufficient biofilm monitoring and process control, challenges in reactor sterilization and scale-up, and issues in recovering dilute products. The key to a successful commercialization of the technology is likely going to be an interdisciplinary approach. Crucial research areas might include genetic engineering combined with the development of specialized biofilm reactors, biofilm carrier development, in-situ biofilm monitoring, model-based process control, mixed microbial biofilm technology, development of suitable biofilm reactor scale-up criteria, and in-situ product recovery.

Effect of Sulfate on Carbon Monoxide Conversion by a Thermophilic Syngas-Fermenting Culture Dominated by a Desulfofundulus Species

A syngas-degrading enrichment culture, culture T-Syn, was dominated by a bacterium closely related to Desulfofundulus australicus strain AB33^T (98% 16S rRNA gene sequence identity). Culture T-Syn could convert high CO concentrations (from pCO ≈ 34 kPa to pCO ≈ 170 kPa), both in the absence and in the presence of sulfate as external electron acceptor. The products formed from CO conversion were H₂ and acetate. With sulfate, a lower H₂/acetate ratio was observed in the product profile, but CO conversion rates were similar to those in the absence of sulfate. The ability of D. australicus strain AB33^T to use CO was also investigated. D. australicus strain AB33^T uses up to 40% CO (pCO ≈ 68 kPa) with sulfate and up to 20% CO (pCO ≈ 34 kPa) without sulfate. Comparison of the metagenome-assembled genome (MAG) of the Desulfofundulus sp. from T-Syn culture with the genome of D. australicus strain AB33^T revealed high similarity, with an ANI value of 99% and only 32 unique genes in the genome of the Desulfofundulus sp. T-Syn. So far, only Desulfotomaculum nigrificans strain CO-1-SRB had been described to grow with CO with and without sulfate. This work further shows the carboxydotrophic potential of Desulfofundulus genus for CO conversion, both in sulfate-rich and low-sulfate environments.

Co-production of hydrogen and caproate for an effective bioprocessing of waste

The objective of the study was to valorize waste stream for the co-production of hydrogen and caproate via open culture fermentation (OCF). Batch studies confirmed that the use of sugar (lactose) together with carboxylates (lactate and acetate) may allow mutual coexistence of chain elongation and dark fermentation processes. During the continuous test in an upflow anaerobic sludge blanket reactor (UASB), acid whey was used as a model feedstock due to a high concentration of lactose and lactate. Shortening hydraulic retention time (HRT) to 2.5 days allowed the co-production of hydrogen and caproate with almost complete methanogenesis inhibition. During the 50 days period, the average hydrogen and caproate production were 1.78 ± 0.75 L_H2/L/d and 133.4 ± 17.9 mmol C/L/d, respectively.

Cryopreservation and fast recovery of enriched syngas-converting microbial communities

Over the last decades, the use of mixed microbial communities has attracted increasing scientific attention due to their potential biotechnological applications in several emerging technological platforms such as the carboxylate, bioplastic, syngas and bio-electrochemical synthesis platforms. However, this increasing interest has not been accompanied by a parallel development of suitable cryopreservation techniques for microbial communities. While cryopreservation methods for the long-term storage of axenic cultures are well established, their effectiveness in preserving the microbial diversity and functionality of microbial communities has rarely been studied. In this study, the effect of the addition of different cryopreservation agents on the long-term storage of microbial communities at -80 °C was studied using a stable enrichment culture converting syngas into acetate and ethanol. The cryopreservation agents considered in the study were glycerol, dimethylsulfoxide, polyvinylpyrrolidone, Tween 80 and yeast extract, as well as with no addition of cryopreservation agent. Their effectiveness was evaluated based on the microbial activity recovery and the maintenance of the microbial diversity and community structure upon revival of the microbial community. The results showed that the commonly used glycerol and no addition of cryopreservation agent were the least recommendable methods for the long-term frozen storage of microbial communities, while Tween 80 and polyvinylpyrrolidone were overall the most effective. Among the cryoprotectants studied, polyvinylpyrrolidone and especially Tween 80 were the only ones assuring reproducible results in terms of microbial activity recovery and microbial community structure preservation.

Species-wide Metabolic Interaction Network for Understanding Natural Lignocellulose Digestion in Termite Gut Microbiota

The structural complexity of lignocellulosic biomass hinders the extraction of cellulose, and it has remained a challenge for decades in the biofuel production process. However, wood-feeding organisms like termite have developed an efficient natural lignocellulolytic system with the help of specialized gut microbial symbionts. Despite having an enormous amount of high-throughput metagenomic data, specific contributions of each individual microbe to achieve this lignocellulolytic functionality remains unclear. The metabolic cross-communication and interdependence that drives the community structure inside the gut microbiota are yet to be explored. We have contrived a species-wide metabolic interaction network of the termite gut-microbiome to have a system-level understanding of metabolic communication. Metagenomic data of Nasutitermes corniger have been analyzed to identify microbial communities in different gut segments. A comprehensive metabolic cross-feeding network of 205 microbes and 265 metabolites was developed using published experimental data. Reconstruction of inter-species influence network elucidated the role of 37 influential microbes to maintain a stable and functional microbiota. Furthermore, in order to understand the natural lignocellulose digestion inside N. corniger gut, the metabolic functionality of each influencer was assessed, which further elucidated 15 crucial hemicellulolytic microbes and their corresponding enzyme machinery.

Syngas-aided anaerobic fermentation for medium-chain carboxylate and alcohol production: the case for microbial communities

Syngas fermentation has been successfully implemented in commercial-scale plants and can enable the biochemical conversion of the driest fractions of biomass through synthesis gas (H₂, CO₂, and CO). The process relies on optimized acetogenic strains able to reach and maintain high productivity of ethanol and acetate. In parallel, microbial communities have shown to be the best choice for the production of valuable medium-chain carboxylates through anaerobic fermentation of biomass, demanding low technical complexity and being able to realize simultaneous hydrolysis of the substrate. Each of the two technologies benefits from different strong points and has different challenges to overcome. This review discusses the rationales for merging these two seemingly disparate technologies by analyzing previous studies and drawing opinions based on the lessons learned from such studies. For keeping the technical demands of the resulting process low, a case is built for using microbial communities instead of pure strains. For that to occur, a shift from conventional syngas-based to "syngas-aided" anaerobic fermentation is suggested. Strategies for tackling the intricacies of working simultaneously with communities and syngas, such as competing pathways, and thermodynamic aspects are discussed as well as the stoichiometry and economic feasibility of the concept. Overall, syngas-aided anaerobic fermentation seems to be a promising concept for the biorefinery of the future. However, the effects of process parameters on microbial interactions have to be understood in greater detail, in order to achieve and sustain feasible medium-chain carboxylate and alcohol productivity.