From Knallgas Bacterium to Promising Biomanufacturing Host: The Evolution of Cupriavidus necator.

The expanding field of synthetic biology requires diversification of microbial chassis to expedite the transition from a fossil fuel-dependent economy to a sustainable bioeconomy. Relying exclusively on established model organisms such as Escherichia coli and Saccharomyces cerevisiae may not suffice to drive the profound advancements needed in biotechnology. In this context, Cupriavidus necator, an extraordinarily versatile microorganism, has emerged as a potential catalyst for transformative breakthroughs in industrial biomanufacturing. This comprehensive book chapter offers an in-depth review of the remarkable technological progress achieved by C. necator in the past decade, with a specific focus on the fields of molecular biology tools, metabolic engineering, and innovative fermentation strategies. Through this exploration, we aim to shed light on the pivotal role of C. necator in shaping the future of sustainable bioprocessing and bioproduct development.

Insights into lignin bioconversion: lignin-derived compounds treatment of a novel marine fungus K-2.

BACKGROUND: The potential for the efficient conversion of lignocellulosic biomass has been extensively explored to produce a wide range of bioproducts. Many approaches have been sought for the deep conversion of lignin to generate products that are toxin-free and beneficial for processing into high-value-added components. RESULTS: This study reported a fungus isolated from the deep sea with strong synthesis of multiple lignocellulases, conversion of lignin and guaiacol (0.1%) by 71.6% and 86.1% within 9 days at 30 °C respectively, and outstanding environmental adaptability (20-50 °C and pH 3-8). Metabolic pathway profiling showed that this fungus utilized lignin to rapidly activate multiple ring-opening reactions including the 2,3- and 3,4-cleavage pathways, with the 2,3-cleavage pathway predominating after 5 days. Conversion of metabolic intermediates confirmed the superb potential of this strain for lignin treatment. Meanwhile, its shikimic acid pathway was metabolically active under lignin. CONCLUSION: This further expands the potential to produce valuable bioproducts during lignin treatment, especially under ambient conditions, which can significantly enhance high-value precursor compound production. © 2024 Society of Chemical Industry.

Biological conversion of lignin-derived ferulic acid from wheat bran into vanillin.

Lignin is a promising feedstock for producing vanillin, one of the most extensively used flavor enhancers. However, the biotransformation performance of lignin derivatives into vanillin is still unsatisfactory. In this study, an efficient conversion strategy of lignin into vanillin was established by employing engineered Saccharomyces cerevisiae as a whole-cell biocatalyst. Optimization of cell culture media and whole-cell bioconversion improved the production efficiency of vanillin. The vanillin titer reached 15.3 mM with a molar yield of 71 % in fed-batch fermentation mode, while incorporating in-situ product separation, demonstrated a remarkable 2.6-fold increase. The whole-cell bioconversion, coupled with in-situ separation, successfully converted real lignin hydrolysate into a record vanillin titer of 21.1 mM, equivalent to 1.8 mg of vanillin per gram of wheat bran biomass. The whole-cell bioconversion process integrated in-situ product separation, represents a sustainable approach for vanillin production and offers a promising pathway for lignin valorization.

Formaldehyde: An Essential Intermediate for C1 Metabolism and Bioconversion.

Formaldehyde is an intermediate metabolite of methylotrophic microorganisms that can be obtained from formate and methanol through oxidation-reduction reactions. Formaldehyde is also a one-carbon (C1) compound with high uniquely reactive activity and versatility, which is more amenable to further biocatalysis. Biosynthesis of high-value-added chemicals using formaldehyde as an intermediate is theoretically feasible and promising. This review focuses on the design of the biosynthesis of high-value-added chemicals using formaldehyde as an essential intermediate. The upstream biosynthesis and downstream bioconversion pathways of formaldehyde as an intermediate metabolite are described in detail, aiming to highlight the important role of formaldehyde in the transition from inorganic to organic carbon and carbon chain elongation. In addition, challenges and future directions of formaldehyde as an intermediate for the chemicals are discussed, with the expectation of providing ideas for the utilization of C1.

The current progress of tandem chemical and biological plastic upcycling.

Each year, millions of tons of plastics are produced for use in such applications as packaging, construction, and textiles. While plastic is undeniably useful and convenient, its environmental fate and transport have raised growing concerns about waste and pollution. However, the ease and low cost of producing virgin plastic have so far made conventional plastic recycling economically unattractive. Common contaminants in plastic waste and shortcomings of the recycling processes themselves typically mean that recycled plastic products are of relatively low quality in some cases. The high cost and high energy requirements of typical recycling operations also reduce their economic benefits. In recent years, the bio-upcycling of chemically treated plastic waste has emerged as a promising alternative to conventional plastic recycling. Unlike recycling, bio-upcycling uses relatively mild process conditions to economically transform pretreated plastic waste into value-added products. In this review, we first provide a précis of the general methodology and limits of conventional plastic recycling. Then, we review recent advances in hybrid chemical/biological upcycling methods for different plastics, including polyethylene terephthalate, polyurethane, polyamide, polycarbonate, polyethylene, polypropylene, polystyrene, and polyvinyl chloride. For each kind of plastic, we summarize both the pretreatment methods for making the plastic bio-available and the microbial chassis for degrading or converting the treated plastic waste to value-added products. We also discuss both the limitations of upcycling processes for major plastics and their potential for bio-upcycling.

Bioconversion of agriculture by-products with functionally enhanced Streptomyces sp. SCUT-3: Fish skin as a model.

With the global population continuously rising, efficient bioconversion of inedible agricultural by-products is crucial for human food and energy sustainability. We here propose solid-state fermentation approaches to efficiently convert biopolymers into oligomers/monomers by accelerating the natural degradation process of the versatile Streptomyces sp. strain SCUT-3. Using fish skin as a representative by-product, 54.3 g amino acids and 14.7 g peptides (91 % < 2500 Da) were recovered from 89.0 g protein in 100 g tilapia skin sample by collagenase-overexpressed SCUT-3 for seven days at a 1:4 substrate:liquid ratio. Fish skin collagen hydrolysates exhibited excellent anti-oxidation, anti-hypertension, scratch-repairing, anti-aging, anti-ultraviolet radiation, and anti-inflammation effects on human skin fibroblasts In vitro and zebrafish larvae in vivo, indicating their potential applications in healthcare/skincare and anti-atopic dermatitis. As Laozi said, the divine law follows nature. This study underscores the efficacy of genetically engineered SCUT-3 according to its natural biomass utilization laws in large-scale biopolymer conversion.

Co-treatment of agri-food waste streams using black soldier fly larvae (Hermetia illucens L.): A sustainable solution for rural waste management.

The management of rural waste, particularly agri-food waste, poses a major challenge to the ecosystem health. This study investigated the efficacy of black soldier fly larvae (Hermetia illucens L., BSFL) bioconversion for agri-food waste under independent treatment or co-treatment strategies using chicken manure and food waste as a model system. The results showed a synergistic effect of co-treating agri-food waste from different sources. The co-treatment strategy enhanced bioconversion efficiency, resulting in a 1.31-fold waste reduction rate and a 1.93-fold bioconversion rate. Additionally, larval growth performance and biomass quality of BSFL were improved, while lauric acid and oleic acid were enriched in the larval fat from the co-treatment strategy. 16S rRNA amplicon sequencing revealed that the co-treatment strategy reshaped both the residue and larval gut microbiota, with distinct enrichment of taxonomical biomarkers. Furthermore, under this strategy, metabolic functions of the residue microbiota were significantly activated, especially carbohydrate, amino acid, and lipid metabolism were enhanced by 16.3%, 23.5%, and 20.2%, respectively. The early colonization of lactic acid bacteria (Weisella and Aerococcus) in the residue, coupled with a symbiotic relationship between Enterococcus in the larval gut and the host, likely promoted organic matter degradation and larval growth performance. Scaling up the findings to a national level in China suggests that the co-treatment strategy can increase waste reduction quantity by 86,329 tonnes annually and produce more larval protein and fat with a market value of approximately US$237 million. Therefore, co-treatment of agri-food waste streams using BSFL presents a sustainable solution for rural waste management that potentially contributes to the achievement of SDG2 (Zero Hunger), SDG3 (Good Health and Well-Being), and SDG12 (Responsible Consumption and Production).

Monitoring corn stover processing by the fungus Ustilago maydis.

A key aspect of sustainable bioeconomy is the recirculation of renewable, agricultural waste streams as substrates for microbial production of high-value compounds. One approach is the bioconversion of corn stover, an abundant maize crop byproduct, using the fungal maize pathogen Ustilago maydis. U. maydis is already used as a unicellular biocatalyst in the production of several industrially-relevant compounds using plant biomass hydrolysates. In this study, we demonstrate that U. maydis can grow using untreated corn stover as its sole carbon source. We developed a small-scale bioreactor platform to investigate U. maydis processing of corn stover, combining online monitoring of fungal growth and metabolic activity profiles with biochemical analyses of the pre- and post-fermentation residues. Our results reveal that U. maydis primarily utilizes soluble sugars i.e., glucose, sucrose and fructose present in corn stover, with only limited exploitation of the abundant lignocellulosic carbohydrates. Thus, we further explored the biotechnological potential of enhancing U. maydis´ lignocellulosic utilization. Additive performance improvements of up to 120 % were achieved when using a maize mutant with increased biomass digestibility, co-fermentation with a commercial cellulolytic enzyme cocktail, and exploiting engineered fungal strains expressing diverse lignocellulose-degrading enzymes. This work represents a key step towards scaling up the production of sustainable compounds from corn stover using U. maydis and provides a tool for the detailed monitoring of the fungal processing of plant biomass substrates.

Enhanced Antioxidant, Antifungal, and Herbicidal Activities through Bioconversion of Diosgenin by Yarrowia lipolytica P01a.

This study explores the bioconversion of diosgenin by Yarrowia lipolytica P01a, focusing on enhancing the antioxidant, antifungal, and herbicidal activities of the resulting extracts. The bioconversion process, involving glycosylation and hydroxylation, produced significant amounts of protodioscin and soyasaponin I. The extracts showed superior antioxidant activity, with up to 97.02% inhibition of ABTS· radicals and 33.30% inhibition of DPPH· radicals at 1000 mg L-1 of diosgenin. Antifungal assays revealed strong inhibitory effects against Botrytis cinerea, Alternaria sp., and Aspergillus niger, with maximum inhibition rates of 67.34%, 35.63%, and 65.53%, respectively. Additionally, the herbicidal activity of the bioconverted extracts was comparable to commercial herbicides, achieving 100% inhibition of seed germination in both monocotyledonous and dicotyledonous plants. These findings suggest that the Y. lipolytica P01a-mediated bioconversion of diosgenin could provide a sustainable and eco-friendly alternative for developing natural biofungicides and bioherbicides.

Identification of Bioactive Substances Derived from the Probiotic-Induced Bioconversion of Lagerstroemia speciosa Pers. Leaf Extract That Have Beneficial Effects on Diabetes and Obesity.

Lagerstroemia speciosa L. (Banaba) has been used as a functional food because of its diuretic, decongestant, antipyretic, anti-hyperglycemic, and anti-adipogenic activities. Triterpene acids, including corosolic acid, oleanolic acid, and asiatic acid, are the principal phytochemicals in Banaba and are potentially anti-diabetic substances, owing to their effect on blood glucose concentration. Bioconversion of Banaba leaf extract (BLE) by Lactobacillus plantarum CBT-LP3 improved the glucose uptake, insulin secretion, and fat browning of this functional food. Furthermore, we identified asiatic acid, which was found to be increased by 3.8-fold during the L. plantarum CBT-LP3-mediated bioconversion process using metabolite profiling. Most previous studies have focused on corosolic acid, another triterpene acid that is a known anti-diabetic compound and is used to standardize BLE preparations. However, asiatic acid is the second most common of the triterpene acids and is also well known to have anti-diabetic properties. The present study has provided strong evidence that asiatic acid represents an alternative to corosolic acid as the most important active compound. These results suggest that the probiotic-mediated bioconversion of BLE may improve the anti-diabetic effects of this functional food. This implies that the consumption of a probiotic should be encouraged for people undergoing BLE treatment to improve its anti-diabetic effects.

The role of black soldier fly (BSF) in eliminating the putrid odor of organic waste and its product application - A comprehensive review.

Organic waste including food garbage (FG) forms a major part of man-made problems that are highly associated with global pollution. This includes emission of greenhouse gases (GHGs) and foul odor which negatively affect human health. Interestingly, bioconversion of FG by black soldier fly larvae (BSFL) has been reported to reduce foul odors released from decaying FG. This paper will give overview on the potential of BSFL in lowering putrid odors from FGs. Thus, various bioconversion treatment methods of managing FG including were compared and discussed. The life cycle and role of BSF in reducing putrid odors from biowastes were also discussed in detail. Lastly, the potential utilization of BSFL in controlling odors and GHGs as well as the economic value of products derived from BSFL bioconversion were also discussed. BSFL inoculation slightly reduces odor compounds by modifying odor-producing compounds and microbes in FG. However, BSFL effectiveness is highly influenced by FG decomposition rate.

Recent progress in one-pot enzymatic synthesis and regeneration of high-value cofactors.

One-pot enzymatic synthesis is flourishing in synthetic chemistry, heralding a sustainable and green era. Recent advancements enable the creation of complex enzymatic prosthetic groups and regeneration of enzymatic cofactors such as S-adenosylmethionine. The next frontier is to develop the effective and innovative cofactors for essential micronutrients, metabolic modulators, and biomedicines.

Candida boidinii isolates from olive curation water: a promising platform for methanol-based biomanufacturing.

Methanol is a promising feedstock for biomanufacturing, but the efficiency of methanol-based bioprocesses is limited by the low rate of methanol utilization pathways and methanol toxicity. Yeast diversity is an attractive biological resource to develop efficient bioprocesses since any effort with strain improvement is more deserving if applied to innate robust strains with relevant catabolic and biosynthetic potential. The present study is in line with such rational and describes the isolation and molecular identification of seven isolates of the methylotrophic species Candida boidinii from waters derived from the traditional curation of olives, in different years, and from contaminated superficial soil near fuel stations. The yeast microbiota from those habitats was also characterized. The four C. boidinii isolates obtained from the curation of olives' water exhibited significantly higher maximum specific growth rates (range 0.15-0.19 h-1), compared with the three isolates obtained from the fuel contaminated soils (range 0.05-0.06 h-1) when grown on methanol as the sole C-source (1% (v/v), in shake flasks, at 30°C). The isolates exhibit significant robustness towards methanol toxicity that increases as the cultivation temperature decreases from 30°C to 25°C. The better methanol-based growth performance exhibited by C. boidinii isolates from olives´ soaking waters could not be essentially attributed to higher methanol tolerance. These methanol-efficient catabolizing isolates are proposed as a promising platform to develop methanol-based bioprocesses.

Quantitative assessment of methane bioconversion based on kinetics and bioenergetics.

The biological conversion of methane under ambient conditions can be performed by methanotrophs that utilize methane as both a sole source of energy and a carbon source. However, compared to the established microbial chassis used for general fermentation with sugar as a feedstock, the productivity of methanotrophs is low. The fundamental knowledge of their metabolic or cellular bottlenecks is limited. In this review, the industrial-scale potential of methane bioconversion was evaluated. In particular, the enzyme kinetics associated with the oxidation and assimilation of methane were investigated to evaluate the potential of methane fermentation. The kinetics of enzymes involved in methane metabolism were compared with those used in the metabolic processes of traditional fermentation (glycolysis). Through this analysis, the current limitations of methane metabolism were identified. Methods for increasing the efficiency of methane bioconversion and directions for the industrial application of methane-based fermentation were discussed.

In situ bioaccumulation of metals by Prosopis juliflora and its detoxification potential at the metal contaminated sites.

Heavy metals emanate from diverse anthropogenic activities and the top soil in the vicinity of these activities acts as an immediate sink and facilitates diffusion of heavy metals into the food chain. In the semi-arid plains of India, Prosopis juliflora is the most common and dominant weed along the motorways and barren lands including industrial environs. This investigation hypothesizes the adaptive nature of Prosopis juliflora in the metal enriched soils and attempts to understand its hyper-accumulating potential of metals besides bioconversion/detoxification capability. Prosopis juliflora samples (root, stem, leaves, and pods) from 100 sites in the environs of anthropogenic activities (vehicular emissions and industrial operations) were analyzed for heavy metal concentrations (Cu, Fe, Cr, Cd, Ni, Pb). Prosopis juliflora accumulate metals at the rate of 0.138 mg/kg/day DW for Copper (Cu), Fe: 0.142 mg/kg/day DW, Cr: 0.114 mg/kg/day DW, Ni: 0.048 mg/kg/day DW, Pb: 0.052 mg/kg/day DW, Cd: 0.009 mg/kg/day DW. Furthermore, X-ray Photoelectron Spectroscopy (XPS) metal oxidation state analysis revealed that in the pods of Prosopis juliflora heavy metals (Fe, Cr, Pb) largely existed in non-toxic form (toxic:non-toxic - 3:6), while in the under canopy soil, metals predominantly existed in toxic form (toxic:non-toxic - 7:2); conclusively XPS results ascertains the heavy metal bioconversion/detoxification potential of the plant. These findings suggest that presence of Prosopis juliflora coppice in the barren landscapes across the transportation corridors and metal based industrial zones may ideally favor phyto-remediation of heavy metals.

Resource recovery and treatment of wastewaters using filamentous fungi.

Industrial wastewater, often characterized by its proximity to neutral pH, presents a promising opportunity for fungal utilization despite the prevalent preference of fungi for acidic conditions. This review addresses this discrepancy, highlighting the potential of certain industrial wastewaters, particularly those with low pH levels, for fungal biorefinery. Additionally, the economic implications of biomass recovery and compound separation, factors that require explicit were emphasized. Through an in-depth analysis of various industrial sectors, including food processing, textiles, pharmaceuticals, and paper-pulp, this study explores how filamentous fungi can effectively harness the nutrient-rich content of wastewaters to produce valuable resources. The pivotal role of ligninolytic enzymes synthesized by fungi in wastewater purification is examined, as well as their ability to absorb metal contaminants. Furthermore, the diverse benefits of fungal biorefinery are underscored, including the production of protein-rich single-cell protein, biolipids, enzymes, and organic acids, which not only enhance environmental sustainability but also foster economic growth. Finally, the challenges associated with scaling up fungal biorefinery processes for wastewater treatment are critically evaluated, providing valuable insights for future research and industrial implementation. This comprehensive analysis aims to elucidate the potential of fungal biorefinery in addressing industrial wastewater challenges while promoting sustainable resource utilization.

Curcumin degradation in a soil microorganism: Screening and characterization of a ß-diketone hydrolase.

Curcumin is a plant-derived secondary metabolite exhibiting antitumor, neuroprotective, antidiabetic activities, and so on. We previously isolated Escherichia coli as an enterobacterium exhibiting curcumin-converting activity from human feces, and discovered an enzyme showing this activity (CurA) and named it NADPH-dependent curcumin/dihydrocurcumin reductase. From soil, here, we isolated a curcumin-degrading microorganism (No. 34) using the screening medium containing curcumin as the sole carbon source and identified as Rhodococcus sp. A curcumin-degrading enzyme designated as CurH was purified from this strain and characterized, and compared with CurA. CurH catalyzed hydrolytic cleavage of a carbon-carbon bond in the ß-diketone moiety of curcumin and its analogs, yielding two products bearing a methyl ketone terminus and a carboxylic acid terminus, respectively. These findings demonstrated that a curcumin degradation reaction catalyzed by CurH in the soil environment was completely different from the one catalyzed by CurA in the human microbiome. Of all the curcumin analogs tested, suitable substrates for the enzyme were curcuminoids (i.e., curcumin and bisdemethoxycurcumin) and tetrahydrocurcuminoids. Thus, we named this enzyme curcuminoid hydrolase. The deduced amino acid sequence of curH exhibited similarity to those of members of acetyl-CoA C-acetyltransferase family. Considering results of oxygen isotope analyses and a series of site-directed mutagenesis experiments on our enzyme, we propose a possible catalytic mechanism of CurH, which is unique and distinct from those of enzymes degrading ß-diketone moieties such as ß-diketone hydrolases known so far.

Biovalorisation of agro-industrial wastes into astaxanthin by Xanthophyllomyces dendrorhous.

Astaxanthin is a red xanthophyll with high economic and industrial value in the pharmaceutical, nutraceutical, cosmetic and food industries. In recent years, the biotechnological production of astaxanthin has attracted much attention as a sustainable alternative to the predominating petrochemical-dependent chemical synthesis. In this regard, Xanthophyllomyces dendrorhous is regarded as a promising microorganism for industrial production of astaxanthin. Unfortunately, biotechnological production of the carotenoid is currently expensive. The present study investigated soy molasses (SM) and residual brewers' yeast as cheap fermentation feedstocks for the cultivation of X. dendrorhous and astaxanthin production. Yeast extract was obtained from residual brewers' yeast using various techniques and then combined with SM to formulate a two-component growth medium which was subsequently used to cultivate X. dendrorhous. Generally, the yeast extract produced from residual brewers' yeast supported X. dendrorhous growth and astaxanthin production at levels comparable to those seen with commercial yeast extract. Overall, cultivating X. dendrorhous in an SM-based medium containing 5% SM and 0.2% yeast extract obtained from residual brewers' yeast resulted in significantly higher (> 20% more) biomass accumulation compared to the control media (YPD). A similar slightly higher astaxanthin output (up to 14% more) was recorded in the SM-based medium compared to YPD. The formulated cultivation medium in this study provides an opportunity to reduce the production cost of astaxanthin from X. dendrorhous while simultaneously reducing the environmental impact related to the disposal of the industrial waste used as feedstock. KEY POINTS: • Cheap culture media were formulated from soy molasses and brewers' spent yeast • The formulated medium resulted in at least 20% more biomass than the control • Up to 14% more astaxanthin was produced in molasses-based medium.