A novel strategy for sequential co-culture of Clostridium thermocellum and Clostridium beijerinckii to produce solvents from alkali extracted corn cobs

Towards the application of nature's catalytic nanomachines: Cellulosomes in 2nd generation biofuel production

Cellulosomes are highly efficient, complex multi-enzyme assemblies, predominantly found in anaerobic bacteria, which offer substantial potential for second-generation biofuel production through efficient lignocellulosic biomass degradation, thus reducing the need for costly pretreatments. Recent advances in cellulosome research have significantly contributed to developing more efficient consolidated bioprocessing (CBP) platforms for biofuel production. This review highlights the latest progress in designing cellulosomes for optimized enzyme synergy and substrate specificity, as well as advances in engineering cellulosome-producing whole-cell biocatalysts tailored for biofuel applications. Apart from recombinant approaches to the development of CBP platforms, metabolic engineering of cellulosome-producing strains (CPS) and co-culture systems that combine CPS with solvent-producing microbes are also discussed. Current challenges and future directions are outlined that emphasize the role of cellulosomes as powerful tools in advancing the efficiency of lignocellulosic biorefineries.

The potential of native and engineered Clostridia for biomass biorefining

Since their first industrial application in the acetone-butanol-ethanol (ABE) fermentation in the early 1900s, Clostridia have found large application in biomass biorefining. Overall, their fermentation products include organic acids (e.g., acetate, butyrate, lactate), short chain alcohols (e.g., ethanol, n-butanol, isobutanol), diols (e.g., 1,2-propanediol, 1,3-propanediol) and H2 which have several applications such as fuels, building block chemicals, solvents, food and cosmetic additives. Advantageously, several clostridial strains are able to use cheap feedstocks such as lignocellulosic biomass, food waste, glycerol or C1-gases (CO2, CO) which confer them additional potential as key players for the development of processes less dependent from fossil fuels and with reduced greenhouse gas emissions. The present review aims to provide a survey of research progress aimed at developing Clostridium-mediated biomass fermentation processes, especially as regards strain improvement by metabolic engineering.

Current progress on engineering microbial strains and consortia for production of cellulosic butanol through consolidated bioprocessing

In the last decades, fermentative production of n-butanol has regained substantial interest mainly owing to its use as drop-in-fuel. The use of lignocellulose as an alternative to traditional acetone-butanol-ethanol fermentation feedstocks (starchy biomass and molasses) can significantly increase the economic competitiveness of biobutanol over production from non-renewable sources (petroleum). However, the low cost of lignocellulose is offset by its high recalcitrance to biodegradation which generally requires chemical-physical pre-treatment and multiple bioreactor-based processes. The development of consolidated processing (i.e., single-pot fermentation) can dramatically reduce lignocellulose fermentation costs and promote its industrial application. Here, strategies for developing microbial strains and consortia that feature both efficient (hemi)cellulose depolymerization and butanol production will be depicted, that is, rational metabolic engineering of native (hemi)cellulolytic or native butanol-producing or other suitable microorganisms; protoplast fusion of (hemi)cellulolytic and butanol-producing strains; and co-culture of (hemi)cellulolytic and butanol-producing microbes. Irrespective of the fermentation feedstock, biobutanol production is inherently limited by the severe toxicity of this solvent that challenges process economic viability. Hence, an overview of strategies for developing butanol hypertolerant strains will be provided.

One-pot fermentation for erythritol production from distillers grains by the co-cultivation of Yarrowia lipolytica and Trichoderma reesei

A co-fermentation process involving Yarrowia lipolytica and Trichoderma reesei was studied, using distillers grains (DGS) as feedstocks for erythritol production. DGS can be effectively hydrolyzed by cellulase in the single-strain culture of T. reesei. One-pot solid state fermentation for erythritol production was then established by co-cultivating Y. lipolytica M53-S with the 12 h delay inoculated T. reesei Rut C-30, in which efficient saccharification of DGS and improved production of erythritol were simultaneously achieved. The 10:1 inoculation proportion of Y. lipolytica and T. reesei contributed to the maximum erythritol production of 267.1 mg/gds under the optimal conditions including initial moisture of 55%, pH of 5.0, NaCl addition of 0.02 g/gds and DGS mass of 200 g in 144 h co-cultivation. Being compared with the attempts to produce erythritol from other raw materials, the one-pot SSF with DGS is proposed to be a potential strategy for efficient and economical erythritol production.

Developing Clostridia as Cell Factories for Short- and Medium-Chain Ester Production

Short- and medium-chain volatile esters with flavors and fruity fragrances, such as ethyl acetate, butyl acetate, and butyl butyrate, are usually value-added in brewing, food, and pharmacy. The esters can be naturally produced by some microorganisms. As ester-forming reactions are increasingly deeply understood, it is possible to produce esters in non-natural but more potential hosts. Clostridia are a group of important industrial microorganisms since they can produce a variety of volatile organic acids and alcohols with high titers, especially butanol and butyric acid through the CoA-dependent carbon chain elongation pathway. This implies sufficient supplies of acyl-CoA, organic acids, and alcohols in cells, which are precursors for ester production. Besides, some Clostridia could utilize lignocellulosic biomass, industrial off-gas, or crude glycerol to produce other branched or straight-chain alcohols and acids. Therefore, Clostridia offer great potential to be engineered to produce short- and medium-chain volatile esters. In the review, the efforts to produce esters from Clostridia via in vitro lipase-mediated catalysis and in vivo alcohol acyltransferase (AAT)-mediated reaction are comprehensively revisited. Besides, the advantageous characteristics of several Clostridia and clostridial consortia for bio-ester production and the driving force of synthetic biology to clostridial chassis development are also discussed. It is believed that synthetic biotechnology should enable the future development of more effective Clostridia for ester production.

Engineering Clostridium cellulovorans for highly selective n-butanol production from cellulose in consolidated bioprocessing

Cellulosic n-butanol from renewable lignocellulosic biomass has gained increased interest. Previously, we have engineered Clostridium cellulovorans, a cellulolytic acidogen, to overexpress the bifunctional butyraldehyde/butanol dehydrogenase gene adhE2 from C. acetobutylicum for n-butanol production from crystalline cellulose. However, butanol production by this engineered strain had a relatively low yield of approximately 0.22 g/g cellulose due to the coproduction of ethanol and acids. We hypothesized that strengthening the carbon flux through the central butyryl-CoA biosynthesis pathway and increasing intracellular NADH availability in C. cellulovorans adhE2 would enhance n-butanol production. In this study, thiolase (thlA^CA ) from C. acetobutylicum and 3-hydroxybutyryl-CoA dehydrogenase (hbd^CT ) from C. tyrobutyricum were overexpressed in C. cellulovorans adhE2 to increase the flux from acetyl-CoA to butyryl-CoA. In addition, ferredoxin-NAD(P)⁺ oxidoreductase (fnr), which can regenerate the intracellular NAD(P)H and thus increase butanol biosynthesis, was also overexpressed. Metabolic flux analyses showed that mutants overexpressing these genes had a significantly increased carbon flux toward butyryl-CoA, which resulted in increased production of butyrate and butanol. The addition of methyl viologen as an electron carrier in batch fermentation further directed more carbon flux towards n-butanol biosynthesis due to increased reducing equivalent or NADH. The engineered strain C. cellulovorans adhE2-fnr^CA -thlA^CA -hbd^CT produced n-butanol from cellulose at a 50% higher yield (0.34 g/g), the highest ever obtained in batch fermentation by any known bacterial strain. The engineered C. cellulovorans is thus a promising host for n-butanol production from cellulosic biomass in consolidated bioprocessing.

A fungus-bacterium co-culture synergistically promoted nitrogen removal by enhancing enzyme activity and electron transfer

The fungus Penicillium citrinum WXP-2 and the bacterium Citrobacter freundii WXP-9 were isolated and found to have poor denitrification performance. Surprisingly, co-culture of the two strains which formed fungus-bacterium pellets (FBPs) promoted the removal efficiency of nitrate (NO₃^--N; 95.78%) and total nitrogen (TN; 81.73%). Nitrogen balance analysis showed that excess degraded NO₃^--N was primarily converted to N₂ (77.53%). Moreover, co-culture increased the dry weight to 0.74 g/L. The diameter of pellets and cell viability also increased by 1.49 and 1.78 times, respectively, indicating that the co-culture exerted a synergistic effect to promote growth. The increase in electron-transmission system activity [99.01 mg iodonitrotetrazolium formazan/(g·L)] and nitrate reductase activity [8.65 mg N/(min·mg protein)] were responsible for denitrification promotion. The FBPs also exhibited the highest degradation rate at 2:1 inoculation ratio and 36 h delayed inoculation of strain WXP-9. Finally, recycling experiments of FBP demonstrated that the high steady TN removal rate could be maintained for five cycles.

Advances and Applications of Clostridium Co-culture Systems in Biotechnology

Clostridium spp. are important microorganisms that can degrade complex biomasses such as lignocellulose, which is a widespread and renewable natural resource. Co-culturing Clostridium spp. and other microorganisms is considered to be a promising strategy for utilizing renewable feed stocks and has been widely used in biotechnology to produce bio-fuels and bio-solvents. In this review, we summarize recent progress on the Clostridium co-culture system, including system unique advantages, composition, products, and interaction mechanisms. In addition, biochemical regulation and genetic modifications used to improve the Clostridium co-culture system are also summarized. Finally, future prospects for Clostridium co-culture systems are discussed in light of recent progress, challenges, and trends.

Microbial cell engineering to improve cellular synthetic capacity

Rapid technological progress in gene assembly, biosensors, and genetic circuits has led to reinforce the cellular synthetic capacity for chemical production. However, overcoming the current limitations of these techniques in maintaining cellular functions and enhancing the cellular synthetic capacity (e.g., catalytic efficiency, strain performance, and cell-cell communication) remains challenging. In this review, we propose a strategy for microbial cell engineering to improve the cellular synthetic capacity by utilizing biotechnological tools along with system biology methods to regulate cellular functions during chemical production. Current strategies in microbial cell engineering are mainly focused on the organelle, cell, and consortium levels. This review highlights the potential of using biotechnology to further develop the field of microbial cell engineering and provides guidance for utilizing microorganisms as attractive regulation targets.

Consolidated bioprocessing for butanol production of cellulolytic Clostridia: development and optimization

Butanol is an important bulk chemical, as well as a promising renewable gasoline substitute, that is commonly produced by solventogenic Clostridia. The main cost of cellulosic butanol fermentation is caused by cellulases that are required to saccharify lignocellulose, since solventogenic Clostridia cannot efficiently secrete cellulases. However, cellulolytic Clostridia can natively degrade lignocellulose and produce ethanol, acetate, butyrate and even butanol. Therefore, cellulolytic Clostridia offer an alternative to develop consolidated bioprocessing (CBP), which combines cellulase production, lignocellulose hydrolysis and co-fermentation of hexose/pentose into butanol in one step. This review focuses on CBP advances for butanol production of cellulolytic Clostridia and various synthetic biotechnologies that drive these advances. Moreover, the efforts to optimize the CBP-enabling cellulolytic Clostridia chassis are also discussed. These include the development of genetic tools, pentose metabolic engineering and the improvement of butanol tolerance. Designer cellulolytic Clostridia or consortium provide a promising approach and resource to accelerate future CBP for butanol production.

Metabolic Engineering of Clostridium cellulovorans to Improve Butanol Production by Consolidated Bioprocessing

Clostridium cellulovorans DSM 743B can produce butyrate when grown on lignocellulose, but it can hardly synthesize butanol. In a previous study, C. cellulovorans was successfully engineered to switch the metabolism from butyryl-CoA to butanol by overexpressing an alcohol aldehyde dehydrogenase gene adhE1 from Clostridium acetobutylicum ATCC 824; however, its full potential in butanol production is still unexplored. In the study, a metabolic engineering approach based on a push-pull strategy was developed to further enhance cellulosic butanol production. In order to accomplish this, the carbon flux from acetyl-CoA to butyryl-CoA was pulled by overexpressing a trans-enoyl-coenzyme A reductase gene (ter), which can irreversibly catalyze crotonyl-CoA to butyryl-CoA. Then an acid reassimilation pathway uncoupled with acetone production was introduced to redirect the carbon flow from butyrate and acetate toward butyryl-CoA. Finally, xylose metabolism engineering was implemented by inactivating xylR (Clocel_0594) and araR (Clocel_1253), as well as overexpressing xylT (CA_C1345), which is expected to supply additional carbon and reducing power for CoA and butanol synthesis pathways. The final engineered strain produced 4.96 g/L of n-butanol from alkali extracted corn cobs (AECC), increasing by 235-fold compared to that of the wild type. It serves as a promising butanol producer by consolidated bioprocessing.

Recent advances of biofuels and biochemicals production from sustainable resources using co-cultivation systems

Microbial communities are ubiquitous in nature and exhibit several attractive features, such as sophisticated metabolic capabilities and strong environment robustness. Inspired by the advantages of natural microbial consortia, diverse artificial co-cultivation systems have been metabolically constructed for biofuels, chemicals and natural products production. In these co-cultivation systems, especially genetic engineering ones can reduce the metabolic burden caused by the complex of metabolic pathway through labor division, and improve the target product production significantly. This review summarized the most up-to-dated co-cultivation systems used for biofuels, chemicals and nature products production. In addition, major challenges associated with co-cultivation systems are also presented and discussed for meeting further industrial demands.

Lignocellulosic biomass for bioethanol: an overview on pretreatment, hydrolysis and fermentation processes

Bioethanol is currently the only alternative to gasoline that can be used immediately without having to make any significant changes in the way fuel is distributed. In addition, the carbon dioxide (CO2) released during the combustion of bioethanol is the same as that used by the plant in the atmosphere for its growth, so it does not participate in the increase of the greenhouse effect. Bioethanol can be obtained by fermentation of plants containing sucrose (beet, sugar cane…) or starch (wheat, corn…). However, large-scale use of bioethanol implies the use of very large agricultural surfaces for maize or sugarcane production. Lignocellulosic biomass (LCB) such as agricultural residues for the production of bioethanol seems to be a solution to this problem due to its high availability and low cost even if its growth still faces technological difficulties. In this review, we present an overview of lignocellulosic biomass, the different methods of pre-treatment of LCB and the various fermentation processes that can be used to produce bioethanol from LCB.

Biochemical engineering in China

Chinese biochemical engineering is committed to supporting the chemical and food industries, to advance science and technology frontiers, and to meet major demands of Chinese society and national economic development. This paper reviews the development of biochemical engineering, strategic deployment of these technologies by the government, industrial demand, research progress, and breakthroughs in key technologies in China. Furthermore, the outlook for future developments in biochemical engineering in China is also discussed.

Synergy of carbon and nitrogen removal of a co-culture of two aerobic denitrifying bacterial strains, Acinetobacter sp. GA and Pseudomonas sp. GP

Two newly isolated aerobic denitrifying bacterial strains (Acinetobacter sp. GA and Pseudomonas sp. GP) were co-cultured to investigate the synergy of carbon and nitrogen removal of different functional bacteria. The co-culture showed higher efficiency for removing total organic carbon (TOC) and total dissolved nitrogen (TDN) than strain GA or GP cultured separately. The inoculation ratio of 50 (strain GA/GP) was advantageous for the TOC and TDN removal efficiencies of the co-culture. The sequential co-culture tests showed that strain GP being inoculated after strain GA was inoculated for 36 h increased the TDN removal efficiency from 53.3% to 86.8%. This finding indicated that the activity of strain GA was important in the co-culture system, and the sequential co-culture could be advantageous to the synergistic effect of strains GA and GP. The co-culture of different functional bacteria can be an alternative method for improving the performance of aerobic denitrifying microorganisms for pollutant removal.

Two newly isolated aerobic denitrifying bacterial strains (Acinetobacter sp. GA and Pseudomonas sp. GP) were co-cultured to investigate the synergy of carbon and nitrogen removal of different functional bacteria.

State of the art review of biofuels production from lignocellulose by thermophilic bacteria

Biofuels, including ethanol and butanol, are mainly produced by mesophilic solventogenic yeasts and Clostridium species. However, these microorganisms cannot directly utilize lignocellulosic materials, which are abundant, renewable and non-compete with human demand. More recently, thermophilic bacteria show great potential for biofuels production, which could efficiently degrade lignocellulose through the cost effective consolidated bioprocessing. Especially, it could avoid contamination in the whole process owing to its relatively high fermentation temperature. However, wild types thermophiles generally produce low levels of biofuels, hindering their large scale production. This review comprehensively summarizes the state of the art development of biofuels production by reported thermophilic microorganisms, and also concludes strategies to improve biofuels production including the metabolic pathways construction, co-culturing systems and biofuels tolerance. In addition, strategies to further improve butanol production are proposed.

Cellulosic ethanol production via consolidated bioprocessing by a novel thermophilic anaerobic bacterium isolated from a Himalayan hot spring

BACKGROUND

Cellulose-degrading thermophilic anaerobic bacterium as a suitable host for consolidated bioprocessing (CBP) has been proposed as an economically suited platform for the production of second-generation biofuels. To recognize the overall objective of CBP, fermentation using co-culture of different cellulolytic and sugar-fermenting thermophilic anaerobic bacteria has been widely studied as an approach to achieving improved ethanol production. We assessed monoculture and co-culture fermentation of novel thermophilic anaerobic bacterium for ethanol production from real substrates under controlled conditions.

RESULTS

In this study, Clostridium sp. DBT-IOC-C19, a cellulose-degrading thermophilic anaerobic bacterium, was isolated from the cellulolytic enrichment cultures obtained from a Himalayan hot spring. Strain DBT-IOC-C19 exhibited a broad substrate spectrum and presented single-step conversion of various cellulosic and hemicellulosic substrates to ethanol, acetate, and lactate with ethanol being the major fermentation product. Additionally, the effect of varying cellulose concentrations on the fermentation performance of the strain was studied, indicating a maximum cellulose utilization ability of 10 g L^-1 cellulose. Avicel degradation kinetics of the strain DBT-IOC-C19 displayed 94.6% degradation at 5 g L^-1 and 82.74% degradation at 10 g L^-1 avicel concentration within 96 h of fermentation. In a comparative study with Clostridium thermocellum DSM 1313, the ethanol and total product concentrations were higher by the newly isolated strain on pretreated rice straw at an equivalent substrate loading. Three different co-culture combinations were used on various substrates that presented two-fold yield improvement than the monoculture during batch fermentation.

CONCLUSIONS

This study demonstrated the direct fermentation ability of the novel thermophilic anaerobic bacteria on various cellulosic and hemicellulosic substrates into ethanol without the aid of any exogenous enzymes, representing CBP-based fermentation approach. Here, the broad substrate utilization spectrum of isolated cellulolytic thermophilic anaerobic bacterium was shown to be of potential utility. We demonstrated that the co-culture strategy involving novel strains is efficient in improving ethanol production from real substrate.

Clostridia: a flexible microbial platform for the production of alcohols

Solventogenic clostridia are native producers of ethanol and many higher alcohols employing a broad range of cheap renewable substrates, such as lignocellulosic materials and C1 gases (CO and CO₂). These characteristics enable solventogenic clostridia to act as flexible microbial platforms for the production of liquid biofuels. With the rapid development of genetic tools in recent years, the intrinsic intractability of clostridia has been largely overcome, thus, engineering clostridia for production of chemicals and fuels has attracted increasing interests. Here, we provide an overview of recent progress in the production of alcohols based on solventogenic clostridia. Saccharolytic, cellulolytic and gas-fermenting clostridia are discussed, with a special focus on strategies for metabolic engineering to enable and to improve clostridia for the production of higher alcohols.

Synthetic Ecology of Microbes: Mathematical Models and Applications

As the indispensable role of natural microbial communities in many aspects of life on Earth is uncovered, the bottom-up engineering of synthetic microbial consortia with novel functions is becoming an attractive alternative to engineering single-species systems. Here, we summarize recent work on synthetic microbial communities with a particular emphasis on open challenges and opportunities in environmental sustainability and human health. We next provide a critical overview of mathematical approaches, ranging from phenomenological to mechanistic, to decipher the principles that govern the function, dynamics and evolution of microbial ecosystems. Finally, we present our outlook on key aspects of microbial ecosystems and synthetic ecology that require further developments, including the need for more efficient computational algorithms, a better integration of empirical methods and model-driven analysis, the importance of improving gene function annotation, and the value of a standardized library of well-characterized organisms to be used as building blocks of synthetic communities.

Role of pretreatment with acid and base on the distribution of the products obtained via lignocellulosic biomass pyrolysis

Analysis of chemicals distribution in pyrolysis liquid following different content of acid and base in pretreatment.