Lignin plays a negative role in the biochemical process for producing lignocellulosic biofuels

Distribution of xylan linked glucuronic acid labelled by molecularly imprinted polymers on pulp fiber surface

Efficiently utilization of plant resources is heavily restricted by the resistance of lignocellulose in plant cells, which is related to the interlinkages of lignocellulose components. Hemicellulose in plant cell wall is bound to cellulose by hydrogen bond and linked with lignin in lignin-carbohydrate complex (LCC). In the xylan chain of hemicellulose, glucuronic acid (GA) is a typical side-group, which provides clues for us to label and locate hemicellulose. The way to label GA on the surface of pulp fibers obtained from pulping process is benefit to explore the deconstruction of lignocellulose. Herein, a new visualization method, fluorescence modified molecularly imprinted polymers (MIP) were applied to recognize and locate GA on the pulp fiber surface. The method combining fluorescence imaging and integrated 3D fiber structure verified the feasibility of the MIP for specific GA recognition. The results showed that xylan (represented by GA) was closely attached to lignin, distributed along the inner wall of pulp fiber cells, and gradually taken off from the inside edge of fiber cells with the deconstruction of lignocellulose. This research provided a basis to develop visualization bioimaging technology to identify biomass components.

Study on the mechanism of lignin non-productive adsorption on cellobiohydrolase

Enzymatic hydrolysis is important for lignocellulosic biomass conversion into fermentable sugars. However, the nonproductive adsorption of enzyme on lignin was major hinderance for the enzymatic hydrolysis efficiency. In this study, non-productive adsorption mechanism of cellulase component cellobiohydrolase (CBH) onto lignin was specific investigated. Research revealed that the adsorption behavior of CBH on eucalyptus alkali lignin (EuA) was affected by reaction conditions. As study on the adsorption kinetic, it was indicated that the adsorption cellulose binding domain (CBD) of CBH onto EuA well fitted with Langmuir adsorption model and pseudo second-order adsorption kinetics model. And the tyrosine site related to the adsorption of CBD onto lignin was proved by the fluorescence and UV spectra analysis. The results of this work provide a theoretical guidance to understanding the nonproductive adsorption mechanism and building method to reduce the adsorption of cellulase on the lignin.

Physiological Responses of C4 Perennial Bioenergy Grasses to Climate Change: Causes, Consequences, and Constraints

C4 perennial bioenergy grasses are an economically and ecologically important group whose responses to climate change will be important to the future bioeconomy. These grasses are highly productive and frequently possess large geographic ranges and broad environmental tolerances, which may contribute to the evolution of ecotypes that differ in physiological acclimation capacity and the evolution of distinct functional strategies. C4 perennial bioenergy grasses are predicted to thrive under climate change-C4 photosynthesis likely evolved to enhance photosynthetic efficiency under stressful conditions of low [CO2], high temperature, and drought-although few studies have examined how these species will respond to combined stresses or to extremes of temperature and precipitation. Important targets for C4 perennial bioenergy production in a changing world, such as sustainability and resilience, can benefit from combining knowledge of C4 physiology with recent advances in crop improvement, especially genomic selection.

Valorization of Lignocellulose with One-Step Acidified Monophasic Phenoxyethanol Fractionation

Effective fractionation of lignocelluosic biomass and subsequent valorization of all three major components under mild conditions were achieved. Pretreatment with acidified monophasic phenoxyethanol (EPH) efficiently removed 92.6 % lignin and 80 % xylan from poplar at 110 °C in 60 min, yielding high-value EPH-xyloside, EPH-modified lignin (EPHL), and a solid residue nearly purely composed of carbohydrates. After removing the grafted acetyl groups using 1 % NaOH at 50 °C, the highest enzymatic digestibility reached 92.3 %. EPHL could be recovered in high yield and purity with an uncondensed structure, while xylose was converted to EPH-xyloside, a potential precursor in biomedical industries. Additionally, the acidified monophasic EPH solvent could effectively fractionate biomass from species other than hardwood, achieving over 70 % delignification from recalcitrant pinewood under the same mild conditions, demonstrating the high potential of monophasic EPH pretreatment.

Grass lignin: biosynthesis, biological roles, and industrial applications

Lignin is a phenolic heteropolymer found in most terrestrial plants that contributes an essential role in plant growth, abiotic stress tolerance, and biotic stress resistance. Recent research in grass lignin biosynthesis has found differences compared to dicots such as Arabidopsis thaliana. For example, the prolific incorporation of hydroxycinnamic acids into grass secondary cell walls improve the structural integrity of vascular and structural elements via covalent crosslinking. Conversely, fundamental monolignol chemistry conserves the mechanisms of monolignol translocation and polymerization across the plant phylum. Emerging evidence suggests grass lignin compositions contribute to abiotic stress tolerance, and periods of biotic stress often alter cereal lignin compositions to hinder pathogenesis. This same recalcitrance also inhibits industrial valorization of plant biomass, making lignin alterations and reductions a prolific field of research. This review presents an update of grass lignin biosynthesis, translocation, and polymerization, highlights how lignified grass cell walls contribute to plant development and stress responses, and briefly addresses genetic engineering strategies that may benefit industrial applications.

Cellulolytic Aerobic Bacteria Isolated from Agricultural and Forest Soils: An Overview

This review provides insights into cellulolytic bacteria present in global forest and agricultural soils over a period of 11 years. It delves into the study of soil-dwelling cellulolytic bacteria and the enzymes they produce, cellulases, which are crucial in both soil formation and the carbon cycle. Forests and agricultural activities are significant contributors to the production of lignocellulosic biomass. Forest ecosystems, which are key carbon sinks, contain 20-30% cellulose in their leaf litter. Concurrently, the agricultural sector generates approximately 998 million tons of lignocellulosic waste annually. Predominant genera include Bacillus, Pseudomonas, Stenotrophomonas, and Streptomyces in forests and Bacillus, Streptomyces, Pseudomonas, and Arthrobacter in agricultural soils. Selection of cellulolytic bacteria is based on their hydrolysis ability, using artificial cellulose media and dyes like Congo red or iodine for detection. Some studies also measure cellulolytic activity in vitro. Notably, bacterial cellulose hydrolysis capability may not align with their cellulolytic enzyme production. Enzymes such as GH1, GH3, GH5, GH6, GH8, GH9, GH10, GH12, GH26, GH44, GH45, GH48, GH51, GH74, GH124, and GH148 are crucial, particularly GH48 for crystalline cellulose degradation. Conversely, bacteria with GH5 and GH9 often fail to degrade crystalline cellulose. Accurate identification of cellulolytic bacteria necessitates comprehensive genomic analysis, supplemented by additional proteomic and transcriptomic techniques. Cellulases, known for degrading cellulose, are also significant in healthcare, food, textiles, bio-washing, bleaching, paper production, ink removal, and biotechnology, emphasizing the importance of discovering novel cellulolytic strains in soil.

Lignin impairs Cel7A degradation of in vitro lignified cellulose by impeding enzyme movement and not by acting as a sink

BACKGROUND

Cellulose degradation by cellulases has been studied for decades due to the potential of using lignocellulosic biomass as a sustainable source of bioethanol. In plant cell walls, cellulose is bonded together and strengthened by the polyphenolic polymer, lignin. Because lignin is tightly linked to cellulose and is not digestible by cellulases, is thought to play a dominant role in limiting the efficient enzymatic degradation of plant biomass. Removal of lignin via pretreatments currently limits the cost-efficient production of ethanol from cellulose, motivating the need for a better understanding of how lignin inhibits cellulase-catalyzed degradation of lignocellulose. Work to date using bulk assays has suggested three possible inhibition mechanisms: lignin blocks access of the enzyme to cellulose, lignin impedes progress of the enzyme along cellulose, or lignin binds cellulases directly and acts as a sink.

RESULTS

We used single-molecule fluorescence microscopy to investigate the nanoscale dynamics of Cel7A from Trichoderma reesei, as it binds to and moves along purified bacterial cellulose in vitro. Lignified cellulose was generated by polymerizing coniferyl alcohol onto purified bacterial cellulose, and the degree of lignin incorporation into the cellulose meshwork was analyzed by optical and electron microscopy. We found that Cel7A preferentially bound to regions of cellulose where lignin was absent, and that in regions of high lignin density, Cel7A binding was inhibited. With increasing degrees of lignification, there was a decrease in the fraction of Cel7A that moved along cellulose rather than statically binding. Furthermore, with increasing lignification, the velocity of processive Cel7A movement decreased, as did the distance that individual Cel7A molecules moved during processive runs.

CONCLUSIONS

In an in vitro system that mimics lignified cellulose in plant cell walls, lignin did not act as a sink to sequester Cel7A and prevent it from interacting with cellulose. Instead, lignin both blocked access of Cel7A to cellulose and impeded the processive movement of Cel7A along cellulose. This work implies that strategies for improving biofuel production efficiency should target weakening interactions between lignin and cellulose surface, and further suggest that nonspecific adsorption of Cel7A to lignin is likely not a dominant mechanism of inhibition.

Supercharging carbohydrate-binding module alone enhances endocellulase thermostability, binding, and activity on cellulosic biomass

Lignocellulosic biomass recalcitrance to enzymatic degradation necessitates high enzyme loadings incurring large processing costs for industrial-scale biofuels or biochemicals production. Manipulating surface charge interactions to minimize non-productive interactions between cellulolytic enzymes and plant cell wall components (e.g., lignin or cellulose) via protein supercharging has been hypothesized to improve biomass biodegradability, but with limited demonstrated success to date. Here we characterize the effect of introducing non-natural enzyme surface mutations and net charge on cellulosic biomass hydrolysis activity by designing a library of supercharged family-5 endoglucanase Cel5A and its native family-2a carbohydrate binding module (CBM) originally belonging to an industrially relevant thermophilic microbe Thermobifida fusca . A combinatorial library of 33 mutant constructs containing different CBM and Cel5A designs spanning a net charge range of -52 to 37 was computationally designed using Rosetta macromolecular modelling software. Activity for all mutants was rapidly characterized as soluble cell lysates and promising mutants (containing mutations either on the CBM, Cel5A catalytic domain, or both CBM and Cel5A domains) were then purified and systematically characterized. Surprisingly, often endocellulases with mutations on the CBM domain alone resulted in improved activity on cellulosic biomass, with three top-performing supercharged CBM mutants exhibiting between 2-5-fold increase in activity, compared to native enzyme, on both pretreated biomass enriched in lignin (i.e., corn stover) and isolated crystalline/amorphous cellulose. Furthermore, we were able to clearly demonstrate that endocellulase net charge can be selectively fine-tuned using protein supercharging protocol for targeting distinct substrates and maximizing biocatalytic activity. Additionally, several supercharged CBM containing endocellulases exhibited a 5-10 °C increase in optimal hydrolysis temperature, compared to native enzyme, which enabled further increase in hydrolytic yield at higher operational reaction temperatures. This study demonstrates the first successful implementation of enzyme supercharging of cellulolytic enzymes to increase hydrolytic activity towards complex lignocellulosic biomass derived substrates.

Kraft Lignin: A Valuable, Sustainable Resource, Opportunities and Challenges

Kraft lignin, a by-product from the production of pulp, is currently incinerated in the recovery boiler during the chemical recovery cycle, generating valuable bioenergy and recycling inorganic chemicals to the pulping process operation. Removing lignin from the black liquor or its gasification lowers the recovery boiler load enabling increased pulp production. During the past ten years, lignin separation technologies have emerged and the interest of the research community to valorize this underutilized resource has been invigorated. The aim of this Review is to give (1) a dedicated overview of the kraft process with a focus on the lignin, (2) an overview of applications that are being developed, and (3) a techno-economic and life cycle asseeements of value chains from black liquor to different products. Overall, it is anticipated that this effort will inspire further work for developing and using kraft lignin as a commodity raw material for new applications undeniably promoting pivotal global sustainability concerns.

Arundo donax L. growth potential under different abiotic stress

Arundo donax L. (giant reed) is a fast-growing, vegetatively multiplying, and rhizomatous perennial grass. It is considered a leading crop for biomass production on marginal and degraded lands under different adverse conditions such as drought, salinity, waterlogging, high and low temperatures, and heavy metal stress. The giant reed tolerance to those stresses is reviewed based on its effects on photosynthetic capacity and biomass production. Possible explanations for the giant reed tolerance against each particular stress were elucidated, as well as changes shown by the plant at a biochemical, physiological and morphological level, that may directly affect its biomass production. The use of giant reed in other areas of interest such as bioconstruction, phytoremediation, and bioremediation, is also reviewed. Arundo donax can be key for circular economy and global warming mitigation.

Bioprospecting of novel ligninolytic bacteria for effective bioremediation of agricultural by-product and synthetic pollutant dyes

Lignin is a significant renewable carbon source that needs to be exploited to manufacture bio-ethanol and chemical feedstocks. Lignin mimicking methylene blue (MB) dye is widely used in industries and causes water pollution. Using kraft lignin, methylene blue, and guaiacol as a full carbon source, 27 lignin-degrading bacteria (LDB) were isolated from 12 distinct traditional organic manures for the current investigation. The ligninolytic potential of 27 lignin-degrading bacteria was assessed by qualitative and quantitative assay. In a qualitative plate assay, the LDB-25 strain produced the largest zone, measuring 6.32 ± 0.297, on MSM-L-kraft lignin plates, while the LDB-23 strain produced the largest zone, measuring 3.44 ± 0.413, on MSM-L-Guaiacol plates. The LDB-9 strain in MSM-L-kraft lignin broth was able to decolorize lignin to a maximum of 38.327 ± 0.011% in a quantitative lignin degradation assay, which was later verified by FTIR assay. In contrast, LDB-20 produced the highest decolorization (49.633 ± 0.017%) in the MSM-L-Methylene blue broth. The highest manganese peroxidase enzyme activity, measuring 6322.314 ± 0.034 U L^-1, was found in the LDB-25 strain, while the highest laccase enzyme activity, measuring 1.5105 ± 0.017 U L^-1, was found in the LDB-23 strain. A preliminary examination into the biodegradation of rice straw using effective LDB was carried out, and efficient lignin-degrading bacteria were identified using 16SrDNA sequencing. SEM investigations also supported lignin degradation. LDB-8 strain had the highest percentage of lignin degradation (52.86%), followed by LDB-25, LDB-20, and LDB-9. These lignin-degrading bacteria have the ability to significantly reduce lignin and lignin-analog environmental contaminants, therefore they can be further researched for effective bio-waste management mediated breakdown.

Additional ratios of hydrolysates from lignocellulosic digestate at different hydrothermal temperatures influencing anaerobic digestion performance

Hydrothermal treatment (HT) is envisaged as a promising technology to treat the lignocellulosic biomass. HT temperature is an important parameter influencing the hydrolysate compositions such as organic compounds and potential inhibitors, and therefore affect the subsequential anaerobic digestion (AD) process. Herein, HT-AD was employed to treat the wheat straw-derived digestate. The HT temperature of 190 °C was proved to be the best performance with a higehst reducing sugar yield (45.05 mg g^-1) in the hydrolysate and a highest methane yield (120.8 mL g_TS^-1) from the AD of the hydrolysate, which was 42.5% higher than the methane yield in the control without the hydrolysate addition (84.8 mL g_TS^-1). 3-Furaldehyde was the dominant organic in the hydrolysates. The HT temperature of 210 °C led to the presence of AD inhibitory moieties (e.g., phenols and furans) in the hydrolysate, resulting in a low methane yield. Although the treatments with the addition of 100% hydrolysate outperformed those of 50% hydrolysate in the methane yields in the late stage, the latter had higher methane yields in the first stage, suggesting that the additional ratios of hydrolysates should be carefully considered in AD, especially the detrimental effects of inhibitors and adaptability issues of AD consortia. The MiSeq sequencing showed that the hydrolysis/acidogenesis was dominant in the first stage, while methanogenesis became dominant in the late stage with the acetoclastic/hydrogenotrophic methanogens (Methanosarcina and Methanobacterium) enriched in the hydrolysate-feeding reactors. These findings demonstrated that a integration of HT-AD was a promising approach for the digestate valorization and to reduce the potential carbon emission from waste treatments.

Transgenic ZmMYB167 Miscanthus sinensis with increased lignin to boost bioenergy generation for the bioeconomy

BACKGROUND

Perennial C₄ grasses from the genus Miscanthus are widely regarded as leading and promising dedicated bioenergy crops due to their high biomass accumulation on marginal land with low environmental impacts and maintenance requirements over its productive life. There is an urgent socio-political and environmental need to ramp up the production of alternative, affordable and green bioenergy sources and to re-direct the net zero carbon emissions trajectory. Hence, up-scaling of Miscanthus cultivation as a source of biomass for renewable energy could play an important role to strategically address sustainable development goals for a growing bio-based economy. Certain Miscanthus sinensis genotypes are particularly interesting for their biomass productivity across a wide range of locations. As the aromatic biomass component lignin exhibits a higher energy density than cell wall polysaccharides and is generally used as an indicator for heating or calorific value, genetic engineering could be a feasible strategy to develop M. sinensis biomass with increased lignin content and thus improving the energetic value of the biomass.

RESULTS

For this purpose, transgenic M. sinensis were generated by Agrobacterium-mediated transformation for expression of ZmMYB167, a MYB transcription factor known for regulating lignin biosynthesis in C₃ and C₄ grasses. Four independent transgenic ZmMYB167 Miscanthus lines were obtained. Agronomic traits such as plant height, tillering and above-ground dry weight biomass of the transgenic plants were not different to that of wild-type control plants. Total lignin content of the transgenic plants was ~ 15-24% higher compared with control plants. However, the structural carbohydrates, glucan and xylan, were decreased by ~ 2-7% and ~ 8-10%, respectively, in the transgenic plants. Moreover, expression of ZmMYB167 in transgenic plants did not alter lignin composition, phenolic compounds or enzymatic saccharification efficiency yields but importantly improved total energy levels in Miscanthus biomass, equivalent to 10% higher energy yield per hectare.

CONCLUSIONS

This study highlights ZmMYB167 as a suitable target for genetic lignin bioengineering interventions aimed at advancing and developing lignocellulosic biomass supply chains for sustainable production of renewable bioenergy.

Genome-wide analysis of the Populus trichocarpa laccase gene family and functional identification of PtrLAC23

INTRODUCTION

Biofuel is a kind of sustainable, renewable and environment friendly energy. Lignocellulose from the stems of woody plants is the main raw material for "second generation biofuels". Lignin content limits fermentation yield and is therefore a major obstacle in biofuel production. Plant laccase plays an important role in the final step of lignin formation, which provides a new strategy for us to obtain ideal biofuels by regulating the expression of laccase genes to directly gain the desired lignin content or change the composition of lignin.

METHODS

Multiple sequence alignment and phylogenetic analysis were used to classify PtrLAC genes; sequence features of PtrLACs were revealed by gene structure and motif composition analysis; gene duplication, interspecific collinearity and Ka/Ks analysis were conducted to identify ancient PtrLACs; expression levels of PtrLAC genes were measured by RNA-Seq data and qRT-PCR; domain analysis combine with cis-acting elements prediction together showed the potential function of PtrLACs. Furthermore, Alphafold2 was used to simulate laccase 3D structures, proLAC23::LAC23-eGFP transgenic Populus stem transects were applied to fluorescence observation.

RESULTS

A comprehensive analysis of the P. trichocarpa laccase gene (PtLAC) family was performed. Some ancient PtrLAC genes such as PtrLAC25, PtrLAC19 and PtrLAC41 were identified. Gene structure and distribution of conserved motifs clearly showed sequence characteristics of each PtrLAC. Combining published RNA-Seq data and qRT-PCR analysis, we revealed the expression pattern of PtrLAC gene family. Prediction results of cis-acting elements show that PtrLAC gene regulation was closely related to light. Through above analyses, we selected 5 laccases and used Alphafold2 to simulate protein 3D structures, results showed that PtrLAC23 may be closely related to the lignification. Fluorescence observation of proLAC23::LAC23-eGFP transgenic Populus stem transects and qRT-PCR results confirmed our hypothesis again.

DISCUSSION

In this study, we fully analyzed the Populus trichocarpa laccase gene family and identified key laccase genes related to lignification. These findings not only provide new insights into the characteristics and functions of Populus laccase, but also give a new understanding of the broad prospects of plant laccase in lignocellulosic biofuel production.

Genomics analysis and degradation characteristics of lignin by Streptomyces thermocarboxydus strain DF3-3

Background

Lignocellulose is an important raw material for biomass-to-energy conversion, and it exhibits a complex but inefficient degradation mechanism. Microbial degradation is promising due to its environmental adaptability and biochemical versatility, but the pathways used by microbes for lignin degradation have not been fully studied. Degradation intermediates and complex metabolic pathways require more study.

Results

A novel actinomycete DF3-3, with the potential for lignin degradation, was screened and isolated. After morphological and molecular identification, DF3-3 was determined to be Streptomyces thermocarboxydus. The degradation of alkali lignin reached 31% within 15 days. Manganese peroxidase and laccase demonstrated their greatest activity levels, 1821.66 UL⁻¹ and 1265.58 UL⁻¹, respectively, on the sixth day. The highest lignin peroxidase activity was 480.33 UL⁻¹ on the fourth day. A total of 19 lignin degradation intermediates were identified by gas chromatography–mass spectrometry (GC–MS), including 9 aromatic compounds. Genome sequencing and annotation identified 107 lignin-degrading enzyme-coding genes containing three core enzymatic systems for lignin depolymerization: laccases, peroxidases and manganese peroxidase. In total, 7 lignin metabolic pathways were predicted.

Conclusions

Streptomyces thermocarboxydus strain DF3-3 has good lignin degradation ability. Degradation products and genomics analyses of DF3-3 show that it has a relatively complete lignin degradation pathway, including the β-ketoadipate pathway and peripheral reactions, gentisate pathway, anthranilate pathway, homogentisic pathway, and catabolic pathway for resorcinol. Two other pathways, the phenylacetate–CoA pathway and the 2,3-dihydroxyphenylpropionic acid pathway, are predicted based on genome data alone. This study provides the basis for future characterization of potential biotransformation enzyme systems for biomass energy conversion.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13068-022-02175-1.

Positive role of non-catalytic proteins on mitigating inhibitory effects of lignin and enhancing cellulase activity in enzymatic hydrolysis: Application, mechanism, and prospective

Fermentable sugar production from lignocellulosic biomass has received considerable attention and has been dramatic progress recently. However, due to low enzymatic hydrolysis (EH) yields and rates, a high dosage of the costly enzyme is required, which is a bottleneck for commercial applications. Over the last decades, various strategies have been developed to reduce cellulase enzyme costs. The progress of the non-catalytic additive proteins in mitigating inhibition in EH is discussed in detail in this review. The low efficiency of EH is mostly due to soluble lignin compounds, insoluble lignin, and harsh thermal and mechanical conditions of the EH process. Adding non-catalytic proteins into the EH is considered a simple and efficient approach to boost hydrolysis yield. This review discussed the multiple mechanical steps involved in the EH process. The effect of physicochemical properties of modified lignin on EH and its interaction with cellulase and cellulose are identified and discussed, which include hydrogen bonding, hydrophobic, electrostatic, and cation-π interactions, as well as physical barriers. Moreover, the effects of different conditions of EH that lead to cellulase deactivation by thermal and mechanical mechanisms are also explained. Finally, recent advances in the development, potential mechanisms, and economic feasibility of non-catalytic proteins on EH are evaluated and perspectives are presented.

Transcriptional and metabolic changes associated with internode development and reduced cinnamyl alcohol dehydrogenase activity in sorghum

The molecular mechanisms associated with secondary cell wall (SCW) deposition in sorghum remain largely uncharacterized. Here, we employed untargeted metabolomics and large-scale transcriptomics to correlate changes in SCW deposition with variation in global gene expression profiles and metabolite abundance along an elongating internode of sorghum, with a major focus on lignin and phenolic metabolism. To gain deeper insight into the metabolic and transcriptional changes associated with pathway perturbations, a bmr6 mutant [with reduced cinnamyl alcohol dehydrogenase (CAD) activity] was analyzed. In the wild type, internode development was accompanied by an increase in the content of oligolignols, p-hydroxybenzaldehyde, hydroxycinnamate esters, and flavonoid glucosides, including tricin derivatives. We further identified modules of genes whose expression pattern correlated with SCW deposition and the accumulation of these target metabolites. Reduced CAD activity resulted in the accumulation of hexosylated forms of hydroxycinnamates (and their derivatives), hydroxycinnamaldehydes, and benzenoids. The expression of genes belonging to one specific module in our co-expression analysis correlated with the differential accumulation of these compounds and contributed to explaining this metabolic phenotype. Metabolomics and transcriptomics data further suggested that CAD perturbation activates distinct detoxification routes in sorghum internodes. Our systems biology approach provides a landscape of the metabolic and transcriptional changes associated with internode development and with reduced CAD activity in sorghum.

An insight into the principles of lignocellulosic biomass-based zero-waste biorefineries: a green leap towards imperishable energy-based future

Lignocellulosic biomass (LCB) is an energy source that has a huge impact in today's world. The depletion of fossil fuels, increased pollution, climatic changes, etc. have led the public and private sectors to move towards sustainability i.e. using LCB for the production of biofuels and value-added compounds. A major bottleneck of the process is the recalcitrant nature of LCB. This can be overcome by using various pretreatment strategies like physical, chemical, biological, physicochemical, etc. Further, the pretreated biomass is made to undergo various steps like hydrolysis, saccharification, etc. for the conversion of value-added products and the remaining waste residues can be further utilized for the synthesis of secondary products thus favouring the zero-waste biorefinery concept. Currently, microorganisms are being explored for their use in biorefinery but the unavailability of commercial strains is a major limitation. Thus, the use of metagenomics can be used to overcome the limitation which is both cost-effective and environmentally friendly. The review deliberates the composition of LCBs, and their recalcitrance nature, followed by the structural changes caused by various pretreatment methods. The further steps in biorefineries, strategies for the development of zero-waste refineries, bottlenecks, and suggestions are also discussed. Special emphasis is given to the use of metagenomics for the discovery of microorganisms efficient for zero-waste biorefineries.

Whole genome duplication of wild-type and CINNAMYL ALCOHOL DEHYDROGENASE1-downregulated hybrid poplar reduces biomass yield and causes a brittle apex phenotype in field-grown wild types

The potential of whole genome duplication to increase plant biomass yield is well-known. In Arabidopsis tetraploids, an increase in biomass yield was accompanied by a reduction in lignin content and, as a result, a higher saccharification efficiency was achieved compared with diploid controls. Here, we evaluated whether the results obtained in Arabidopsis could be translated into poplar and whether the enhanced saccharification yield upon alkaline pretreatment of hairpin-downregulated CINNAMYL ALCOHOL DEHYDROGENASE1 (hpCAD) transgenic poplar could be further improved upon a whole genome duplication. Using a colchicine treatment, wild-type (WT) Populus tremula x P. alba cv. INRA 717-1B4, a commonly used model clone in tree biotechnology research, and hpCAD tetraploids were generated and grown in the greenhouse. In parallel, WT tetraploid poplars were grown in the field. In contrast to Arabidopsis, a whole genome duplication of poplar had a negative impact on the biomass yield of both greenhouse- and field-grown trees. Strikingly, field-grown WT tetraploids developed a brittle apex phenotype, i.e., their tip broke off just below the apex. In addition, the chromosome doubling altered the biomass composition of field-grown, but not of greenhouse-grown tetraploid poplars. More specifically, the lignin content of field-grown tetraploid poplars was increased at the expense of matrix polysaccharides. This increase in lignin deposition in biomass is likely the cause of the observed brittle apex phenotype, though no major differences in stem anatomy or in mechanical properties could be found between di- and tetraploid WT poplars grown in the field. Finally, without biomass pretreatment, the saccharification efficiency of greenhouse- and field-grown WT diploids was not different from that of tetraploids, whereas that of greenhouse-grown hpCAD tetraploids was higher than that of greenhouse-grown diploids. Upon alkaline pretreatment, the saccharification yield of diploids was similar to that of tetraploids for all genotypes and growth conditions tested. This study showed that a whole genome duplication in hybrid WT and hpCAD poplar did neither result in further improvements in biomass yield, nor in improved biomass composition and, hence, saccharification performance.

H-lignin can be deposited independently of CINNAMYL ALCOHOL DEHYDROGENASE C and D in Arabidopsis

Lignin contributes substantially to the recalcitrance of biomass toward saccharification. To circumvent this problem, researchers have genetically altered lignin, although, in a number of cases, these efforts have resulted in an undesirable yield penalty. Recent findings have shown that by knocking out two subunits (MED5A and MED5B) of the transcriptional regulatory complex Mediator, the stunted growth phenotype of mutants in p-coumaroyl shikimate 3'-hydroxylase, reduced epidermal fluorescence 8-1 (ref8-1), can be alleviated. Furthermore, these plants synthesize a lignin polymer almost entirely derived from p-coumaryl alcohol. Plants deficient in cinnamyl alcohol dehydrogenase (CAD) are notable in that they primarily incorporate coniferaldehyde and sinapaldehyde into their lignin. We tested the hypothesis that by stacking mutations in the genes encoding for the CAD paralogs C and D on an Arabidopsis (Arabidopsis thaliana) med5a/5b ref8-1 genetic background, the biosynthesis of p-coumaryl alcohol would be blocked, making p-coumaraldehyde available for polymerization into a novel kind of lignin. The med5a/5b ref8-1 cadc cadd plants are viable, but lignin analysis demonstrated that they continue to synthesize p-hydroxyphenyl lignin despite being mutated for the CADs typically considered to be required for monolignol biosynthesis. In addition, enzyme activity tests showed that even in the absence of CADC and CADD, there is high CAD activity in stems. We tested the potential involvement of other CADs in p-coumaraldehyde biosynthesis in the quintuple mutant by mutating them using the CRISPR/Cas9 system. Lignin analysis demonstrated that the resulting hextuple mutant plants continue to deposit p-coumaryl alcohol-derived lignin, demonstrating a route for the synthesis of p-hydroxyphenyl lignin in Arabidopsis independent of four CAD isoforms.

Transcriptome and metabolite profiling to identify genes associated with rhizome lignification and the function of ZoCSE in ginger (Zingiber officinale)

Ginger (Zingiber officinale Roscoe) is an important spice crop in China, and fresh ginger rhizomes are consumed as vegetable in Sichuan and Chongqing. However, tissue lignification accelerates with rhizome maturation, resulting in the loss of edible quality. To understand the molecular mechanisms of texture modification during rhizome development, we investigated lignin accumulation patterns and identified the key genes associated with lignin biosynthesis using gas chromatography-mass spectrometry (GC-MS), liquid chromatography-tandem mass spectrometry (LC-MS/MS) and RNA-sequencing (RNA-Seq). Results showed that the contents of total lignin and its precursors exhibited notable declines with tissue maturation. However, the lignin composition was remarkably modified and syringyl lignin was deposited in mature rhizomes, leading to ginger lignification. Transcriptome analysis displayed 32 lignin biosynthetic genes were dramatically downregulated with rhizome development, including caffeoylshikimate esterase (CSE ), 4-coumarate-CoA ligase , laccase , cinnamoyl-CoA reductase , cinnamyl-alcohol dehydrogenase , peroxidase and caffeic acid 3-O-methyltransferase , indicating that lignin reduction might be attributed to deficiency in intermediates or the downregulation of key biosynthetic enzymes. Furthermore, overexpressing ZoCSE in Nicotiana benthamiana L. enhanced the total lignin content, suggesting its fundamental role in lignin biosynthesis. RNA-Seq also identified candidate lignin production regulators, including hormone-related genes and NAC/MYB transcription factors (ZoNAC1 , ZoNAC4 , ZoMYB14 and ZoMYB17 ). This result provides a molecular basis for lignin accumulation in ginger.

Structural elucidation and targeted valorization of poplar lignin from the synergistic hydrothermal-deep eutectic solvent pretreatment

Elucidating the structural variations of lignin during the pretreatment is very important for lignin valorization. Herein, poplar wood was pretreated with an integrated process, which was composed of AlCl₃-catalyzed hydrothermal pretreatment (HTP, 130-150 °C, 1.0 h) and mild deep-eutectic solvents (DES, 100 °C, 10 min) delignification for recycling lignin fractions. Confocal Raman Microscopy (CRM) was developed to visually monitor the delignification process during the HTP-DES pretreatment. NMR characterizations (2D-HSQC and ³¹P NMR) and elemental analysis demonstrated that the lignin fractions had undergone the following structural changes, such as dehydration, depolymerization, condensation. Molecular weights (GPC), microstructure (SEM and TEM), and antioxidant activity (DPPH analysis) of the lignins revealed that the DES delignification resulted in homogeneous lignin fragments (1.32 < PDI < 1.58) and facilitated the rapid assemblage of lignin nanoparticles (LNPs) with controllable nanoscale sizes (30-210 nm) and excellent antioxidant activity. These findings will enhance the understanding of structural transformations of the lignin during the integrated process and maximize the lignin valorization in a current biorefinery process.

Dissolved xylan inhibits cellulosome-based saccharification by binding to the key cellulosomal component of Clostridium thermocellum

Polysaccharides derived from lignocellulose are promising sustainable carbon sources. Cellulosome is a supramolecular machine integrating multi-function enzymes for effective lignocellulose bio-saccharification. However, how various non-cellulose components of lignocellulose affect the cellulosomal saccharification is hitherto unclear. This study first investigated the stability and oxygen sensitivity of the cellulosome from Clostridium thermocellum during long-term saccharification process. Then, the differential inhibitory effects of non-cellulose components, including lignin, xylan, and arabinoxylan, on the cellulosome-based saccharification were determined. The results showed that lignin played inhibitory roles by non-productively adsorbing extracellular proteins of C. thermocellum. Differently, arabinoxylan preferred to bind with the cellulosomal components. Almost no adsorption of cellulosomal proteins on solid xylan was detected. Instead, xylan in water-dissolved form interacted with the cellulosomal proteins, especially the key exoglucanase Cel48S, leading to the xylan inhibitory effect. Compared to xylan, xylooligosaccharides influenced the cellulosome activity slightly. Hence, this work demonstrates that the timely hydrolysis or removal of dissolved xylan is important for cellulosome-based lignocellulose saccharification.

Extraction and Characterization of Cellulose from Agricultural By-Products of Chiang Rai Province, Thailand

Cellulose is an abundant component of the plant biomass in agricultural waste valorization that may be exploited to mitigate the excessive use of synthetic non-biodegradable materials. This work aimed to investigate the cellulose utilized by alkaline extraction with a prior bleaching process from rice straw, corncob, Phulae pineapple leaves, and Phulae pineapple peels. The bleaching and alkaline extraction process was performed using 1.4% acidified sodium chlorite (NaClO2) and 5% potassium hydroxide (KOH) in all the samples. All the samples, without and with the alkaline process, were characterized for their physico-chemical, microstructure, thermal properties and compared to commercial cellulose (COM-C). The extraction yield was the highest in alkaline-extracted cellulose from the corncob (AE-CCC) sample (p < 0.05), compared to the other alkaline-treated samples. The undesired components, including mineral, lignin, and hemicellulose, were lowest in the AE-CCC sample (p < 0.05), compared to raw and alkaline-treated samples. The microstructure displayed the flaky AE-CCC structure that showed a similar visibility in terms of morphology with that of the alkaline-treated pineapple peel cellulose (AE-PPC) and COM-C samples compared to other alkaline-treated samples with a fibrous structure. Fourier Transform Infrared (FTIR) and X-ray Diffraction (XRD) of AE-CCC samples showed the lowest amorphous regions, possibly due to the elimination of hemicellulose and lignin during bleaching and alkaline treatment. The highest crystallinity index obtained in the AE-CCC sample showed a close resemblance with the COM-C sample. Additionally, the AE-CCC sample showed the highest thermal stability, as evidenced by its higher Tonset (334.64 °C), and Tmax (364.67 °C) compared to the COM-C and alkaline-treated samples. Therefore, agricultural wastes after harvesting in the Chiang Rai province of Thailand may be subjected to an alkaline process with a prior bleaching process to yield a higher cellulose content that is free of impurities. Thus, the extracted cellulose could be used as an efficient, eco-friendly, and biodegradable material for packaging applications.

Fluorescence Microscopy Methods for the Analysis and Characterization of Lignin

Lignin is one of the most studied and analyzed materials due to its importance in cell structure and in lignocellulosic biomass. Because lignin exhibits autofluorescence, methods have been developed that allow it to be analyzed and characterized directly in plant tissue and in samples of lignocellulose fibers. Compared to destructive and costly analytical techniques, fluorescence microscopy presents suitable alternatives for the analysis of lignin autofluorescence. Therefore, this review article analyzes the different methods that exist and that have focused specifically on the study of lignin because with the revised methods, lignin is characterized efficiently and in a short time. The existing qualitative methods are Epifluorescence and Confocal Laser Scanning Microscopy; however, other semi-qualitative methods have been developed that allow fluorescence measurements and to quantify the differences in the structural composition of lignin. The methods are fluorescence lifetime spectroscopy, two-photon microscopy, Föster resonance energy transfer, fluorescence recovery after photobleaching, total internal reflection fluorescence, and stimulated emission depletion. With these methods, it is possible to analyze the transport and polymerization of lignin monomers, distribution of lignin of the syringyl or guaiacyl type in the tissues of various plant species, and changes in the degradation of wood by pulping and biopulping treatments as well as identify the purity of cellulose nanofibers though lignocellulosic biomass.

Current understanding and optimization strategies for efficient lignin-enzyme interaction: A review

From energy perspective, with abundant polysaccharides (45-85%), the renewable lignocellulosic is recognized as the 2nd generation feedstock for bioethanol and bio-based products production. Enzymatic hydrolysis is a critical pathway to yield fermentable monosaccharides from pretreated substrates of lignocellulose. Nevertheless, the lignin presence in lignocellulosic substrates leads to the low substrate enzymatic digestibility ascribed to the nonproductive adsorption. It has been reported that the water-soluble lignin (low molecular weight, sulfonated/sulfomethylated and graft polymer) enhance the rate of enzymatic digestibility, however, the catalytic mechanism of lignin-enzyme interaction remains elusive. In this review, optimization strategies for enzymatic hydrolysis based on the lignin structural modification, enzyme engineering, and different additives are critically reviewed. Lignin-enzyme interaction mechanism is also discussed (lignin and various cellulases). In addition, the mathematical models and simulation of lignin, cellulose and enzyme aims for promoting an integrated biomass-conversion process for sustainable production of value-added biofuels.

Degradation of lignin by Bacillus altitudinis SL7 isolated from pulp and paper mill effluent

Lignin is a major by-product of pulp and paper industries, and is resistant to depolymerization due to its heterogeneous structure. Degradation of lignin can be achieved by the use of potential lignin-degrading bacteria. The current study was designed to evaluate the degradation efficiency of newly isolated Bacillus altitudinis SL7 from pulp and paper mill effluent. The degradation efficiency of B. altitudinis SL7 was determined by color reduction, lignin content, and ligninolytic activity from degradation medium supplemented with alkali lignin (3 g/L). B. altitudinis SL7 reduced color and lignin content by 26 and 44%, respectively, on the 5th day of incubation, as evident from the maximum laccase activity. Optimum degradation was observed at 40 °C and pH 8.0. FT-IR spectroscopy and GC-MS analysis confirmed lignin degradation by emergence of the new peaks and identification of low-molecular-weight compounds in treated samples. The identified compounds such as vanillin, 2-methyoxyhenol, 3-methyl phenol, oxalic acid and ferulic acid suggested the degradation of coniferyl and sinapyl groups of lignin. Degradation efficiency of B. altitudinis SL7 towards high lignin concentration under alkaline pH indicated the potential application of this isolate in biological treatment of the lignin-containing effluents.

Algae biorefinery: a promising approach to promote microalgae industry and waste utilization

Microalgae have a number of intriguing characteristics that make them a viable raw material aimed at usage in a variety of applications when refined using a bio-refining process. They offer unique capabilities that allow them to be used in biotechnology-related applications. As a result, this review explores how to increase the extent to which microalgae may be integrated with various additional biorefinery uses in order to improve their maintainability. In this study, the use of microalgae as potential animal feed, manure, medicinal, cosmeceutical, ecological, and other biotechnological uses is examined in its entirety. It also includes information on the boundaries, openings, and improvements of microalgae and the possibilities of increasing the range of microalgae through techno-economic analysis. According to the findings of this review, financing supported research and shifting the focus of microalgal investigations from biofuels production to biorefinery co-products can help guarantee that they remain a viable resource. Furthermore, innovation collaboration is unavoidable if one wishes to avoid the high cost of microalgae biomass handling. This review is expected to be useful in identifying the possible role of microalgae in biorefinery applications in the future.

Biological Activities and Emerging Roles of Lignin and Lignin-Based Products─A Review

Bioactive substances, displaying excellent biocompatibility, chemical stability, and processability, could be extensively applied in biomedicine and tissue engineering. In recent years, plant-based bioactive substances such as flavonoids, vitamins, terpenes, and lignin have received considerable attention due to their human health benefits and pharmaceutical/medical applications. Among them is lignin, an amorphous biomacromolecule mainly derived from the combinatorial radical coupling of three phenylpropane units (p-hydroxypenyl, guaiacyl, and syringyl) during lignification. Lignin possesses intrinsic bioactivities (antioxidative, antibacterial, anti-UV activities, etc.) against phytopathogens. Lignin also enhances the plant resistance (adaptability) against environmental stresses. The abundant structural features of lignin offer other significant bioactivities including antitumor and antivirus bioactivities, regulation of plant growth, and enzymatic hydrolysis of cellulose. This Review reports the latest research results on the bioactive potential of lignin and lignin-based substances in biomedicine, agriculture, and biomass conversion. Moreover, the interfacial reactions and bonding mechanisms of lignin with biotissue/cells and other constituents were also discussed, aiming at promoting the conversion or evolution of lignin from industrial wastes to value-added bioactive materials.

Short-time deep eutectic solvents pretreatment enhanced production of fermentable sugars and tailored lignin nanoparticles from abaca

Deep eutectic solvents (DES) pretreatment is a promising approach to decrease "biomass recalcitrance" and boost the cellulose bioconversion as well as lignin valorization. In this study, a short-time DES pretreatment strategy was performed to enhance the production of high-yield fermentable sugars and tailored lignin nanoparticles (LNPs) from abaca. The glucose yield reached 92.4% under the optimal pretreatment condition (110 °C, 30 min), which was dramatically increased in comparison with that (9.5%) of control abaca. Simultaneously, nuclear magnetic resonance (NMR) and gel permeation chromatography (GPC) techniques indicated that the removed and regenerated DES lignin fractions displayed depolymerized structures and have relatively low molecular weight with relatively homogeneous morphology and narrow size distribution. Transmission electron microscope (TEM) analysis indicated that these lignin fractions are LNPs and the size of the optimal LNPs fraction is ranged from 30 nm to 50 nm. Moreover, all the DES lignin exhibited excellent antioxidant activities as compared to the commercial antioxidant butylated hydroxytoluene (BHT), which can be used as a promising natural antioxidant in industry. In short, this study demonstrated that the short-time DES pretreatment will improve the enzymatic digestibility and facilitate the controllable production and valorization of LNPs from abaca biomass, which will further promote the economic and overall benefits of biorefinery.

Comparative Analysis of Herbaceous and Woody Cell Wall Digestibility by Pathogenic Fungi

Fungal pathogens have evolved combinations of plant cell-wall-degrading enzymes (PCWDEs) to deconstruct host plant cell walls (PCWs). An understanding of this process is hoped to create a basis for improving plant biomass conversion efficiency into sustainable biofuels and bioproducts. Here, an approach integrating enzyme activity assay, biomass pretreatment, field emission scanning electron microscopy (FESEM), and genomic analysis of PCWDEs were applied to examine digestibility or degradability of selected woody and herbaceous biomass by pathogenic fungi. Preferred hydrolysis of apple tree branch, rapeseed straw, or wheat straw were observed by the apple-tree-specific pathogen Valsa mali, the rapeseed pathogen Sclerotinia sclerotiorum, and the wheat pathogen Rhizoctonia cerealis, respectively. Delignification by peracetic acid (PAA) pretreatment increased PCW digestibility, and the increase was generally more profound with non-host than host PCW substrates. Hemicellulase pretreatment slightly reduced or had no effect on hemicellulose content in the PCW substrates tested; however, the pretreatment significantly changed hydrolytic preferences of the selected pathogens, indicating a role of hemicellulose branching in PCW digestibility. Cellulose organization appears to also impact digestibility of host PCWs, as reflected by differences in cellulose microfibril organization in woody and herbaceous PCWs and variation in cellulose-binding domain organization in cellulases of pathogenic fungi, which is known to influence enzyme access to cellulose. Taken together, this study highlighted the importance of chemical structure of both hemicelluloses and cellulose in host PCW digestibility by fungal pathogens.

Lignin-to-chemicals: Application of catalytic hydrogenolysis of lignin to produce phenols and terephthalic acid via metal-based catalysts

Lignin is the only renewable aromatic material in nature and contains a large number of oxygen-containing functional groups. High-value and green utilization of "lignin-to-chemicals" can be realized via using lignin to produce fine chemicals such as phenols and carboxylic acids, which can not only reduce the waste of lignin in the process of lignocellulosic biomass treatment, but gradually make the substitution of traditional fossil fuels come true. The hydrogenolysis process under catalysis of metal catalyst has high product selectivity and less impurity, which is suitable for the production of same type or single fine chemicals. Hydrogenolysis of lignin via metal catalysts to produce lignin oil, and further modification of functional groups (e.g. methoxyl, alkyl and hydroxyl group) of depolymerized monomers in the bio-oil to yeild phenols and terephthalic acid are reviewed, and catalytic mechanisms are briefly summarized in this paper. Finally, the problems of lignin catalytic conversion existing currently are investigated, and the future development of this field is also prospected.

Net Energy Analysis and Techno-Economic Assessment of Co-Production of Bioethanol and Biogas from Cellulosic Biomass

Co-production is a process based on the biorefinery concept that maximizes the benefit of biomass by reusing residue from the production of one product to produce others. In this regard, biogas is one of the most researched second products for the production of ethanol from cellulosic biomass. However, operating this scheme requires additional investment in biogas processing equipment. This review compiles data from research studies on the co-production of bioethanol and biogas from lignocellulosic biomass to determine which is more worthwhile: leaving the residue or investing more to benefit from the second product. According to previous research, ethanol stillage can be converted to biogas via anaerobic digestion, increasing energy output by 2–3 fold. Techno-economic studies demonstrated that the co-production process reduces the minimum ethanol selling price to a level close to the market price of ethanol, implying the possibility of industrializing cellulosic ethanol production through this scheme.

Microbial valorization of underutilized and nonconventional waste streams

The growing burden of waste disposal coupled with natural resource scarcity has renewed interest in the remediation, valorization, and/or repurposing of waste. Traditional approaches such as composting, anaerobic digestion, use in fertilizers or animal feed, or incineration for energy production extract very little value out of these waste streams. In contrast, waste valorization into fuels and other biochemicals via microbial fermentation is an area of growing interest. In this review, we discuss microbial valorization of nonconventional, aqueous waste streams such as food processing effluents, wastewater streams, and other industrial wastes. We categorize these waste streams as carbohydrate-rich food wastes, lipid-rich wastes, and other industrial wastes. Recent advances in microbial valorization of these nonconventional waste streams are highlighted, along with a discussion of the specific challenges and opportunities associated with impurities, nitrogen content, toxicity, and low productivity.

CRISPR-Knockout of CSE Gene Improves Saccharification Efficiency by Reducing Lignin Content in Hybrid Poplar

Caffeoyl shikimate esterase (CSE) has been shown to play an important role in lignin biosynthesis in plants and is, therefore, a promising target for generating improved lignocellulosic biomass crops for sustainable biofuel production. Populus spp. has two CSE genes (CSE1 and CSE2) and, thus, the hybrid poplar (Populus alba × P. glandulosa) investigated in this study has four CSE genes. Here, we present transgenic hybrid poplars with knockouts of each CSE gene achieved by CRISPR/Cas9. To knockout the CSE genes of the hybrid poplar, we designed three single guide RNAs (sg1-sg3), and produced three different transgenic poplars with either CSE1 (CSE1-sg2), CSE2 (CSE2-sg3), or both genes (CSE1/2-sg1) mutated. CSE1-sg2 and CSE2-sg3 poplars showed up to 29.1% reduction in lignin deposition with irregularly shaped xylem vessels. However, CSE1-sg2 and CSE2-sg3 poplars were morphologically indistinguishable from WT and showed no significant differences in growth in a long-term living modified organism (LMO) field-test covering four seasons. Gene expression analysis revealed that many lignin biosynthetic genes were downregulated in CSE1-sg2 and CSE2-sg3 poplars. Indeed, the CSE1-sg2 and CSE2-sg3 poplars had up to 25% higher saccharification efficiency than the WT control. Our results demonstrate that precise editing of CSE by CRISPR/Cas9 technology can improve lignocellulosic biomass without a growth penalty.

Biorefinery Concept Employing Bacillus coagulans: LX-Lignin and L-(+)-Lactic Acid from Lignocellulose

A new biorefinery concept is proposed that integrates the novel LX-Pretreatment with the fermentative production of L-(+)-lactic acid. Lignocellulose was chosen as a substrate that does not compete with the provision of food or feed. Furthermore, it contains lignin, a promising new chemical building material which is the largest renewable source for aromatic compounds. Two substrates were investigated: rye straw (RS) as a residue from agriculture, as well as the fibrous digestate of an anaerobic biogas plant operated with energy corn (DCS). Besides the prior production of biogas from energy corn, chemically exploitable LX-Lignin was produced from both sources, creating a product with a low carbohydrate and ash content (90.3% and 88.2% of acid insoluble lignin). Regarding the cellulose fraction of the biomass, enzymatic hydrolysis and fermentation experiments were conducted, comparing a separate (SHF), simultaneous (SSF) and prehydrolyzed simultaneous saccharification and fermentation (PSSF) approach. For this purpose, thermophilic B. coagulans 14-300 was utilized, reaching 38.0 g L⁻¹ LA in 32 h SSF from pretreated RS and 18.3 g L⁻¹ LA in 30 h PSSF from pretreated DCS with optical purities of 99%.

Interdependence between lignocellulosic biomasses, enzymatic hydrolysis and yeast cell factories in biorefineries

Biorefineries have a pivotal role in the bioeconomy scenario for the transition from fossil‐based processes towards more sustainable ones relying on renewable resources. Lignocellulose is a prominent feedstock since its abundance and relatively low cost. Microorganisms are often protagonists of biorefineries, as they contribute both to the enzymatic degradation of lignocellulose complex polymers and to the fermentative conversion of the hydrolyzed biomasses into fine and bulk chemicals. Enzymes have therefore become crucial for the development of sustainable biorefineries, being able to provide nutrients to cells from lignocellulose. Enzymatic hydrolysis can be performed by a portfolio of natural enzymes that degrade lignocellulose, often combined into cocktails. As enzymes can be deployed in different operative settings, such as separate hydrolysis and fermentation (SHF) or simultaneous saccharification and fermentation (SSF), their characteristics need to be combined with microbial ones to maximize the process. We therefore reviewed how the optimization of lignocellulose enzymatic hydrolysis can ameliorate bioethanol production when Saccharomyces cerevisiae is used as cell factory. Expanding beyond biofuels, enzymatic cocktail optimization can also be pivotal to unlock the potential of non‐Saccharomyces yeasts, which, thanks to broader substrate utilization, inhibitor resistance and peculiar metabolism, can widen the array of feedstocks and products of biorefineries.

Growth-defense trade-offs and yield loss in plants with engineered cell walls

As a major component of plant secondary cell walls, lignin provides structural integrity and rigidity, and contributes to primary defense by providing a physical barrier to pathogen ingress. Genetic modification of lignin biosynthesis has been adopted to reduce the recalcitrance of lignified cell walls to improve biofuel production, tree pulping properties and forage digestibility. However, lignin-modification is often, but unpredictably, associated with dwarf phenotypes. Hypotheses suggested to explain this include: collapsed vessels leading to defects in water and solute transport; accumulation of molecule(s) that are inhibitory to plant growth or deficiency of metabolites that are critical for plant growth; activation of defense pathways linked to cell wall integrity sensing. However, there is still no commonly accepted underlying mechanism for the growth defects. Here, we discuss recent data on transcriptional reprogramming in plants with modified lignin content and their corresponding suppressor mutants, and evaluate growth-defense trade-offs as a factor underlying the growth phenotypes. New approaches will be necessary to estimate how gross changes in transcriptional reprogramming may quantitatively affect growth. Better understanding of the basis for yield drag following cell wall engineering is important for the biotechnological exploitation of plants as factories for fuels and chemicals.

Integrated NIRS and QTL assays reveal minor mannose and galactose as contrast lignocellulose factors for biomass enzymatic saccharification in rice

BACKGROUND

Identifying lignocellulose recalcitrant factors and exploring their genetic properties are essential for enhanced biomass enzymatic saccharification in bioenergy crops. Despite genetic modification of major wall polymers has been implemented for reduced recalcitrance in engineered crops, it could most cause a penalty of plant growth and biomass yield. Alternatively, it is increasingly considered to improve minor wall components, but an applicable approach is required for efficient assay of large population of biomass samples. Hence, this study collected total of 100 rice straw samples and characterized all minor wall monosaccharides and biomass enzymatic saccharification by integrating NIRS modeling and QTL profiling.

RESULTS

By performing classic chemical analyses and establishing optimal NIRS equations, this study examined four minor wall monosaccharides and major wall polymers (acid-soluble lignin/ASL, acid-insoluble lignin/AIL, three lignin monomers, crystalline cellulose), which led to largely varied hexoses yields achieved from enzymatic hydrolyses after two alkali pretreatments were conducted with large population of rice straws. Correlation analyses indicated that mannose and galactose can play a contrast role for biomass enzymatic saccharification at P < 0.0 l level (n = 100). Meanwhile, we found that the QTLs controlling mannose, galactose, lignin-related traits, and biomass saccharification were co-located. By combining NIRS assay with QTLs maps, this study further interpreted that the mannose-rich hemicellulose may assist AIL disassociation for enhanced biomass enzymatic saccharification, whereas the galactose-rich polysaccharides should be effectively extracted with ASL from the alkali pretreatment for condensed AIL association with cellulose microfibrils.

CONCLUSIONS

By integrating NIRS assay with QTL profiling for large population of rice straw samples, this study has identified that the mannose content of wall polysaccharides could positively affect biomass enzymatic saccharification, while the galactose had a significantly negative impact. It has also sorted out that two minor monosaccharides could distinctively associate with lignin deposition for wall network construction. Hence, this study demonstrates an applicable approach for fast assessments of minor lignocellulose recalcitrant factors and biomass enzymatic saccharification in rice, providing a potential strategy for bioenergy crop breeding and biomass processing.

Selective delignification of poplar wood with a newly isolated white-rot basidiomycete Peniophora incarnata T-7 by submerged fermentation to enhance saccharification

BACKGROUND

Pretreatment is a critical step required for efficient conversion of woody biomass into biofuels and platform chemicals. Fungal pretreatment is regarded as one of the most promising technology for woody biomass conversion but remains challenging for industrial application. The exploration of potential fungus strain with high efficient delignification and less processing time for woody biomass pretreatment will be valuable for development of biorefinery industry. Here, a newly isolated white-rot basidiomycete Peniophora incarnate T-7 was employed for poplar wood pretreatment.

RESULTS

The chemical component analysis showed that cellulose, hemicellulose and lignin from poplar wood declined by 16%, 48% and 70%, respectively, after 7 days submerged fermentation by P. incarnate T-7. Enzymatic saccharification analysis revealed that the maximum yields of glucose and xylose from 7 days of P. incarnate T-7 treated poplar wood reached 33.4% and 27.6%, respectively, both of which were enhanced by sevenfold relative to the untreated group. Fourier transform infrared spectroscopy (FTIR), scanning electron microscope (SEM), X-ray diffraction (XRD) and pyrolysis gas chromatography-mass spectrometry (Py-GC/MS) characterization confirmed that lignocellulosic structure of poplar wood was largely broken by P. incarnate T-7, including delignification and de-crystalline of cellulose. Meanwhile, lignin component of poplar wood was selectively degraded by P. incarnate T-7, and G-type unit of lignin was preferentially attacked by the strain. Furthermore, quantitative proteomic analysis revealed that a considerable amount of lignocellulolytic enzymes were detected in the secretory proteins of P. incarnate T-7, especially with high abundance of lignin-degrading enzymes and hemicellulases. Combination of quantitative proteomic with transcriptomic analysis results showed that most of those lignocellulolytic enzymes were highly upregulated on poplar wood substrate compared to glucose substrate.

CONCLUSIONS

This study showed that P. incarnate T-7 could selectively delignify poplar wood by submerged fermentation with short time of 7 days, which greatly improved its enzymatic saccharification efficiency. Our results suggested that P. incarnate T-7 might be a promising candidate for industrial woody biomass pretreatment.

Coffee cell walls—composition, influence on cup quality and opportunities for coffee improvements

The coffee beverage is the second most consumed drink worldwide after water. In coffee beans, cell wall storage polysaccharides (CWSPs) represent around 50 per cent of the seed dry mass, mainly consisting of galactomannans and arabinogalactans. These highly abundant structural components largely influence the organoleptic properties of the coffee beverage, mainly due to the complex changes they undergo during the roasting process. From a nutritional point of view, coffee CWSPs are soluble dietary fibers shown to provide numerous health benefits in reducing the risk of human diseases. Due to their influence on coffee quality and their health-promoting benefits, CWSPs have been attracting significant research attention. The importance of cell walls to the coffee industry is not restricted to beans used for beverage production, as several coffee by-products also present high concentrations of cell wall components. These by-products include cherry husks, cherry pulps, parchment skin, silver skin, and spent coffee grounds, which are currently used or have the potential to be utilized either as food ingredients or additives, or for the generation of downstream products such as enzymes, pharmaceuticals, and bioethanol. In addition to their functions during plant development, cell walls also play a role in the plant’s resistance to stresses. Here, we review several aspects of coffee cell walls, including chemical composition, biosynthesis, their function in coffee’s responses to stresses, and their influence on coffee quality. We also propose some potential cell wall–related biotechnological strategies envisaged for coffee improvements.

Cost-effective production of biocatalysts using inexpensive plant biomass: a review

Enzymes are the complex protein moieties, catalyze the rate of chemical reactions by transforming various substrates to specific products and play an integral part in multiple biochemical cycles. Advancement in enzyme research and its integration with industries have reformed the biotech industries. It provides a superior monetary and ecological exchange to traditional material measures in an efficient and environmentally sustainable manner. The cost-effective production of pure and highly active enzymes is still a challenge for the biocatalyst industries. The use of high purity substrates further raises the cost of a typical biocatalyst. The use of low-cost plant-based biomasses as an enticing and sustainable substrate for enzyme production is the most cost-effective approach to these problems. Given the relevance of biomass as a substrate for enzyme development, this review article focuses on the key source, composition and major enzyme generated using various biomass residues. Furthermore, the difficulties associated with the use of biomass as a substrate and technical developments in this area, are also addressed. The use of waste biomass as a substrate lowers the ultimate cost for the production of biocatalysts while simultaneously reduces the waste burden from the environment.

Targeted plant improvement through genome editing: from laboratory to field

This review illustrates how far we have come since the emergence of GE technologies and how they could be applied to obtain superior and sustainable crop production. The main challenges of today's agriculture are maintaining and raising productivity, reducing its negative impact on the environment, and adapting to climate change. Efficient plant breeding can generate elite varieties that will rapidly replace obsolete ones and address ongoing challenges in an efficient and sustainable manner. Site-specific genome editing in plants is a rapidly evolving field with tangible results. The technology is equipped with a powerful toolbox of molecular scissors to cut DNA at a pre-determined site with different efficiencies for designing an approach that best suits the objectives of each plant breeding strategy. Genome editing (GE) not only revolutionizes plant biology, but provides the means to solve challenges related to plant architecture, food security, nutrient content, adaptation to the environment, resistance to diseases and production of plant-based materials. This review illustrates how far we have come since the emergence of these technologies and how these technologies could be applied to obtain superior, safe and sustainable crop production. Synergies of genome editing with other technological platforms that are gaining significance in plants lead to an exciting new, post-genomic era for plant research and production. In previous months, we have seen what global changes might arise from one new virus, reminding us of what drastic effects such events could have on food production. This demonstrates how important science, technology, and tools are to meet the current time and the future. Plant GE can make a real difference to future sustainable food production to the benefit of both mankind and our environment.

Association of gene expression with syringyl to guaiacyl ratio in sugarcane lignin

A transcriptome analysis reveals the transcripts and alleles differentially expressed in sugarcane genotypes with contrasting lignin composition. Sugarcane bagasse is a highly abundant resource that may be used as a feedstock for the production of biofuels and bioproducts in order to meet increasing demands for renewable replacements for fossil carbon. However, lignin imparts rigidity to the cell wall that impedes the efficient breakdown of the biomass into fermentable sugars. Altering the ratio of the lignin units, syringyl (S) and guaiacyl (G), which comprise the native lignin polymer in sugarcane, may facilitate the processing of bagasse. This study aimed to identify genes and markers associated with S/G ratio in order to accelerate the development of sugarcane bioenergy varieties with modified lignin composition. The transcriptome sequences of 12 sugarcane genotypes that contrasted for S/G ratio were compared and there were 2019 transcripts identified as differentially expressed (DE) between the high and low S/G ratio groups. These included transcripts encoding possible monolignol biosynthetic pathway enzymes, transporters, dirigent proteins and transcriptional and post-translational regulators. Furthermore, the frequencies of single nucleotide polymorphisms (SNPs) were compared between the low and high S/G ratio groups to identify specific alleles expressed with the phenotype. There were 2063 SNP loci across 787 unique transcripts that showed group-specific expression. Overall, the DE transcripts and SNP alleles identified in this study may be valuable for breeding sugarcane varieties with altered S/G ratio that may provide desirable bioenergy traits.