Decoding reactive structures in dilute alloy catalysts
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Correction to: Nature Communicationshttps://doi.org/10.1038/s41467-024-53784-3, published online 4 November 2024 In the version of this article initially published, Table 1 did not include the properties of the taxa being proposed or refer directly to another location in the main manuscript describing the properties. As such, the original manuscript did not comply with Rule 27 (2)(c) of the ICNP. Also, Table 1 listed the order Fervidibacterales as the nomenclatural type for the class Fervidibacteria, which violates latest emended version of Rule 15 stating that the nomenclatural type for a class must be a genus. Below we provide a modification of Table 1 containing protologues with these errors corrected. We have also changed the order of the taxa in the table to meet the most common ordering. (Table presented.) Taxon names proposed under the ICNP Proposed taxon Etymology Description Genus Fervidibacter Fer.vi.di.bac’ter. L. masc. adj. fervidus, hot, steaming; N.L. masc. n. bacter, a rod; N.L. masc. n. Fervidibacter, a hot rod Thermophilic or hyperthermophilic inhabitants of freshwater thermal environments. All members are likely polysaccharide-degrading chemoheterotrophs with numerous carbohydrate-active enzymes encoded in their genomes. Aerobic, with high-affinity and/or low-affinity terminal oxidases present in the genomes. The oxidative pentose phosphate pathway and the tricarboxylic acid cycle are complete in genomes belonging to the genus. Gram-stain-negative and diderm cell envelope structure. Ovoid- to rod-shaped morphology. Spores are not formed. The genus is a distinct phylogenetic lineage in the family Fervidibacteraceae, the order Fervidibacterales, and the class Fervidibacteria in the phylum Armatimonadota. The type species is Fervidibacter sacchariT. Species Fervidibacter sacchari sac’cha.ri. N.L. gen. n. sacchari, of sugar Hyperthermophilic, microaerophilic, facultatively anaerobic, and grows chemoheterotrophically on monosaccharides and polysaccharides. Cells are ovoid- to rod-shaped, Gram-stain negative, and are 0.9–1.3 µm in width and 1.6–3.6 µm in length. Grows between 65 and 87.5 °C and an optimum temperature of 80 °C, and a pH range of 6.5–8.6 with an optimum pH of 7.5. Grows at an optimum O2 concentration of 5–10%. Grows on D-arabinose, D-galactose, D-glucose, D-rhamnose, D-ribose, D-xylose, chondroitin sulfate, colloidal chitin, galactan, gellan gum, guar gum, karaya gum, locust bean gum, xantham gum, xyloglucan, β-glucan, glycogen, starch, AFEX-pretreated corn stover, miscanthus, sugarcane bagasse, acetate and casamino acids. Grows weakly on xyloglucan under fermentation conditions. The major fatty acids (>10%) are C16:0, C18:0 and/or cyclo-C17:0, and iso-C16:0. The major respiratory quinones (>10%) are MK-8 and MK-9. The isolate and genomes of the species have been recovered from geothermal springs in the Great Basin, Nevada, USA. GC content of genomes range between 51–52%. Subunits for both the high-affinity and low-affinity terminal oxidases are encoded in the genomes. Genomes also encode a Group 3d [NiFe] hydrogenase, which produces hydrogen as an electron sink for NAD+ regeneration. The type strain PD1T (= JCM 39283T = DSM 113467T) was isolated from Great Boiling Spring in Nevada, USA. Family Fervidibacteraceae Fer.vi.di.bac.te.ra’ce.ae. N.L. masc. n. Fervidibacter type genus of the family; L. suff. -aceae ending to denote a family; N.L. fem. pl. n. Fervidibacteraceae the family of the genus Fervidibacter Thermophilic or hyperthermophilic inhabitants of freshwater thermal environments. All members are likely polysaccharide-degrading chemoheterotrophs with numerous carbohydrate-active enzymes encoded in their genomes. Aerobic, with high-affinity and/or low-affinity terminal oxidases present in the genomes. The oxidative pentose phosphate pathway and the tricarboxylic acid cycle are complete in genomes belonging to the family. The family is a distinct phylogenetic lineage in the order Fervidibacterales and the class Fervidibacteria in the phylum Armatimonadota. The type genus is Fervidibacter. Order Fervidibacterales Fer.vi.di.bac.te.ra’les. N.L. masc. n. Fervidibacter type genus of the order; L. suff. -ales ending to denote an order; N.L. fem. pl. n. Fervidibacterales the order of the genus Fervidibacter Thermophilic or hyperthermophilic inhabitants of freshwater thermal environments. All members are likely polysaccharide-degrading chemoheterotrophs with numerous carbohydrate-active enzymes encoded in their genomes. Aerobic or strictly anaerobic. Phylogenomic placement of this lineage within the Fervidibacteria and relative evolutionary divergence supports delineation of this lineage as an order within the class Fervidibacteria and phylum Armatimonadota. The type genus is Fervidibacter. Class Fervidibacteria Fer.vi.di.bac.te’ri.a. N.L. masc. n. Fervidibacter type genus of the type order of the class; L. suff. -ia ending to denote a class; N.L. neut. pl. n. Fervidibacteria the class of the order Fervidibacterales Thermophilic or hyperthermophilic inhabitants of freshwater thermal environments. All members are likely polysaccharide-degrading chemoheterotrophs with numerous carbohydrate-active enzymes encoded in their genomes. Aerobic or strictly anaerobic. Phylogenomic placement of this lineage within the Armatimonadota and relative evolutionary divergence supports delineation of this lineage as a class within the Armatimonadota. The type genus is Fervidibacter. 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Enzymatic depolymerization has the potential to contribute to nylon waste recycling. However, the implementation of a viable industrial process still lags far behind progress in enzymatic polyester recycling. Here we review the current biocatalytic nylon recycling landscape, highlighting biochemical, structural, and materials science barriers that currently limit depolymerization extents. We detail efforts to identify, engineer, and characterize new nylon depolymerases, where currently even the best biocatalysts rarely exceed ~1 wt% conversion of solid polymer to products. Based on our analyses, we suggest that limited substrate accessibility due to substrate crystallinity and hydrogen bonding, rather than intrinsic enzyme inefficiency or instability, is the primary bottleneck to enhanced depolymerization. Guided by successes in polyester enzymatic recycling, we outline a research roadmap combining nylonase engineering with polymer pretreatment, chemo-enzymatic cascades, and process analyses to accelerate development of viable enzymatic nylon recycling processes.
Given our vast lignocellulosic biomass reserves and the difficulty in bioprocessing them without expensive pretreatment and fuel separation steps, the conversion of lignocellulosic biomass directly into electricity would be beneficial. Here we report the previously unexplored capabilities of thermophilic Geobacillus sp. strain WSUCF1 to generate electricity directly from such complex substrates in microbial fuel cells. This process obviates the need for exogenous enzymes and redox mediator supplements. Cyclic voltammetry and chromatography studies revealed the electrochemical signatures of riboflavin molecules that reflect mediated electron transfer capabilities of strain WSUCF1. Proteomics and genomics analysis corroborated that WSUCF1 biofilms uses type-II NADH dehydrogenase and demethylmenaquinone methyltransferase to transfer the electrons to conducting anode via the redox active pheromone lipoproteins localized at the cell membrane.
Lignocellulosic biomass is composed of three major biopolymers: cellulose, hemicellulose and lignin. Analytical tools capable of quickly detecting both glycan and lignin deconstruction are needed to support the development and characterization of efficient enzymes/enzyme cocktails. Previously we have described nanostructure-initiator mass spectrometry-based assays for the analysis of glycosyl hydrolase and most recently an assay for lignin modifying enzymes. Here we integrate these two assays into a single multiplexed assay against both classes of enzymes and use it to characterize crude commercial enzyme mixtures. Application of our multiplexed platform based on nanostructure-initiator mass spectrometry enabled us to characterize crude mixtures of laccase enzymes from fungi Agaricus bisporus (Ab) and Myceliopthora thermophila (Mt) revealing activity on both carbohydrate and aromatic substrates. Using time-series analysis we determined that crude laccase from Ab has the higher GH activity and that laccase from Mt has the higher activity against our lignin model compound. Inhibitor studies showed a significant reduction in Mt GH activity under low oxygen conditions and increased activities in the presence of vanillin (common GH inhibitor). Ultimately, this assay can help to discover mixtures of enzymes that could be incorporated into biomass pretreatments to deconstruct diverse components of lignocellulosic biomass.
Novel Immunological and Mass Spectrometry Methods for Comprehensive Analysis of Recalcitrant Oligosaccharides in AFEX Pretreated Corn Stover. Lignocellulosic biomass is a sustainable alternative to fossil fuel and is extensively used for developing bio-based technologies to produce products such as food, feed, fuel, and chemicals. The key to these technologies is to develop cost competitive processes to convert complex carbohydrates present in plant cell wall to simple sugars such as glucose, xylose, and arabinose. Since lignocellulosic biomass is highly recalcitrant, it must undergo a combination of thermochemical treatment such as Ammonia Fiber Expansion (AFEX), dilute acid (DA), Ionic Liquid (IL) and biological treatment such as enzyme hydrolysis and microbial fermentation to produce desired products. However, when using commercial fungal enzymes during hydrolysis, only 75–85% of the soluble sugars generated are monomeric sugars, while the remaining 15–25% are soluble recalcitrant oligosaccharides that cannot be easily utilized by microorganisms. Previously, we successfully separated and purified the soluble recalcitrant oligosaccharides using a combination of charcoal and celite-based separation followed by size exclusion chromatography and studies their inhibitory properties on enzymes. We discovered that the oligosaccharides with higher degree of polymerization (DP) containing methylated uronic acid substitutions were more recalcitrant towards commercial enzyme mixtures than lower DP and neutral oligosaccharides. Here, we report the use of several complementary techniques that include glycome profiling using plant biomass glycan specific monoclonal antibodies (mAbs) to characterize sugar linkages in plant cell walls and enzymatic hydrolysate, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) using structurally-informative diagnostic peaks offered by negative ion post-secondary decay spectra, gas chromatography followed by mass spectrometry (GC–MS) to characterize oligosaccharide sugar linkages with and without derivatization. Since oligosaccharides (DP 4–20) are small, it is challenging to mobilize these molecules for mAbs binding and characterization. To overcome this problem, we have applied a new biotin-coupling based oligosaccharide immobilization method that successfully tagged most of the low DP soluble oligosaccharides on to a micro-plate surface followed by specific linkage analysis using mAbs in a high-throughput system. This new approach will help develop more advanced versions of future high throughput glycome profiling methods that can be used to separate and characterize oligosaccharides present in biomarkers for diagnostic applications.
Abstract Cocultures of engineered thermophilic bacteria can ferment lignocellulose without costly pretreatment or added enzymes, an ability that can be exploited for low cost biofuel production from renewable feedstocks. The hemicellulose-fermenting species Thermoanaerobacterium thermosaccharolyticum was engineered for high ethanol yield, but we found that the strains switched from growth-coupled production of ethanol to growth uncoupled production of acetate and 1,2-propanediol upon growth cessation, producing up to 6.7 g/L 1,2-propanediol from 60 g/L cellobiose. The unique capability of this species to make 1,2-propanediol from sugars was described decades ago, but the genes responsible were not identified. Here we deleted genes encoding methylglyoxal reductase, methylglyoxal synthase and glycerol dehydrogenase. Deletion of the latter two genes eliminated propanediol production. To understand how carbon flux is redirected in this species, we hypothesized that high ATP levels during growth cessation downregulate the activity of alcohol and aldehyde dehydrogenase activities. Measurements with cell free extracts show approximately twofold and tenfold inhibition of these activities by 10 mM ATP, supporting the hypothesized mechanism of metabolic redirection. This result may have implications for efforts to direct and maximize flux through alcohol dehydrogenase in other species.
Lignin is composed of phenylpropanoid monomers linked by ether and carbon-carbon bonds to form a complex heterogeneous structure. Bond-specific studies of lignin-modifying enzymes (LMEs; e.g., laccases and peroxidases) are limited by the polymerization of model lignin substrates and repolymerization of cleavage products. Here we present a high throughput platform to screen LME activities on four tagged model lignin compounds that represent the β-O-4’, β-β’, 5–5’, and 4-O-5’ linkages in lignin. We utilized nanostructure-initiator mass spectrometry (NIMS) and model lignin compounds with tags containing perfluorinated and cationic moieties, which effectively limit polymerization and condensation of the substrates and their degrading products. Sub-microliter sample droplets were printed on the NIMS chip with a novel robotics method. This rapid platform enabled characterization of LMEs across a range of pH 3–10 and relative quantification of modified (typically oxidized), cleaved, and polymerized products. All tested enzymes oxidized the four substrates and cleaved the β-O-4’ and β-β’ substrates to monomeric products. We discovered that the active pH range depended on both the substrate and the enzyme type. This has important applications for biomass conversion to biofuels and bioproducts, where the relative percentages of different bond types in lignin varies depending on feedstock and chemical pretreatment methods.
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Plant cells are elaborate three-dimensional polymer nano-constructs with complex chemistry. The bulk response of plants to light, in the far-field, is ultimately encoded by optical scattering from these nano-constructs. Their chemical and physical properties may be acquired through their interaction with a modulated nano-tip using scattering scanning near-field optical microscopy. Here, using this technique, we present 20 nm spatial resolution mechanical, spectral and optical mappings of plant cell walls. We first address the problem of plant polymers tracking through pretreatment and processing. Specifically, cellulose and lignin footprints are traced within a set of delignified specimen, establishing the factors hindering complete removal of lignin, an important industrial polymer. Furthermore, we determine the frequency dependent dielectric function ${\epsilon }(\omega)={(n+ik)}^{2}$ of plant material in the range 28 ≤ ω ≤ 58 THz, and show how the environmental chemical variation is imprinted in the nanoscale variability of n and k . This nanometrology is a promise for further progress in the development of plant-based (meta-)materials.
A circular plastics economy can leverage the lightweight, strong and durable characteristics of macromolecular materials, while simultaneously reducing the negative environmental impacts associated with polymer waste. Advanced recycling technologies provide an opportunity to valorize plastics waste and extend the lifespan of these materials by converting waste into new monomers, polymers or specialty chemicals. Although many advanced technologies appear promising, assessments of economic and environmental sustainability are often not conducted in a standardized fashion and neglect factors such as plastics waste transportation, sorting and pretreatment. These shortcomings can lead to inaccurate or misleading predictions, reduce opportunities for optimization and limit industrial relevance. In this Review, we highlight select industrial case studies to underscore the notable consequences of underestimating the complexity of real-life consumer plastics waste. In addition, the current challenges associated with the assessment of the industrial viability of laboratory-scale processes are explored. Here, by discussing relevant analysis frameworks and system boundaries, along with potential analytical pitfalls, future research will be guided beyond chemical considerations and toward impactful circular solutions.
Cellulose, an abundant, renewable, and sustainable non-edible carbon source from agriculture and forestry, has attracted great attention for producing diverse value-added chemicals and fuels. However, the rigid 3D structure of cellulose, maintained by an extensive hydrogen bonding network, hinders chemical conversion, requiring effective pretreatment to break down the crystalline structure. High-value cellulose-derived compounds such as 5-hydroxymethylfurfural (5-HMF), levulinate esters, and sorbitol, recognized as critical platform chemicals by the U.S. Department of Energy, are particularly attractive for versatile applications. This review provides a comprehensive overview of methodologies for the chemical synthesis of 5-HMF, levulinate esters, and sorbitol, focusing on direct catalytic conversion of cellulose. It delves into recent advancements in reaction systems and catalysts, highlighting catalytic pathways, selectivity, strategies for process optimization, and computational approaches, while discussing the challenges associated with the catalytic conversion of cellulose into these high-value products and offering potential strategies for enhancing future catalytic processes.
Although the use of ionic liquids (ILs) for the pretreatment of lignocellulosic biomass has been limited due to high costs, recent efforts to develop low-cost protic ILs show promise for achieving cost-effectiveness for biorefineries. However, an additional challenge remains in that ILs present in biomass hydrolysates are toxic to most microbial hosts, resulting in poor growth phenotypes. To address this issue, we applied an adaptive laboratory evolution (ALE) approach for tolerizing Pseudomonas putida KT2440, an industrially relevant bacterial host, to two low-cost ILs (triethanolammonium acetate [TEOH][OAc] and triethylammonium hydrogen sulfate [TEA][HS]). After continuous cultivations with gradually increased IL levels, we obtained evolved strains showing significant improvements in their growth performance under high concentrations of the ILs (maximum 4% [TEOH][OAc] and 8% [TEA][HS], in w/v) at which the wild-type strain cannot grow. Sequencing of evolved strains revealed multiple regions where mutations were associated with improved performance in minimal media conditions (relA, gacS, oprB/PP_1446, fleQ, tktA, and uvrY/PP_4100) and in IL-specific conditions (PP_5350, PP_4929/emrE, oprD, and PP_5324). We further validated the causality of the PP_5350 and emrE genes for improved IL tolerance via reverse engineering and transcriptomic analysis. Here, a common mutation in the PP_5350 gene, encoding a RpiR family transcriptional regulator, was shown to significantly upregulate the glyoxylate cycle for efficient acetate catabolism. In addition, it was suggested that the emrE gene encodes an efflux pump which can export [TEA][HS]. Finally, the cultivation of two of the best performing evolved strains with IL-treated biomass hydrolysates demonstrated their considerable potential to be used as platform strains. Taken as a whole, this work provides strains for utilization of IL-treated biomass and a mechanistic understanding that could be further leveraged to develop efficient microbial bioprocesses.
An integrated acetic acid based one-pot protic ionic liquid pretreatment and saccharification enables the near full conversion of poplar polysaccharides.
This work demonstrates the feasibility of applying dual functional solvents called alkanolamines for biomass pretreatment, deconstruction, and conversion into biofuels.
Biological lignin conversion to medium chain length-polyhydroxyalkanoates (mcl-PHA) has recently emerged as an attractive alternative to petroleum-based plastics due to the renewable nature of lignin and the value-added applications of mcl-PHA. Previous reports suggested that addition of limited glucose can improve mcl-PHA accumulation in Pseudomonas putida KT2440 grown in lignin substrates. Herein, we propose a biorefinery process to systematically release lignin and sugars from lignocellulosic biomass and evaluate the potential of co-utilization of all biomass components for conversion to mcl-PHA. Our results indicate that a sequential treatment composed of acid pretreatment, enzymatic hydrolysis and alkaline treatment produces a suitable lignin stream for mcl-PHA production in engineered P. putida. In addition, the PHA titer could be increased by 71% when the lignin stream (AH) was combined with the enzymatic hydrolysate (EH) at a ratio of 75 : 25. Higher ratios of EH : AH negatively affect mcl-PHA accumulation as well as mixtures with sugars from the acid hydrolysate. The optimization of the fermentation conditions, including the inoculum (OD 600 ) and substrate (soluble solid content (SSC)), was carried out by a central composite design. The optimal conditions were achieved at OD 600 = 2.17 and SSC = 68.28 g L –1 . Under these conditions, the titer increased 4.3 fold, achieving a mcl-PHA production of 1.38 g L –1 . Lignin characterization before and after fermentation by nuclear magnetic resonance and gas chromatography showed that p-coumarates were mainly consumed during the fermentation for mcl-PHA production. Overall, this biorefinery strategy allowed us to increase mcl-PHA production by utilizing the different lignocellulosic fractions. Unlike previous studies, no model substrates were utilized at any stage of the fermentation process, representing a step forward towards process feasibility.
Lignocellulosic biomass conversion to renewable, carbon-neutral materials, fuels, and chemicals is the cornerstone of the transition to a sustainable future bioeconomy. Green energy in the form of electricity needs to be coupled with or substitute conventional thermally driven processes to realize small-scale, economically viable and environmentally friendly biorefineries. Gas discharge plasmas enable the conversion of renewable electric energy, supplied in the form of an electric field, to chemical energy through the formation of a highly reactive environment that can induce several transformations related to agricultural waste valorization processes. Herein, we review the application of plasma technology to lignocellulosic biomass upgrade, aiming to provide the scientific background and technical challenges in this rapidly emerging research field. To bridge the gap between plasma science and biomass valorization technologies, we initially present the technical aspects of plasma reactors related to biomass processing and further discuss the advances in plasma processing for each biomass conversion technology, providing insights into the related plasma chemistry and interaction mechanisms. Here, we first focus on the low and medium-temperature biomass conversion processes, including biomass pretreatment and delignification to promote enzyme or acid-catalyzed hydrolysis to sugars and biomass liquefaction using plasma electrolysis. Then we discuss the high and very high-temperature conversion processes, such as plasma-assisted pyrolysis and gasification to syngas and plasma application to tar removal, combustion, and vitrification. Overall, this review provides knowledge at the interface of plasma science and biomass conversion technology to promote the interaction between the individual communities, which is crucial for the further advancement of the field.
The solubility parameter (SP) of a molecular species is a vital feature that indicates polarity and quantifies the ‘like-seeks-like’ principle, which is used in chemistry to screen solvents for dissolution. Recent studies have demonstrated that ionic liquids (ILs) and deep eutectic solvents (DESs) efficiently solubilize lignocellulosic biomass and promote enzymatic saccharification into sugars used for the production of biofuels and value-added chemicals. Understanding the solubility of plant biopolymers, particularly lignin, in ILs and DESs is critical for selecting candidate ILs and DESs for biomass pretreatment; however, experimentally measuring SPs is challenging. Thus, the present study investigates lignin dissolution mechanisms in IL/DES and prediction of the solubility parameters (Hildebrand and Hansen) of lignin, ILs, and DESs using multi-resolution simulation approaches. Here, solubility parameters of the studied compounds were predicted using molecular dynamics (MD) simulations, and the SP of lignin was determined to be 23–27 MPa 1/2 , which was close to the polymeric lignin solubility parameter (24.3–25.5 MPa 1/2 ). The SPs of ILs namely [Ch][Lys], [Ch][Oct], and [Emim][Lys] were predicted to be ~26 MPa 1/2 , which is close to lignin's SPs and resulted in increased biomass delignification. The MD simulated SPs were validated by both the COSMO-RS model and experimental investigations, with the results showing a close agreement between the predicted and experimentally obtained SPs. In addition, the enthalpy of vaporization (ΔH vap ) of ILs/DESs was predicted based on the potential energy of the system, and the ΔH vap of ILs/DESs was around 40–65 kcal mol –1 , which is 5–8 times higher than that of traditional organic solvents.