Bioconversion of Plant Hydrolysate Biomass into Biofuels Using an Engineered Bacillus subtilis and Escherichia coli Mixed-whole Cell Biotransformation

Sustainable extraction of phytoestrogens from soybean and okara using green solvents

Soy extract waste, okara, is a rich source of bioactive compounds such as isoflavones, which are phytoestrogens with potential health benefits. To develop a green approach to recovering these compounds and valorizing okara, a study was developed to screen variables for the extraction of isoflavones from okara and soybean (for comparison) using Deep Eutectic Solvents (DES) composed with choline chloride ([Ch]Cl) and acetic acid (AA) ([Ch]Cl: AA, 1:2). A fractional design (24-1) was used to evaluate variables in the extraction of isoflavones, followed by a Central Composite Rotatable Design (CCRD). The variables analyzed included temperature, % water, solid-liquid ratio, and stirring speed. Furthermore, cytotoxicity tests were carried out using Caco-2 cells from the extracts obtained under best conditions, and the solid matrices were evaluated by scanning electron microscopy (SEM). This study showed that 1194.56 µg TIC/g of dried soybeans were extracted using [Ch]Cl: AA with 70 % water added at low temperature (25 °C), 500 rpm, S/L ratio of 10 mg/mL and extraction time of 2 h. For okara, 450.9 µg TIC/g of dry okara were extracted at 40 °C, 500 rpm, 61.5 % water in DES, S/L ratio of 10 mg/mL, and extraction time of 1 h. In the cytotoxicity tests, it was observed that the neutralization step of the extracts is necessary to reduce the cytotoxic effects caused by the high acidity of the solvents. In summary, this work has shown that aqueous mixtures of DES can be used as sustainable alternative techniques for recovering isoflavones from soybean residue and can replace toxic conventional solvents.

Innovative approaches for amino acid production via consolidated bioprocessing of agricultural biomass

Agricultural plantations in Indonesia and Malaysia yield substantial waste, necessitating proper disposal to address environmental concerns. Yet, these wastes, rich in starch and lignocellulosic content, offer an opportunity for value-added product development, particularly amino acid production. Traditional methods often rely on costly commercial enzymes to convert biomass into fermentable sugars for amino acid production. An alternative, consolidated bioprocessing, enables the direct conversion of agricultural biomass into amino acids using selected microorganisms. This review provides a comprehensive assessment of the potential of agricultural biomass in Indonesia and Malaysia for amino acid production through consolidated bioprocessing. It explores suitable microorganisms and presents a case study on using Bacillus subtilis ATCC 6051 to produce 9.56 mg/mL of amino acids directly from pineapple plant stems. These findings contribute to the advancement of sustainable amino acid production methods using agricultural biomass especially in Indonesia and Malaysia through consolidated bioprocessing, reducing waste and enhancing environmental sustainability.

Top-down and bottom-up microbiome engineering approaches to enable biomanufacturing from waste biomass

Growing environmental concerns and the need to adopt a circular economy have highlighted the importance of waste valorization for resource recovery. Microbial consortia-enabled biotechnologies have made significant developments in the biomanufacturing of valuable resources from waste biomass that serve as suitable alternatives to petrochemical-derived products. These microbial consortia-based processes are designed following a top-down or bottom-up engineering approach. The top-down approach is a classical method that uses environmental variables to selectively steer an existing microbial consortium to achieve a target function. While high-throughput sequencing has enabled microbial community characterization, the major challenge is to disentangle complex microbial interactions and manipulate the structure and function accordingly. The bottom-up approach uses prior knowledge of the metabolic pathway and possible interactions among consortium partners to design and engineer synthetic microbial consortia. This strategy offers some control over the composition and function of the consortium for targeted bioprocesses, but challenges remain in optimal assembly methods and long-term stability. In this review, we present the recent advancements, challenges, and opportunities for further improvement using top-down and bottom-up approaches for microbiome engineering. As the bottom-up approach is relatively a new concept for waste valorization, this review explores the assembly and design of synthetic microbial consortia, ecological engineering principles to optimize microbial consortia, and metabolic engineering approaches for efficient conversion. Integration of top-down and bottom-up approaches along with developments in metabolic modeling to predict and optimize consortia function are also highlighted.

ONE-SENTENCE SUMMARY

This review highlights the microbial consortia-driven waste valorization for biomanufacturing through top-down and bottom-up design approaches and describes strategies, tools, and unexplored opportunities to optimize the design and stability of such consortia.

Bioupgrading of the aqueous phase of pyrolysis oil from lignocellulosic biomass: a platform for renewable chemicals and fuels from the whole fraction of biomass

Pyrolysis, a thermal decomposition without oxygen, is a promising technology for transportable liquids from whole fractions of lignocellulosic biomass. However, due to the hydrophilic products of pyrolysis, the liquid oils have undesirable physicochemical characteristics, thus requiring an additional upgrading process. Biological upgrading methods could address the drawbacks of pyrolysis by utilizing various hydrophilic compounds as carbon sources under mild conditions with low carbon footprints. Versatile chemicals, such as lipids, ethanol, and organic acids, could be produced through microbial assimilation of anhydrous sugars, organic acids, aldehydes, and phenolics in the hydrophilic fractions. The presence of various toxic compounds and the complex composition of the aqueous phase are the main challenges. In this review, the potential of bioconversion routes for upgrading the aqueous phase of pyrolysis oil is investigated with critical challenges and perspectives.

Strategy for efficiently utilizing Escherichia coli cells producing isobutanol by combining isobutanol and indigo production systems

Isobutanol is a potential biofuel, and its microbial production systems have demonstrated promising results. In a microbial system, the isobutanol produced is secreted into the media; however, the cells remaining after fermentation cannot be used efficiently during the isobutanol recovery process and are discarded as waste. To address this, we aimed to investigate the strategy of utilizing these remaining cells by combining the isobutanol production system with the indigo production system, wherein the product accumulates intracellularly. Accordingly, we constructed E. coli systems with genes, such as acetolactate synthase gene (alsS), ketol-acid reductoisomerase gene (ilvC), dihydroxyl-acid dehydratase (ilvD), and alpha-ketoisovalerate decarboxylase gene (kivD), for isobutanol production and genes, such as tryptophanase gene (tnaA) and flavin-containing monooxygenase gene (FMO), for indigo production. This system produced isobutanol and indigo simultaneously while accumulating indigo within cells. The production of isobutanol and indigo exhibited a strong linear correlation up to 72 h of production time; however, the pattern of isobutanol and indigo production varied. To our knowledge, this study is the first to simultaneously produce isobutanol and indigo and can potentially enhance the economy of biochemical production.

Enhanced isobutanol production using engineered E. coli and B. subtilis host by UV-induced mutation

Recombinant Escherichia coli and Bacillus subtilis strains were engineered by simultaneous chemical and ultraviolet-induced random mutagenesis to enhance bio-alcohol production. Our study investigated the bio-alcohol production of six variants of E. coli (EM1-6) and B. subtilis mutants (BM1-6). The induced mutation in the EM variants increased isobutanol (C4 alcohol) production most effectively, whereas pH adjustment and additional l-valine feeding increased isobutanol production by the BM variants. In contrast, pH adjustment or l-valine addition negatively affected isobutanol production by the EM variants. The highest titer of 5.07 g/L of isobutanol from a 40 g/L yeast extract medium (YEM) was achieved by the EM1 variant, whereas 0.57 g/L of isobutanol from YEM supplemented with 5 g/L of l-valine was obtained from the BM5 variant. These results can be applied in further research on engineering production hosts and improving production titers to utilize heterogenous bioresources in the future.

Microbial production of 2-pyrone-4,6-dicarboxylic acid from lignin derivatives in an engineered Pseudomonas putida and its application for the synthesis of bio-based polyester

Lignin valorization depends on microbial upcycling of various aromatic compounds in the form of a complex mixture, including p-coumaric acid and ferulic acid. In this study, an engineered Pseudomonas putida strain utilizing lignin-derived monomeric compounds via biological funneling was developed to produce 2-pyrone-4,6-dicarboxylic acid (PDC), which has been considered a promising building block for bioplastics. The biosynthetic pathway for PDC production was established by introducing the heterologous ligABC genes under the promoter P_tac in a strain lacking pcaGH genes to accumulate a precursor of PDC, i.e., protocatechuic acid. Based on the culture optimization, fed-batch fermentation of the final strain resulted in 22.7 g/L PDC with a molar yield of 1.0 mol/mol and productivity of 0.21 g/L/h. Subsequent purification of PDC at high purity was successfully implemented, which was consequently applied for the novel polyester.

Improving the catalytic performance of xylanase from Bacillus circulans through structure-based rational design

Endo-1,4-β-xylanase is one of the most important enzymes employed in biorefineries for obtaining fermentable sugars from hemicellulosic components. Herein, we aimed to improve the catalytic performance of Bacillus circulans xylanase (Bcx) using a structure-guided rational design. A systematic analysis of flexible motions revealed that the R49 component of Bcx (i) constrains the global conformational changes essential for substrate binding and (ii) is involved in modulating flexible motion. Site-saturated mutagenesis of the R49 residue led to the engineering of the active mutants with the trade-off between flexibility and rigidity. The most active mutant R49N improved the catalytic performance, including its catalytic efficiency (7.51-fold), conformational stability (0.7 °C improvement), and production of xylose oligomers (2.18-fold higher xylobiose and 1.72-fold higher xylotriose). The results discussed herein can be applied to enhance the catalytic performance of industrially important enzymes by controlling flexibility.

Metabolic engineering of Lactobacillus reuteri DSM 20,016 for improved 1,3-propanediol production from glycerol

The production of 1,3-propanediol (1,3-PDO) from glycerol was studied by GRAS and native 1,3-PDO producer, Lactobacillus reuteri DSM 20016. This strain ferments glucose with production of lactate, acetate, ethanol, and converts glycerol to 1,3-PDO using NADH generated by glucose metabolism. To improve 1,3-PDO production, alcohol dehydrogenases (ADH) were disrupted and 1,3-PDO oxidoreductases (PDOR) were overexpressed. Deletion of ADH (adh2) enhanced 1,3-PDO production yield on glucose by reducing ethanol synthesis, and overexpression of PDOR (pduQ) elevated 1,3-PDO production rate and cell growth rate. The strain with simultaneous adh2 deletion, pduQ overexpression (Δadh2pduQ⁺⁺) could produce 687 mM 1,3-PDO with the yield of 1.2 ± 0.08 mol 1,3-PDO/mol glucose by fed-batch bioreactor cultivation in 48 h. However, the 1,3-PDO production rate was greatly reduced in the late period of bioreactor culture, mainly due to high lactate accumulation. This is the first report on rational metabolic engineering of L. reuteri for improved 1,3-PDO production.

Cell-free synthesis of industrial chemicals and biofuels from carbon feedstocks

The power of biological systems can be harnessed with higher efficiency when biosynthetic reactions are decoupled from cellular physiology. This can be achieved by cell-free synthesis, which relies on the in vitro use of cellular machinery under optimized reaction conditions. As exemplified by the recent development of mRNA vaccines and therapeutics, the cell-free synthesis of biomolecules is fast, efficient and flexible. Cell-free synthesis of industrial chemicals and biofuels is drawing considerable attention as a promising alternative to microbial fermentation processes, which currently show low conversion yields and toxicity to host cells. Here, we provide a brief overview of the history of cell-free synthesis systems and the state-of-the-art cell-free technologies used to produce diverse chemicals and biofuels. We also discuss the future directions of cell-free synthesis that can fully harness the synthetic power of biological systems.

Collagen peptide provides Streptomyces coelicolor CGMCC 4.7172 with abundant precursors for enhancing undecylprodigiosin production

Abstract

Effective and ecofriendly converting biomass to chemicals is important for sustainable engineering based on the foreseeable shortage of fossil resources. Undecylprodigiosin (UP) is a promising antibiotic, but the direct feeding of pure precursor amino acids makes it costly for large-scale production. Here, collagen peptide (CP), a renewable animal-derived biomass contains abundant precursor amino acids of UP. CP can act as carbon and nitrogen source for the growth of Streptomyces coelicolor CGMCC 4.7172. The plant biomasses including soybean meal, wheat bran, and malt extract were unsuitable for UP prodution. However, 365.40 µg/L UP was detected after 24 h in the media containing CP, and its highest concentration reached 1198.01 µg/L. UP was also detected in the media containing meat hydrolysates of domestic animals, but its initial production time was delayed, and final concentration was lower than that in the medium containing CP only. Compared the fermentation performances of CP and other proteins, CP has a special superiority for UP production. These results revealed that UP biosynthesis may be dependent on amino acid availability of substrates and CP is beneficial for UP production because of its specific amino acid composition.

Graphical abstract

Improved Sugar Recovery from Orange Peel by Statistical Optimization of Thermo-Alkaline Pretreatment

Orange peel, which is a by-product of oranges, contains carbohydrates that can be converted into sugars and used in the fermentation process. In this study, the thermal alkaline pretreatment process was chosen because of its simplicity and lesser reaction time. In addition, the reaction factors were optimized using response surface methodology. The determined optimal conditions were as follows: 60.1 g/L orange peels loading, 3% KOH and 30 min. Under the optimal conditions, glucan content (GC) and enzymatic digestibility (ED) were found to be 32.8% and 87.8%, respectively. Enzymatic hydrolysis was performed with pretreated and non-pretreated orange peels using three types of enzyme complex (cellulase, cellobiase and xylanase). The minimum concentrations of enzyme complex required to obtain maximum ED were 30 FPU (filter paper unit), 15 CBU (cellobiase unit), and 30 XNU (xylanase unit) based on 1 g-biomass. Additionally, ED of the treated group was approximately 3.7-fold higher than that of the control group. In conclusion, the use of orange peel as a feedstock for biorefinery can be a strategic solution to reduce wastage of resources and produce sustainable bioproducts.

Bacillus subtilis as a robust host for biochemical production utilizing biomass

Bacillus subtilis is regarded as a suitable host for biochemical production owing to its excellent growth and bioresource utilization characteristics. In addition, the distinct endogenous metabolic pathways and the suitability of the heterologous pathways have made B. subtilis a robust and promising host for producing biochemicals, such as: bioalcohols; bioorganic acids (lactic acids, α-ketoglutaric acid, and γ-aminobutyric acid); biopolymers (poly(γ-glutamic acid, polyhydroxyalkanoates (PHA), and polysaccharides and monosaccharides (N-acetylglucosamine, xylooligosaccharides, and hyaluronic acid)); and bioflocculants. Also for producing oligopeptides and functional peptides, owing to its efficient protein secretion system. Several metabolic and genetic engineering techniques, such as target gene overexpression and inactivation of bypass pathways, have led to the improvement in production titers and product selectivity. In this review article, recent progress in the utilization of robust B. subtilis-based host systems for biomass conversion and biochemical production has been highlighted, and the prospects of such host systems are suggested.

New Bacterial Surface Display System Development and Application Based on Bacillus subtilis YuaB Biofilm Component as an Anchoring Motif

Bacterial surface display system has been adopted in various biotechnological applications. In the case of Bacillus subtilis, most of the studies have been developed using spore based surface display system utilizing the inherent rigidity of spore against heat, alkali, and shear stress. But, spore harvest, purification and separation need additional cost and labor. To eliminate this procedure and to use the gram-positive nature of B. subtilis, YuaB, which is one of the major B. subtilis biofilm components and locates in the cell wall, based cell surface display system, is developed. P43 promoter driven overexpression of YuaB-His₆ tag does not hamper bacterial cell growth and promoted biofilm formation of recombinant strain. Flow cytometry of recombinant strain and its protoplast using FITC-Anti His₆ antibody, verified that YuaB locate in plasma membrane and protrude to the outside of cell wall, which means YuaB can be used as very efficient anchoring motif. Using surface expressed YuaB-His₆ tag, removal of divalent metal ion, Cu²⁺ and Ni²⁺, was tried to test its possibility for the environmental application of developed system.

Improved Glucose Recovery from Sicyos angulatus by NaOH Pretreatment and Application to Bioethanol Production

As greenhouse gases and environmental pollution become serious, the demand for alternative energy such as bioethanol has rapidly increased, and a large supply of biomass is required for bioenergy production. Lignocellulosic biomass is the most abundant on the planet and a large part of it, the second-generation biomass, has the advantage of not being a food resource. In this study, Sicyos angulatus, known as an invasive plant (harmful) species, was used as a raw material for bioethanol production. In order to improve enzymatic hydrolysis, S. angulatus was pretreated with different NaOH concentration at 121 °C for 10 min. The optimal NaOH concentration for the pretreatment was determined to be 2% (w/w), and the glucan content (GC) and enzymatic digestibility (ED) were 46.7% and 55.3%, respectively. Through NaOH pretreatment, the GC and ED of S. angulatus were improved by 2.4-fold and 2.5-fold, respectively, compared to the control (untreated S. angulatus). The hydrolysates from S. angulatus were applied to a medium for bioethanol fermentation of Saccharomyces cerevisiae K35. Finally, the maximum ethanol production was found to be 41.3 g based on 1000 g S. angulatus, which was 2.4-fold improved than the control group.

Biorefinery: The Production of Isobutanol from Biomass Feedstocks

Environmental issues have prompted the vigorous development of biorefineries that use agricultural waste and other biomass feedstock as raw materials. However, most current biorefinery products are cellulosic ethanol. There is an urgent need for biorefineries to expand into new bioproducts. Isobutanol is an important bulk chemical with properties that are close to gasoline, making it a very promising biofuel. The use of microorganisms to produce isobutanol has been extensively studied, but there is still a considerable gap to achieving the industrial production of isobutanol from biomass. This review summarizes current metabolic engineering strategies that have been applied to biomass isobutanol production and recent advances in the production of isobutanol from different biomass feedstocks.