Cellulase-free xylanases from Bacillus and other microorganisms

Production of a bacterial secretome highly efficient for the deconstruction of xylans

Bacteria within the Paenibacillus genus are known to secrete a diverse array of enzymes capable of breaking down plant cell wall polysaccharides. We studied the extracellular xylanolytic activity of Paenibacillus xylanivorans and examined the complete range of secreted proteins when grown on carbohydrate-based carbon sources of increasing complexity, including wheat bran, sugar cane straw, beechwood xylan and sucrose, as control. Our data showed that the relative abundances of secreted proteins varied depending on the carbon source used. Extracellular enzymatic extracts from wheat bran (WB) or sugar cane straw (SCR) cultures had the highest xylanolytic activity, coincidently with the largest representation of carbohydrate active enzymes (CAZymes). Scaling-up to a benchtop bioreactor using WB resulted in a significant enhancement in productivity and in the overall volumetric extracellular xylanase activity, that was further concentrated by freeze-drying. The enzymatic extract was efficient in the deconstruction of xylans from different sources as well as sugar cane straw pretreated by alkali extrusion (SCRe), resulting in xylobiose and xylose, as primary products. The overall yield of xylose released from SCRe was improved by supplementing the enzymatic extract with a recombinant GH43 β-xylosidase (EcXyl43) and a GH62 α-L-arabinofuranosidase (CsAbf62A), two activities that were under-represented. Overall, we showed that the extracellular enzymatic extract from P. xylanivorans, supplemented with specific enzymatic activities, is an effective approach for targeting xylan within lignocellulosic biomass.

A novel endo-1,4-β-xylanase from Alicyclobacillus mali FL18: Biochemical characterization and its synergistic action with β-xylosidase in hemicellulose deconstruction

A novel endo-1,4-β-xylanase-encoding gene was identified in Alicyclobacillus mali FL18 and the recombinant protein, named AmXyn, was purified and biochemically characterized. The monomeric enzyme worked optimally at pH 6.6 and 80 °C on beechwood xylan with a specific activity of 440.00 ± 0.02 U/mg and a good catalytic efficiency (kcat/KM = 91.89 s-1mLmg-1). In addition, the enzyme did not display any activity on cellulose, suggesting a possible application in paper biobleaching processes. To develop an enzymatic mixture for xylan degradation, the association between AmXyn and the previously characterized β-xylosidase AmβXyl, deriving from the same microorganism, was assessed. The two enzymes had similar temperature and pH optima and showed the highest degree of synergy when AmXyn and AmβXyl were added sequentially to beechwood xylan, making this mixture cost-competitive and suitable for industrial use. Therefore, this enzymatic cocktail was also employed for the hydrolysis of wheat bran residue. TLC and HPAEC-PAD analyses revealed a high conversion rate to xylose (91.56 %), placing AmXyn and AmβXyl among the most promising biocatalysts for the saccharification of agricultural waste.

Molecular and Biochemical Characterization of Xylanase Produced by Streptomyces viridodiastaticus MS9, a Newly Isolated Soil Bacterium

A xylan-degrading bacterial strain, MS9, was recently isolated from soil samples collected in Namhae, Gyeongsangnam-do, Republic of Korea. This strain was identified as a variant of Streptomyces viridodiastaticus NBRC13106T based on 16S rRNA gene sequencing, DNA-DNA hybridization analysis, and other chemotaxonomic characteristics, and was named S. viridodiastaticus MS9 (=KCTC29014= DSM42055). In this study, we aimed to investigate the molecular and biochemical characteristics of a xylanase (XynCvir) identified from S. viridodiastaticus MS9. XynCvir (molecular weight ≍ 21 kDa) was purified from a modified Luria-Bertani medium, in which cell growth and xylanase production considerably increased after addition of xylan. Thin layer chromatography of xylan-hydrolysate showed that XynCvir is an endo-(1,4)-β-xylanase that degrades xylan into a series of xylooligosaccharides, ultimately converting it to xylobiose. The Km and Vmax values of XynCvir for beechwood xylan were 1.13 mg/ml and 270.3 U/mg, respectively. Only one protein (GHF93985.1, 242 amino acids) containing an amino acid sequence identical to the amino-terminal sequence of XynCvir was identified in the genome of S. viridodiastaticus. GHF93985.1 with the twin-arginine translocation signal peptide is cleaved between Ala-50 and Ala-51 to form the mature protein (21.1 kDa; 192 amino acids), which has the same amino-terminal sequence (ATTITTNQT) and molecular weight as XynCvir, indicating GHF93985.1 corresponds to XynCvir. Since none of the 100 open reading frames most homologous to GHF93985.1 listed in GenBank have been identified for their biochemical functions, our findings greatly contribute to the understanding of their biochemical characteristics.

A Glycosyl Hydrolase 30 Family Xylanase from the Rumen Metagenome and Its Effects on In Vitro Ruminal Fermentation of Wheat Straw

The challenge of wheat straw as a ruminant feed is its low ruminal digestibility. This study investigated the impact of a xylanase called RuXyn, derived from the rumen metagenome of beef cattle, on the in vitro ruminal fermentation of wheat straw. RuXyn encoded 505 amino acids and was categorized within subfamily 8 of the glycosyl hydrolase 30 family. RuXyn was heterologously expressed in Escherichia coli and displayed its highest level of activity at pH 6.0 and 40 °C. RuXyn primarily hydrolyzed xylan, while it did not show any noticeable activity towards other substrates, including carboxymethylcellulose and Avicel. At concentrations of 5 mM, Mn2+ and dithiothreitol significantly enhanced RuXyn's activity by 73% and 20%, respectively. RuXyn's activity was almost or completely inactivated in the presence of Cu2+, even at low concentrations. The main hydrolysis products of corncob xylan by RuXyn were xylopentose, xylotriose, and xylotetraose. RuXyn hydrolyzed wheat straw and rice straw more effectively than it did other agricultural by-products. A remarkable synergistic effect was observed between RuXyn and a cellulase cocktail on wheat straw hydrolysis. Supplementation with RuXyn increased dry matter digestibility; acetate, propionate, valerate, and total volatile fatty acid yields; NH3-N concentration, and total bacterial number during in vitro fermentation of wheat straw relative to the control. RuXyn's inactivity at 60 °C and 70 °C was remedied by mutating proline 151 to phenylalanine and aspartic acid 204 to leucine, boosting activity to 20.3% and 21.8% of the maximum activity at the respective temperatures. As an exogenous enzyme preparation, RuXyn exhibits considerable potential to improve ruminal digestion and the utilization of wheat straw in ruminants. As far as we know, this is the first study on a GH30 xylanase promoting the ruminal fermentation of agricultural straws. The findings demonstrate that the utilization of RuXyn can significantly enhance the ruminal digestibility of wheat straw by approximately 10 percentage points. This outcome signifies the emergence of a novel and highly efficient enzyme preparation that holds promise for the effective utilization of wheat straw, a by-product of crop production, in ruminants.

Enzymatic potential of endophytic fungi: xylanase production by Colletotrichum boninense from sugarcane biomass

Endophytic fungi constitute a major part of the still unexplored fungal diversity and have gained interest as new biological sources of natural active compounds, including enzymes. Endophytic fungi were isolated from soybean leaves and initially screened on agar plates for the production of CMCase (carboxymethylcellulase), xylanase, amylase and protease. The highest Enzymatic Indexes (IE) were verified for xylanase (2.14 and 1.31) with the fungi M6-A6P5F2 and M12-A5P3F1.2 and CMCase (1.92 and 1.62) with the fungi M13-A9P2F1 and M12-A5P3F1.2, respectively. The production of xylanase and CMCase by the selected fungi was evaluated in submerged cultivation using beechwood xylan and carboxymethylcellulose (CMC), as well as sugarcane straw and bagasse in different ratios as carbon sources. Both types of lignocellulosic biomass proved to be good inducers of enzymatic activity. The best xylanase producer among the isolates was identified as Colletotrichum boninense. With this fungus, the highest xylanase activity was obtained with a sugarcane straw-bagasse mixture in a 50:50 ratio (383.63 U mL-1), a result superior to that obtained with the use of beechwood xylan (296.65 U mL-1). Regardingthe kinetic behavior of the crude xylanase, there was found optimal pH of 5.0 and optimal temperatures of 50°C and 60°C. At 40°C and 50°C, xylanase retained 87% and 76% of its initial catalytic activity, respectively. These results bring new perspectives on bioprospecting endophytic fungi for the production of enzymes, mainly xylanase, as well as the exploitation of agro-industrial by-products, such as sugarcane straw and bagasse.

A Combined Study on Optimization, In Silico Modeling, and Genetic Modification of Large Scale Microbial Cellulase Production

Cellulase is a biocatalyst that hydrolyzes cellulosic biomass and is considered a major group of industrial enzymes for its applications. Extensive work has been done on microbial cellulase but fungi are considered a novel strain for their maximum cellulase production. Production cost and novel microbial strains are major challenges for its improvement where cheap agro wastes can be essential sources of cellulose as substrates. The researcher searches for more cellulolytic microbes from natural sources but the production level of isolated strains is comparatively low. So genetic modification or mutation can be employed for large-scale cellulase production before optimization. After genetic modification than in silico molecular modeling can be evaluated for substrate molecule's binding affinity. In this review, we focus not only on the conventional methods of cellulase production but also on modern biotechnological approaches applied to cellulase production by a sequential study on common cellulase-producing microbes, modified microbes, culture media, carbon sources, substrate pretreatment process, and the importance of optimum pH and temperature on fermentation. In this review, we also compare different cellulase activity determination methods. As a result, this review provides insights into the interrelationship between the characteristics of optimizing different culture conditions, genetic modification, and in silico enzyme modeling for the production of cellulase enzymes, which may aid in the advancement of large-scale integrated enzyme manufacturing of substrate-specific enzymes.

Fusarium graminearum as a producer of xylanases with low cellulases when grown on wheat bran

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Endophytic fungi of cacao had important xylanase activity when grown on wheat bran.

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F. graminearum strain Ec220 produced xylanases with low cellulolytic activity.

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Xylanase production was optimized using response surface methodology.

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Proteomic analysis revealed similarities with previously reported xylanases.

The xylanolytic potential of endophytic fungi isolated from leaves of Theobroma cacao was explored for the first time. Four fungal strains showed significant amounts of xylanase activity and low cellulase levels when grown on wheat bran as the sole carbon source. Strain Ec220 of Fusarium graminearum had the highest xylanase production (1.79 U/ml), whereas its cellulase activity was minimal (0.24 U/ml). Optimal conditions for xylanase production were: 154 h of incubation time, pH 5.79 and 29.8 °C. Furthermore, two protein spots detected by two-dimensional gel electrophoresis showed molecular weights (26.05 and 27.70 kDa) and isoelectric points (6.18 and 9.20) corresponding to previously reported F. graminearum xylanases, Xyl A and Xyl B, respectively. Therefore, endophytic fungi of T. cacao can be an important source of xylanolytic activities when cultured on wheat bran, and xylanases with low cellulases found in strain Ec220 require further characterization as they show promise for possible industrial applications.

Complete genome sequencing and investigation on the fiber-degrading potential of Bacillus amyloliquefaciens strain TL106 from the tibetan pig

Background

Cellulolytic microorganisms are considered a key player in the degradation of feed fiber. These microorganisms can be isolated from various resources, such as animal gut, plant surfaces, soil and oceans. A new strain of Bacillus amyloliquefaciens, TL106, was isolated from faeces of a healthy Tibetan pigs. This strain can produce cellulase and shows strong antimicrobial activity in mice. Thus, in this study, to better understand the strain of B. amyloliquefaciens TL106 on degradation of cellulose, the genome of the strain TL106 was completely sequenced and analyzed. In addition, we also explored the cellulose degradation ability of strain TL106 in vitro.

Results

TL106 was completely sequenced with the third generation high-throughput DNA sequencing. In vitro analysis with enzymatic hydrolysis identified the activity of cellulose degradation. TL106 consisted of one circular chromosome with 3,980,960 bp and one plasmid with 16,916 bp, the genome total length was 3.99 Mb and total of 4,130 genes were predicted. Several genes of cellulases and hemicellulase were blasted in Genbank, including β-glucosidase, endoglucanase, ß-glucanase and xylanase genes. Additionally, the activities of amylase (20.25 U/mL), cellulase (20.86 U/mL), xylanase (39.71 U/mL) and β-glucanase (36.13 U/mL) in the fermentation supernatant of strain TL106 were higher. In the study of degradation characteristics, we found that strain TL106 had a better degradation effect on crude fiber, neutral detergent fiber, acid detergent fiber, starch, arabinoxylan and β-glucan of wheat and highland barley .

Conclusions

The genome of B. amyloliquefaciens TL106 contained several genes of cellulases and hemicellulases, can produce carbohydrate-active enzymes, amylase, cellulase, xylanase and β-glucanase. The supernatant of fermented had activities of strain TL106. It could degrade the fiber fraction and non-starch polysaccharides (arabinoxylans and β-glucan) of wheat and highland barley. The present study demonstrated that the degradation activity of TL106 to crude fiber which can potentially be applied as a feed additive to potentiate the digestion of plant feed by monogastric animals.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-022-02599-7.

Glycosyl hydrolase 11 (xynA) gene with xylanase activity from thermophilic bacteria isolated from thermal springs

Background

Hemicellulose is one of the copious polymer in lignocellulosic biomass (LCB). It is primarily composed of xylan linked by β-1,4 glycosidic bonds. Xylanase preferentially cleaves the β-1,4-glycosidic bonds in the xylan backbone resulting in complete hydrolysis of the biomass. Thermostable variants of glycoside hydrolases act as robust catalysts, not only in degradation but also during processing, to obtain specific carbohydrate-containing chemicals and materials (Ramasamy et al. in Madras Agric J 107(special):1. 10.29321/MAJ.2020.000382, 2020).

Results

The xylanase production by two thermophilic bacteria isolated from thermal springs was evaluated. In addition, the gene encoding this industrially vital enzyme was isolated and characterized, and its protein structure was analyzed. The thermophilic bacteria producing xylanases were isolated from augmented sawdust and banana fiber biomass from hot springs of Himachal Pradesh and identified as Bacillus subtilis VSDB5 and Bacillus licheniformis KBFB4 using 16S rRNA gene sequencing. The persistent xylanase activity revealed that the enzyme is secreted extracellularly with the maximum activity of 0.76 IU mL−1 and 1.0 IU mL−1 at 6 h and 12 h of growth by KBFB4 and VSDB5, respectively, under submerged fermentation. Both the strains exhibited the maximum activity at pH 6 and a temperature of 50 °C. The xylanases of KBFB4 and VSDB5 were thermostable and retained 40% of their activity at 60 °C after incubation for 30 min. Xylanase of VSDB5 had wide thermotolerance and retained 20% of its activity from 60 to 80 °C, whereas xylanase of KBFB4 showed wide alkali tolerance and retained 80% of its activity until pH 10. The xylanase (xynA)-encoding gene (650 bp) cloned from both the strains using specific primers showed 98 to 99% homology to β-1,4-endoxylanase gene. Further in silico analysis predicted that the xylanase protein, with a molecular weight of 23 kDa, had a high pI (9.44–9.65), which explained the alkaline nature of the enzyme and greater aliphatic index (56.29). This finding suggested that the protein is thermostable. Multiple sequence alignment and homology modeling of the protein sequence revealed that the gene product belonged to the GH11 family, indicating its possible application in bioconversion.

Conclusion

The strains B. subtilis VSDB5 and B. licheniformis KBFB4 obtained from hot springs of Himachal Pradesh produced potent and alkali-tolerant thermostable xylanases, which belong to the GH11 family. The enzyme can be supplemented in industrial applications for biomass conversion at high temperatures and pH (or in processes involving alkali treatment).

Graphical Abstract

Biological pretreatment of corn stover for enhancing enzymatic hydrolysis using Bacillus sp. P3

The biological pretreatment for the enzymatic hydrolysis of lignocellulosic biomasses depends exclusively on the effective pretreatment process. Herein, we report a significant enhancement of enzymatic saccharification obtained with corn stover using a bacterial strain Bacillus sp. P3. The hemicellulose removal from corn stover by the strain Bacillus sp. P3 was evaluated for enhancing subsequent enzymatic hydrolysis. Therefore, our study revealed that an alkaline-resistant xylanase as well as other enzymes produced by Bacillus sp. P3 in fermentation broth led to a substantially enhanced hemicellulose removal rate from corn stover within pH 9.36–9.68. However, after a 20-day pretreatment of corn stover by the strain P3, the glucan content was increased by 51% and the xylan content was decreased by 35%. After 72 h of saccharification using 20 U/g of commercial cellulase, the yield of reducing sugar released from 20-day pretreated corn stover was increased by 56% in comparison to the untreated corn stover. Therefore, the use of the strain P3 could be a promising approach to pretreat corn stover for enhancing the enzymatic hydrolysis process of industrial bioenergy productions.

XynDZ5: A New Thermostable GH10 Xylanase

Xylanolytic enzymes have a broad range of applications in industrial biotechnology as biocatalytic components of various processes and products, such as food additives, bakery products, coffee extraction, agricultural silage and functional foods. An increasing market demand has driven the growing interest for the discovery of xylanases with specific industrially relevant characteristics, such as stability at elevated temperatures and in the presence of other denaturing factors, which will facilitate their incorporation into industrial processes. In this work, we report the discovery and biochemical characterization of a new thermostable GH10 xylanase, termed XynDZ5, exhibiting only 26% amino acid sequence identity to the closest characterized xylanolytic enzyme. This new enzyme was discovered in an Icelandic hot spring enrichment culture of a Thermoanaerobacterium species using a recently developed bioinformatic analysis platform. XynDZ5 was produced recombinantly in Escherichia coli, purified and characterized biochemically. This analysis revealed that it acts as an endo-1,4-β-xylanase that performs optimally at 65–75°C and pH 7.5. The enzyme is capable of retaining high levels of catalytic efficiency after several hours of incubation at high temperatures, as well as in the presence of significant concentrations of a range of metal ions and denaturing agents. Interestingly, the XynDZ5 biochemical profile was found to be atypical, as it also exhibits significant exo-activity. Computational modeling of its three-dimensional structure predicted a (β/α)₈ TIM barrel fold, which is very frequently encountered among family GH10 enzymes. This modeled structure has provided clues about structural features that may explain aspects of its catalytic performance. Our results suggest that XynDZ5 represents a promising new candidate biocatalyst appropriate for several high-temperature biotechnological applications in the pulp, paper, baking, animal-feed and biofuel industries.

Parageobacillus thermantarcticus, an Antarctic Cell Factory: From Crop Residue Valorization by Green Chemistry to Astrobiology Studies

Knowledge of Antarctic habitat biodiversity, both marine and terrestrial, has increased considerably in recent years, causing considerable development in the studies of life science related to Antarctica. In the Austral summer 1986–1987, a new thermophilic bacterium, Parageobacillus thermantarcticus strain M1 was isolated from geothermal soil of the crater of Mount Melbourne (74°22′ S, 164°40′ E) during the Italian Antarctic Expedition. In addition to the biotechnological potential due to the production of exopolysaccharides and thermostable enzymes, successful studies have demonstrated its use in the green chemistry for the transformation and valorization of residual biomass and its employment as a suitable microbial model for astrobiology studies. The recent acquisition of its genome sequence opens up new opportunities for the use of this versatile bacterium in still unexplored biotechnology sectors.

Optimization of the Cellulase Free Xylanase Production by Immobilized Bacillus Pumilus

Background

The extracellular xylanase secreted by microorganisms is a hydrolytic enzyme, which arbitrarily cleaves the β-1, 4 backbone of the polysaccharide xylan; an enzyme used in the food processing, bio-pulping and bio-bleaching. The commercial production of the xylanase is limited because of a higher cost involvement, which can be overcome by the cost-effective production of the xylanase through immobilization of the microbial cell by the non-toxic substances.

Objectives

In this work, the optimization of the extra-cellular cellulase free xylanase production by the immobilized cell of the Bacillus pumilus IMAU80221 strain using Ca-alginate beads along with standardization of the various parameters for a higher xylanase production were studied.

Materials and Methods

Following to sterilization, the Na-alginate solution was mixed with the bacterial suspension of the Bacillus pumilus IMAU80221 and was added drop by drop into the 1 M calcium chloride solution for 1 h for obtaining a uniform sized polymeric bead of the Ca-alginate. For xylanase production, the Ca-alginate beads were then transferred into 100 mL Erlenmeyer flasks with 20 mL of the culture medium containing (w/v) 0.02% NaCl, 0.02% MgSO₄, 0.04% (KH₄)₂PO₄, 0.1% peptone, and 0.5% xylan and incubated at 34 °C in an incubator shaker (150 rpm) for 24 h. The resultant supernatant (crude enzyme) was used for enzyme assay.

Results

The maximum xylanase production by the free cell (1.9 U.mL^-1.min^-1) was recorded at 48 h which was 40.5% lower than the xylanase production by the immobilized cell (2.67 U.mL^-1.min^-1) at the same time. The beads containing the immobilized cells could be reused up to eight fermentation cycles for xylanase production and retained 83.5% of the productivity at the fourth cycle. The entrapped cells were stable after six months of storage at 4 °C and retained 68% of the xylanase productivity.

Conclusion

Cellulase free xylanase production from the immobilized Bacillus pumilus IMAU80221 was optimized. The xylanase production by the immobilized cells of Bacillus pumilus was higher by 40.5 and 132.6 % over the free cells respectively after 48 and 72 h of the incubation.

Statistical based experimental optimization for co-production of endo-glucanase and xylanase from Bacillus sonorensis BD92 with their application in biomass saccharification

Endo-glucanase (cellulase) and xylanase have high industrial demand due to their vast application in industrial processes. This study reports statistical based experimental optimization for co-production of endo-glucanase and xylanase from Bacillus sonorensis BD92. Response surface methodology (RSM) involving central composite design (CCD) with full factorial experiments (2³) was applied to elucidate the components that significantly affect co-production of endo-glucanase and xylanase. The optimum co-production conditions for endo-glucanase and xylanase were as follows: carboxymethyl cellulose (CMC) 20 g/L, yeast extract 15 g/L, and time 72 h. The maximum endo-glucanase and xylanase production obtained was 1.46 and 5.69 U/mL, respectively, while the minimum endo-glucanase and xylanase production obtained was 0.66 and 0.25 U/mL, respectively. This statistical model was efficient because only 20 experimental runs were necessary to assess the highest production conditions, and the model accuracy was very satisfactory as coefficient of determination (R²) was 0.95 and 0.89 for endo-glucanase and xylanase, respectively. Further, potential application of these enzymes for saccharification of lignocellulosic biomass (wheat bran, wheat straw, rice straw, and cotton stalk) was also investigated. The results revealed that the biomass was susceptible to enzymatic saccharification and the amount of reducing sugars (glucose and xylose) increased with increase in incubation time. In conclusion, Bacillus sonorensis BD92 reveals a promise as a source of potential endo-glucanase and xylanase producer that could be useful for degrading plant biomass into value-added products of economic importance using precise statistically optimized conditions.

Isolation, Identification and Partial Optimization of Novel Xylanolytic Bacterial Isolates from Bhilai-Durg Region, Chhattisgarh, India

Background

Plant biomass and agricultural waste products disposal is a serious problem in agriculture based countries. These wastes, usually rich in xylan can be satisfactorily converted to industrially important and useful products by efficient biotechnological application of potent xylanase producing bacteria which generally have high temperature and pH optima.

Objective

The aim was to isolate and identify xylanolytic bacterial isolates from Bhilai-Durg region of Chhattisgarh, India which was otherwise unexplored for isolation of thermoalkalophilic xylanase producing bacteria. Partial scale up of process development was performed.

Materials and Methods

Xyalanse producing bacteria were isolated from probable samples following three stages of screening procedures. The potent isolates were identified and various parameters affecting xylanase production were optimized using the conventional one-factor-at-a-time approach.

Results

Two potent indigenous bacterial isolates belonged to genus Bacillus and designated as Bacillus sp. MCC2728 and Bacillus sp. MCC2727 were isolated from forest soils with the ability to degrade xylan. Significant differences were observed in their morphology and phenotypic characters amongst themselves and with its closest type strains implying the novelty of the two isolates. After optimization, maximum xylanase levels were obtained at pH 9.0, 55 °C for Bacillus sp. MCC2728 and 50 °C for Bacillus sp. MCC2727, 5% inoculum, agitation speed (150 rpm). Yeast extract and peptone are best nitrogen sources and wheat bran, the best carbon source. The GenBank/EMBL/DDBJ accession numbers of strains Bacillus sp. MCC2728 and Bacillus sp. MCC2727 are KP742971 and KT444621 respectively. Wheat bran, Yeast extract and peptone proved to be the best carbon and nitrogen sources respectively and xylose as an additive was found to be contributing to maximize the xylanase yields.

Conclusion

Two potent thermoalkalophilic novel bacterial isolates were successfully isolated with xylan degrading ability which may be used as promising xylanase producing candidates for various industrial purposes using agricultural based waste residues.

Exploration of Rice Husk Compost as an Alternate Organic Manure to Enhance the Productivity of Blackgram in Typic Haplustalf and Typic Rhodustalf

The present study was aimed at using cellulolytic bacterium Enhydrobacter and fungi Aspergillus sp. for preparing compost from rice husk (RH). Further, the prepared compost was tested for their effect on blackgram growth promotion along with different levels of recommended dose of fertilizer (RDF) in black soil (typic Haplustalf) and red soil (typic Rhodustalf) soil. The results revealed that, inoculation with lignocellulolytic fungus (LCF) Aspergillus sp. @ 2% was considered as the most efficient method of composting within a short period. Characterization of composted rice husk (CRH) was examined through scanning electron microscope (SEM) for identifying significant structural changes. At the end of composting, N, P and K content increased with decrease in CO₂ evolution, C:N and C:P ratios. In comparison to inorganic fertilization, an increase in grain yield of 16% in typic Haplustalf and 17% in typic Rhodustalf soil over 100% RDF was obtained from the integrated application of CRH@ 5 t ha⁻¹ with 50% RDF and biofertilizers. The crude protein content was maximum with the combined application of CRH, 50% RDF and biofertilizers of 20% and 21% in typic Haplustalf and typic Rhodustalf soils, respectively. Nutrient rich CRH has proved its efficiency on crop growth and soil fertility.

Biochemical properties of a new thermo- and solvent-stable xylanase recovered using three phase partitioning from the extract of Bacillus oceanisediminis strain SJ3

The present study investigates the production and partial biochemical characterization of an extracellular thermostable xylanase from the Bacillus oceanisediminis strain SJ3 newly recovered from Algerian soil using three phase partitioning (TPP). The maximum xylanase activity recorded after 2 days of incubation at 37 °C was 20.24 U/ml in the presence of oat spelt xylan. The results indicated that the enzyme recovered in the middle phase of TPP system using the optimum parameters were determined as 50% ammonium sulfate saturation with 1.0:1.5 ratio of crude extract: t-butanol at pH and temperature of 8.0 and 10 °C, respectively. The xylanase was recovered with 3.48 purification fold and 107% activity recovery. The enzyme was optimally active at pH 7.0 and was stable over a broad pH range of 5.0–10. The optimum temperature for xylanase activity was 55 °C and the half-life time at this temperature was of 6 h. At this time point the enzyme retained 50% of its activity after incubation for 2 h at 95 °C. The crude enzyme resist to sodium dodecyl sulfate and β-mercaptoethanol, while all the tested ions do not affect the activity of the enzyme. The recovered enzyme is, at least, stable in tested organic solvents except in propanol where a reduction of 46.5% was observed. Further, the stability of the xylanase was higher in hydrophobic solvents where a maximum stability was observed with cyclohexane. These properties make this enzyme to be highly thermostable and may be suggested as a potential candidate for application in some industrial processes. To the best of our knowledge, this is the first report of xylanase activity and recoverey using three phase partitioning from B. oceanisediminis.

Bacterial xylanases: biology to biotechnology

In this review, a comprehensive discussion exclusively on bacterial xylanases; their gene organization; different factors and conditions affecting enzyme yield and activity; and their commercial application have been deliberated in the light of recent research findings and extensive information mining. Improved understanding of biological properties and genetics of bacterial xylanase will enable exploitation of these enzymes for many more ingenious biotechnological and industrial applications.

C-Terminal proline-rich sequence broadens the optimal temperature and pH ranges of recombinant xylanase from Geobacillus thermodenitrificans C5

Efficient utilization of hemicellulose entails high catalytic capacity containing xylanases. In this study, proline rich sequence was fused together with a C-terminal of xylanase gene from Geobacillus thermodenitrificans C5 and designated as GthC5ProXyl. Both GthC5Xyl and GthC5ProXyl were expressed in Escherichia coli BL21 host in order to determine effect of this modification. The C-terminal oligopeptide had noteworthy effects and instantaneously extended the optimal temperature and pH ranges and progressed the specific activity of GthC5Xyl. Compared with GthC5Xyl, GthC5ProXyl revealed improved specific activity, a higher temperature (70°C versus 60°C) and pH (8 versus 6) optimum, with broad ranges of temperature and pH (60-80°C and 6.0-9.0 versus 40-60°C and 5.0-8.0, respectively). The modified enzyme retained more than 80% activity after incubating in xylan for 3h at 80°C as compared to wild -type with only 45% residual activity. Our study demonstrated that proper introduction of proline residues on C-terminal surface of xylanase family might be very effective in improvement of enzyme thermostability. Moreover, this study reveals an engineering strategy to improve the catalytic performance of enzymes.

Production and Characterization of Highly Thermostable β-Glucosidase during the Biodegradation of Methyl Cellulose by Fusarium oxysporum

Production of β-glucosidase from Fusarium oxysporum was investigated during degradation of some cellulosic substrates (Avicel, α-cellulose, carboxymethyl cellulose (CMC), and methylcellulose). Optimized production of β-glucosidase using the cellulosic substrate that supported highest yield of enzyme was examined over 192 h fermentation period and varied pH of 3.0–11.0. The β-glucosidase produced was characterized for its suitability for industrial application. Methyl cellulose supported the highest yield of β-glucosidase (177.5 U/mg) at pH 6.0 and 30°C at 96 h of fermentation with liberation of 2.121 μmol/mL glucose. The crude enzyme had optimum activity at pH 5.0 and 70°C. The enzyme was stable over broad pH range of 4.0–7.0 with relative residual activity above 60% after 180 min of incubation. β-glucosidase demonstrated high thermostability with 83% of its original activity retained at 70°C after 180 min of incubation. The activity of β-glucosidase was enhanced by Mn²⁺ and Fe²⁺ with relative activities of 167.67% and 205.56%, respectively, at 5 mM and 360% and 315%, respectively, at 10 mM. The properties shown by β-glucosidase suggest suitability of the enzyme for industrial applications in the improvement of hydrolysis of cellulosic compounds into fermentable sugars that can be used in energy generation and biofuel production.

Expression of the Thermobifida fusca xylanase Xyn11A in Pichia pastoris and its characterization

BACKGROUND

Xylan is a major component of plant cells and the most abundant hemicellulose. Xylanases degrade xylan into monomers by randomly cleaving β-1,4-glycosidic bonds in the xylan backbone, and have widespread potential applications in various industries. The purpose of our study was to clone and express the endoxylanase gene xynA of Thermobifida fusca YX in its native form and with a C-terminal histidine (His) tag in Pichia pastoris X-33. We analyzed and compared these two forms of the protein and examined their potential applications in various industries.

RESULTS

The xynA gene from T. fusca YX was successfully cloned and expressed using P. pastoris X-33. We produced a recombinant native form of the protein (rXyn11A) and a C-terminal His-tagged form of the desired protein (rXyn11A-(His)6). The specific activities of rXyn11A and rXyn11A-(His)6 in culture supernatants approached 149.4 and 133.4 U/mg, respectively. These activities were approximately 4- and 3.5-fold higher than those for the non-recombinant wild-type Xyn11A (29.3 U/mg). Following purification, the specific activities of rXyn11A and rXyn11A-(His)6 were 557.35 and 515.84 U/mg, respectively. The specific activity of rXyn11A was 8% higher than that of rXyn11A-(His)6. Both recombinant xylanases were optimally active at 80°C and pH 8.0, and exhibited greater than 60% activity between pH 6-9 and 60-80°C. They exhibited similar pH stability, while rXyn11A exhibited better thermostability; N-glycosylation enhanced the thermostability of both recombinant xylanases. The products of beechwood xylan hydrolyzed by both xylanases included xylobiose, xylotriose, xylotetraose and xylopentaose.

CONCLUSIONS

The C-terminal His tag had adverse effects when added to the Xyn11A protein. The thermostability of both recombinant xylanases was enhanced by N-glycosylation. Their stabilities at a high pH and temperature indicate their potential for application in various industries.

Population, diversity and characteristics of cellulolytic microorganisms from the Indo-Burma Biodiversity hotspot

Forest ecosystem harbour a large number of biotic components where cellulolytic microorganisms participate actively in the biotransformation of dead and decaying organic matter and soil nutrient cycling. This study explores the aerobic culturable cellulolytic microorganisms in the forest soils of North East India. Soil samples rich in dead and decaying organic matter were collected from eight conserved forests during the season when microbes were found to be most active. Cellulolytic microorganisms were isolated using selective media in which cellulose was the sole carbon source. Population of culturable, aerobic, cellulolytic microorganisms were found to be higher at the incubation temperature that corresponds to the natural ambient temperature of the site of sample collection. Bacterial population was higher in all of the sites than fungal population. Bacterial population ranged from 1.91 × 10(5) to 3.35 × 10(6) CFU g(-1) dry soil while actinomycetes and fungal population ranged from 9.13 × 10(2) to 3.46 × 10(4) CFU g(-1) dry soil and 9.36 × 10(2) to 4.31 × 10(4) CFU g(-1) dry soil, respectively. It was observed that though many isolates showed activity on the CMC plate assay, very few isolates showed significant filter paper activity. Three cellulolytic fungal isolates showing high FPase activity were characterised, identified and submitted to GenBank as Talaromyces verruculosus SGMNPf3 (KC937053), Trichoderma gamsii SGSPf7 (KC937055) and Trichoderma atroviride SGBMf4 (KC937054).

Modulation of xylanase production from alkaliphilic Bacillus pumilus VLK-1 through process optimization and temperature shift operation

This study was aimed at enhancing the production of xylanase from an alkaliphilic Bacillus pumilus VLK-1 in submerged fermentation using wheat bran, a cheap and abundantly available agro-residue, through process optimization and to monitor the effect of temperature shift operation on it. The potential of xylanase in saccharification of wheat straw was also investigated. The results showed that optimization of the fermentation process by one variable approach increased the enzyme yield from 402 to 4,986 IU/ml. Subsequently, optimization of nitrogen and carbon sources through response surface methodology led to high level xylanase production (7,295 IU/ml) which was 1.46-fold greater than one variable approach after 56 h of cultivation at 30 °C. Temperature shift operation during fermentation resulted in maximum xylanase production in lesser duration (48 h instead of 56 h). Enzymatic hydrolysis of the alkali pre-treated wheat straw with 500 IU xylanase alone released 173 ± 8 mg sugars/g whereas in combination with cellulase and β-glucosidase released 553 ± 12 mg sugars/g dry substrate in 6 h, indicating its potential in saccharification of the lignocellulosic substrate. Temperature shift operation is likely to be attractive for large scale industrial fermentation due to significant reduction in the operating cost. To our knowledge, this is the first report which showed the effect of temperature shift operation on xylanase production from bacteria. The xylanase production from Bacillus sp. in the present study is close to the highest titre reported in the literature. An enhanced xylanase production using wheat bran, a cheap and abundantly available agro-residue, will apparently reduce the enzyme cost, which would be beneficial for industry.

Isolation and characterization of Bacillus subtilis strain BY-3, a thermophilic and efficient cellulase-producing bacterium on untreated plant biomass

Bioconversion of biomass, particularly crop wastes, into biofuels is being developed as an alternative approach in meeting the high energy demand. In this study, a thermophilic bacterial strain BY-3 that exhibits cellulolytic potential was isolated from faecal samples of Tibetan pigs; this strain was identified as Bacillus subtilis. The strain can produce cellulase when grown on various substrates, including carboxymethyl cellulose, rice straw, corn stover, soluble starch and wheat bran. The maximum cellulase activity of the strain was up to 4·323 ± 0·065 U ml(-1) when cultivated in the medium containing corn stover (30 g l(-1) ) for 24 h. The results demonstrated that corn stover is the most suitable substrate for cellulase production by the strain BY-3. The crude cellulase of strain BY-3 was most active at pH 5·5 and 60°C, and the enzyme in acetate buffer (50 mmol l(-1) ) demonstrated a good stability at 60°C for at least 1 h. The crude cellulase exhibited a strong antibacterial activity against Staphylococcus aureus. The strain can be used in cost-efficient cellulase production for bioconversion of agricultural residual biomass into biofuels.

SIGNIFICANCE AND IMPACT OF THE STUDY

The increased consumption of fossil fuels has caused serious energy crisis and environmental problem. Thus, an alternative energy source is necessary. Bioconversion of biomass, particularly agricultural residuals, into value-added bioproducts, such as biofuels and chemical solvents, has received considerable attention. In this study, the newly isolated thermophilic Bacillus subtilis strain BY-3 produces cellulase efficiently with the use of untreated corn stover as a sole carbon source. This strain possesses the thermostable cellulase that is active with diverse crop wastes with a broad pH range and is a highly promising candidate for agricultural waste management.

Production of xylanases by mangrove fungi from the Philippines and their application in enzymatic pretreatment of recycled paper pulps

Mangrove fungi are vastly unexplored for enzymes with industrial application. This study aimed to assess the biocatalytic activity of mangrove fungal xylanases on recycled paper pulp. Forty-four mangrove fungal (MF) isolates were initially screened for xylanolytic activity in minimal medium with corn cob xylan as the sole carbon source. Eight MF were further cultivated under submerged fermentation for the production of crude xylanases. These crude enzymes were then characterized and tested for the pretreatment of recycled paper pulps. Results showed that 93 % of the tested MF isolates exhibited xylanolytic activity in solid medium. In submerged fermentation, salinity improved the growth of the fungal isolates but did not influence xylanase production. The crude xylanases were mostly optimally active at 50 °C and pH 7. Changes in pH had a greater effect on xylanase stability than temperature. More than half of the activity was lost at pH 9 for majority of the crude enzymes. However, two thermophilic xylanases from Fusarium sp. KAWIT-A and Aureobasidium sp. 2LIPA-M and one alkaliphilic xylanase from Phomopsis sp. MACA-J were also produced. All crude enzymes exhibited cellulase activities ranging from 4 to 21 U/ml. Enzymatic pretreatment of recycled paper pulps with 5 % consistency produced 70-650 mg of reducing sugars per gram of pulp at 50 °C after 60 min. The release of high amounts of reducing sugars showed the potential of mangrove fungal crude xylanases in the local paper and pulp industry. The diverse properties shown by the tested crude enzymes also indicate its potential applications to other enzyme-requiring industries.

Molecular and biochemical characterization of a new alkaline active multidomain xylanase from alkaline wastewater sludge

A xylanase gene, xyn-b39, coding for a multidomain glycoside hydrolase (GH) family 10 protein was cloned from the genomic DNA of the alkaline wastewater sludge of a paper mill. Its deduced amino acid sequence of 1,481 residues included two carbohydrate-binding modules (CBM) of family CBM_4_9, one catalytic domain of GH 10, one family 9 CBM and three S-layer homology (SLH) domains. xyn-b39 was expressed heterologously in Escherichia coli, and the recombinant enzyme was purified and characterized. Xyn-b39 exhibited maximum activity at pH 7.0 and 60 °C, and remained highly active under alkaline conditions (more than 80 % activity at pH 9.0 and 40 % activity at pH 10.0). The enzyme was thermostable at 55 °C, retaining more than 90 % of the initial activity after 2 h pre-incubation. Xyn-b39 had wide substrate specificity and hydrolyzed soluble substrates (birchwood xylan, beechwood xylan, oat spelt xylan, wheat arabinoxylan) and insoluble substrates (oat spelt xylan and wheat arabinoxylan). Hydrolysis product analysis indicated that Xyn-b39 was an endo-type xylanase. The K (m) and V (max) values of Xyn-b39 for birchwood xylan were 1.01 mg/mL and 73.53 U/min/mg, respectively. At the charge of 10 U/g reed pulp for 1 h, Xyn-b39 significantly reduced the Kappa number (P < 0.05) with low consumption of chlorine dioxide alone.

Purification and biochemical characterization of a novel thermo-stable carboxymethyl cellulase from Azorean isolate Bacillus mycoides S122C

Bacillus mycoides S122C was identified as carboxymethyl cellulase (CMcellulase)-producing bacteria from the Azorean Bacillus collection (Lab collection), which was isolated from local soil samples. The bacteria was identified by 16S rRNA sequence and designated as B. mycoides S122C. NCBI blast analysis showed that the B. mycoides S122C 16S rRNA sequence has high identity compared to other B. mycoides strains. CMcellulase was purified from the culture filtrates using anion-exchange chromatography. After mono-Q purification, the protein folds and recovery were 13.7 and 0.76 %, respectively. SDS-PAGE analysis showed that the molecular weight of the purified CMcellulase protein was estimated to be about 62 kDa and that it was composed of a single subunit. MALDI-MS/MS analysis yielded each four peptides of the purified protein; it has identity to other cellulases. The purified CMcellulase showed high activity with CMcellulose followed by β-glucan as a substrate. Optimum temperature and pH for the purified CMcellulase activity were found to be at 50 °C and pH 7.0, respectively. The purified CMcellulase was stable with about 60 % activity in broad pH ranges from 5 to 10 and temperature of 40 to 60 °C. However, purified CMcellulase was stable at about 70 % at 70 °C and also stable overall at 78 % for surfactants. CMcellulase activity was inhibited by ions such as HgCl(2), followed by CuSo(4), FeCl(2), and MnCl(2), while CoCl(2) activated CMcellulase activity. The purified CMcellulase activity was strongly inhibited by EDTA.

Production of alkali tolerant cellulase free xylanase in high levels by Bacillus pumilus SV-205

The fermentation conditions were optimized for hyper production of xylanase from Bacillus pumilus SV-205. The bacterium secretes high levels (7382.7±1200 IU/mL) of cellulase-free xylanase using wheat bran led to 21.63 fold increase in activity. A combination of yeast extract and peptone stimulated highest xylanase production (2448.0 IU/mL) as compared to other combinations. The most important characteristic of the enzyme is its high pH stability (100%) over a broad pH range of 6-11 for 24h. Thermostability studies revealed that enzyme retained 65% activity after an incubation of 2h at 60°C. The level of production is remarkable as compared to earlier reports.

Hydrolysis of lignocellulosic feedstock by novel cellulases originating from Pseudomonas sp. CL3 for fermentative hydrogen production

A newly isolated indigenous bacterium Pseudomonas sp. CL3 was able to produce novel cellulases consisting of endo-β-1,4-d-glucanase (80 and 100 kDa), exo-β-1,4-d-glucanase (55 kDa) and β-1,4-d-glucosidase (65 kDa) characterized by enzyme assay and zymography analysis. In addition, the CL3 strain also produced xylanase with a molecular weight of 20 kDa. The optimal temperature for enzyme activity was 50, 45, 45 and 55 °C for endo-β-1,4-d-glucanase, exo-β-1,4-d-glucanase, β-1,4-d-glucosidase and xylanase, respectively. All the enzymes displayed optimal activity at pH 6.0. The cellulases/xylanase could hydrolyze cellulosic materials very effectively and were thus used to hydrolyze natural agricultural waste (i.e., bagasse) for clean energy (H2) production by Clostridium pasteurianum CH4 using separate hydrolysis and fermentation process. The maximum hydrogen production rate and cumulative hydrogen production were 35 ml/L/h and 1420 ml/L, respectively, with a hydrogen yield of around 0.96 mol H2/mol glucose.

Alkalistable endo-β-1,4-xylanase production from a newly isolated alkalitolerant Penicillium sp. SS1 using agro-residues

Thermostable and alkalitolerant xylanases have got intense research focus due to their vast applications in various industries including pulp and paper, food, feed, textile, biofuel, etc. In the present investigation, a Penicillum sp. SS1 isolated from degrading woody material was found to produce moderately thermoactive and alkalistable endo-β-1,4-xylanase (xylanase). Maximum xylanase production was observed after fourth day of fermentation (43.84 IU/ml). The organism produced substantial quantities of xylanase using agricultural residues like wheat bran (20.6 IU/ml), rice bran (21.8 IU/ml) and sawdust (10.7 IU/ml) as carbon sources. The enzyme preparation was totally free of filter paper activity (FPase) and possessed negligible carboxymethyl cellulase (CMCase) activity; this could be an important feature of enzyme if the intended application of enzyme is in pulp and paper industries. Among nitrogen sources examined, yeast extract supported maximum xylanase production (45.74 IU/ml), and was followed by soybean meal (22.2 IU/ml) and ammonium sulphate (20 IU/ml). Maximum xylanase production was observed at initial medium pH 9 (25.6 IU/ml); however, at pH 8 and 10 also significantly high enzyme titre was observed (24 and 21.2 IU/ml, respectively). Thus, Penicillium sp. SS1 displayed capability of growing and producing xylanase at high alkaline pH (8-10). Maximum xylanase activity was reported at 50 °C, however, significantly high activity was observed at 60 °C (65.4%), however, at 70-80 °C activity was lost considerably. At 50-60 °C the enzyme retained very high activity up to 30-60 min (91-100%), however, prolonged incubation (90 min) caused considerable activity reduction (residual activity 63-68%).

Purification and characterization studies of a thermostable β-xylanase from Aspergillus awamori

This study presents data on the production, purification, and properties of a thermostable β-xylanase produced by an Aspergillus awamori 2B.361 U2/1 submerged culture using wheat bran as carbon source. Fractionation of the culture filtrate by membrane ultrafiltration followed by Sephacryl S-200 and Q-Sepharose chromatography allowed for the isolation of a homogeneous xylanase (PXII-1), which was 32.87 kDa according to MS analysis. The enzyme-specific activity towards soluble oat spelt xylan, which was found to be 490 IU/mg under optimum reaction conditions (50°C and pH 5.0-5.5), was 17-fold higher than that measured in the culture supernatant. Xylan reaction products were identified as xylobiose, xylotriose, and xylotetraose. K (m) values (mg ml(-1)) for soluble oat spelt and birchwood xylan were 11.8 and 9.45, respectively. Although PXII-1 showed 85% activity retention upon incubation at 50 °C and pH 5.0 for 20 days, incubation at pH 7.0 resulted in 50% activity loss within 3 days. PXII-1 stability at pH 7.0 was improved in the presence of 20 mM cysteine, which allowed for 85% activity retention for 25 days. This study on the production in high yields of a remarkably thermostable xylanase is of significance due to the central role that this class of biocatalyst shares, along with cellulases, for the much needed enzymatic hydrolysis of biomass. Furthermore, stable xylanases are important for the manufacture of paper, animal feed, and xylooligosaccharides.

A novel microbial habitat of alkaline black liquor with very high pollution load: microbial diversity and the key members in application potentials

A microbial community which developed naturally in alkaline black liquor was investigated by culture-based and culture-independent techniques. The community was effective in lowering pH, color, and chemical oxygen demand (COD) of black liquor, and the community activities varied in different seasons. Both 16S ribosomal DNA (rDNA) clone library and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analyses suggested that the seasonal bacterial communities had obvious differences in diversities and compositions. Clostridium species were suggested to be the key agents in black liquor treatment. Moreover, the isolates of the genera Halomonas and Bacillus were shown to be effective in treating very heavily polluted black liquor. The strains of Halomonas, Clostridium and especially Bacillus, might be the key producers of xylanase and CMCase in the community. The worldwide problem of black liquor treatment and renewable resource utilization would benefit from these microorganisms in application potentials.