Role of various bacterial enzymes in complete depolymerization of lignin: A review

Paper-based electrodes as a tool for detecting ligninolytic enzymatic activities

Lignin is the most important natural source of aromatic compounds. The valorisation of lignin into aromatics requires fractionation steps that can be catalysed by ligninolytic enzymes. However, one of the main limitations of biological lignin fractionation is the low efficiency of biocatalysts; it is therefore crucial to enhance or to identify new ligninolytic enzymes. Currently, the screening of ligninolytic activities on lignin polymers represents a technological bottenleck and hinders the characterization and the discovery of efficient ligninolytic biocatalysts. An efficient and fast method for the measurement of such enzymatic activities is therefore required. In this work, we present a new electrochemical tool based on lignin-coated paper electrodes for the detection and the characterization of ligninolytic activity. The suitability of this method is demonstrated using a catalase-peroxidase isolated from Thermobacillus xylanilyticus.

Development of functional consortia for the pretreatment of compostable lignocellulosic waste: A simple and effective solution to a large-scale problem

Microorganisms drive the degradation of organic matter thanks to their enzymatic versatility. However, the structure of lignocellulose poses a great challenge for the microbiota inhabiting a compost pile. Our purpose was to increase the biodegradability of vegetable waste in the early stages of the composting process by applying a microbial consortium with lignocelllulolytic capacity. For this, a previous screening was performed among the culturable microbiota from different composting processes to find inoculants with ligninocellulolytic activity. Selected strains were applied as a pure culture and as a microbial consortium. The starting material was composed of tomato plant and pruning remains mixed in a ratio (50:50 v/v), whose humidity was adjusted to around 65%. To determine the ability of both treatments to activate the biodegradation of the mixtures, moisture, organic matter, ash, C/N ratio, 4-day cumulative respirometric index (AT4) and degradation rates of cellulose, hemicellulose and lignin were evaluated. Subsequently, a real composting process was developed in which the performance of the microbial consortium was compared with the composting process without inoculum (control). According to our tests, three microbial strains (Bacillus safensis, Bacillus licheniformis and Fusarium oxysporum) were selected. The results showed that the application of the bacteria strains at low doses (104 CFU g-1 on the complete residual material of the pile) resulted in higher rates of lignocelullose degradation after 10 days of treatment compared to that observed after application of the fungus in pure culture or untreated controls. The implementation of the strategy described in this work resulted in obtaining compost with better agronomic quality than the uninoculated controls. Therefore, the application of this consortium could be considered as an interesting tool for bioactivation of lignocellulosic waste prior to the composting process.

pH-dependent and whole-cell catalytic decolorization of dyes using recombinant dye-decolorizing peroxidase from Rhodococcus jostii

Dyes in wastewater have adverse effects on the environment and human health. Dye-decolorizing peroxidase (DyP) is a promising biocatalyst to dyes degradation, but the decolorization rates varied greatly which influencing factors and mechanisms remain to be fully disclosed. To explore an effective decolorizing approach, we have studied a DyP from Rhodococcus jostii (RhDyPB) which was overexpressed in Escherichia coli to decolorize four kinds of dyes, Reactive blue 19, Eosin Y, Indigo carmine, and Malachite green. We found the decolorization rates of the dyes by purified RhDyPB were all pH-dependent and the highest one was 94.4% of Malachite green at pH 6.0. ESI-MS analysis of intermediates in the decolorization process of Reactive blue 19 proved the degradation was due to peroxidase catalysis. Molecular docking predicated the interaction of RhDyPB with dyes, and a radical transfer reaction. In addition, we performed decolorization of dyes with whole E. coli cell with and without expressing RhDyPB. It was found that decolorization of dyes by E. coli cell was due to both cell absorption and degradation, and RhDyPB expression improved the degradation rates towards Reactive blue 19, Indigo carmine and Malachite green. The effective decolorization of Malachite green and the successful application of whole DyP-overexpressed cells in dye decolorization is conducive to the bioremediation of dye-containing wastewaters by DyPs.

Lignin bioconversion based on genome mining for ligninolytic genes in Erwinia billingiae QL-Z3

BACKGROUND

Bioconversion of plant biomass into biofuels and bio-products produces large amounts of lignin. The aromatic biopolymers need to be degraded before being converted into value-added bio-products. Microbes can be environment-friendly and efficiently degrade lignin. Compared to fungi, bacteria have some advantages in lignin degradation, including broad tolerance to pH, temperature, and oxygen and the toolkit for genetic manipulation.

RESULTS

Our previous study isolated a novel ligninolytic bacterial strain Erwinia billingiae QL-Z3. Under optimized conditions, its rate of lignin degradation was 25.24% at 1.5 g/L lignin as the sole carbon source. Whole genome sequencing revealed 4556 genes in the genome of QL-Z3. Among 4428 protein-coding genes are 139 CAZyme genes, including 54 glycoside hydrolase (GH) and 16 auxiliary activity (AA) genes. In addition, 74 genes encoding extracellular enzymes are potentially involved in lignin degradation. Real-time PCR quantification demonstrated that the expression of potential ligninolytic genes were significantly induced by lignin. 8 knock-out mutants and complementary strains were constructed. Disruption of the gene for ELAC_205 (laccase) as well as EDYP_48 (Dyp-type peroxidase), ESOD_1236 (superoxide dismutase), EDIO_858 (dioxygenase), EMON_3330 (monooxygenase), or EMCAT_3587 (manganese catalase) significantly reduced the lignin-degrading activity of QL-Z3 by 47-69%. Heterologously expressed and purified enzymes further confirmed their role in lignin degradation. Fourier transform infrared spectroscopy (FTIR) results indicated that the lignin structure was damaged, the benzene ring structure and groups of macromolecules were opened, and the chemical bond was broken under the action of six enzymes encoded by genes. The abundant enzymatic metabolic products by EDYP_48, ELAC_205 and ESOD_1236 were systematically analyzed via liquid chromatography-mass spectrometry (LC-MS) analysis, and then provide a speculative pathway for lignin biodegradation. Finally, The activities of ligninolytic enzymes from fermentation supernatant, namely, LiP, MnP and Lac were 367.50 U/L, 839.50 U/L, and 219.00 U/L by orthogonal optimization.

CONCLUSIONS

Our findings provide that QL-Z3 and its enzymes have the potential for industrial application and hold great promise for the bioconversion of lignin into bioproducts in lignin valorization.

Bacterial transformation of lignin: key enzymes and high-value products

Lignin, a natural organic polymer that is recyclable and inexpensive, serves as one of the most abundant green resources in nature. With the increasing consumption of fossil fuels and the deterioration of the environment, the development and utilization of renewable resources have attracted considerable attention. Therefore, the effective and comprehensive utilization of lignin has become an important global research topic, with the goal of environmental protection and economic development. This review focused on the bacteria and enzymes that can bio-transform lignin, focusing on the main ways that lignin can be utilized to produce high-value chemical products. Bacillus has demonstrated the most prominent effect on lignin degradation, with 89% lignin degradation by Bacillus cereus. Furthermore, several bacterial enzymes were discussed that can act on lignin, with the main enzymes consisting of dye-decolorizing peroxidases and laccase. Finally, low-molecular-weight lignin compounds were converted into value-added products through specific reaction pathways. These bacteria and enzymes may become potential candidates for efficient lignin degradation in the future, providing a method for lignin high-value conversion. In addition, the bacterial metabolic pathways convert lignin-derived aromatics into intermediates through the "biological funnel", achieving the biosynthesis of value-added products. The utilization of this "biological funnel" of aromatic compounds may address the heterogeneous issue of the aromatic products obtained via lignin depolymerization. This may also simplify the separation of downstream target products and provide avenues for the commercial application of lignin conversion into high-value products.

Laccase and dye-decolorizing peroxidase-modified lignin incorporated with keratin-based biodegradable film: An elucidation of structural characterization, antibacterial and antioxidant properties

Lignin valorization to produce functionalized materials is challenging. This study harnessed the versatile properties of lignin through a grafting reaction involving the aryl hydroxyl group of alkali lignin (AL) and enzymatically modified-alkali lignin (EMAL) using Bacillus ligninphilus-derived laccase (Lacc) L1 and C. seriivinvornas-derived dye-decolorizing peroxidase (DyP) with keratin (K) amide group. This reaction was executed utilizing an eco-friendly solvent with the aim of generating thin films. A thorough investigation was conducted, focusing on grafting AL and EMAL onto K. The incorporation of EMAL into the films enhanced tensile strength (TS) (14.8±1.8 MPa) and elongation at break (EAB) (23.7±0.3 %). Additionally, it enhanced thermal stability, suppressed the proliferation of Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli), and mitigated oxidative stress. This study introduces a novel approach for lignin valorization, offering the potential to tailor mechanical properties, antibacterial and antioxidant properties of the final material, making it sustainable substitute for petroleum-based products.

Effects of adding corn steep liquor on bacterial community composition and carbon and nitrogen transformation during spent mushroom substrate composting

BACKGROUND

Carbon and nitrogen are essential energy and nutrient substances in the composting process. Corn steep liquor (CSL) is rich in soluble carbon and nitrogen nutrients and active substances and is widely used in the biological industry. Nonetheless, limited research has been done on the effect of CSL on composting. This work firstly reveals the effect of adding CSL to bacterial community composition and carbon and nitrogen conversion during composting. This study provides the choice of auxiliary materials for the spent mushroom substrate compost (SMS) and some novel knowledge about the effect of bacterial community on C and N cycling during composting of SMS and CSL. Two treatments were set up in the experiment: 100% spent mushroom substrate (SMS) as CK and SMS + 0.5% CSL (v/v) as CP.

RESULTS

The results showed that the addition of CSL enhanced the initial carbon and nitrogen content of the compost, altered the bacterial community structure, and increased the bacterial diversity and relative abundance, which might be beneficial to the conversion and retention of carbon and nitrogen in the composting process. In this paper, network analysis was used to screen the core bacteria involved in carbon and nitrogen conversion. In the CP network, the core bacteria were divided into two categories, synthesizing and degrading bacteria, and there were more synthesizing bacteria than degrading bacteria, so the degradation and synthesis of organic matter were carried out simultaneously, while only degrading bacteria were found in the CK network. Functional prediction by Faprotax identified 53 groups of functional bacteria, among which 20 (76.68% abundance) and 14 (13.15% abundance) groups of functional bacteria were related to carbon and nitrogen conversion, respectively. Adding CSL stimulated the compensatory effect of core and functional bacteria, enhanced the carbon and nitrogen transformation ability, stimulated the activity of low-abundance bacteria, and reduced the competitive relationship between the bacterial groups. This may be why the addition of CSL accelerated the organic matter degradation and increased carbon and nitrogen preservation.

CONCLUSIONS

These findings indicate that the addition of CSL promoted the cycling and preservation of carbon and nitrogen in the SMS composts, and the addition of CSL to the compost may be an effective way to dispose of agricultural waste.

Effect of calcium peroxide assisted microwave irradiation pretreatment on humus formation and microbial community in straw and dairy manure composting

In this study, the effects of four pretreatment methods on the crystallinity of maize straw were compared, and the CaO₂ assisted microwave pretreatment was selected for straw and dairy manure composting. The humification and microbial community were investigated. Results showed that the pretreatment increased the initial water-soluble carbon, which favored the microbial activity, and the CO₂ release increased by 15.71%. Pretreatment promoted the lignocellulose degradation, with total degradation ratio of 37.06%. The final humic acid content was 11.39 g/kg higher than the control. Spearman correlation analysis indicated that polyphenols and amino acids were significantly related to humus formation. In addition, pretreatment rendered the Firmicutes the most dominant phylum, and increased the metabolic intensity of reducing sugar metabolism, aromatic amino acid biosynthesis and carbon fixation pathways. Redundancy analysis revealed that the dominant genus of Firmicutes was significantly positively correlated with humus, while that of Actinobacteriota was correlated with CO₂ release.

Effects of high-strength landfill leachate effluent on stress-induced microalgae lipid production and post-treatment micropollutant degradation

This research investigates the effects of landfill leachate effluent concentrations from moving bed biofilm reactor (MBBR) on stress-induced Chlorella vulgaris and Scenedesmus armatus lipid production and post-treatment micropollutant degradation. The effluent concentrations were varied between 25%, 50%, 75%, and 100% (v/v). The landfill leachate influent was treated using two-stage moving bed biofilm reactor under 24 h and 18 h hydraulic retention time (HRT). The results indicated that the effluent concentration was positively correlated with the stress-induced microalgae lipid production in the post-treatment of residual micropollutants. C. vulgaris and S. armatus completely remove residual micropollutants in the effluent. The superoxide dismutase and peroxidase activity were positively correlated with the cellular lipid content. The lipid content of C. vulgaris and S. armatus cultivated in the 18 h HRT effluent were 31-51% and 51-64%, while those in the 24 h HRT effluent were 15-16% and 5-19%. The optimal condition of microalgae cultivation for the post-treatment of residual micropollutants was 50-75% (v/v) effluent concentrations under 18 h HRT, achieving the highest lipid production of 113-116 mg/L for C. vulgaris and 74-75 mg/L for S. armatus. Essentially, the MBBR landfill leachate effluent holds promising potential as a substrate for microalgae lipid production.

Lignocellulose biohydrogen towards net zero emission: A review on recent developments

This review mainly determines novel and advance physical, chemical, physico-chemical, microbiological and nanotechnology-based pretreatment techniques in lignocellulosic biomass pretreatment for bio-H2 production. Further, aim of this review is to gain the knowledge on the lignocellulosic biomass pretreatment and its priority on the efficacy of bio-H2 and positive findings. The influence of various pretreatment techniques on the structure of lignocellulosic biomass have presented with the pros and cons, especially about the cellulose digestibility and the interference by generation of inhibitory compounds in the bio-enzymatic technique as such compounds is toxic. The result implies that the stepwise pretreatment technique only can ensure eventually the lignocellulosic biomass materials fermentation to yield bio-H2. Though, the mentioned pretreatment steps are still a challenge to procure cost-effective large-scale conversion of lignocellulosic biomass into fermentable sugars along with low inhibitory concentration.

Role of psychrotrophic bacteria and cold-active enzymes in composting methods adopted in cold regions

Temperature-dependent composting is a challenging task but is worthy if it is done in the right manner. Cold composting has been known to be practiced since ancient times but there were not enough advancements to overcome the long mesophilic phase and bring the compost maturation to a short period. The composting processes that have been well practiced are discussed and the role of psychrotrophic bacteria that produce cold tolerant hydrolytic enzymes has been highlighted. In this chapter, the mechanism of substrate degradation has been elaborated to better understand the need of specific bacteria for a specific kind of substrate allowing fast and efficient decomposition. This chapter attempts to pave an appropriate way and suggest the best-suited method of composting for efficient production of compost by the conservation of heat in cold regions.

Looking into the world's largest elephant population in search of ligninolytic microorganisms for biorefineries: a mini-review

Gastrointestinal tracts (GIT) of herbivores are lignin-rich environments with the potential to find ligninolytic microorganisms. The occurrence of the microorganisms in herbivore GIT is a well-documented mutualistic relationship where the former benefits from the provision of nutrients and the latter benefits from the microorganism-assisted digestion of their recalcitrant lignin diets. Elephants are one of the largest herbivores that rely on the microbial anaerobic fermentation of their bulky recalcitrant low-quality forage lignocellulosic diet given their inability to break down major components of plant cells. Tapping the potential of these mutualistic associations in the biggest population of elephants in the whole world found in Botswana is attractive in the valorisation of the bulky recalcitrant lignin waste stream generated from the pulp and paper, biofuel, and agro-industries. Despite the massive potential as a feedstock for industrial fermentations, few microorganisms have been commercialised. This review focuses on the potential of microbiota from the gastrointestinal tract and excreta of the worlds' largest population of elephants of Botswana as a potential source of extremophilic ligninolytic microorganisms. The review further discusses the recalcitrance of lignin, achievements, limitations, and challenges with its biological depolymerisation. Methods of isolation of microorganisms from elephant dung and their improvement as industrial strains are further highlighted.

Variations in lignin monomer contents and stable hydrogen isotope ratios in methoxy groups during the biodegradation of garden biomass

Lignin, a highly polymerized organic component of plant cells, is one of the most difficult aromatic substances to degrade. Selective biodegradation under mild conditions is a promising method, but the dynamic variations in lignin monomers during the biodegradation of lignocellulose are not fully understood. In this study, we evaluated the differences in lignin degradation under different microbial inoculation based on the lignin monomer content, monomer ratio, and stable hydrogen isotope ratio of lignin methoxy groups (δ2HLM). The weight loss during degradation and the net loss of lignocellulosic components improved dramatically with fungal inoculation. Syringyl monolignol (S-lignin), which contains two methoxy groups, was more difficult to degrade than guaiacyl (G-lignin), which contains only one methoxy group. The co-culture of Pseudomonas mandelii and Aspergillus fumigatus produced the greatest decrease in the G/S ratio, but δ2HLM values did not differ significantly among the three biodegradation experiments, although the enrichment was done within the fungal inoculation. The fluctuation of δ2HLM values during the initial phase of biodegradation may be related to the loss of pectic polysaccharides (another methoxy donor), which mainly originate from fallen leaves. Overall, the relative δ2HLM signals were preserved despite decreasing G/S ratios in the three degradation systems. Nevertheless, some details of lignin δ2HLM as a biomarker for biogeochemical cycles need to be explored further.

The Use of Baikal Psychrophilic Actinobacteria for Synthesis of Biologically Active Natural Products from Sawdust Waste

One of the relevant areas in microbiology and biotechnology is the study of microorganisms that induce the destruction of different materials, buildings, and machines and lead to negative effects. At the same time, the positive ecological effects of degradation can be explained by the detoxication of industrial and agricultural wastes, chemical substances, petroleum products, xenobiotics, pesticides, and other chemical pollutants. Many of these industrial wastes include hard-to-degrade components, such as lignocellulose or plastics. The biosynthesis of natural products based on the transformation of lignocellulosic wastes is of particular interest. One of the world’s unique ecosystems is presented by Lake Baikal. This ecosystem is characterized by the highest level of biodiversity, low temperatures, and a high purity of the water. Here, we studied the ability of several psychrophilic representatives of Baikal Actinobacteria to grow on sawdust wastes and transform them into bioactive natural products. Different strains of both widely spread genus of Actinobacteria and rare genera of Actinobacteria were tested. We used the LC-MS methods to show that Actinobacteria living in sawmill wastes can produce both known and novel natural products with antibiotic activity. We demonstrated that the type of sawmill wastes and their concentration influence the Actinobacteria biosynthetic potential. We have shown for the first time that the use of Baikal psychrophilic microorganisms as a factory for biodegradation is applicable for the transformation of lignocellulosic wastes. Thus, the development of techniques for screening novel natural products leads to an elaboration on the active ingredients for novel drugs.

Lignocellulosics in plant cell wall and their potential biological degradation

Lignocellulosic materials are composed of three main structural polymers: hemicellulose, cellulose, and lignin. Cellulose is a long chain molecule of glucose requiring a small number of enzymes for degradation due to its simple structure while lignin is a complex polymer of phenylpropane making its biochemical decomposition difficult. Under anaerobic conditions, lignocellulose breakdown is much easier and more rapid than aerobic conditions. Various studies have been carried out to estimate the rate of degradation of lignocellulosic materials. Microorganisms play a key role in the degradation of lignocellulosic materials because they produce a variety of hydrolytic enzymes including cellulase, proteases, xylanases, lipases, laccase, and phosphatases during the degradation of lignocellulosic materials. Based on the body of literature, microorganismal activity can provide useful information about the process of organic matter decomposition.

Harnessing the potential use of cellulolytic Klebsiella oxytoca (M21WG) and Klebsiella sp. (Z6WG) isolated from the guts of termites (Isoptera)

Background

For many years, denim-heavy quality cotton twill colored with indigo colors and with a well-worn/faded look has held a lot of appeal. Machine damage, drainage system blockage, and other issues come with the conventional usage of pumice stones for “stone-washing” denims. In view of the abovementioned information, a range of works has been done to investigate the economic prospects of bacterial cellulase enzymes for use in industrial processes, including biopolishing in the textile sector. Ethiopia has excellent termite diversity to isolate bacterial gut-associated cellulose enzymes for biostoning applications. The main purpose of this study was, therfore, to decipher how to isolate and characterize cellulase enzymes from termite (Isoptera) gut bacteria with the intention of employing it for biostoning of textiles.

Purpose

To use cellulolytic enzymes of Klebsiella oxytoca (M21WG) and Klebsiella sp. (Z6WG) isolated from termite guts in biostoning of textiles and improving garment quality.

Methods

Cellulase enzyme-producing bacteria were isolated and screened from the guts of worker termites sampled from Meki and Zeway termite mounds in the Central Rift Valley region of Ethiopia. Bacterial screening, biochemical, morphological, and 16S rRNA sequence identification techniques were employed to characterize the bacterial strains. In addition, the production, optimization, and purification of the associated cellulase enzymes were employed, and the potential application of the enzymes for biostoning of a textile was demonstrated.

Result

The isolated M21WG was found to be 99% identical to the Klebsiella oxytoca (MT104573.1) strain, while the isolated Z6WG showed 97.3% identity to the Klebsiella sp. strain (MN629242.1). At an ideal pH of 7, a temperature of 37 °C, a 72-h incubation time, and a substrate concentration of 1.5% carboxymethylcellulose sodium, the maximum activity of the crude cellulase extract from these bacteria was assessed. These bacteria produced cellulase enzymes that were moderately efficient. Consequently, it was determined that the cellulase enzymes were effective for biostoning of denim cloth.

Conclusion

It was determined that Klebsiella oxytoca (M21WG) and Klebsiella sp. (Z6WG) could be used as a doorway to better understand harnessing the use of these cellulase-producing bacteria from termite (Isoptera) guts. In this study, it was also attempted to assess the effectiveness of the two bacterial isolates in biostoning in anticipation of their potential application in the textile realm.

Next generation applications of lignin derived commodity products, their life cycle, techno-economics and societal analysis

The pulp and biorefining industries produce their waste as lignin, which is one of the most abundant renewable resources. So far, lignin has been remained severely underutilized and generally burnt in a boiler as a low-value fuel. To demonstrate lignin's potential as a value-added product, we will review market opportunities for lignin related applications by utilizing the thermo-chemical/biological depolymerization strategies (with or without catalysts) and their comparative evaluation. The application of lignin and its derived aromatics in various sectors such as cement industry, bitumen modifier, energy materials, agriculture, nanocomposite, biomedical, H2 source, biosensor and bioimaging have been summarized. This comprehensive review article also highlights the technical, economic, environmental, and socio-economic variable that affect the market value of lignin-derived by-products. The review shows the importance of lignin, and its derived products are a platform for future bioeconomy and sustainability.

Microbial valorization of lignin: Prospects and challenges

Lignin is the world's second most prevalent biomaterial, but its effective value-added product valorization methods are still being developed. The most common preparation processes for converting lignin to platform chemicals and biofuels are fragmentation and depolymerization. Due to its structural diversity, fragmentation generally produces a variety of products, necessitating tedious separation and purifying methods to isolate the desired products. Bacterial-based techniques are commonly utilized for lignin fragmentation due to their high metabolitic activity. Recent advancements in lignin valorization utilizing bacteria, such as lignin decomposing microbes and major pathways involved that can breakdown lignin into various valuable products namely lipids, furfural, vanillin, polyhydroxybutyrate, poly lactic acid blends were discussed in this review. This review also covers the genetic and fermentation methodologies to enhance lignin decomposition, challenges and future trends of microbe based lignin valorization.

Lignocellulose biomass bioconversion during composting: Mechanism of action of lignocellulase, pretreatment methods and future perspectives

Composting is a biodegradation and transformation process that converts lignocellulosic biomass into value-added products, such as humic substances (HSs). However, the recalcitrant nature of lignocellulose hinders the utilization of cellulose and hemicellulose, decreasing the bioconversion efficiency of lignocellulose. Pretreatment is an essential step to disrupt the structure of lignocellulosic biomass. Many pretreatment methods for composting may cause microbial inactivation and death. Thus, the pretreatment methods suitable for composting can promote the degradation and transformation of lignocellulosic biomass. Therefore, this review summarizes the pretreatment methods suitable for composting. Microbial consortium pretreatment, Fenton pretreatment and surfactant-assisted pretreatment for composting may improve the bioconversion process. Microbial consortium pretreatment is a cost-effective pretreatment method to enhance HSs yields during composting. On the other hand, the efficiency of enzyme production during composting is very important for the degradation of lignocellulose, whose action mechanism is unknown. Therefore, this review describes the mechanism of action of lignocellulase, the predominant microbes producing lignocellulase and their related genes. Finally, optimizing pretreatment conditions and increasing enzymatic hydrolysis to improve the quality of composts by controlling suitable microenvironmental factors and core target microbial activities as a research focus in the bioconversion of lignocellulose during composting in the future.

Bioconversion of Lignocellulosic Biomass into Value Added Products under Anaerobic Conditions: Insight into Proteomic Studies

Production of biofuels and other value-added products from lignocellulose breakdown requires the coordinated metabolic activity of varied microorganisms. The increasing global demand for biofuels encourages the development and optimization of production strategies. Optimization in turn requires a thorough understanding of the microbial mechanisms and metabolic pathways behind the formation of each product of interest. Hydrolysis of lignocellulosic biomass is a bottleneck in its industrial use and often affects yield efficiency. The accessibility of the biomass to the microorganisms is the key to the release of sugars that are then taken up as substrates and subsequently transformed into the desired products. While the effects of different metabolic intermediates in the overall production of biofuel and other relevant products have been studied, the role of proteins and their activity under anaerobic conditions has not been widely explored. Shifts in enzyme production may inform the state of the microorganisms involved; thus, acquiring insights into the protein production and enzyme activity could be an effective resource to optimize production strategies. The application of proteomic analysis is currently a promising strategy in this area. This review deals on the aspects of enzymes and proteomics of bioprocesses of biofuels production using lignocellulosic biomass as substrate.

Microbial succession of lignocellulose degrading bacteria during composting of corn stalk

The discarding and burning of corn stalks in the fields after harvesting lead to environmental pollution and waste of resources. Composting is an effective way to disposal of the crop straws. Composting is a complex biochemical process and need a detail studied in cold region. Hence, the succession process of bacteria and Actinomycetes in the process of corn stalk composting in cold region was studied by 16SrRNA. Alpha diversity analysis showed that the detection results could represent the real situation. The bacterial community diversity from high to low was F50 > F90 > F0 > F10 > F20. The results of beta analysis showed that F20 and F50 had the most similar microbial structure at the phylum level, and the difference between F0 and F20 was the largest. The dominant microbes changed from Proteobacteria and Bacteroidetes in F0 in heating stage to Firmicutes and Proteobacteria, Actinobacteria and Firmicutes in F10 during early high temperature stage, and Actinobacteria, Proteobacteria and Bacteroidetes in cooling and post composting phases. Actinobacteria and Firmicutes were the dominant bacteria in the whole composting process. In the composting process, the microbial community was mainly involved in amino acid metabolism related to nitrogen transformation and carbohydrate metabolism related to lignocellulose degradation. Lignin and hemicellulose were mainly degraded in thermophilic stage. The conversion of nitrogen and degradation of cellulose occurred mainly in the early stages of composting. The research will be helpful to understand the biochemical process of composting in cold region.

Enzyme-assisted bioremediation approach for synthetic dyes and polycyclic aromatic hydrocarbons degradation

Environmental protection from emerging pollutants has become a significant challenge for mankind as an increasing number of contaminants, including synthetic dyes and polycyclic aromatic hydrocarbons (PAHs), represent a serious risk to ecological and environmental balance. Most synthetic dyes have complex aromatic structures and are resistant to degrade by classical approaches, such as physical and chemical processes, including adsorption, chemical coagulation, flocculation, ion exchange, membrane separation, froth flotation, and reverse osmosis. Enzymes-assisted catalytic transformation of pollutants has become a potential alternative to classical methods because of their ability to react with complex compounds, a quick degradation rate, and producing less harmful by-products. Plant peroxidases, and microbial laccase and lignin-degrading peroxidases (manganese and lignin peroxidase) have gained significant attention for treating aromatic waste due to their capability of oxidizing and detoxifying a wide range of recalcitrant xenobiotics, including PAHs and synthetic dyes. Peroxidases being efficient biocatalysts detoxify an array of toxic compounds by simple free-radical mechanism resulting in the formation of oxidized and depolymerized products of significantly reduced toxicity. Moreover, it is an ecofriendly and economically favorable approach towards the biodegradation of recalcitrant and toxic industrial waste. Among microbial and plant peroxidases, bacterial enzymes have broad substrate specificity and can transform a wide range of recalcitrant substrates. Ligninolytic enzymes oxidize the aromatic ring into quinones and acids by producing free hydroxyl radicals instead of dihydrodiols and mineralize aromatic hydrocarbon in combination with cytochrome P450, monooxygenases, and epoxide hydrolases. In the review, an attempt has been made to provide detailed knowledge about the availability of inexpensive peroxidases sources, their mechanism of action, and degradation potential. The present review summarizes the exploitation of peroxidases from plants, bacteria, and fungus (manganese peroxidase, lignin peroxidase, and laccases) for detoxification and degradation of textile dyes as well as PAHs. Conclusively, peroxidases have great potential to react with almost all classes of synthetic dyes and most PAHs due to broad substrate specificity and transformed them into less harmful metabolites.

Bioremediation of lignin derivatives and phenolics in wastewater with lignin modifying enzymes: Status, opportunities and challenges

Lignin modifying enzymes from fungi and bacteria are potential biocatalysts for sustainable mitigation of different potentially toxic pollutants in wastewater. Notably, the paper and pulp industry generates enormous amounts of wastewater containing high amounts of complex lignin-derived chlorinated phenolics and sulfonated pollutants. The presence of these compounds in wastewater is a critical issue from environmental and toxicological perspectives. Some chloro-phenols are harmful to the environment and human health, as they exert carcinogenic, mutagenic, cytotoxic, and endocrine-disrupting effects. In order to address these most urgent concerns, the use of oxidative lignin modifying enzymes for bioremediation has come into focus. These enzymes catalyze modification of phenolic and non-phenolic lignin-derived substances, and include laccase and a range of peroxidases, specifically lignin peroxidase (LiP), manganese peroxidase (MnP), versatile peroxidase (VP), and dye-decolorizing peroxidase (DyP). In this review, we explore the key pollutant-generating steps in paper and pulp processing, summarize the most recently reported toxicological effects of industrial lignin-derived phenolic compounds, especially chlorinated phenolic pollutants, and outline bioremediation approaches for pollutant mitigation in wastewater from this industry, emphasizing the oxidative catalytic potential of oxidative lignin modifying enzymes in this regard. We highlight other emerging biotechnical approaches, including phytobioremediation, bioaugmentation, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-based technology, protein engineering, and degradation pathways prediction, that are currently gathering momentum for the mitigation of wastewater pollutants. Finally, we address current research needs and options for maximizing sustainable biobased and biocatalytic degradation of toxic industrial wastewater pollutants.

Biotransformation of Lignin by an Artificial Heme Enzyme Designed in Myoglobin With a Covalently Linked Heme Group

The conversion of Kraft lignin in plant biomass into renewable chemicals, aiming at harvesting aromatic compounds, is a challenge process in biorefinery. Comparing to the traditional chemical methods, enzymatic catalysis provides a gentle way for the degradation of lignin. Alternative to natural enzymes, artificial enzymes have been received much attention for potential applications. We herein achieved the biodegradation of Kraft lignin using an artificial peroxidase rationally designed in myoglobin (Mb), F43Y/T67R Mb, with a covalently linked heme cofactor. The artificial enzyme of F43Y/T67R Mb has improved catalytic efficiencies at mild acidic pH for phenolic and aromatic amine substrates, including Kraft lignin and the model lignin dimer guaiacylglycerol-β-guaiacyl ether (GGE). We proposed a possible catalytic mechanism for the biotransformation of lignin catalyzed by the enzyme, based on the results of kinetic UV-Vis studies and UPLC-ESI-MS analysis, as well as molecular modeling studies. With the advantages of F43Y/T67R Mb, such as the high-yield by overexpression in E. coli cells and the enhanced protein stability, this study suggests that the artificial enzyme has potential applications in the biodegradation of lignin to provide sustainable bioresource.

Screening and Comparison of Lignin Degradation Microbial Consortia from Wooden Antiques

Lignin, which is a component of wood, is difficult to degrade in nature. However, serious decay caused by microbial consortia can happen to wooden antiques during the preservation process. This study successfully screened four microbial consortia with lignin degradation capabilities (J-1, J-6, J-8 and J-15) from decayed wooden antiques. Their compositions were identified by genomic sequencing, while the degradation products were analyzed by GC-MS. The lignin degradation efficiency of J-6 reached 54% after 48 h with an initial lignin concentration of 0.5 g/L at pH 4 and rotation speed of 200 rpm. The fungal consortium of J-6 contained Saccharomycetales (98.92%) and Ascomycota (0.56%), which accounted for 31% of the total biomass. The main bacteria in J-6 were Shinella sp. (47.38%), Cupriavidus sp. (29.84%), and Bosea sp. (7.96%). The strongest degradation performance of J-6 corresponded to its composition, where Saccharomycetales likely adapted to the system and improved lignin degradation enzymes activities, and the abundant bacterial consortium accelerated lignin decomposition. Our work demonstrated the potential utilization of microbial consortia via the synergy of microbial consortia, which may overcome the shortcomings of traditional lignin biodegradation when using a single strain, and the potential use of J-6 for lignin degradation/removal applications.

Complementary Contribution of Fungi and Bacteria to Lignocellulose Digestion in the Food Stored by a Neotropical Higher Termite

Lignocellulose digestion in termites is achieved through the functional synergy between gut symbionts and host enzymes. However, some species have evolved additional associations with nest microorganisms that collaborate in the decomposition of plant biomass. In a previous study, we determined that plant material packed with feces inside the nests of Cornitermes cumulans (Syntermitinae) harbors a distinct microbial assemblage. These food nodules also showed a high hemicellulolytic activity, possibly acting as an external place for complementary lignocellulose digestion. In this study, we used a combination of ITS sequence analysis, metagenomics, and metatranscriptomics to investigate the presence and differential expression of genes coding for carbohydrate-active enzymes (CAZy) in the food nodules and the gut of workers and soldiers. Our results confirm that food nodules express a distinct set of CAZy genes suggesting that stored plant material is initially decomposed by enzymes that target the lignin and complex polysaccharides from fungi and bacteria before the passage through the gut, where it is further targeted by a complementary set of cellulases, xylanases, and esterases produced by the gut microbiota and the termite host. We also showed that the expression of CAZy transcripts associated to endoglucanases and xylanases was higher in the gut of termites than in the food nodules. An additional finding in this study was the presence of fungi in the termite gut that expressed CAZy genes. This study highlights the importance of externalization of digestion by nest microbes and provides new evidence of complementary digestion in the context of higher termite evolution.

Depolymerization and conversion of lignin to value-added bioproducts by microbial and enzymatic catalysis

Lignin, the most abundant renewable aromatic compound in nature, is an excellent feedstock for value-added bioproducts manufacturing; while the intrinsic heterogeneity and recalcitrance of which hindered the efficient lignin biorefinery and utilization. Compared with chemical processing, bioprocessing with microbial and enzymatic catalysis is a clean and efficient method for lignin depolymerization and conversion. Generally, lignin bioprocessing involves lignin decomposition to lignin-based aromatics via extracellular microbial enzymes and further converted to value-added bioproducts through microbial metabolism. In the review, the most recent advances in degradation and conversion of lignin to value-added bioproducts catalyzed by microbes and enzymes were summarized. The lignin-degrading microorganisms of white-rot fungi, brown-rot fungi, soft-rot fungi, and bacteria under aerobic and anaerobic conditions were comparatively analyzed. The catalytic metabolism of the microbial lignin-degrading enzymes of laccase, lignin peroxidase, manganese peroxidase, biphenyl bond cleavage enzyme, versatile peroxidase, and β-etherize was discussed. The microbial metabolic process of H-lignin, G-lignin, S-lignin based derivatives, protocatechuic acid, and catechol was reviewed. Lignin was depolymerized to lignin-derived aromatic compounds by the secreted enzymes of fungi and bacteria, and the aromatics were converted to value-added compounds through microbial catalysis and metabolic engineering. The review also proposes new insights for future work to overcome the recalcitrance of lignin and convert it to value-added bioproducts by microbial and enzymatic catalysis.

Physicochemical Properties and Lignin Degradation of Thermal-Pretreated Oil Palm Empty Fruit Bunch

Oil palm empty fruit bunches (EFB) are recoverable lignocellulosic biomass serving as feedstock for biofuel production. The major hurdle in producing biofuel from biomass is the abundance of embedded recalcitrant lignin. Pretreatment is a key step to increase the accessibility of enzymes to fermentable sugars. In this study, thermal pretreatments at moderate temperatures ranging from 150 °C to 210 °C, at different durations (30–120 min) and EFB particle sizes (1–10 mm), were employed to maximize lignin degradation. Observation through a scanning electron microscope (SEM) revealed disruptions in EFB structure and the removal of silica bodies and other impurities upon thermal pretreatment. Remarkable changes on the elemental contents and functional groups occurred, as was evident from the energy dispersive X-ray (EDX) and Fourier transform infrared (FTIR) analyses. The smallest EFB size yielded higher lignin degradation—about 2.3-fold and 1.2-fold higher—than the biggest and moderate tested EFB sizes, indicating a smaller particle size provides a higher surface area for bioreaction. Furthermore, applying a longer duration of treatment and a higher temperature enhanced lignin degradation by up to 58%. This study suggests that moderate thermal treatment could enhance lignin degradation by altering the physicochemical structure of EFB, which is beneficial in improving biofuel production.