Enzymatic saccharification of pretreated rice straw by cellulases from Aspergillus niger BK01

Cloning, expression and purification of cellobiohydrolase gene from Caldicellulosiruptor bescii for efficient saccharification of plant biomass

Anthropogenic activities have led to a drastic shift from natural fuels to alternative renewable energy reserves that demand heat-stable cellulases. Cellobiohydrolase is an indispensable member of cellulases that play a critical role in the degradation of cellulosic biomass. This article details the process of cloning the cellobiohydrolase gene from the thermophilic bacterium Caldicellulosiruptor bescii and expressing it in Escherichia coli (BL21) CondonPlus DE3-(RIPL) using the pET-21a(+) expression vector. Multi-alignments and structural modeling studies reveal that recombinant CbCBH contained a conserved cellulose binding domain III. The enzyme's catalytic site included Asp-372 and Glu-620, which are either involved in substrate or metal binding. The purified CbCBH, with a molecular weight of 91.8 kDa, displayed peak activity against pNPC (167.93 U/mg) at 65°C and pH 6.0. Moreover, it demonstrated remarkable stability across a broad temperature range (60-80°C) for 8 h. Additionally, the Plackett-Burman experimental model was employed to assess the saccharification of pretreated sugarcane bagasse with CbCBH, aiming to evaluate the cultivation conditions. The optimized parameters, including a pH of 6.0, a temperature of 55°C, a 24-hour incubation period, a substrate concentration of 1.5% (w/v), and enzyme activity of 120 U, resulted in an observed saccharification efficiency of 28.45%. This discovery indicates that the recombinant CbCBH holds promising potential for biofuel sector.

An overview on the current status and future prospects in Aspergillus cellulase production

Cellulase is a new research point besides glucoamylase, amylase, and protease in the enzyme industry. Cellulase can decompose lignocellulosic biomass into small-molecule sugars, which facilitates microbial utilization; thus, it has a vast market potential in the field of feed, food, energy, and chemistry. The Aspergillus was the first strain used in cellulase preparation because of its safety and non-toxicity, strong growth ability, and high enzyme yield. This review provides the latest research and advances on preparing cellulase from Aspergillus. The metabolic mechanisms of cellulase secretion by Aspergillus, the selection of fermentation substrates, the comparison of the fermentation modes, and the effect of fermentation conditions have been discussed in this review. Also, the subsequent separation and purification techniques of Aspergillus cellulase, including salting out, organic solvent precipitation, ultrafiltration, and chromatography, have been declared. Further, bottlenecks in Aspergillus cellulase preparation and corresponding feasible approaches, such as genetic engineering, mixed culture, and cellulase immobilization, have also been proposed in this review. This paper provides theoretical support for the efficient production and application of Aspergillus cellulase.

On-site enriched production of cellulase enzyme using rice straw waste and its hydrolytic performance evaluation through systematic dynamic modeling

The application of on-site produced cellulolytic enzymes in place of commercial enzymes towards hydrolytic preparations of reducing sugars using inexpensive lignocellulosic wastes is considered the most efficient strategy to accomplish a cost-effective biofuel production process. Along with improved production, intrinsic and systematic performance evaluation of the produced enzyme during the hydrolysis process through kinetic intervention remains a crucial requirement for achieving the improved performance of the process. With this motivation, the present study primarily deals with the nutritionally optimized production strategy of cellulases from rice straw (RS) waste using Trichoderma reesei (MTCC 164). The highest cellulase production was obtained 8.09 ± 0.32 g/l in batch mode at optimized combinations of 3.5% (w/v) RS inducer, 3.0% (w/v) lactose, and 1.5% (w/v) peptone. Production was further improved through pH-regulated (pH 5.5 to 6.5) fed-batch fermentations. The enzyme produced at pH 6 was considered for hydrolysis studies at 4 to 10% (w/w) solid loading due to reasonable exoglucanase, endoglucanase, and maximum β-glucosidase activity levels of 9.3 U/ml, 3.87 U/ml, and 2.65 U/ml respectively. Multi-reaction systematic kinetic modeling was implemented to evaluate enzyme performance during hydrolysis, and the values of inhibitory kinetic parameters (K_2r = 7.1 < K₁r = 18.5 < K₃r = 276.6) suggested that sequential conversion of cellulose to glucose by existing enzyme components was more dominant over direct conversion.

Integration of agricultural residues as biomass source to saccharification bioprocess and for the production of cellulases from filamentous fungi

The production of second-generation bioethanol has several challenges, among them finding cheap and efficient enzymes for a sustainable process. In this work, we analyzed two native fungi, Cladosporium cladosporioides and Penicillium funiculosum, as a source of cellulolytic enzyme production, and corn stover, wheat bran, chickpeas, and bean straw as a carbon source in two fermentation systems: submerged and solid fermentation. Corn stover was selected for cellulase production in both fermentation systems, because we found the highest enzymatic activities when carboxymethyl cellulase activity (CMCase) was assessed using CMC as substrate. C. cladosporioides showed the highest CMCase activity (1.6 U/mL), while P. funiculosum had the highest filter paper activity (Fpase) (0.39 U/mL). The ß-glucosidase activities produced by both fungi were similar in submerged fermentation using corn stover as substrate. Through in-gel zymography, three polypeptides with cellulolytic activities were identified in each fungus: with molecular weights of ~ 38, 45 and 70 kDa in C. cladosporioides and ~ 21, 63 and 100 kDa in P. funiculosum. The best results for saccharification (10.11 g/L of reducing sugars) of diluted acid pretreated corn stover were obtained after 36 h of the hydrolytic process at pH 5 and 50 °C using the enzyme extract of P. funiculosum. This is the first report of cellulase identification in C. cladosporioides and the saccharification of corn stover using enzymes of this fungus. Enzymatic extracts of C. cladosporioides and P. funiculosum obtained from low-cost lignocellulosic biomass have great potential for use in the production of second-generation bioethanol.

Molecular modeling and dynamics simulation of alcohol dehydrogenase enzyme from high efficacy cellulosic ethanol-producing yeast mutant strain Pichia kudriavzevii BGY1-γm

One of the major constraints limiting the use of abundantly available lignocellulosic biomass as potential feedstock for alcohol industry is the lack of C₆/C₅ co-sugar fermenting yeast. The present study explores a mutant yeast Pichia kudriavzevii BGY1-γm as a potential strain for bioconversion of glucose/xylose sugars of green biomass into ethanol under batch fermentation. The mutant strain having higher alcohol dehydrogenase activity (11.31%) showed significantly higher ethanol concentration during co-fermentation of glucose/xylose sugars (14.2%) as compared to the native strain. Based on 99% sequence similarity of ADH encoding gene from the mutant with the gene sequences from other yeast strains, the ADH enzyme was identified as ADH-1 type. The study reveals first three-dimensional model of ADH-1 utilizing glucose/xylose sugars from P. kudriavzevii BGY1-γm (PkADH mutant). The refined and validated model of PkADH mutant was used for molecular docking against the substrate (acetaldehyde) and product (ethanol). Molecular docking results showed that substrate and product exhibited a binding affinity of -4.55 and -4.5 kcal/mol with PkADH mutant. Acetaldehyde and ethanol interacted at the active site of PkADH mutant via hydrogen bonds (Ser42, His69 and Asp163) and hydrophobic interactions (Cys40, Ser42, His69, Cys95, Trp123 and Asp163) to form the stable protein-ligand complex. Molecular dynamics analysis revealed that PkADH-mutant acetaldehyde and PkADH-mutant ethanol complexes were more stable than PkADH mutant. MMPBSA binding energy confirmed that binding of substrate and product results in the formation of a lower energy stable protein-ligand complex.Communicated by Ramaswamy H. Sarma.

Enhancing Antioxidants Extraction from Agro-Industrial By-Products by Enzymatic Treatment

Nowadays, agro-industrial by-products are of increasing interest as a source of antioxidant compounds. Thus, alternative green techniques to extract antioxidant compounds have been pursued. The use of enzymes to release bioactive compounds through antioxidant activity reduces the environmental impact caused by traditional extraction systems using organic solvents. A crude enzymatic extract containing carbohydrolases was produced by solid-state fermentation (SSF) of an olive pomace and brewery spent-grain combination. The crude extract was evaluated at different temperatures and pH values and its thermostability was studied. Results showed that β-glucosidase and cellulase were more stable than xylanase, particularly cellulase, which kept 91% of its activity for 72 h at 45 °C. The extract was also applied in enzymatic treatments (ET) to liberate antioxidant compounds from winery, olive mill and brewery by-products under optimal conditions for enzymatic activities. The highest antioxidant activity was found in extracts obtained after enzymatic treatment of exhausted olive pomace (EOP). Enzymatic crude extract produced by SSF was successfully applied in the extraction of antioxidant compounds from winery, olive mill and brewery by-products. Thus, integrating SSF and enzymatic technologies is a valuable approach to implement circular economy practices in the agro-food industry.

Unique pool of carbohydrate-degrading enzymes in novel bacteria assembled from cow and buffalo rumen metagenomes

Reconstruction of genomes from environmental metagenomes offers an excellent prospect for studying the metabolic potential of organisms resilient to isolation in laboratory conditions. Here, we assembled 12 high-quality metagenome-assembled genomes (MAGs) with an estimated completion of ≥ 90% from cow and buffalo rumen metagenomes. Average nucleotide identity (ANI) score-based screening with an existing database suggests the novelty of these genomes. Gene prediction led to the identification of 30,359 protein-encoding genes (PEGs) across 12 genomes, of which only 44.8% were annotated against a specific functional attribute. Further analysis revealed the presence of 985 carbohydrate-active enzymes (CAZymes) from more than 50 glycoside hydrolase families, of which 90% do not have a proper match in the CAZy database. Genome mining revealed the presence of a high frequency of plant biomass deconstructing genes in Bacteroidetes MAGs compared to Firmicutes. The results strongly indicate that the rumen chamber harbors high numbers of deeply branched and as-yet uncultured microbes that encode novel CAZymes, candidates for prospective usage in plant biomass-hydrolyzing and biofuels industries. KEY POINTS: • Genome binning plays a crucial role in revealing the metabolic potential of uncultivable microbes. • Assembled 12 novel genomes from cow and buffalo rumen metagenome datasets. • High frequency of plant biomass deconstructing genes identified in Bacteroidetes MAGs.

Agricultural waste management strategies for environmental sustainability

Globally, abundant agricultural wastes (AWs) are being generated each day to fulfil the increasing demands of the fast-growing population. The limited and/or improper management of the same has created an urgent need to devise strategies for their timely utilization and valorisation, for agricultural sustainability and human-food and health security. The AWs are generated from different sources including crop residue, agro-industries, livestock, and aquaculture. The main component of the crop residue and agro-industrial waste is cellulose, (the most abundant biopolymer), followed by lignin and hemicellulose (lignocellulosic biomass). The AWs and their processing are a global issue since its vast majority is currently burned or buried in soil, causing pollution of air, water and global warming. Traditionally, some crop residues have been used in combustion, animal fodder, roof thatching, composting, soil mulching, matchsticks and paper production. But, lignocellulosic biomass can also serve as a sustainable source of biofuel (biodiesel, bioethanol, biogas, biohydrogen) and bioenergy in order to mitigate the fossil fuel shortage and climate change issues. Thus, valorisation of lignocellulosic residues has the potential to influence the bioeconomy by producing value-added products including biofertilizers, bio-bricks, bio-coal, bio-plastics, paper, biofuels, industrial enzymes, organic acids etc. This review encompasses circular bioeconomy based various AW management strategies, which involve 'reduction', 'reusing' and 'recycling' of AWs to boost sustainable agriculture and minimise environmental pollution.

Fermentation Quality and Microbial Community of Corn Stover or Rice Straw Silage Mixed with Soybean Curd Residue

The objective of this study was to investigate the fermentation quality and microbial community of corn stover (CS) or rice straw (RS) silage mixed with soybean curd residue (SCR). In this study, SCR and CS or RS were mixed at ratios of 75:25, 70:30, and 65:35, respectively, and measured for nutrient content, fermentation indices, and bacterial diversity after 30 days of ensiling. The results showed an increase in lactic acid (LA) concentration (p < 0.01) and crude protein (CP) content (p < 0.0001), a decrease in pH value (p < 0.01), the content of NDF (p < 0.01) and ADF (p < 0.01), and ammonia nitrogen (AN) concentration (p < 0.01) as the proportion of SCR in raw materials (CS or RS) increased. The addition of SCR to silage led to a decrease in bacterial diversity and contributed to an increased relative abundance of beneficial microorganisms, such as Lactobacillus, and a corresponding decrease in the relative abundance of undesirable microorganisms, such as Clostridium and Enterobacter. Collectively, the mixed silage of soybean curd residue with corn stover or rice straw preserved more nutrients and helped improve fermentation quality.

Biological activity of chitosan inducing resistance efficiency of rice (Oryza sativa L.) after treatment with fungal based chitosan

Reduced pathogen resistance and management of the left-over rice stubble are among the most important challenges faced in rice cultivation. A novel and eco-friendly strategy to synthesise 'Fungal Chitosan' (FC) from Aspergillus niger using rice straw could serve as a sustainable treatment approach to improve both disease resistance and yields, while also effectively managing the rice stubble waste. The FC treatment promoted germination as well as growth parameters in rice varieties, TN1 (high yielding-susceptible) and PTB33 (low yielding-resistant) better than a commercial chitosan (PC). Treatments of exogenously applied FC to plants produced direct toxicity to Xoo, and reduced the BLB disease index by 39.9% in TN1. The capability of FC to trigger a cascade of defense pathways was evident from the measurable changes in the kinetics of defense enzymes, peroxidase (POD) and polyphenol oxidase (PPO). FC treatment increased levels of POD in TN1 by 59.4%, which was 35.3% greater than that of untreated PTB33. Therefore, the study demonstrated the effectiveness of FC treatments for use in agriculture as a potential biostimulant as well as protective agent against bacterial leaf blight, BLB, of rice (Oryza sativa) that could be produced from stubble waste and improve rice stubble management strategies.

Understanding the alteration in rumen microbiome and CAZymes profile with diet and host through comparative metagenomic approach

Rumen microbial community harbors a distinct genetic reservoir of potent carbohydrate-active enzymes (CAZyme) that functions efficiently for the deconstruction of plant biomass. Based on this premise, metagenomics approach was applied to characterize the rumen microbial community and identify carbohydrate-active genes of Bos taurus (cow) and Bubalus bubalis (buffalo) fed on green or dry roughage. Metadata was generated from the samples: green roughage-fed cow (NDC_GR), buffalo (NDB_GR) and dry roughage-fed cow (NDC_DR), buffalo (NDB_DR). Phylogenetic analysis revealed the dominance of Bacteroidetes, Firmicutes, Proteobacteria, Actinobacteria and Fibrobacter in all the four samples, covering 90-96% of the total bacterial population. On finer resolution, higher abundance of bacterial genera Fibrobacter, Bacteroides, Clostridium, Prevotella and Ruminococcus involved in plant biomass hydrolysis was observed in NDB_DR. Functional annotation using dbCAN annotation algorithm identified 28.13%, 8.08% 10.93% and 12.53% of the total contigs as putatively carbohydrate-active against NDC_GR, NDB_GR, NDC_DR and NDB_DR, respectively. Additional profiling of CAZymes revealed an over representation and diversity of putative glycoside hydrolases (GHs) in the animals fed on dry roughage with substantial enrichments of genes encoding GHs from families GH2, GH3, GH13 and GH43. GHs of families GH45, GH12, GH113, GH128, GH54 and GH27 were observed exclusively in NDB_DR metagenome. A higher abundance of cellulases, hemicellulases, debranching and oligosaccharide hydrolyzing enzymes was revealed in NDB_DR metagenome. Accordingly, it can be concluded that buffalo rumen microbiome are more efficient in plant biomass hydrolysis. The present study provides a deep understanding of the shifts in microbial community and plant polysaccharide deconstructing capabilities of rumen microbiome in response to changes in the feed type and host animal. Activity-specific microbial consortia procured from these animals can be used further for efficient plant biomass hydrolysis. The study also establishes the utility of rumen microbiome as a unique resource for mining diverse lignocellulolytic enzymes.

Rice straw fermentation by Schizophyllum commune ARC-11 to produce high level of xylanase for its application in pre-bleaching

Rice straw is valuable resource that has been used as substrate for cost effective production of xylanase under solid-state fermentation by a newly isolated white rot fungi, S. commune ARC-11. Out of eleven carbon sources tested, rice straw was found most effective for the induction of xylanase that produced 4288.3 IU/gds of xylanase by S. commune ARC-11. Maximum xylanase production (6721.9 IU/gds) was observed on 8th day of incubation at temperature (30 °C), initial pH (7.0) and initial moisture content (70.0%). The supplementation of ammonium sulphate (0.08% N, as available nitrogen) enhanced the xylanase production up to 8591.4 IU/gds. The xylanase production by S. commune ARC-11 was further improved by the addition of 0.10%, (w/v) of Tween-20 as surfactant. The maximum xylanase activities were found at pH 5.0 and temperature 55 °C with a longer stability (180 min) at temperature 45, 50 and 55 °C. This xylanase preparation was also evaluated for the pre-bleaching of ethanol-soda pulp from Eulaliopsis binata. An enzyme dosage of 10 IU/g of xylanase resulted maximum decrease in kappa number (14.51%) with a maximum improvement 2.9% in ISO brightness compared to control.

Paenibacillus polymyxa ND25: candidate genome for lignocellulosic biomass utilization

Genome sequence of Paenibacillus polymyxa ND25 isolated from cow rumen is reported for being a potential candidate in hydrolysis of lignocellulosic plant biomass. Draft genome sequence generated 5.73 Mb data containing 4922 putative protein coding genes, of which 140 are annotated for glycoside hydrolases. P. polymyxa ND25 strain comprises diverse lignocellulolytic components, especially 12 cellulase along with 23 hemicellulases and 11 esterases, signifying its potential for lignocellulose hydrolysis. Subsequent enzyme assay exhibited the potential of strain to produce 0.49, 0.24 and 0.44 U/ml U/ml of endoglucanase, exoglucanase and β-glucosidase, respectively, utilizing sugarcane bagasse as the sole carbon source. This study signifies the efficient application of P. polymyxa ND25 for facilitating plant-biomass utilization.