Improved lignocellulose conversion to biofuels with thermophilic bacteria and thermostable enzymes

Characterization of Thermophilic Microorganisms in the Geothermal Water Flow of El Chichón Volcano Crater Lake

This study reports for the first time the isolation, identification and characterization of lipase-producing thermophilic strain from the geothermal water of the El Chichón volcano crater lake. Two strains were identified by 16S rRNA sequencing as Geobacillus jurassicus CHI2 and Geobacillus stearothermophilus CHI1. Results showed that G. jurassicus CHI2 is Gram-positive, able to ferment maltose, fructose and sucrose and to hydrolyze starch and casein; while G. stearothermophilus CHI1 showed to be Gram-variable, able to ferment maltose and fructose and to hydrolyze starch. Colonies of both strains presented irregular shape, umbilicated elevation of gummy texture and cells presented flagellar movement to survive in fluids with high temperature and mass gradients due to complex phenomena of heat and mass transfer present in the geothermal fluids. Lipase production for G. stearothermophilus CHI1 was also evaluated. It was found that this strain possesses a growth associated with extracellular lipase production with a high activity of 143 U/mL at 8.3 h of incubation time, superior to the activities reported for other microorganisms of genus Geobacillus; for this reason, it can be said that the thermal flow of the El Chichón volcano crater lake can be a useful source of lipase-producing thermophilic bacteria.

Thermotolerant glycosyl hydrolases-producing Bacillus aerius CMCPS1 and its saccharification efficiency on HCR-laccase (LccH)-pretreated corncob biomass

BACKGROUND

The current production of bioethanol based on lignocellulosic biomass (LCB) highly depends on thermostable enzymes and extremophiles owing to less risk of contamination. Thermophilic bacterial cellulases are preferred over fungi due to their higher growth rate, presence of complex multi-enzymes, stability, and enhanced bioconversion efficiency. Corncob, underutilized biomass, ensures energy conservation due to high lignocellulosic and more fermentable sugar content. In the present study, the thermophilic bacterium Bacillus aerius CMCPS1, isolated from the thermal springs of Manikaran, Himachal Pradesh, India, was characterized in terms of its activity, stability, and hydrolytic capacity. A two-step process comprising: (i) a combined strategy of hydrodynamic cavitation reaction (HCR)-coupled enzymatic (LccH at 6.5 U) pretreatment for delignification and (ii) subsequent hydrolysis of pre-treated (HCR-LccH) corncob biomass (CCB) using a thermostable cocktail of CMCPS1 was adopted to validate the efficiency of the process. Some of the parameters studied include lignin reduction, cellulose increase, and saccharification efficiency.

RESULT

Among the five isolates obtained by in situ enrichment on various substrates, B. aerius CMCPS1, isolated from hot springs, exhibited the maximum hydrolytic activity of 4.11. The GH activity of the CMCPS1 strain under submerged fermentation revealed maximum filter paper activity (FPA) and endoglucanase activity of 4.36 IU mL-1 and 2.98 IU mL-1, respectively, at 44 h. Similarly, the isolate produced exoglucanase and β-glucosidase with an activity of 1.76 IU mL-1 and 1.23 IU mL-1 at 48 h, respectively. More specifically, the enzyme endo-1,4-β-d glucanase E.C.3.2.1.4 (CMCase) produced by B. aerius CMCPS1 displayed wider stability to pH (3-9) and temperature (30-90 °C) than most fungal cellulases. Similarly, the activity of CMCase increased in the presence of organic solvents (118% at 30% acetone v/v). The partially purified CMCase from the culture supernatant of CMCPS1 registered 64% yield with twofold purification. The zymogram and SDS-PAGE analyses further confirmed the CMCase activity with an apparent molecular mass of 70 kDa. The presence of genes specific to cellulases, such as cellulose-binding domain CelB, confirmed the presence of GH family 46 and β-glucosidase activity (GH3). The multifunctional cellulases of CMCPS1 were evaluated for their saccharification efficiency on laccase (LccH, a fungal laccase from Hexagonia hirta MSF2)-pretreated corncob in a HCR. The lignin and hemicelluloses removal efficiency of HCR-LccH was 54.1 and 6.57%, respectively, with an increase in cellulose fraction (42.25%). The saccharification efficiency of 55% was achieved with CMCPS1 multifunctional cellulases at 50 °C and pH 5.0.

CONCLUSION

The multifunctional cellulase complex of B. aerius CMCPS1 is a potential biocatalyst for application in lignocellulosic biomass-based biorefineries. The saccharification ability of HCR-LccH-pretreated corncob at elevated temperatures would be an advantage for biofuel production from lignocellulosic biomass.

Recent Development of Extremophilic Bacteria and Their Application in Biorefinery

The biorefining technology for biofuels and chemicals from lignocellulosic biomass has made great progress in the world. However, mobilization of laboratory research toward industrial setup needs to meet a series of criteria, including the selection of appropriate pretreatment technology, breakthrough in enzyme screening, pathway optimization, and production technology, etc. Extremophiles play an important role in biorefinery by providing novel metabolic pathways and catalytically stable/robust enzymes that are able to act as biocatalysts under harsh industrial conditions on their own. This review summarizes the potential application of thermophilic, psychrophilic alkaliphilic, acidophilic, and halophilic bacteria and extremozymes in the pretreatment, saccharification, fermentation, and lignin valorization process. Besides, the latest studies on the engineering bacteria of extremophiles using metabolic engineering and synthetic biology technologies for high-efficiency biofuel production are also introduced. Furthermore, this review explores the comprehensive application potential of extremophiles and extremozymes in biorefinery, which is partly due to their specificity and efficiency, and points out the necessity of accelerating the commercialization of extremozymes.

Adaptive Enrichment of a Thermophilic Bacterial Isolate for Enhanced Enzymatic Activity

The mimicking of evolution on a laboratory timescale to enhance biocatalyst specificity, substrate utilization activity, and/or product formation, is an effective and well-established approach that does not involve genetic engineering or regulatory details of the microorganism. The present work employed an evolutionary adaptive approach to improve the lignocellulose deconstruction capabilities of the strain by inducing the expression of laccase, a multicopper oxidase, in Geobacillus sp. strain WSUCF1. This bacterium is highly efficient in depolymerizing unprocessed lignocellulose, needing no preprocessing/pretreatment of the biomasses. However, it natively produces low levels of laccase. After 15 rounds of serially adapting this thermophilic strain in the presence of unprocessed corn stover as the selective pressure, we recorded a 20-fold increase in catalytic laccase activity, at 9.23 ± 0.6 U/mL, in an adapted yet stable strain of Geobacillus sp. WSUCF1, compared with the initial laccase production (0.46 ± 0.04 U/mL) obtained with the unadapted strain grown on unprocessed corn stover before optimization. Chemical composition analysis demonstrated that lignin removal by the adapted strain was 22 wt.% compared with 6 wt.% removal by the unadapted strain. These results signify a favorable prospect for fast, cost competitive bulk production of this thermostable enzyme. Also, this work has practical importance, as this fast adaptation of the Geobacillus sp. strain WSUCF1 suggests the possibility of growing industrial quantities of Geobacillus sp. strain WSUCF1 cells as biocatalysts on reasonably inexpensive carbon sources for commercial use. This work is the first application of the adaptive laboratory evolution approach for developing the desired phenotype of enhanced ligninolytic capability in any microbial strain.

Extremophile Microalgae: the potential for biotechnological application

Microalgae are photosynthetic microorganisms that use sunlight as an energy source, and convert water, carbon dioxide, and inorganic salts into algal biomass. The isolation and selection of microalgae, which allow one to obtain large amounts of biomass and valuable compounds, is a prerequisite for their successful industrial production. This work provides an overview of extremophile algae, where their ability to grow under harsh conditions and the corresponding accumulation of metabolites are addressed. Emphasis is placed on the high-value products of some prominent algae. Moreover, the most recent applications of these microorganisms and their potential exploitation in the context of astrobiology are taken into account.

Real-Time QCM-D Monitoring of the Adsorption-Desorption of Expansin on Lignin

Expansin has nonhydrolytic disruptive activity and synergistically acts with cellulases to enhance the hydrolysis of cellulose. The adsorption-desorption of expansin on noncellulosic lignin can greatly affect the action of expansin on lignocellulose. In this study, three lignins with different sources (kraft lignin (KL), sodium lignin sulfonate (SLS), and enzymatic hydrolysis lignin (EHL)) were selected as the substrates. The real-time adsorption-desorption of Bacillus subtilis expansin (BsEXLX1) on lignins was monitored using quartz crystal microgravimetry with dissipation (QCM-D). The effects of temperature and Tween 80 on the adsorption-desorption behaviors were also investigated. The results show that BsEXLX1 exhibited high binding ability on lignin and achieved maximum adsorption of 283.2, 273.8, and 266.9 ng cm^-2 at 25 °C on KL, SLS, and EHL, respectively. The maximum adsorption decreased to 148.2-192.8 ng cm^-2 when the temperature increased from 25 to 45 °C. Moreover, Tween 80 competitively bound to lignin and significantly prevented expansin adsorption. After irreversible adsorption of Tween 80, the maximum adsorption of BsEXLX1 greatly decreased to 33.3, 37.2, and 10.3 ng cm^-2 at 25 °C on KL, SLS, and EHL, respectively. Finally, a kinetic model was developed to analyze the adsorption-desorption process of BsEXLX1. BsEXLX1 has a higher adsorption rate constant (k_A) and a lower desorption rate constant (k_D) on KL than on SLS and EHL. The findings of this study provide useful insights into the adsorption-desorption of expansin on lignin.

Agave Leaves as a Substrate for the Production of Cellulases by Penicillium sp. and the Obtainment of Reducing Sugars

Lignocellulosic biomass can be used to obtain fermentable sugars by enzymatic hydrolysis, and also it serves as a carbon source to produce cellulases by solid-state fermentation. In this study, we propose the use of leaves of Agave salmiana as a carbon source to produce cellulases by the fungus Penicillium sp., isolated from the same plant. The crude enzymatic extract was used to obtain sugars from the hydrolysis of the parenchymal cells of the leaves. The enzymes produced were characterized (endoglucanase 14.4 U/g; exoglucanase 3.5 U/g; β-glucosidase 4.14 U/g). The enzymes showed activities at elevated temperatures: 50°C for endoglucanase and exoglucanase and 70°C for β-glucosidase. Furthermore, the crude enzymatic extract obtained was able to hydrolyze the parenchyma in 51.6% in 48 h. The evidence presented in this paper shows the potential of the agave leaves as a source of carbon in the production of enzymes by fermentation with the consequent production of reducing sugars. In addition, the enzymes produced by Penicillium sp. could be used in the production of bioethanol, since they work at high temperatures.

Identification and Characterization of a Novel Hyperthermostable Bifunctional Cellobiohydrolase- Xylanase Enzyme for Synergistic Effect With Commercial Cellulase on Pretreated Wheat Straw Degradation

The novel cellobiohydrolase gene ctcel7 was identified from Chaetomium thermophilum, and its recombinant protein CtCel7, a member of glycoside hydrolase family 7, was heterologously expressed in Pichia pastoris and biochemically characterized. Compared with commercial hydrolases, purified CtCel7 exhibited superior bifunctional cellobiohydrolase and xylanase activities against microcrystalline cellulose and xylan, respectively, under optimal conditions of 60°C and pH 4.0. Moreover, CtCel7 displayed remarkable thermostability with over 90% residual activity after heat (60°C) treatment for 180 min. CtCel7 was insensitive to most detected cations and reagents and preferentially cleaved the β-1,4-glycosidic bond to generate oligosaccharides through the continuous saccharification of lignocellulosic substrates, which are crucial for various practical applications. Notably, the hydrolysis effect of a commercial cellulase cocktail on pretreated wheat straw was substantively improved by its combination with CtCel7. Taken together, these excellent properties distinguish CtCel7 as a robust candidate for the biotechnological production of biofuels and biobased chemicals.

Mixing of Prosopis africana pods and corn cob exerts contrasting effects on the production and quality of Bacillus thuringiensis crude endoglucanase

Recently, attention has shifted to the use of mixed lignocellulosic substrates for the production of cellulolytic enzymes. However, researchers have focused mainly on achieving increased enzyme yields while neglecting other properties of the enzymes when using such mixtures. In this first-ever report of the application of Prosopis africana pod (PAP) in cellulase production, we investigated the effect of its combination with corn cob (CC), as an inducing carbon source, on the amounts and quality of crude endoglucanase produced by Bacillus thuringiensis SS12. The organism was grown on PAP, CC or their 1:1% w/w mixture (MS) and the crude endoglucanases produced were tested for activity, hydrolytic efficiency, and thermostability. PAP supported the highest enzyme activity (0.138 U/mL) and its endoglucanase was the most effective in hydrolyzing CMC and filter paper while CC-derived endoglucanase was the best for hydrolysis of alkali-pretreated CC. Enzyme activity of MS-derived endoglucanase (0.110 U/mL) was intermediate to that of PAP and CC (0.091 U/mL) and was the most stable at elevated temperatures (70 and 80 °C). It also liberated the least amount of reducing sugars from all tested substrates. Combination of both the substrates, thus, favored enzyme production and thermostability but was detrimental to hydrolytic efficiency.

CRISPR interference (CRISPRi) as transcriptional repression tool for Hungateiclostridium thermocellum DSM 1313

Hungateiclostridium thermocellum DSM 1313 has biotechnological potential as a whole-cell biocatalyst for ethanol production using lignocellulosic renewable sources. The full exploitation of H. thermocellum has been hampered due to the lack of simple and high-throughput genome engineering tools. Recently in our research group, a thermophilic bacterial CRISPR-Cas9-based system has been developed as a transcriptional suppression tool for regulation of gene expression. We applied ThermoCas9-based CRISPR interference (CRISPRi) to repress the H. thermocellum central metabolic lactate dehydrogenase (ldh) and phosphotransacetylase (pta) genes. The effects of repression on target genes were studied based on transcriptional expression and product formation. Single-guide RNA (sgRNA) under the control of native intergenic 16S/23S rRNA promoter from H. thermocellum directing the ThermodCas9 to the promoter region of both pta and ldh silencing transformants reduced expression up to 67% and 62% respectively. This resulted in 24% and 17% decrease in lactate and acetate production, correspondingly. Hence, the CRISPRi approach for H. thermocellum to downregulate metabolic genes can be used for remodelling of metabolic pathways without the requisite for genome engineering. These data established for the first time the feasibility of employing CRISPRi-mediated gene repression of metabolic genes in H. thermocellum DSM 1313.

An overview on bioethanol production from lignocellulosic feedstocks

Lignocellulosic ethanol has been proposed as a green alternative to fossil fuels for many decades. However, commercialization of lignocellulosic ethanol faces major hurdles including pretreatment, efficient sugar release and fermentation. Several processes were developed to overcome these challenges e.g. simultaneous saccharification and fermentation (SSF). This review highlights the various ethanol production processes with their advantages and shortcomings. Recent technologies such as singlepot biorefineries, combined bioprocessing, and bioenergy systems with carbon capture are promising. However, these technologies have a lower technology readiness level (TRL), implying that additional efforts are necessary before being evaluated for commercial availability. Solving energy needs is not only a technological solution and interlinkage of various factors needs to be assessed beyond technology development.

A Recombinant β-Mannanase from Thermoanaerobacterium aotearoense SCUT27: Biochemical Characterization and Its Thermostability Improvement

β-Mannanase was expressed in Thermoanaerobacterium aotearoense SCUT27 induced by locust bean gum (LBG). The open reading frame encoding a GH26 β-mannanase was identified and encoded a preprotein of 515 amino acids with a putative signal peptide. The enzyme without a signal sequence (Man25) was overexpressed in Escherichia coli with a specific activity of 1286.2 U/mg. Moreover, a facile method for β-mannanase activity screening was established based on agar plates. The optimum temperature for the purified Man25 using LBG as a substrate was 55 °C. The catalytic activity and thermostability of Man25 displayed a strong dependence on calcium ions. Through saturation mutagenesis at the putative Ca²⁺ binding sites in Man25, the best mutant ManM3-3 (D143A) presented improvements in thermostability with 3.6-fold extended half-life at 55 °C compared with that of the wild-type. The results suggest that mutagenesis at metal binding sites could be an efficient approach to increase enzyme thermostability.

A highly thermostable crude endoglucanase produced by a newly isolated Thermobifida fusca strain UPMC 901

A thermophilic Thermobifida fusca strain UPMC 901, harboring highly thermostable cellulolytic activity, was successfully isolated from oil palm empty fruit bunch compost. Its endoglucanase had the highest activity at 24 hours of incubation in carboxymethyl-cellulose (CMC) and filter paper. A maximum endoglucanase activity of 0.9 U/mL was achieved at pH 5 and 60 °C using CMC as a carbon source. The endoglucanase properties were further characterized using crude enzyme preparations from the culture supernatant. Thermal stability indicated that the endoglucanase activity was highly stable at 70 °C for 24 hours. Furthermore, the activity was found to be completely maintained without any loss at 50 °C and 60 °C for 144 hours, making it the most stable than other endoglucanases reported in the literature. The high stability of the endoglucanase at an elevated temperature for a prolonged period of time makes it a suitable candidate for the biorefinery application.

Engineered Thermoanaerobacterium aotearoense with nfnAB knockout for improved hydrogen production from lignocellulose hydrolysates

BACKGROUND

As a renewable and clean energy carrier, the production of biohydrogen from low-value feedstock such as lignocellulose has increasingly garnered interest. The NADH-dependent reduced ferredoxin:NADP⁺ oxidoreductase (NfnAB) complex catalyzes electron transfer between reduced ferredoxin and NAD(P)⁺, which is critical for production of NAD(P)H-dependent products such as hydrogen and ethanol. In this study, the effects on end-product formation of deletion of nfnAB from Thermoanaerobacterium aotearoense SCUT27 were investigated.

RESULTS

Compared with the parental strain, the NADH/NAD⁺ ratio in the ∆nfnAB mutant was increased. The concentration of hydrogen and ethanol produced increased by (41.1 ± 2.37)% (p < 0.01) and (13.24 ± 1.12)% (p < 0.01), respectively, while the lactic acid concentration decreased by (11.88 ± 0.96)% (p < 0.01) when the ∆nfnAB mutant used glucose as sole carbon source. No obvious inhibition effect was observed for either SCUT27 or SCUT27/∆nfnAB when six types of lignocellulose hydrolysate pretreated with dilute acid were used for hydrogen production. Notably, the SCUT27/∆nfnAB mutant produced 190.63-209.31 mmol/L hydrogen, with a yield of 1.66-1.77 mol/mol and productivity of 12.71-13.95 mmol/L h from nonsterilized rice straw and corn cob hydrolysates pretreated with dilute acid.

CONCLUSIONS

The T. aotearoense SCUT27/∆nfnAB mutant showed higher hydrogen yield and productivity compared with those of the parental strain. Hence, we demonstrate that deletion of nfnAB from T. aotearoense SCUT27 is an effective approach to improve hydrogen production by redirecting the electron flux, and SCUT27/∆nfnAB is a promising candidate strain for efficient biohydrogen production from lignocellulosic hydrolysates.

A novel neutral and thermophilic endoxylanase from Streptomyces ipomoeae efficiently produced xylobiose from agricultural and forestry residues

Endoxylanases capable of producing high ratios of xylobiose from agricultural and forestry residues in neutral and high temperature conditions are attractive for the prebiotic and alternative sweetener industries. In this study, a putative glycosyl hydrolase gene from Streptomyces ipomoeae was cloned and expressed in Escherichia coli. The recombinant enzyme, named as SipoEnXyn10A, hydrolyzed beechwood xylan in endo-action mode releasing xylobiose as its main end product. It was most active at pH 6.5 and 75-80 °C and showed remarkable stability at 65 °C. The xylobiose yield from 10 g corncob and moso bamboo reached 1.123 ± 0.021 and 0.229 ± 0.005 g, respectively, at pH 6.5 and 70 °C, whichwas higher than other reports using the same material. Moreover, high ratios of xylobiose in the xylose-based product of about 85% were obtained from corncob, moso bamboo sawdust, cassava stem and Chinese fir sawdust. These results demonstrated that SipoEnXyn10A has potential for industrial application.

Dextran Aldehyde in Biocatalysis: More Than a Mere Immobilization System

Dextran aldehyde (dexOx), resulting from the periodate oxidative cleavage of 1,2-diol moiety inside dextran, is a polymer that is very useful in many areas, including as a macromolecular carrier for drug delivery and other biomedical applications. In particular, it has been widely used for chemical engineering of enzymes, with the aim of designing better biocatalysts that possess improved catalytic properties, making them more stable and/or active for different catalytic reactions. This polymer possesses a very flexible hydrophilic structure, which becomes inert after chemical reduction; therefore, dexOx comes to be highly versatile in a biocatalyst design. This paper presents an overview of the multiple applications of dexOx in applied biocatalysis, e.g., to modulate the adsorption of biomolecules on carrier surfaces in affinity chromatography and biosensors design, to serve as a spacer arm between a ligand and the support in biomacromolecule immobilization procedures or to generate artificial microenvironments around the enzyme molecules or to stabilize multimeric enzymes by intersubunit crosslinking, among many other applications.

A design of experiments approach for the rapid formulation of a chemically defined medium for metabolic profiling of industrially important microbes

Geobacillus thermoglucosidans DSM2542 is an industrially important microbe, however the complex nutritional requirements of Geobacilli confound metabolic engineering efforts. Previous studies have utilised semi-defined media recipes that contain complex, undefined, biologically derived nutrients which have unknown ingredients that cannot be quantified during metabolic profiling. This study used design of experiments to investigate how individual nutrients and interactions between these nutrients contribute to growth. A mathematically derived defined medium has been formulated that has been shown to robustly support growth of G. thermoglucosidans in two different environmental conditions (96-well plate and shake flask) and with a variety of lignocellulose-based carbohydrates. This enabled the catabolism of industrially relevant carbohydrates to be investigated.

Genome Sequencing Revealed the Biotechnological Potential of an Obligate Thermophile Geobacillus thermoleovorans Strain RL Isolated from Hot Water Spring

In the present study, we report the draft genome sequence of an obligate thermophile Geobacillus thermoleovorans strain RL isolated from Manikaran hot water spring located atop the Himalayan ranges, India. Strain RL grew optimally at 70 °C but not below 45 °C. The draft genome (3.39 Mb) obtained by Illumina sequencing contains 138 contigs with an average G + C content of 52.30%. RAST annotation showed that amino acid metabolism pathways were most dominant followed by carbohydrate metabolism. Genome-wide analysis using NCBI's Prokaryotic Genome Annotation Pipeline revealed that strain RL encodes for a cocktail of industrially important hydrolytic enzymes glycoside hydrolase, α-and β-glucosidase, xylanase, amylase, neopullulanase, pullulanase and lipases required for white biotechnology. In addition, the presence of genes encoding green biocatalyst multicopper polyphenol oxidase (laccase) and an anticancer enzyme l-glutaminase reflects the significance of strain RL in gray and red biotechnology, respectively. Strain RL is a thermophilic multi-enzyme encoding bacterium which could be the source for the recombinant production of biotechnologically significant enzymes. In, addition whole cells of strain RL may be used in bioremediation studies.

Improvements of thermophilic enzymes: From genetic modifications to applications

Thermozymes (from thermophiles or hyperthermophiles) offer obvious advantages due to their excellent thermostability, broad pH adaptation, and hydrolysis ability, resulting in diverse industrial applications including food, paper, and textile processing, biofuel production. However, natural thermozymes with low yield and poor adaptability severely hinder their large-scale applications. Extensive studies demonstrated that using genetic modifications such as directed evolution, semi-rational design, and rational design, expression regulations and chemical modifications effectively improved enzyme's yield, thermostability and catalytic efficiency. However, mechanism-based techniques for thermozymes improvements and applications need more attention. In this review, stabilizing mechanisms of thermozymes are summarized for thermozymes improvements, and these improved thermozymes eventually have large-scale industrial applications.

A novel thermostable GH10 xylanase with activities on a wide variety of cellulosic substrates from a xylanolytic Bacillus strain exhibiting significant synergy with commercial Celluclast 1.5 L in pretreated corn stover hydrolysis

BACKGROUND

Cellulose and hemicellulose are the two largest components in lignocellulosic biomass. Enzymes with activities towards cellulose and xylan have attracted great interest in the bioconversion of lignocellulosic biomass, since they have potential in improving the hydrolytic performance and reducing the enzyme costs. Exploring glycoside hydrolases (GHs) with good thermostability and activities on xylan and cellulose would be beneficial to the industrial production of biofuels and bio-based chemicals.

RESULTS

A novel GH10 enzyme (XynA) identified from a xylanolytic strain Bacillus sp. KW1 was cloned and expressed. Its optimal pH and temperature were determined to be pH 6.0 and 65 °C. Stability analyses revealed that XynA was stable over a broad pH range (pH 6.0-11.0) after being incubated at 25 °C for 24 h. Moreover, XynA retained over 95% activity after heat treatment at 60 °C for 60 h, and its half-lives at 65 °C and 70 °C were about 12 h and 1.5 h, respectively. More importantly, in terms of substrate specificity, XynA exhibits hydrolytic activities towards xylans, microcrystalline cellulose (filter paper and Avicel), carboxymethyl cellulose (CMC), cellobiose, p-nitrophenyl-β-d-cellobioside (pNPC), and p-nitrophenyl-β-d-glucopyranoside (pNPG). Furthermore, the addition of XynA into commercial cellulase in the hydrolysis of pretreated corn stover resulted in remarkable increases (the relative increases may up to 90%) in the release of reducing sugars. Finally, it is worth mentioning that XynA only shows high amino acid sequence identity (88%) with rXynAHJ14, a GH10 xylanase with no activity on CMC. The similarities with other characterized GH10 enzymes, including xylanases and bifunctional xylanase/cellulase enzymes, are no more than 30%.

CONCLUSIONS

XynA is a novel thermostable GH10 xylanase with a wide substrate spectrum. It displays good stability in a broad range of pH and high temperatures, and exhibits activities towards xylans and a wide variety of cellulosic substrates, which are not found in other GH10 enzymes. The enzyme also has high capacity in saccharification of pretreated corn stover. These characteristics make XynA a good candidate not only for assisting cellulase in lignocellulosic biomass hydrolysis, but also for the research on structure-function relationship of bifunctional xylanase/cellulase.

Enhancement of bioethanol production from Moso bamboo pretreated with biodiesel crude glycerol: Substrate digestibility, cellulase absorption and fermentability

Utilization of sustainable energy is limited by energy requirement for the manufacturing of renewable fuels. Moso bamboo was pretreated with industrially derived crude glycerol obtained from different sources at 150/160 °C for 3 h. This bamboo, pretreated with base biodiesel glycerol with pressure filtration removal method, showed a high glucose yield of 94.95% and an ethanol yield of 73.10% of the theoretical. Major glycerol content was removed by pressure filtration, leaving a small amount of fatty acid soap in the pretreated sample, which formed an emulsion that reduced lignin redisposition onto the biomass surface and effectively blocked lignin absorption of cellulase, allowing greater enzymatic hydrolysis and fermentation system function. The surface was more hydrophilic and a higher lignin removal was achieved: 39.24% with base biodiesel glycerol pretreatment compared to 26.08% with sodium hydroxide glycerol pretreatment. This study provides a useful and cost-effective process, BBGP, for high-yield ethanol production.

Optimization of cell culture and cell disruption processes to enhance the production of thermophilic cellulase FnCel5A in E.coli using response surface methodology

FnCel5A from Fervidobacterium nodosum is one of the most thermostable endoglucanases that have phenomenal characteristics, such as high activity, pH stability, and multi-specificity towards various substrates. However, large-scale thermophilic enzyme production is still a challenge. Herein, we focus on an optimization approach based on response surface methodology to improve the production of this enzyme. First, a Box-Behnken design was used to examine physiochemical parameters such as induction temperatures, isopropylβ-D-1-thiogalactopyranoside concentrations and induction times on the heterogeneous expression of FnCel5A gene in E. coli. The best culture was collected after adding 0.56 mM IPTG and incubating it for 29.5 h at 24°C. The highest enzymatic activity observed was 3.31 IU/mL. Second, an economical "thermolysis" cell lysis method for the liberation of the enzymes was also optimized using Box-Behnken design. The optimal levels of the variables were temperature 77°C, pH 7.71, and incubation time of 20 min, which gave about 74.3% higher activity than the well-established bead-milling cell disruption method. The maximum productivity of FnCel5A achieved (5772 IU/L) illustrated that its production increased significantly after combining both optimal models. This strategy can be scaled-up readily for overproduction of FnCel5A from recombinant E.coli to facilitate its usage in biomass energy production.

Waste-to-wealth: biowaste valorization into valuable bio(nano)materials

The waste-to-wealth concept aims to promote a future sustainable lifestyle where waste valorization is seen not only for its intrinsic benefits to the environment but also to develop new technologies, livelihoods and jobs.

A novel strategy to enhance biohydrogen production using graphene oxide treated thermostable crude cellulase and sugarcane bagasse hydrolyzate under co-culture system

Graphene oxide (GO) treated thermostable crude cellulase has been obtained via fungal co-cultivation of strain Cladosporium cladosporioides NS2 and Emericella variecolor NS3 using mix substrate of orange peel and rice straw under solid state fermentation (SSF). Enzyme activity of 60 IU/gds FP, 300 IU/gds EG and 400 IU/gds BGL are recorded in the presence of 1.0% GO in 96 h. This crude enzyme showed 50 °C as optimum incubation temperature, thermally stable at 55 °C for 600 min and stability in the pH range 4.5-8.0. Further, 70.04 g/L of sugar hydrolyzate is obtained from enzymatic conversion of 3.0% alkali pre-treated baggase using GO treated crude cellulase. Finally, 2870 ml/L cumulative biohydrogen production having bacterial biomass ∼2.2 g/L and the complimentary initial pH 7.0 is recorded from sugar hydrolyzate via dark fermentation using co-culture of Clostridium pasteurianum (MTCC116) and a newly isolated Bacillus subtilis PF_1.

Ig-like Domain in Endoglucanase Cel9A from Alicyclobacillus acidocaldarius Makes Dependent the Enzyme Stability on Calcium

Endoglucanase Cel9A from Alicyclobacillus acidocaldarius (AaCel9A) has an Ig-like domain and the enzyme stability is dependent to calcium. In this study the effect of calcium on the structure and stability of the wild-type enzyme and the truncated form (the wild-type enzyme without Ig-like domain, AaCel9AΔN) was investigated. Fluorescence quenching results indicated that calcium increased and decreased the rigidity of the wild-type and truncated enzymes, respectively. RMSF results indicated that AaCel9A has two flexible regions (regions A and B) and deleting the Ig-like domain increased the truncated enzyme stability by decreasing the flexibility of region B probably through increasing the hydrogen bonds. Calcium contact map analysis showed that deleting the Ig-like domain decreased the calcium contacting residues and their calcium binding affinities, especially, in region B which has a role in calcium binding site in AaCel9A. Metal depletion and activity recovering as well as stability results showed that the structure and stability of the wild-type and truncated enzymes are completely dependent on and independent of calcium, respectively. Finally, one can conclude that the deletion of Ig-like domain makes AaCel9AΔN independent of calcium via decreasing the flexibility of region B through increasing the hydrogen bonds. This suggests a new role for the Ig-like domain which makes AaCel9A structure dependent on calcium.

Bioprospecting thermophilic glycosyl hydrolases, from hot springs of Himachal Pradesh, for biomass valorization

The harnessing of biocatalysts from extreme environment hot spring niche for biomass conversion is significant and promising owing to the special characteristics of extremozymes attributed by intriguing biogeochemistry and extreme conditions of these environments. Hence, in the present study 38 bacterial isolates obtained from hot springs of Manikaran (~ 95 °C), Kalath (~ 50 °C) and Vasist (~ 65 °C) of Himachal Pradesh were screened for glycosyl hydrolases by in situ enrichment technique using lignocellulosic biomass (LCB). Based on their hydrolytic potential 5 isolates were selected and they were Bacillus tequilensis (VCB1, VCB2 and VSDB4), and B. licheniformis (KBFB2 and KBFB3). Cellulolytic activity assayed by growth under submerged fermentation showed that B. tequilensis VCB1 had maximum FPA activity (3.38 IU ml⁻¹) in 48 h, while B. licheniformis KBFB3 excelled for endoglucanase (EGA of 4.81 IU ml⁻¹ in 24 h) and cellobiase (0.71 IU ml⁻¹ in 48 h) activities. Among all the thermophilic biocatalysts evaluated, highest exoglucanase (0.06 IU ml⁻¹) activity was observed in B. tequilensis VSDB4 while endoglucanase of B. licheniformis KBFB3 showed optimum specific activity at pH 7 and 70 °C. Further, the presence of celS, celB and xlnB genes in the isolates suggest their possible role in biomass conversion. Protein profiling by SDS-PAGE analysis revealed that cellulase isoforms migrated with molecular masses of 75 kDa. The endoglucanase activity of promising strain B. licheniformis KBFB3 was enhanced in the presence of Ca²⁺, mercaptoethanol and sodium hypochlorite whereas moderately inhibited by Cu²⁺, Zn²⁺, urea, SDS and H₂O₂. The results of this study indicate scope for the possible development of novel biocatalysts with multifunctional thermostable glycosyl hydrolases from hot springs for efficient hydrolysis of the complex lignocellulosic biomass into simple sugars and other derived bioproducts leading to biomass valorization.

Single pot bioconversion of prairie cordgrass into biohydrogen by thermophiles

The aim of the present work was to use a thermophilic consortium for H₂ production using lignocellulosic biomass in a single pot. The thermophilic consortium, growing at 60 °C utilized both glucose and xylose, making it an ideal source of microbes capable of utilizing and fermenting both hexose and pentose sugars. The optimization of pH, temperature, and substrate concentration increased the H₂ production from 1.07 mmol H₂/g of prairie cordgrass (PCG) to 2.2 mmol H₂/g PCG by using the thermophilic consortium. A sequential cultivation of a thermostable lignocellulolytic enzyme producing strain Geobacillus sp. strain WSUCF1 (aerobic) with the thermophilic consortium (anaerobic) further increased H₂ production with PCG 3-fold (3.74 mmol H₂/g PCG). A single pot sequential culturing of aerobic and anaerobic microbes can be sustainable and advantageous for industrial scale production of biofuels.

Thermostable Xylanase Production by Geobacillus sp. Strain DUSELR13, and Its Application in Ethanol Production with Lignocellulosic Biomass

The aim of the current study was to optimize the production of xylanase, and its application for ethanol production using the lignocellulosic biomass. A highly thermostable crude xylanase was obtained from the Geobacillus sp. strain DUSELR13 isolated from the deep biosphere of Homestake gold mine, Lead, SD. Geobacillus sp. strain DUSELR13 produced 6 U/mL of the xylanase with the beechwood xylan. The xylanase production was improved following the optimization studies, with one factor at a time approach, from 6 U/mL to 19.8 U/mL with xylan. The statistical optimization with response surface methodology further increased the production to 31 U/mL. The characterization studies revealed that the crude xylanase complex had an optimum pH of 7.0, with a broad pH range of 5.0⁻9.0, and an optimum temperature of 75 °C. The ~45 kDa xylanase protein was highly thermostable with t_1/2 of 48, 38, and 13 days at 50, 60, and 70 °C, respectively. The xylanase activity increased with the addition of Cu^+2, Zn⁺², K^+, and Fe⁺² at 1 mM concentration, and Ca⁺², Zn⁺², Mg⁺², and Na⁺ at 10 mM concentration. The comparative analysis of the crude xylanase against its commercial counterpart Novozymes Cellic HTec and Dupont, Accellerase XY, showed that it performed better at higher temperature, hydrolyzing 65.4% of the beechwood at 75 °C. The DUSEL R13 showed the mettle to hydrolyze, and utilize the pretreated, and untreated lignocellulosic biomass: prairie cord grass (PCG), and corn stover (CS) as the substrate, and gave a maximum yield of 20.5 U/mL with the untreated PCG. When grown in co-culture with Geobacillus thermoglucosidasius, it produced 3.53 and 3.72 g/L ethanol, respectively with PCG, and CS. With these characteristics the xylanase under study could be an industrial success for the high temperature bioprocesses.

The Genome of a Thermo Tolerant, Pathogenic Albino Aspergillus fumigatus

Biotechnologists are interested in thermo tolerant fungi to manufacture enzymes active and stable at high temperatures, because they provide improved catalytic efficiency, strengthen enzyme substrate interactions, accelerate substrate enzyme conversion rates, enhance mass transfer, lower substrate viscosity, lessen contamination risk and offer the potential for enzyme recycling. Members of the genus Aspergillus live a wide variety of lifestyles, some embrace GRAS status routinely employed in food processing while others such as Aspergillus fumigatus are human pathogens. A. fumigatus produces melanins, pyomelanin protects the fungus against reactive oxygen species and DHN melanin produced by the pksP gene cluster confers the gray-greenish color. pksP mutants are attenuated in virulence. Here we report on the genomic DNA sequence of a thermo tolerant albino Aspergillus isolated from rain forest composted floors. Unexpectedly, the nucleotide sequence was 95.7% identical to the reported by Aspergillus fumigatus Af293. Genome size and predicted gene models were also highly similar, however differences in DNA content and conservation were observed. The albino strain, classified as Aspergillus fumigatus var. niveus, had 160 gene models not present in A. fumigatus Af293 and A. fumigatus Af293 had 647 not found in the albino strain. Furthermore, the major pigment generating gene cluster pksP appeared to have undergone genomic rearrangements and a key tyrosinase present in many aspergilli was missing from the genome. Remarkably however, despite the lack of pigmentation A. fumigatus var. niveus killed neutropenic mice and survived macrophage engulfment at similar rates as A. fumigatus Af293.

Cellulases from Thermophiles Found by Metagenomics

Cellulases are a heterogeneous group of enzymes that synergistically catalyze the hydrolysis of cellulose, the major component of plant biomass. Such reaction has biotechnological applications in a broad spectrum of industries, where they can provide a more sustainable model of production. As a prerequisite for their implementation, these enzymes need to be able to operate in the conditions the industrial process requires. Thus, cellulases retrieved from extremophiles, and more specifically those of thermophiles, are likely to be more appropriate for industrial needs in which high temperatures are involved. Metagenomics, the study of genes and gene products from the whole community genomic DNA present in an environmental sample, is a powerful tool for bioprospecting in search of novel enzymes. In this review, we describe the cellulolytic systems, we summarize their biotechnological applications, and we discuss the strategies adopted in the field of metagenomics for the discovery of new cellulases, focusing on those of thermophilic microorganisms.

Microbial diversity of thermophiles with biomass deconstruction potential in a foliage-rich hot spring

The ability of thermophilic microorganisms and their enzymes to decompose biomass have attracted attention due to their quick reaction time, thermostability, and decreased risk of contamination. Exploitation of efficient thermostable glycoside hydrolases (GHs) could accelerate the industrialization of biofuels and biochemicals. However, the full spectrum of thermophiles and their enzymes that are important for biomass degradation at high temperatures have not yet been thoroughly studied. We examined a Malaysian Y-shaped Sungai Klah hot spring located within a wooded area. The fallen foliage that formed a thick layer of biomass bed under the heated water of the Y-shaped Sungai Klah hot spring was an ideal environment for the discovery and analysis of microbial biomass decay communities. We sequenced the hypervariable regions of bacterial and archaeal 16S rRNA genes using total community DNA extracted from the hot spring. Data suggested that 25 phyla, 58 classes, 110 orders, 171 families, and 328 genera inhabited this hot spring. Among the detected genera, members of Acidimicrobium, Aeropyrum, Caldilinea, Caldisphaera, Chloracidobacterium, Chloroflexus, Desulfurobacterium, Fervidobacterium, Geobacillus, Meiothermus, Melioribacter, Methanothermococcus, Methanotorris, Roseiflexus, Thermoanaerobacter, Thermoanaerobacterium, Thermoanaerobaculum, and Thermosipho were the main thermophiles containing various GHs that play an important role in cellulose and hemicellulose breakdown. Collectively, the results suggest that the microbial community in this hot spring represents a good source for isolating efficient biomass degrading thermophiles and thermozymes.

Effect of CBM1 and linker region on enzymatic properties of a novel thermostable dimeric GH10 xylanase (Xyn10A) from filamentous fungus Aspergillus fumigatus Z5

Xylanase with a high thermostability will satisfy the needs of raising the temperature of hydrolysis to improve the rheology of the broth in industry of biomass conversion. In this study, a xylanase gene (xyn10A), predicted to encode a hydrolase domain of GH10, a linker region and a CBM1 domain, was cloned from a superior lignocellulose degrading strain Aspergillus fumigatus Z5 and successfully expressed in Pichia pastoris X33. Xyn10A has a specific xylanase activity of 34.4 U mg⁻¹, and is optimally active at 90 °C and pH 6.0. Xyn10A shows quite stable at pHs ranging from 3.0 to 11.0, and keeps over 40% of xylanase activity after incubation at 70 °C for 1 h. Removal of CBM1 domain has a slight negative effect on its thermostability, but the further cleavage of linker region significantly decreased its stability at high temperature. The transfer of CBM1 and linker region to another GH10 xylanase can help to increase the thermostability. In addition, hydrolase domains between the two Xyn10A proteins naturally formed a dimer structure, which became more thermostable after removing the CBM1 or/and linker region. This thermostable Xyn10A is a suitable candidate for the highly efficient fungal enzyme cocktails for biomass conversion.

Functional Genomics in the Study of Metabolic Pathways in Medicago truncatula: An Overview

In addition to its value as a model system for studies on symbiotic nitrogen fixation, Medicago truncatula has recently become an organism of choice for dissection of complex pathways of secondary metabolism. This work has been driven by two main reasons, both with practical implications. First Medicago species possess a wide range of flavonoid and terpenoid natural products, many of which, for example, the isoflavonoids and triterpene saponins, have important biological activities impacting both plant and animal (including human) health. Second, M. truncatula serves as an excellent model for alfalfa, the world's major forage legume, and forage quality is determined in large part by the concentrations of products of secondary metabolism, particularly lignin and condensed tannins. We here review recent progress in understanding the pathways leading to flavonoids, lignin, and triterpene saponins through utilization of genetic resources in M. truncatula.

Glycoside hydrolase gene transcription by Alicyclobacillus acidocaldarius during growth on wheat arabinoxylan and monosaccharides: a proposed xylan hydrolysis mechanism

BACKGROUND

Metabolism of carbon bound in wheat arabinoxylan (WAX) polysaccharides by bacteria requires a number of glycoside hydrolases active toward different bonds between sugars and other molecules. Alicyclobacillus acidocaldarius is a Gram-positive thermoacidophilic bacterium capable of growth on a variety of mono-, di-, oligo-, and polysaccharides. Nineteen proposed glycoside hydrolases have been annotated in the A. acidocaldarius Type Strain ATCC27009/DSM 446 genome. Experiments were performed to understand the effect of monosaccharides on gene expression during growth on the polysaccharide, WAX.

RESULTS

Molecular analysis using high-density oligonucleotide microarrays was performed on A. acidocaldarius strain ATCC27009 when growing on WAX. When a culture growing exponentially at the expense of arabinoxylan saccharides was challenged with glucose or xylose, most glycoside hydrolases were downregulated. Interestingly, regulation was more intense when xylose was added to the culture than when glucose was added, showing a clear departure from classical carbon catabolite repression demonstrated by many Gram-positive bacteria. In silico analyses of the regulated glycoside hydrolases, along with the results from the microarray analyses, yielded a potential mechanism for arabinoxylan metabolism by A. acidocaldarius. Glycoside hydrolases expressed by this strain may have broad substrate specificity, and initial hydrolysis is catalyzed by an extracellular xylanase, while subsequent steps are likely performed inside the growing cell.

CONCLUSIONS

Glycoside hydrolases, for the most part, appear to be found in clusters, throughout the A. acidocaldarius genome. Not all of the glycoside hydrolase genes found at loci within these clusters were regulated during the experiment, indicating that a specific subset of the 19 glycoside hydrolase genes found in A. acidocaldarius were used during metabolism of WAX. While specific functions of the glycoside hydrolases were not tested as part of the research discussed, many of the glycoside hydrolases found in the A. acidocaldarius Type Strain appear to have a broader substrate range than that represented by the glycoside hydrolase family in which the enzymes were categorized.

State of the art review of biofuels production from lignocellulose by thermophilic bacteria

Biofuels, including ethanol and butanol, are mainly produced by mesophilic solventogenic yeasts and Clostridium species. However, these microorganisms cannot directly utilize lignocellulosic materials, which are abundant, renewable and non-compete with human demand. More recently, thermophilic bacteria show great potential for biofuels production, which could efficiently degrade lignocellulose through the cost effective consolidated bioprocessing. Especially, it could avoid contamination in the whole process owing to its relatively high fermentation temperature. However, wild types thermophiles generally produce low levels of biofuels, hindering their large scale production. This review comprehensively summarizes the state of the art development of biofuels production by reported thermophilic microorganisms, and also concludes strategies to improve biofuels production including the metabolic pathways construction, co-culturing systems and biofuels tolerance. In addition, strategies to further improve butanol production are proposed.