Characterization of efficient xylanases from industrial-scale pulp and paper wastewater treatment microbiota

Heterologous expression and structure prediction of a xylanase identified from a compost metagenomic library

Xylanases are key biocatalysts in the degradation of the β-1,4-glycosidic linkages in the xylan backbone of hemicellulose. These enzymes are potentially applied in a wide range of bioprocessing industries under harsh conditions. Metagenomics has emerged as powerful tools for the bioprospection and discovery of interesting bioactive molecules from extreme ecosystems with unique features, such as high temperatures. In this study, an innovative combination of function-driven screening of a compost metagenomic library and automatic extraction of halo areas with in-house MATLAB functions resulted in the identification of a promising clone with xylanase activity (LP4). The LP4 clone proved to be an effective xylanase producer under submerged fermentation conditions. Sequence and phylogenetic analyses revealed that the xylanase, Xyl4, corresponded to an endo-1,4-β-xylanase belonging to glycosyl hydrolase family 10 (GH10). When xyl4 was expressed in Escherichia coli BL21(DE3), the enzyme activity increased about 2-fold compared to the LP4 clone. To get insight on the interaction of the enzyme with the substrate and establish possible strategies to improve its activity, the structure of Xyl4 was predicted, refined, and docked with xylohexaose. Our data unveiled, for the first time, the relevance of the amino acids Glu133 and Glu238 for catalysis, and a close inspection of the catalytic site suggested that the replacement of Phe316 by a bulkier Trp may improve Xyl4 activity. Our current findings contribute to enhancing the catalytic performance of Xyl4 towards industrial applications. KEY POINTS: • A GH10 endo-1,4-β-xylanase (Xyl4) was isolated from a compost metagenomic library • MATLAB's in-house functions were developed to identify the xylanase-producing clones • Computational analysis showed that Glu133 and Glu238 are crucial residues for catalysis.

Precision enzyme discovery through targeted mining of metagenomic data

Metagenomics has opened new avenues for exploring the genetic potential of uncultured microorganisms, which may serve as promising sources of enzymes and natural products for industrial applications. Identifying enzymes with improved catalytic properties from the vast amount of available metagenomic data poses a significant challenge that demands the development of novel computational and functional screening tools. The catalytic properties of all enzymes are primarily dictated by their structures, which are predominantly determined by their amino acid sequences. However, this aspect has not been fully considered in the enzyme bioprospecting processes. With the accumulating number of available enzyme sequences and the increasing demand for discovering novel biocatalysts, structural and functional modeling can be employed to identify potential enzymes with novel catalytic properties. Recent efforts to discover new polysaccharide-degrading enzymes from rumen metagenome data using homology-based searches and machine learning-based models have shown significant promise. Here, we will explore various computational approaches that can be employed to screen and shortlist metagenome-derived enzymes as potential biocatalyst candidates, in conjunction with the wet lab analytical methods traditionally used for enzyme characterization.

Discovery of novel alkaline-tolerant xylanases from fecal microbiota of dairy cows

Xylo-oligosaccharides (XOS) are considered as a promising type of prebiotics that can be used in foods, feeds, and healthcare products. Xylanases play a key role in the production of XOS from xylan. In this study, we conducted a metagenomic analysis of the fecal microbiota from dairy cows fed with different types of fodders. Despite the diversity in their diets, the main phyla observed in all fecal microbiota were Firmicutes and Bacteroidetes. At the genus level, one group of dairy cows that were fed probiotic fermented herbal mixture-containing fodders displayed decreased abundance of Methanobrevibacter and increased growth of beneficial Akkermansia bacteria. Additionally, this group exhibited a high microbial richness and diversity. Through our analysis, we obtained a comprehensive dataset comprising over 280,000 carbohydrate-active enzyme genes. Among these, we identified a total of 163 potential xylanase genes and subsequently expressed 34 of them in Escherichia coli. Out of the 34 expressed genes, two alkaline xylanases with excellent temperature stability and pH tolerance were obtained. Notably, CDW-xyl-8 exhibited xylanase activity of 96.1 ± 7.5 U/mg protein, with an optimal working temperature of 55 ℃ and optimal pH of 8.0. CDW-xyl-16 displayed an activity of 427.3 ± 9.1 U/mg protein with an optimal pH of 8.5 and an optimal temperature at 40 ℃. Bioinformatic analyses and structural modeling suggest that CDW-xyl-8 belongs to GH10 family xylanase, and CDW-xyl-16 is a GH11 family xylanase. Both enzymes have the ability to hydrolyze beechwood xylan and produce XOS. In conclusion, this metagenomic study provides valuable insights into the fecal microbiota composition of dairy cows fed different fodder types, revealing main microbial groups and demonstrating the abundance of xylanases. Furthermore, the characterization of two novel xylanases highlights their potential application in XOS production.

Production, Characterization and Prebiotic Potential of Xylooligosaccharides Produced from Wheat Bran using Enterobacter hormaechei KS1 Xylanase

In the present investigation, xylooligosaccharides were produced from wheat bran and wheat bran extracted xylan through enzymatic hydrolysis using xylanase from novel Enterobacter hormaechei KS1. Xylooligosaccharides/reducing sugars production from wheat bran was found maximum (374 mg/g) when 4.0% of wheat bran was treated with 375 units (IU/mL) of Enterobacter hormaechei KS1 xylanase at pH 6.0 and incubated at 50 °C for 24 h of incubation. In case of wheat bran extracted xylan 419 mg/g of xylooligosaccharides were produced when 3% of extracted xylan was incubate for 8 h. Analysis of the enzymatic hydrolysate through high performance liquid chromatography equipped with refractive index detector showed the presence of xylose, xylopentose and xylohexose. The decrease in pH with 1.0% dose of xylooligosacchaides produced from extracted xylan hydrolysis using E. hormaechei KS1 xylanase showed more decrease with L. rhamnosus (6.72 to 5.94) followed by L. brevis (6.71 to 6.15) and L. plantarum (6.71 to 6.41). In case of increase in optical density both wheat bran and wheat bran extracted xylan generated xylooligosaccharides exhibited similar pattern i.e., L. rhamnosus > L. plantarum > L. brevis.

Research advances in probiotic fermentation of Chinese herbal medicines

Chinese herbal medicines (CHM) have been used to cure diseases for thousands of years. However, the bioactive ingredients of CHM are complex, and some CHM natural products cannot be directly absorbed by humans and animals. Moreover, the contents of most bioactive ingredients in CHM are low, and some natural products are toxic to humans and animals. Fermentation of CHM could enhance CHM bioactivities and decrease the potential toxicities. The compositions and functions of the microorganisms play essential roles in CHM fermentation, which can affect the fermentation metabolites and pharmaceutical activities of the final fermentation products. During CHM fermentation, probiotics not only increase the contents of bioactive natural products, but also are beneficial for the host gut microbiota and immune system. This review summarizes the advantages of fermentation of CHM using probiotics, fermentation techniques, probiotic strains, and future development for CHM fermentation. Cutting-edge microbiome and synthetic biology tools would harness microbial cell factories to produce large amounts of bioactive natural products derived from CHM with low-cost, which would help speed up modern CHM biomanufacturing.

Utilization of Corncob as an Immobilization Matrix for a Xylanolytic Yeast Strain

Immobilization of microbial cells for the production of industrially important enzymes has been reported to offer the advantages of recyclability, higher yields and cost effectiveness. The search for an appropriate matrix that is affordable and easy to prepare is a significant topic in microbial biotechnology. Here, an abundant type of agro-industrial waste-corncob-was utilized as an immobilization matrix for the production of xylanase from an indigenous yeast strain, Saccharomyces cerevisiae MK-157. This is the first report describing xylanase production from immobilized S. cerevisiae. To render the corncob matrix more porous, alkaline pretreatment was undertaken and yeast cells were immobilized on the matrix by cultivating at 30 °C for 48 h in Sabouraud dextrose broth. After incubation, the immobilized matrix was transferred to mineral salt medium containing 1% xylan and incubated at 30 °C for 24 h. Xylanase production was determined in cell-free culture supernatant and the matrix was recycled for up to seven cycles. Moreover, xylanase-mediated saccharification was carried out using sugarcane bagasse as a substrate and the release of reducing sugars was monitored. The results showed that the immobilized yeast produced 4.97 IU mL-1 xylanase in the first production cycle, indicating a >tenfold increase compared to the free cells. Xylanase production further increased to its maximum levels (9.23 IU mL-1) in the fourth production cycle. Nonetheless, the cells retained 100% productivity for up to seven cycles. The volumetric and specific productivity of xylanase were also the highest in the fourth cycle. Scanning electron microscopy images revealed the rough surface of the untreated corncob, which became more porous after alkaline pretreatment. Immobilized yeast cells were also visible on the corncob pieces. The saccharification of a natural resource-sugarcane bagasse-using xylanase preparation yielded 26 mg L-1 of reducing sugars. Therefore, it can be concluded that yeast strains can yield sufficient quantities of xylanase, allowing possible biotechnological applications. Moreover, corncob can serve as a cost-effective matrix for industrially important yeast strains.

Enhancement of functional activity and biosynthesis of exopolysaccharides in Monascus purpureus by genistein treatments

The exopolysaccharides (EPS) produced by the edible medicinal fungus Monascus purpureus (EMP) become the center of growing interest due to their techno-functional properties and their numerous applications in the food industries; however, the low EPS yields limit its application. In this study, the effect of genistein supplementation on the production, rheological and antioxidant properties of EPS by M. purpureus and its biosynthesis mechanism were explored. The results indicated that the addition of genistein (3 g/L) generated a 110% and 59% increase in the maximum mycelial biomass and EPS yield, respectively. The genistein supplementation group (G-EMP) had higher molar percentages of Xyl and Man, and significantly decreased molecule weight and particle size of EPS, which resulted in stronger antioxidant effect and cell growth promotion. Rheological analysis showed that both EMP and G-EMP demonstrated pseudoplastic fluid behavior and G-EMP exhibited strong gel-like elastic behavior (G' > G"). Furthermore, genistein not only facilitated the production of EPS by regulating cell membrane permeability, enhancing cellular respiratory metabolism and monosaccharide precursor synthesis pathways, and enhancing antioxidant enzyme activity to reduce oxidative stress damage, but also affected the composition of the monosaccharides by increasing enzyme activity in the underlying synthesis pathways. These findings expand the application of M. purpureus resources and provide a paradigm for future study of the structural and functional characteristics of EPS.

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Genistein (3 g/L) significantly stimulate yield of biomass and exopolysaccharides (EPS) from M. purpureus.

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The physicochemical and rheological properties of EPS were significantly changed.

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Their antioxidant and cytoprotective effect were compared.

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A possible mechanism for the response of genistein to increase EPS yield is proposed.

Characterization of Novel Pectinolytic Enzymes Derived from the Efficient Lignocellulose Degradation Microbiota

Diverse pectinolytic enzymes are widely applied in the food, papermaking, and other industries, and they account for more than 25% of the global industrial enzyme demands. Efficient lignocellulose degradation microbiota are reservoirs of pectinolytic enzymes and other lignocellulose-degrading genes. Metagenomics has been widely used to discover new pectinolytic enzymes. Here, we used a metagenomic strategy to characterize pectinolytic genes from one efficient lignocellulose-degrading microbiota derived from pulp and paper wastewater treatment microbiota. A total of 23 predicted full-length GH28 and PL1 family pectinolytic genes were selectively cloned and expressed in Escherichia coli, and 5 of the expressed proteins had pectinolytic activities. Among them, the characterization of one pectinolytic enzyme, PW-pGH28-3, which has a 58.4% identity with an exo-polygalacturonase gene of Aquipluma nitroreducens, was further investigated. The optimal pH and optimal temperature of PW-pGH28-3 were 8.0 and 40 °C, respectively, and its pectinolytic activity at the optimal condition was 13.5 ± 1.1 U/mg protein. Bioinformatics analyses and structural modeling suggest that PW-pGH28-3 is a novel secretory exo-polygalacturonase, which is confirmed by its hydrolysates of polygalacturonic acid. The detection of PW-pGH28-3 and other pectinolytic genes showed that efficient lignocellulose degradation microbiota could provide potential efficient pectinolytic enzymes for industrial application. In the future, improving metagenomic screening efficiency would discover efficient lignocellulose-degrading enzymes and lead to the sustainable and green utilization of lignocellulose.

Characterization of a novel GH10 alkali-thermostable xylanase from a termite microbiome

The aim of the present study was to assess the biochemical and molecular structural characteristics of a novel alkali-thermostable GH10 xylanase (Xyl10B) identified in a termite gut microbiome by a shotgun metagenomic approach. This endoxylanase candidate was amplified, cloned, heterologously expressed in Escherichia coli and purified. The recombinant enzyme was active at a broad range of temperatures (37-60 ºC) and pH values (4-10), with optimal activity at 50 ºC and pH 9. Moreover, its activity remained at more than 80% of its maximum at 50 °C for 8 h. In addition, Xyl10B was found to be stable in the presence of salt and several ions and chemical reagents frequently used in the industry. These characteristics make this enzyme an interesting candidate for pulp and paper bleaching industries, since this process requires enzymes without cellulase activity and resistant to high temperatures and alkaline pH (thermo-alkaliphilic enzymes). The products of xylan hydrolysis by Xyl10B (short xylooligosaccharides, xylose and xylobiose) could be suitable for application as prebiotics and in the production of bioethanol.

Metagenomic Approaches as a Tool to Unravel Promising Biocatalysts from Natural Resources: Soil and Water

Natural resources are considered a promising source of microorganisms responsible for producing biocatalysts with great relevance in several industrial areas. However, a significant fraction of the environmental microorganisms remains unknown or unexploited due to the limitations associated with their cultivation in the laboratory through classical techniques. Metagenomics has emerged as an innovative and strategic approach to explore these unculturable microorganisms through the analysis of DNA extracted from environmental samples. In this review, a detailed discussion is presented on the application of metagenomics to unravel the biotechnological potential of natural resources for the discovery of promising biocatalysts. An extensive bibliographic survey was carried out between 2010 and 2021, covering diverse metagenomic studies using soil and/or water samples from different types and locations. The review comprises, for the first time, an overview of the worldwide metagenomic studies performed in soil and water and provides a complete and global vision of the enzyme diversity associated with each specific environment.

Advances in Studies on Microbiota Involved in Nitrogen Removal Processes and Their Applications in Wastewater Treatment

The discharge of excess nitrogenous pollutants in rivers or other water bodies often leads to serious ecological problems and results in the collapse of aquatic ecosystems. Nitrogenous pollutants are often derived from the inefficient treatment of industrial wastewater. The biological treatment of industrial wastewater for the removal of nitrogen pollution is a green and efficient strategy. In the initial stage of the nitrogen removal process, the nitrogenous pollutants are converted to ammonia. Traditionally, nitrification and denitrification processes have been used for nitrogen removal in industrial wastewater; while currently, more efficient processes, such as simultaneous nitrification-denitrification, partial nitrification-anammox, and partial denitrification-anammox processes, are used. The microorganisms participating in nitrogen pollutant removal processes are diverse, but information about them is limited. In this review, we summarize the microbiota participating in nitrogen removal processes, their pathways, and associated functional genes. We have also discussed the design of efficient industrial wastewater treatment processes for the removal of nitrogenous pollutants and the application of microbiome engineering technology and synthetic biology strategies in the modulation of the nitrogen removal process. This review thus provides insights that would help in improving the efficiency of nitrogen pollutant removal from industrial wastewater.