Potential halophilic cellulases for in situ enzymatic saccharification of ionic liquids pretreated lignocelluloses

Developing endophytic Penicillium oxalicum as a source of lignocellulolytic enzymes for enhanced hydrolysis of biorefinery relevant pretreated rice straw

Endophytic fungi, as plant symbionts, produce an elaborate array of enzymes for efficient disintegration of lignocellulosic biomass into constituent monomeric sugars, making them novel source of lignocellulolytic CAZymes with immense potential in future biorefineries. The present study reports lignocellulolytic enzymes production potential of an endophytic halotolerant Penicillium oxalicum strain isolated from Citrus limon, under submerged and solid-state fermentation (SmF & SSF, respectively), in the presence and absence of salt (1 M NaCl). The comparative QTOF-LC/MS-based exoproteome analysis of the culture extracts unveiled differential expression of CAZymes, with the higher abundance of GH6 and GH7 family cellobiohydrolase in the presence of 1 M salt. The strain improvement program, employing cyclic mutagenesis and diploidization, was utilized to develop hyper-cellulase producing mutant strains of P. oxalicum. The enzyme production of the developed strain (POx-M35) was further enhanced through statistical optimization of the culture conditions utilizing glucose mix disaccharides (GMDs) as an inducer. This optimization process resulted in the lignocellulolytic cocktail that contained high titers (U/mL) of endoglucanase (EG) (146.16), cellobiohydrolase (CBHI) (6.99), β-glucosidase (β-G) (26.21), xylanase (336.05) and FPase (2.02 U/mL), which were 5.47-, 5.54-, 8.55-, 4.96-, and 4.39-fold higher when compared to the enzyme titers obtained in wild HP1, respectively. Furthermore, the lignocellulolytic cocktails designed by blending secretome produced by mutant POx-M35 with xylanases (GH10 and GH11) derived from Malbranchea cinnamomea resulted in efficient hydrolysis of unwashed acid pretreated (UWAP) rice straw slurry and mild alkali deacetylated (MAD) rice straw. This study underscores the potential of bioprospecting novel fungus and developing an improved strain for optimized production and constitution of lignocellulolytic cocktails that can be an important determinant in advancing biomass conversion technologies.

Ion-combination specific effects driving the enzymatic activity of halophilic alcohol dehydrogenase 2 from Haloferax volcanii in aqueous ionic liquid solvent mixtures

Biocatalysis in ionic liquids enables novel routes for bioprocessing. Enzymes derived from extremophiles promise greater stability and activity under ionic liquid (IL) influence. Here, we probe the enzyme alcohol dehydrogenase 2 from the halophilic archaeon Haloferax volcanii in thirteen different ion combinations for relative activity and analyse the results against molecular dynamics (MD) simulations of the same IL systems. We probe the ionic liquid property space based on ion polarizability and molecular electrostatic potential. Using the radial distribution functions, survival probabilities and spatial distribution functions of ions, we show that cooperative ion-ion interactions determine ion-protein interactions, and specifically, strong ion-ion interactions equate to higher enzymatic activity if neither of the ions interact strongly with the protein surface. We further demonstrate a tendency for cations interacting with the protein surface to be least detrimental to enzymatic activity if they show a low polarizability when combined with small hydrophilic anions. We also find that the IL ion influence is not mitigated by the surplus of negatively charged residues of the halophilic enzyme. This is shown by free energy landscape analysis in root mean square deviation and distance variation plots of active site gating residues (Trp43 and His273) demonstrating no protection of specific structural elements relevant to preserving enzymatic activity. On the other hand, we observe a general effect across all IL systems that a tight binding of water at acidic residues is preferentially interrupted at these residues through the increased presence of potassium ions. Overall, this study demonstrates a co-ion interaction dependent influence on allosteric surface residues controlling the active/inactive conformation of halophilic alcohol dehydrogenase 2 and the necessity to engineer ionic liquid systems for enzymes that rely on the integrity of functional surface residues regardless of their halophilicity or thermophilicity for use in bioprocessing.

Halophilic filamentous fungi and their enzymes: Potential biotechnological applications

Recently, interest in the study of microorganisms growing under extreme conditions, particularly halophiles, has increased due to their potential use in industrial processes. Halophiles are the class of microorganisms that grow optimally at high NaCl concentrations and are capable of producing halophilic enzymes capable of catalyzing reactions under harsh conditions. So far, fungi are the least studied halophilic microorganisms, even though they have been shown to counteract these extreme conditions by producing secondary metabolites with very interesting properties. This review highlights mechanisms that allow halophilic fungi to adapt high salinity and the specificity of their enzymes to a spectrum of action in industrial and environmental applications. The peculiarities of these enzymes justify the urgent need to apply green alternative compounds in industries.

Biosynthesis and biodegradation of poly(3-hydroxybutyrate) from Priestia flexa; A promising mangrove halophyte towards the development of sustainable eco-friendly bioplastics

The protracted persistence of petrochemical plastics in the environment and their non-biodegradability impede the survival of living creatures. Recently, biopolymers are being thoroughly researched as a potential replacement for conventional plastics. This present study sought to locate Poly(3-hydroxybutyrate) synthesizing bacterial species prevalent in the mangrove ecosystem. Six halophilic bacterial isolates were obtained from the mangrove habitat, four isolates displayed superior cell dry weight as well as PHB accumulation. Isolate PMPHB5 showed the highest cell dry weight (4.92 ± 0.02 g/L), while the maximum PHA yield (80%) was found with PMPHB7. Hence, PMPHB7 was chosen for further optimization of carbon source wherein glucose demonstrated improved cell growth as well as PHB production. The characterization of the PHB granules was performed by FT-IR spectroscopy and FE-SEM EDX. The presence of characteristic elements in the sample was confirmed using EDX. Isolate PMPHB7 was further identified as Priestia flexa through 16S rRNA gene sequencing (GenBank accession number: ON362236) and a phylogenetic tree was constructed to reveal the molecular relationships of this organism with others. The solvent-cast biopolymer film was made to check the biodegradability of the extracted PHB. When buried in soil, it was found that the biopolymer film exhibited approximately 73% biodegradation after 21 days. Thus, the present study sheds light on the potential of mangrove-associated halophytes to efficiently produce PHB that is readily biodegradable in soil.

Halophilic and Halotolerant Actinomycetes of Sambhar Salt Lake, India: Screening and Optimization of Cellulolytic Activity

Actinomycetes are Gram-positive filamentous bacteria well known for the production of bioactive compounds. Recently, many halophilic habitats have been explored for isolation of actinomycetes that exhibit biotechnological potentials. In this investigation, a saline habitat of Rajasthan, Sambhar Salt Lake (SSL) was selected to study the actinomycetes population and Carboxy Methyl Cellulase (CMCase) production by native isolates. A total of sixteen actinomycete isolates, halotolerant and moderately halophilic, were obtained using culture-dependent methods and characterized morphologically and biochemically. They were identified as members of Streptomyces, Nocardiopsis, Pseudonocardia, Saccharospolyspora, and Microbispora. Streptomyces was the most dominating genus, followed by Nocardiopsis. Agar plate assay was used for screening the isolates for CMCase production. Thirteen were found to produce the enzyme, apparent by hydrolysis observed on media plates. The highest relative activity of 22.04 was shown by isolate SSL 14 identified as Nocardiopsis sp. by 16S rDNA sequencing studies and thus selected for further optimization studies. Maximum enzyme (1.08 ± 0.09 U/ml) was produced using medium containing Carboxy Methyl Cellulose (Carbon source) and yeast extract (nitrogen source) at 12% NaCl and pH 9.0, incubated at 30 °C for 96 h. Maximum CMCase production at high salt concentration and pH suggests that Nocardiopsis SSL 14 can be used for industrial processes that operate under excessive saline and alkaline conditions.

Turning mannitol-rich agricultural waste to poly(3-hydroxybutyrate) with Cobetia amphilecti fermentation and recovery with methyl levulinate as a green solvent

The present study explored the use of mannitol and mannitol-rich agro-industrial wastes as substrates for PHB production by Cobetia amphilecti isolated from the green Ulva sp. seaweed. Cultivation of C. amphilecti on mannitol, celery, and olive leaves (OLs) waste led to 4.20, 6.00, and 5.16 g L^-1 of cell dry mass (CDM), 76.3, 25.5, and 12.0% of PHB content in CDM and 3.2, 1.53, and 0.62 g L^-1 of PHB concentration, respectively; which suggested that they can be exploited as carbon substrates for the production of PHB. Extraction of PHB from C. amphilecti cultures by solubilization in the green solvent methyl levulinate (ML) (2% w/w, 140 °C, 1 h) indicated that the recovery yield and purity of PHB are above 97 and 90% w/w, respectively. The use of ML could be an attractive method for the recovery of PHB when safe and non-toxic solvents are required.

Seawater-based biorefineries: A strategy to reduce the water footprint in the conversion of lignocellulosic biomass

Biorefineries are an essential step towards implementing a circular economy in the long term. They are based on renewable raw materials and must be designed holistically, recovering building blocks from being converted into several products. Lignocellulosic biomass is considered a critical pillar for a biologically based economy and a high value-added feedstock. The separation of the structural complexity that makes up the biomass allows the development of different product flows. Chemical, physical, and biological processes are evaluated for fractionation, hydrolysis, and fermentation processes in biorefineries; however, the volume of freshwater used affects water safety and increases the economic costs. Non-potable-resources-based technologies for biomass bioconversion are essential for biorefineries to become environmentally and economically sustainable systems. Studies are being carried out to substitute freshwater with seawater to reduce the water footprint. Accordingly, this review addresses a comprehensive discussion about seawater-based biorefineries focusing on lignocellulosic biomass conversion in biofuel and value-added products.

Isolation of Halomicroarcula pellucida strain GUMF5, an archaeon from the Dead Sea-Israel possessing cellulase

A strain designated GUMF5 was isolated in Goa-India from sediments of Dead Sea-Israel  and identified as haloarchaeon Halomicroarcula pellucida based on 16S rRNA gene analysis similarity value of 99.84%. Strain GUMF5 grew on mineral salts medium with 20% NaCl and 0.5% carboxymethyl cellulose-sodium (CMC-Na) as a sole source of carbon and produced haloextremozyme cellulase. The enzyme was concentrated using Sephadex G20, precipitated with ethanol, dialyzed and retentate purified using Sephadex G200, the size exclusion chromatography. A yield of 78.53% cellulase with an activity of 131.13 U/mg and 1.24-fold purity was obtained. The purified cellulase had optimum activity at 20% NaCl, at 40 ºC, 0.5% CMC-Na, pH 7 and 150 rpm. SDS-PAGE combined with zymographic analysis revealed the molecular weight of cellulase as 240 kDa, 40 kDa and 17.4 kDa. The activity of the enzyme was stimulated by metallic cations in the order of Ca⁺² > Mn⁺² > Mg⁺² > SO₄ ^2- > NH₄ ⁺ and was inhibited by Ag⁺  > Fe⁺² > Cu⁺². Methanol and ethanol enhanced the cellulase activity by 6% and 26%, respectively. The haloextremozyme cellulase degraded Whatman No. 1 filter paper indicated in scanning electron micrographs, exposure of open pores and fibers without any intra connectivity corresponding to paperase activity and implicating the possible use of enzyme to bio-convert cellulosic waste. Conclusively, Halomicroarcula pellucida GUMF5 (Accession number: MH244431), globally, is the only Halomicroarcula pellucida isolated from the sediments of Dead Sea producing haloextremozyme cellulase, and hence is an important biotechnological resource.

Bioreactor and Bioprocess Design Issues in Enzymatic Hydrolysis of Lignocellulosic Biomass

Saccharification of lignocellulosic biomass is a fundamental step in the biorefinery of second generation feedstock. The physicochemical and enzymatic processes for the depolymerization of biomass into simple sugars has been achieved through numerous studies in several disciplines. The present review discusses the development of technologies for enzymatic saccharification in industrial processes. The kinetics of cellulolytic enzymes involved in polysaccharide hydrolysis has been discussed as the starting point for the design of the most promising bioreactor configurations. The main process configurations—proposed so far—for biomass saccharification have been analyzed. Attention was paid to bioreactor configurations, operating modes and possible integrations of this operation within the biorefinery. The focus is on minimizing the effects of product inhibition on enzymes, maximizing yields and concentration of sugars in the hydrolysate, and reducing the impact of enzyme cost on the whole process. The last part of the review is focused on an emerging process based on the catalytic action of laccase applied to lignin depolymerization as an alternative to the consolidated physicochemical pretreatments. The laccases-based oxidative process has been discussed in terms of characteristics that can affect the development of a bioreactor unit where laccases or a laccase-mediator system can be used for biomass delignification.

Marine bacteria associated with the green seaweed Ulva sp. for the production of polyhydroxyalkanoates

This work aimed to isolate a series of bacterial strains associated with the green seaweed Ulva sp. and evaluate their capability to manufacture PHA. The effect of the type of supplemented sugars found to be in macroalgae, on the growth and PHA productivity of the strains was studied. Analysis of the 16S rRNA gene sequence of the isolated strains revealed that the PHA-producing bacteria were phylogenetically related to the genus Cobetia, Bacillus, Pseudoaltermonas and Sulfitobacter, which showed high PHA contents among the isolates. The highest PHA content was observed in the case of Cobetia strain, with up to 61% w/w in the presence of mannitol and 12% w/w on Ulva sp. acid hydrolysate as a substrate.

Efficient enzymatic saccharification of alkaline and ionic liquid-pretreated bamboo by highly active extremozymes produced by the co-culture of two halophilic fungi

Herein, we studied two strains of halophilic fungi (Aspergillus flavus and Aspergillus penicillioides) as potential potent sources of hydrolases under solid-state fermentation conditions. We found that the co-culture of these two fungal species was associated with maximal CMCase, FPase, xylanase, and β-xylosidase activity under optimized fermentation conditions. These enzymes functioned optimally at pH values from 9.0 to 10.0, at temperatures from 50 °C to 60 °C, and in the presence of 15-20% NaCl. These enzymes were also stable in metal salt solutions and the presence of ionic liquids. Reducing sugar yields following the cellulase-hemicellulase co-treatment of untreated, alkaline-pretreated, and ionic liquid-pretreated bamboo were higher than those associated with separate cellulase and hemicellulase treatments, thus confirming the synergistic activity of cellulase-hemicellulase co-treatment in the context of bamboo saccharification. These results indicate that these two fungi are promising hydrolase producers that can facilitate the bioconversion of bamboo biomass.

Revealing of sugar utilization systems in Halomonas sp. YLGW01 and application for poly(3-hydroxybutyrate) production with low-cost medium and easy recovery

Poly(3-hydroxybutyrate) (PHB) is a common polyhydroxyalkanoate (PHA) with potential as an alternative for petroleum-based plastics. Previously, we reported a new strain, Halomonas sp. YLGW01, which hyperproduces PHB with 94% yield using fructose. In this study, we examined the PHB production machinery of Halomonas sp. YLGW01 in more detail by deep-genome sequencing, which revealed a 3,453,067-bp genome with 65.1% guanine-cytosine content and 3054 genes. We found two acetyl-CoA acetyltransferases (Acetoacetyl-CoA thiolase, PhaA), one acetoacetyl-CoA reductase (PhaB), two PHB synthases (PhaC1, PhaC2), PHB depolymerase (PhaZ), and Enoyl-CoA hydratase (PhaJ) in the genome, along with two fructose kinases and fructose transporter systems, including the phosphotransferase system (PTS) and ATP-binding transport genes. We then examined the PHB production by Halomonas sp. YLGW01 using high-fructose corn syrup (HFCS) containing fructose, glucose, and sucrose in sea water medium, resulting in 7.95 ± 0.11 g/L PHB (content, 67.39 ± 0.34%). PHB was recovered from Halomonas sp. YLGW01 using different detergents; the use of Tween 20 and SDS yielded micro-sized granules with high purity. Overall, these results reveal the distribution of PHB synthetic genes and the sugar utilization system in Halomonas sp. YLGW01 and suggest a possible method for PHB recovery.

Effects of soluble dietary fiber from soybean residue fermented by Neurospora crassa on the intestinal flora in rats

In this study, soluble dietary fiber (SDF, including oligosaccharides and polysaccharides) of soybean residue (SR) fermented by Neurospora crassa was used as a research object. In vitro fermentation technology was used to analyze the fermentation properties of SDF from fermented soybean residue (FSR). Moreover, the effects of SDF from FSR on the composition and diversity of intestinal microflora of rats were studied by high-throughput sequencing technology. Results showed that the SDF content of fermented soybean residue was 27.21%. The addition of SDF in the range 2 to 10 g L-1 could increase the levels of gas production and short-chain fatty acids (SCFAs), as well as decrease the pH and ammonia N concentration after 24 h fermentation in the fermentation broth compared with the control group (p < 0.05). The animal-based experiments showed that Bacteroidetes and Firmicutes were the major dominant phyla in all the groups. Compared with the control group, oligosaccharides and polysaccharides of FSR changed the relative abundance and diversity of the bacterial community, and increased the numbers of beneficial flora, such as Prevotellaceae and Lactobacillales. It was shown that SDF of SR fermented by Neurospora crassa had great effects on the intestinal environment and the composition of intestinal flora in rats.

Fermented Soybean Dregs by Neurospora crassa: a Traditional Prebiotic Food

Soybean dregs fermented by Neurospora crassa is a typical traditional food in Gannan district of China. In this study, in vitro imitated gut fermentation was carried out to evaluate whether the oligosaccharides from this fermented soybean dregs had potential prebiotic properties. 11.91% of oligosaccharides were extracted from the fermented soybean dregs at the optimized condition which of 1:25 for ratio of soybean dregs (g) to 50% ethanol (ml), 90 min of extracted duration at 70 °C for twice. The soybean dreg oligosaccharides (SBOS) were progressively purified with Sevag method and on columns filled with AB-8 macroporous resin, and then identified as cellobiose by HPLC-ESI-MS and FT-IR. Oligosaccharides of soybean dregs with 800 mg/L significantly decreased pH value (p < 0.05) and ammonia N concentration (p < 0.05), and increased short chain fatty acid (SCFA) level (p < 0.05) in imitated gut fermentation compared with control group. It was shown that this fermented soybean dregs could be a potential prebiotic food.

Biosynthesis of butyl esters from crude oil of palm fruit and kernel using halophilic lipase secretion by Marinobacter litoralis SW-45

Initially, a new moderate halophilic strain was locally isolated from seawater. The partial 16S rRNA sequence analysis positioned the organism in Marinobacter genus and was named 'Marinobacter litoralis SW-45'. This study further demonstrates successful utilization of the halophilic M. litoralis SW-45 lipase (MLL) for butyl ester synthesis from crude palm fruit oil (CPO) and kernel oil (CPKO) in heptane and solvent-free system, respectively, using hydroesterification. Hydrolysis and esterification of enzymatic [Thermomyces lanuginosus lipase (TLL)] hydrolysis of CPO and CPKO to free fatty acids (FFA) followed by MLL-catalytic esterification of the concentrated FFAs with butanol (acyl acceptor) to synthesize butyl esters were performed. A one-factor-at-a-time technique (OFAT) was used to study the influence of physicochemical factors on the esterification reaction. Under optimal esterification conditions of 40 and 45 °C, 150 and 230 rpm, 50% (v/v) biocatalyst concentration, 1:1 and 5:1 butanol:FFA, 9% and 15% (w/v) NaCl, 60 and 15 min reaction time for CPO- and CPKO-derived FFA esterification system, maximum ester conversion of 62.2% and 69.1%, respectively, was attained. Gas chromatography (GC) analysis confirmed the products formed as butyl esters. These results showed halophilic lipase has promising potential to be used for biosynthesis of butyl esters in oleochemical industry.

Proteins in Ionic Liquids: Reactions, Applications, and Futures

Biopolymer processing and handling is greatly facilitated by the use of ionic liquids, given the increased solubility, and in some cases, structural stability imparted to these molecules. Focussing on proteins, we highlight here not just the key drivers behind protein-ionic liquid interactions that facilitate these functionalities, but address relevant current and potential applications of protein-ionic liquid interactions, including areas of future interest.

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.

Characterization of the Microbial Population Inhabiting a Solar Saltern Pond of the Odiel Marshlands (SW Spain)

The solar salterns located in the Odiel marshlands, in southwest Spain, are an excellent example of a hypersaline environment inhabited by microbial populations specialized in thriving under conditions of high salinity, which remains poorly explored. Traditional culture-dependent taxonomic studies have usually under-estimated the biodiversity in saline environments due to the difficulties that many of these species have to grow at laboratory conditions. Here we compare two molecular methods to profile the microbial population present in the Odiel saltern hypersaline water ponds (33% salinity). On the one hand, the construction and characterization of two clone PCR amplified-16S rRNA libraries, and on the other, a high throughput 16S rRNA sequencing approach based on the Illumina MiSeq platform. The results reveal that both methods are comparable for the estimation of major genera, although massive sequencing provides more information about the less abundant ones. The obtained data indicate that Salinibacter ruber is the most abundant genus, followed by the archaea genera, Halorubrum and Haloquadratum. However, more than 100 additional species can be detected by Next Generation Sequencing (NGS). In addition, a preliminary study to test the biotechnological applications of this microbial population, based on its ability to produce and excrete haloenzymes, is shown.

Microbial Community Structure and Functional Potential Along a Hypersaline Gradient

Salinity is one of the strongest environmental drivers of microbial evolution and community composition. Here we aimed to determine the impact of salt concentrations (2.5, 7.5, and 33.2%) on the microbial community structure of reclaimed saltern ponds near San Francisco, California, and to discover prospective enzymes with potential biotechnological applications. Community compositions were determined by 16S rRNA amplicon sequencing revealing both higher richness and evenness in the pond sediments compared to the water columns. Co-occurrence network analysis additionally uncovered the presence of microbial seed bank communities, potentially primed to respond to rapid changes in salinity. In addition, functional annotation of shotgun metagenomic DNA showed different capabilities if the microbial communities at different salinities for methanogenesis, amino acid metabolism, and carbohydrate-active enzymes. There was an overall shift with increasing salinity in the functional potential for starch degradation, and a decrease in degradation of cellulose and other oligosaccharides. Further, many carbohydrate-active enzymes identified have acidic isoelectric points that have potential biotechnological applications, including deconstruction of biofuel feedstocks under high ionic conditions. Metagenome-assembled genomes (MAGs) of individual halotolerant and halophilic microbes were binned revealing a variety of carbohydrate-degrading potential of individual pond inhabitants.

Halotolerant microbial consortia able to degrade highly recalcitrant plant biomass substrate

The microbial degradation of plant-derived compounds under salinity stress remains largely underexplored. The pretreatment of lignocellulose material, which is often needed to improve the production of lignocellulose monomers, leads to high salt levels, generating a saline environment that raises technical considerations that influence subsequent downstream processes. Here, we constructed halotolerant lignocellulose degrading microbial consortia by enriching a salt marsh soil microbiome on a recalcitrant carbon and energy source, i.e., wheat straw. The consortia were obtained after six cycles of growth on fresh substrate (adaptation phase), which was followed by four cycles on pre-digested (highly-recalcitrant) substrate (stabilization phase). The data indicated that typical salt-tolerant bacteria made up a large part of the selected consortia. These were “trained” to progressively perform better on fresh substrate, but a shift was observed when highly recalcitrant substrate was used. The most dominant bacteria in the consortia were Joostella marina, Flavobacterium beibuense, Algoriphagus ratkowskyi, Pseudomonas putida, and Halomonas meridiana. Interestingly, fungi were sparsely present and negatively affected by the change in the substrate composition. Sarocladium strictum was the single fungal strain recovered at the end of the adaptation phase, whereas it was deselected by the presence of recalcitrant substrate. Consortia selected in the latter substrate presented higher cellulose and lignin degradation than consortia selected on fresh substrate, indicating a specialization in transforming the recalcitrant regions of the substrate. Moreover, our results indicate that bacteria have a prime role in the degradation of recalcitrant lignocellulose under saline conditions, as compared to fungi. The final consortia constitute an interesting source of lignocellulolytic haloenzymes that can be used to increase the efficiency of the degradation process, while decreasing the associated costs.

Screening of potential IL-tolerant cellulases and their efficient saccharification of IL-pretreated lignocelluloses

Lignocellulosic biomass as one of the most abundant and renewable resources has great potential for biofuel production. The complete conversion of biomass to biofuel is achieved through the effective pretreatment process and the following enzyme saccharification. Ionic liquids (ILs) are considered as a green solvent for lignocellulose pretreatment. However, ILs exhibit an inhibitory effect on cellulase activity, leading to a subsequent decrease in the efficiency of saccharification. The screening of new potential IL-tolerant cellulases is important. In the current study, a fungal strain with a relatively high cellulase production was isolated and identified as Penicillium oxalicum HC6. The culture conditions were optimized using corn stover and peptone as the carbon source and nitrogen source at pH 4.0 and 30 °C with an inoculation size of 2% (v/v) for 8 days. It was found that P. oxalicum HC6 exhibited potential salt tolerance with the increase of the enzyme production at a salt concentration of 5.0% (w/v). In addition, high enzyme activities were obtained at pH 4.0–6.0 and 50–65 °C. The crude enzyme from P. oxalicum HC6 with good thermal stability was also stable in the presence of salt and ILs. Good yields of reducing sugar were obtained by the crude enzyme from P. oxalicum HC6 after the saccharification of corn stover that was pretreated by ILs. P. oxalicum HC6 with potentially salt-tolerant and IL-tolerant enzymes has great potential application in the enzymatic saccharification of lignocellulose.

Lignocellulosic biomass as one of the most abundant and renewable resources has great potential for biofuel production.

Facing the challenge of sustainable bioenergy production: Could halophytes be part of the solution?

Due to steadily growing population and economic transitions in the more populous countries, renewable sources of energy are needed more than ever. Plant biomass as a raw source of bioenergy and biofuel products may meet the demand for sustainable energy; however, such plants typically compete with food crops, which should not be wasted for producing energy and chemicals. Second-generation or advanced biofuels that are based on renewable and non-edible biomass resources are processed to produce cellulosic ethanol, which could be further used for producing energy, but also bio-based chemicals including higher alcohols, organic acids, and bulk chemicals. Halophytes do not compete with conventional crops for arable areas and freshwater resources, since they grow naturally in saline ecosystems, mostly in semi-arid and arid areas. Using halophytes for biofuel production may provide a mid-term economically feasible and environmentally sustainable solution to producing bioenergy, contributing, at the same time, to making saline areas – which have been considered unproductive for a long time – more valuable. This review emphasises on halophyte definition, global distribution, and environmental requirements. It also examines their enzymatic valorization, focusing on salt-tolerant enzymes from halophilic microbial species that may be deployed with greater advantage compared to their conventional mesophilic counterparts for faster degradation of halophyte biomass.

Thermal Inactivation Kinetics and Secondary Structure Change of a Low Molecular Weight Halostable Exoglucanase from a Marine Aspergillus niger at High Salinities

Two kinds of exoglucanase were purified from a marine Aspergillus niger. Catalytic ability of halophilic exoglucanase with a lower molecular weight and secondary structure change was analyzed at different salinities. Activity of the low molecular weight exoglucanase in 10% NaCl solution (w/v) was 1.69-fold higher of that in NaCl-free solution. Half-life time in 10% NaCl solution (w/v) was over 1.27-fold longer of that in NaCl-free solution. Free energy change of the low molecular weight exoglucanase denaturation, △G, in 10% NaCl solution (w/v) was 0.54 kJ/mol more than that in NaCl-free solution. Melt point in 10% NaCl solution (w/v), 52.01 °C, was 4.21 °C higher than that in NaCl-free solution, 47.80 °C. K _m value, 0.179 mg/ml in 10% NaCl solution (w/v) was less 0.044 mg/ml than that, 0.224 mg/ml, in NaCl-free solution. High salinity made content of α-helix increased. Secondary structure change caused by high salinities improved exoglucanase thermostability and catalysis activity. The halophilic exoglucanase from a marine A. niger was valuable for hydrolyzing cellulose at high salinities.

Isolation, one-step affinity purification, and characterization of a polyextremotolerant laccase from the halophilic bacterium Aquisalibacillus elongatus and its application in the delignification of sugar beet pulp

The aim of the present work was to study the ability of a halophilic bacterial laccase to efficient delignification in extreme conditions. Here, a highly stable extracellular laccase showing ligninolytic activity from halophilic Aquisalibacillus elongatus is described. The laccase production was strongly influenced by NaCl and CuSO₄ and under optimal conditions reached 4.8UmL^-1. The monomeric enzyme of 75kDa was purified by a synthetic affinity column with 68.2% yield and 99.8-fold purification. The enzyme showed some valuable features viz. stability against a wide range of organic solvents, salts, metals, inhibitors, and surfactants and specificity to a wide spectrum of substrates diverse in structure and redox potential. It retained more than 50% of the original activity at 25-75°C and pH 5.0-10.0. Furthermore, the enzyme was found to be effective in the delignification of sugar beet pulp in an ionic liquid that makes it useful for industrial applications.

Enzyme kinetics approach to assess biocatalyst inhibition and deactivation caused by [bmim][Cl] ionic liquid during cellulose hydrolysis

The aim of this work was to study the inhibition and deactivation of commercial enzyme cocktail (Cellic® Htec2) in the presence of [bmim][Cl] ionic liquid employing model cellulosic substrate, carboxymethyl cellulose (CMC). It turned out from the experiments - relying on enzyme kinetics approach - that [bmim][Cl] could act as a competitive inhibitor. Furthermore, depending on the process conditions i.e. contact of enzyme solution with high concentration [bmim][Cl], severe biocatalyst inactivation should be also taken into account as a potential risk during the enzymatic cellulose hydrolysis even in as short process times as few minutes.

Characterization of lignocellulolytic activities from fungi isolated from the deep-sea sponge Stelletta normani

Extreme habitats have usually been regarded as a source of microorganisms that possess robust proteins that help enable them to survive in such harsh conditions. The deep sea can be considered an extreme habitat due to low temperatures (<5°C) and high pressure, however marine sponges survive in these habitats. While bacteria derived from deep-sea marine sponges have been studied, much less information is available on fungal biodiversity associated with these sponges. Following screening of fourteen fungi isolated from the deep-sea sponge Stelletta normani sampled at a depth of 751 metres, three halotolerant strains (TS2, TS11 and TS12) were identified which displayed high CMCase and xylanase activities. Molecular based taxonomic approaches identified these strains as Cadophora sp. TS2, Emericellopsis sp. TS11 and Pseudogymnoascus sp. TS 12. These three fungi displayed psychrotolerance and halotolerant growth on CMC and xylan as sole carbon sources, with optimal growth rates at 20°C. They produced CMCase and xylanase activities, which displayed optimal temperature and pH values of between 50-70°C and pH 5-8 respectively, together with good thermostability and halotolerance. In solid-state fermentations TS2, TS11 and TS12 produced CMCases, xylanases and peroxidase/phenol oxidases when grown on corn stover and wheat straw. This is the first time that CMCase, xylanase and peroxidase/phenol oxidase activities have been reported in these three fungal genera isolated from a marine sponge. Given the biochemical characteristics of these ligninolytic enzymes it is likely that they may prove useful in future biomass conversion strategies involving lignocellulosic materials.

Enzymatic in situ saccharification of chestnut shell with high ionic liquid-tolerant cellulases from Galactomyces sp. CCZU11-1 in a biocompatible ionic liquid-cellulase media

In this study, it was the first time to report that the cellulases of Galactomyces sp. CCZU11-1 showed high activity and stability in the culture and reaction media containing IL [Mmim]DMP. Using untreated chestnut shell (CNS) as carbon source in the culture media containing IL [Mmim]DMP (5%, w/v), high activity of FPA (28.6U/mL), xylanase (186.2U/mL), and CMCase (107.3U/mL) were obtained, and 184.9mg/L of total protein was achieved. Furthermore, the changes in the structural features (crystallinity, morphology, and porosity) of the solid residue of CNS utilized with Galactomyces sp. CCZU11-1 were characterized with Fourier transform infrared spectroscopy, scanning electron microscopy, and X-ray diffraction. After was enzymatically hydrolyzed with the prepared crude enzymes in IL diluted to 20% (w/v), a high yield of reducing sugars, 62.1%, was obtained. Significantly, Galactomyces sp. CCZU11-1 showed high potential for the efficient transformation of lignocellulosic materials to glucose in a single-step process.

Advances in improving the performance of cellulase in ionic liquids for lignocellulose biorefinery

Ionic liquids (ILs) have been considered as a class of promising solvents that can dissolve lignocellulosic biomass and then provide enzymatic hydrolyzable holocellulose. However, most of available cellulases are completely or partially inactivated in the presence of even low concentrations of ILs. To more fully exploit the benefits of ILs to lignocellulose biorefinery, it is critical to improve the compatibility between cellulase and ILs. Various attempts have been made to screen natural IL-tolerant cellulases from different microhabitats. Several physical and chemical methods for stabilizing cellulases in ILs were also developed. Moreover, recent advances in protein engineering have greatly facilitated the rational engineering of cellulases by site-directed mutagenesis for the IL stability. This review is aimed to provide the first detailed overview of the current advances in improving the performance of cellulase in non-natural IL environments. New ideas from the most representative progresses and technical challenges will be summarized and discussed.

Genome Sequence of Halomonas sp. Strain KO116, an Ionic Liquid-Tolerant Marine Bacterium Isolated from a Lignin-Enriched Seawater Microcosm

Halomonas sp. strain KO116 was isolated from Nile Delta Mediterranean Sea surface water enriched with insoluble organosolv lignin. It was further screened for growth on alkali lignin minimal salts medium agar. The strain tolerates the ionic liquid 1-ethyl-3-methylimidazolium acetate. Its complete genome sequence is presented in this report.

Applicability evaluation of Deep Eutectic Solvents-Cellulase system for lignocellulose hydrolysis

Deep Eutectic Solvents (DESs) have recently emerged as a new generation of ionic liquids for lignocellulose pretreatment. However, DESs contain salt components which tend to inactivate cellulase in the subsequent saccharification process. To alleviate this problem, it is necessary to evaluate the applicability of the DESs-Cellulase system. This was accomplished in the present study by first studying the stability of cellulase in the presence of selected DESs followed by applicability evaluation based on glucose production, energy consumption and kinetic performance. Results showed that the cellulase was able to retain more than 90% of its original activity in the presence of 10% (v/v) for glycerol based DES (GLY) and ethylene glycol based DES (EG). Furthermore, both DESs system exhibited higher glucose percentage enhancement and lower energy consumption as compared to diluted alkali system. Among the two DESs studied, EG showed comparatively better kinetic performance.