Wood biodegradation and enzyme production by Ceriporiopsis subvermispora during solid-state fermentation of Eucalyptus grandis

CRISPR/Cas9 using a transient transformation system in Ceriporiopsis subvermispora

Ceriporiopsis subvermispora is a white-rot fungus with great potential for industrial and biotechnological applications, such as the pretreatment of lignocellulose in biorefineries, as it decomposes the lignin in the plant cell wall without causing severe cellulose degradation. A genetic transformation system was recently developed; however, gene-targeting experiments to disrupt or modify the gene(s) of interest remain challenging, and this is a bottleneck for further molecular genetic studies and breeding of C. subvermispora. Herein, we report efficient clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9)-assisted gene mutagenesis in this fungus. Two plasmids expressing Cas9 together with a different pyrG-targeting single-guide RNA were separately introduced into the monokaryotic C. subvermispora strain FP-90031-Sp/1, which frequently generated strains that exhibited resistance to 5-fluoroorotic acid and uridine/uracil auxotrophy. Southern blot analyses and genomic polymerase chain reaction followed by DNA sequencing of some mutants revealed that they were pyrG mutants. We also observed that hygromycin resistance of the pyrG mutants was frequently lost after repeated subcultivations, indicating that a maker-free genome editing occurred successfully. It is also suggested that a gene mutation(s) can be introduced via a transient expression of Cas9 and a single-guide RNA; this feature, together with high-frequency gene targeting using the CRISPR/Cas9 system, would be helpful for studies on lignocellulose-degrading systems in C. subvermispora. KEY POINTS: • Efficient plasmid-based CRISPR/Cas9 was established in C. subvermispora. • The mutations can be introduced via a transient expression of Cas9 and sgRNA. • A maker-free CRISPR/Cas9 is established in this fungus.

Comparative Analysis of Enzyme Production Patterns of Lignocellulose Degradation of Two White Rot Fungi: Obba rivulosa and Gelatoporia subvermispora

The unique ability of basidiomycete white rot fungi to degrade all components of plant cell walls makes them indispensable organisms in the global carbon cycle. In this study, we analyzed the proteomes of two closely related white rot fungi, Obba rivulosa and Gelatoporia subvermispora, during eight-week cultivation on solid spruce wood. Plant cell wall degrading carbohydrate-active enzymes (CAZymes) represented approximately 5% of the total proteins in both species. A core set of orthologous plant cell wall degrading CAZymes was shared between these species on spruce suggesting a conserved plant biomass degradation approach in this clade of basidiomycete fungi. However, differences in time-dependent production of plant cell wall degrading enzymes may be due to differences among initial growth rates of these species on solid spruce wood. The obtained results provide insight into specific enzymes and enzyme sets that are produced during the degradation of solid spruce wood in these fungi. These findings expand the knowledge on enzyme production in nature-mimicking conditions and may contribute to the exploitation of white rot fungi and their enzymes for biotechnological applications.

Overview of lignocellulolytic enzyme systems with special reference to valorization of lignocellulosic biomass

Lignocellulosic biomass, one of the most valuable natural resources, is abundantly present on earth. Being a renewable feedstock, it harbors a great potential to be exploited as a raw material, to produce various value-added products. Lignocellulolytic microorganisms hold a unique position regarding the valorization of lignocellulosic biomass as they contain efficient enzyme systems capable of degrading this biomass. The ubiquitous nature of these microorganisms and their survival under extreme conditions have enabled their use as an effective producer of lignocellulolytic enzymes with improved biochemical features crucial to industrial bioconversion processes. These enzymes can prove to be an exquisite tool when it comes to the eco-friendly manufacturing of value-added products using waste material. This review focuses on highlighting the significance of lignocellulosic biomass, microbial sources of lignocellulolytic enzymes and their use in the formation of useful products.

Amplicon-Based Sequencing of Soil Fungi from Wood Preservative Test Sites

Soil samples were collected from field sites in two AWPA (American Wood Protection Association) wood decay hazard zones in North America. Two field plots at each site were exposed to differing preservative chemistries via in-ground installations of treated wood stakes for approximately 50 years. The purpose of this study is to characterize soil fungal species and to determine if long term exposure to various wood preservatives impacts soil fungal community composition. Soil fungal communities were compared using amplicon-based DNA sequencing of the internal transcribed spacer 1 (ITS1) region of the rDNA array. Data show that soil fungal community composition differs significantly between the two sites and that long-term exposure to different preservative chemistries is correlated with different species composition of soil fungi. However, chemical analyses using ICP-OES found levels of select residual preservative actives (copper, chromium and arsenic) to be similar to naturally occurring levels in unexposed areas. A list of indicator species was compiled for each treatment-site combination; functional guild analyses indicate that long-term exposure to wood preservatives may have both detrimental and stimulatory effects on soil fungal species composition. Fungi with demonstrated capacity to degrade industrial pollutants were found to be highly correlated with areas that experienced long-term exposure to preservative testing.

Lignocellulose degradation patterns, structural changes, and enzyme secretion by Inonotus obliquus on straw biomass under submerged fermentation

This study examined the white rot fungus I. obliquus on the degradation of three types of straw biomass and the production of extracellular lignocellulolytic enzymes under submerged fermentation. The fungus process resulted in a highest lignin loss of 72%, 39%, and 47% in wheat straw, rice straw, and corn stover within 12days, respectively. In merely two days, the fungus selectively degraded wheat straw lignin by 37%, with only limited cellulose degradation (13%). Fourier transform infrared spectroscopy revealed that the fungus most effectively degraded the wheat straw lignin and rice straw crystalline cellulose. Scanning electronic microscopy showed the most pronounced structural changes in wheat straw. High activities of manganese peroxidase (159.0U/mL) and lignin peroxidase (123.4U/mL) were observed in wheat straw culture on Day 2 and 4, respectively. Rice straw was the best substrate to induce the production of cellulase and xylanase.

Differences between two strains of Ceriporiopsis subvermispora on improving the nutritive value of wheat straw for ruminants

AIM

This study evaluated differences between two strains of Ceriporiopsis subvermispora on improving the nutritive value and in vitro degradability of wheat straw.

METHODS AND RESULTS

Wheat straw was treated with the fungi for 7 weeks. Weekly samples were analysed for ergosterol content, in vitro gas production (IVGP), chemical composition and lignin-degrading enzyme activity. Ergosterol data showed CS1 to have a faster initial growth than CS2 and reaching a stationary phase after 3 weeks. The IVGP of CS1-treated wheat straw exceeded the control earlier than CS2 (4 vs 5 weeks). CS1 showed a significantly higher (P < 0·001) selectivity in lignin degradation compared to CS2. Both strains showed peak activity of laccase and manganese peroxidase (MnP) at week 1. CS1 showed a significantly higher (P < 0·001) laccase activity, but lower (P = 0·008) MnP activity compared to CS2.

CONCLUSION

Both CS strains improved the nutritive value of wheat straw. Variation between strains was clearly demonstrated by their growth pattern and enzyme activities.

SIGNIFICANCE AND IMPACT OF THE STUDY

The differences among the two strains provide an opportunity for future selection and breeding programs in improving the extent and selectivity of lignin degradation in agricultural biomass.

Anaerobic digestion of lignocellulosic biomasses pretreated with Ceriporiopsis subvermispora

Fungal pretreatment by Ceriporiopsis subvermispora of two forest residues (hazel and acacia branches) and two agricultural lignocellulosic residues (barley straw and sugarcane bagasse) were studied as a pretreatment to improve their subsequent anaerobic digestion for methane production. Biomass samples were grinded to 2 ranges of particle sizes (<4 or 1 mm), autoclaved, inoculated with two strains of C. subvermispora (ATCC 90467 and ATCC 96608) and incubated at 28 °C for 28 days. The effects of fungal pretreatment were assessed by analyzing the samples before and after incubations for dry solids mass, biochemical composition, bio-methane production (BMP) and availability of cellulose to hydrolysis. The production of ligninolytic enzymes MnP and/or laccase was observed with both strains during incubation on most of the samples tested. It almost doubled the hazel branches BMP per unit mass of dry solids but did not improve however the BMP of the agricultural residues and acacia branches. These observations were explained by the fact that although both strains were able to degrade 20-25% of lignin in <1 mm and <4 mm hazel branches samples, none of them was successful however to significantly degrade lignin in the other samples, except for sugarcane bagasse.

Evaluation of selected white-rot fungal isolates for improving the sugar yield from wheat straw

Biological pretreatment of lignocellulosic biomass by fungi can represent a low-cost and eco-friendly alternative to physicochemical methods to facilitate enzymatic hydrolysis. However, fungal metabolism can cause cellulose loss and it is therefore necessary to use the appropriate fungal strain-biomass type combination. In this work, the effects of biological pretreatments carried out by five different fungi on enzymatic hydrolysis of wheat straw were investigated. The best results were obtained with a Ceriporiopsis subvermispora strain, which minimized weight and cellulose losses and gave the highest net sugar yield (calculated with respect to the holocellulose content of the untreated straw), up to 44 % after a 10-week pretreatment, more than doubling the yields obtained with the other isolates. Moreover, prolonging the pretreatment from 4 up to 10 weeks produced a 2-fold increase, up to 60 %, in digestibility (sugar yield, calculated considering the holocellulose content of the pretreated material). The hemicellulose content of the pretreated material resulted inversely correlated with digestibility, and it could thus be utilized as an index of the pretreatment efficacy. Finally, a correlation was also found between digestibility and the difference between the absorbance values at 290 and 320 nm of pretreated wheat straw extracts.

Optimization of ligninolytic enzyme activity and production rate with Ceriporiopsis subvermispora for application in bioremediation by varying submerged media composition and growth immobilization support

Response surface methodology (central composite design of experiments) was employed to simultaneously optimize enzyme production and productivities of two ligninolytic enzymes produced by Ceriporiopsis subvermispora. Concentrations of glucose, ammonium tartrate and Polysorbate 80 were varied to establish the optimal composition of liquid media (OLM), where the highest experimentally obtained activities and productivities were 41 U L⁻¹ and 16 U L⁻¹ day⁻¹ for laccase (Lac), and 193 U L⁻¹ and 80 U L⁻¹ day⁻¹ for manganese peroxidase (MnP). Considering culture growth in OLM on various types of immobilization support, the best results were obtained with 1 cm beech wood cubes (BWCM). Enzyme activities in culture filtrate were 152 U L⁻¹ for Lac and 58 U L⁻¹ for MnP, since the chemical composition of this immobilization material induced higher Lac activity. Lower enzyme activities were obtained with polyurethane foam. Culture filtrates of OLM and BWCM were applied for dye decolorization. Remazol Brilliant Blue R (RBBR) was decolorized faster and more efficiently than Copper(II)phthalocyanine (CuP) with BWCM (80% and 60%), since Lac played a crucial role. Decolorization of CuP was initially faster than that of RBBR, due to higher MnP activities in OLM. The extent of decolorization after 14 h was 60% for both dyes.

Effect of hot water extraction and liquid hot water pretreatment on the fungal degradation of biomass feedstocks

Exhaustive hot water extraction (HWE) and liquid hot water (LHW) pretreatment were evaluated for their effects on degradation of biomass feedstocks (i.e., corn stover, wheat straw, and soybean straw) by Ceriporiopsis subvermispora. HWE (85 °C for 10 min) partially removed water soluble extractives and subsequently improved fungal degradation on wheat straw while it had little or no effect on the fungal degradation of corn stover and soybean straw. In contrast, LHW pretreatment at 170 °C for 3 min improved the fungal degradation of soybean straw; thus, lignin removal of 36.70% and glucose yield of 64.25% were obtained from the combined LHW and fungal pretreatment. However, corn stover, which was effectively degraded by fungal pretreatment alone, was less affected by this combined pretreatment. Our results indicated that a HWE or LHW pretreatment conducted under mild conditions worked synergistically with fungal degradation for some recalcitrant feedstocks.

Two-stage fungal biopulping for improved enzymatic hydrolysis of wood

A novel two-stage, whole organism fungal biopulping method was examined for increasing the yield of enzymatic hydrolysis of wood into soluble glucose. Liriodendron tulipifera wood chips (1g) were exposed to liquid culture suspensions of white rot (Ceriporiopsis subvermispora) or brown rot (Postia placenta) fungi and incubated at 28°C, either alone in single-stage 30 day (one fungal species applied) or two-stage 60 day (both fungal species applied in alternative succession) treatments. Fungi grew in all treatments, but did not significantly decrease the percent carbohydrate content of the wood. Two-stage treatments differed significantly in mass loss depending on order of exposure, suggesting additive or inhibitory fungal interactions occurred. Treatments consisting of C. subvermispora followed by P. placenta exhibited 6 ± 0.5% mass loss and increased the yield of enzymatic hydrolysis by 67-119%. This significant hydrolysis improvement suggests that fungal biopulping technologies could support commercial lignocellulosic ethanol production efforts if further developed.

Effectiveness of microbial pretreatment by Ceriporiopsis subvermispora on different biomass feedstocks

Different types of feedstocks, including corn stover, wheat straw, soybean straw, switchgrass, and hardwood, were tested to evaluate the effectiveness of fungal pretreatment by Ceriporiopsis subvermispora. After 18-d pretreatment, corn stover, switchgrass, and hardwood were effectively delignified by the fungus through manganese peroxidase and laccase. Correspondingly, glucose yields during enzymatic hydrolysis reached 56.50%, 37.15%, and 24.21%, respectively, which were a 2 to 3-fold increase over those of the raw materials. A further 10-30% increase in glucose yields was observed when pretreatment time extended to 35d. In contrast, cellulose digestibility of wheat straw and soybean straw was not significantly improved by fungal pretreatment. When external carbon sources and enzyme inducers were added during fungal pretreatment of wheat straw and soybean straw, only glucose and malt extract addition improved cellulose digestibility of wheat straw. The cellulose digestibility of soybean straw was not improved.

Effect of manganese on the secretion of manganese-peroxidase by the basidiomycete Ceriporiopsis subvermispora

The ligninolytic machinery of the widely used model fungus Ceriporiopsis subvermispora includes the enzymes manganese-peroxidase (MnP) and laccase (Lcs). In this work the effect of Mn(II) on the secretion of MnP was studied. Cultures grown in the absence of Mn(II) showed high levels of mnp transcripts. However, almost no MnP enzyme was detected in the extracellular medium, either by enzymatic activity assays or Western blot hybridizations. In the corresponding mycelia, immuno-electron microscopy experiments showed high levels of MnP enzyme within intracellular compartments. These results suggest that in addition to its well-known effect on transcription regulation of mnp genes, manganese influences secretion of MnP to the extracellular medium. Experiments carried out in the presence of cycloheximide confirmed that the metal is required to secrete MnP already synthesized and retained within the cell.

Cellobiose dehydrogenase from the ligninolytic basidiomycete Ceriporiopsis subvermispora

Cellobiose dehydrogenase (CDH), an extracellular flavocytochrome produced by several wood-degrading fungi, was detected in cultures of the selective delignifier Ceriporiopsis subvermispora when grown on a cellulose- and yeast extract-based liquid medium. CDH amounted to up to 2.5% of total extracellular protein during latter phases of the cultivation and thus suggested an important function for the fungus under the given conditions. The enzyme was purified 44-fold to apparent homogeneity. It was found to be present in two glycoforms of 98 kDa and 87 kDa with carbohydrate contents of 16 and 4%, respectively. The isoelectric point of both glycoforms is around 3.0, differing by 0.1 units, which is the most acidic value so far reported for a CDH. By using degenerated primers of known CDH sequences, one cdh gene was found in the genomic DNA, cloned, and sequenced. Alignment of the 774-amino-acid protein sequence revealed a high similarity to CDH from other white rot fungi. One notable difference was found in the longer interdomain peptide linker, which might affect the interdomain electron transfer at higher temperatures. The preferred substrate of C. subvermispora CDH is cellobiose, while glucose conversion is strongly discriminated by a 155,000-fold-lower catalytic efficiency. This is a typical feature of a basidiomycete CDH, as are the acidic pH optima for all tested electron acceptors in the range from 2.5 to 4.5.

Evaluation of the white-rot fungi Ganoderma australe and Ceriporiopsis subvermispora in biotechnological applications

Ganoderma australe is a white-rot fungus that causes a selective wood biodelignification in some hardwoods found in the Chilean rainforest. Ceriporiopsis subvermispora is also a lignin-degrading fungus used in several biopulping studies. The enzymatic system responsible for lignin degradation in wood can also be used to degrade recalcitrant organic pollutants in liquid effluents. In this work, two strains of G. australe and one strain of C. subvermipora were comparatively evaluated in the biodegradation of ABTS and the dye Poly R-478 in liquid medium, and in the pretreatment of Eucalyptus globulus wood chips for further kraft biopulping. Laccase was detected in liquid and wood cultures with G. australe. Ceriporiopsis subvermispora produce laccase and manganese peroxidase when grown in liquid medium and only manganese peroxidase was detected during wood decay. ABTS was totally depleted by all strains after 8 days of incubation while Poly R-478 was degraded up to 40% with G. australe strains and up to 62% by C. subvermispora after 22 days of incubation. Eucalyptus globulus wood chips decayed for 15 days presented 1-6% of lignin loss and less than 2% of glucan loss. Kraft pulps with kappa number 15 were produced from biotreated wood chips with 2% less active alkali, with up to 3% increase in pulp yield and up to 20% less hexenuronic acids than pulps from undecayed control. Results showed that G. australe strains evaluated were not as efficient as C. subvermispora for dye and wood biodegradation, but could be used as a feasible alternative in biotechnological processes such as bioremediation and biopulping.

Mycelium growth and degradation of creosote-treated wood by basydiomycetes

Tolerance of wood decay fungi of the genera Agrocybe, Armillaria, Auricularia, Daedalea, Pleurotus, Trametes to the presence of various amounts of creosote-treated wood (CTW) in the growth medium was compared. In the case of the most tolerant strain, Pleurotus ostreatus SMR 684, extracellular laccase and peroxidase specific activities were monitored during growth in the presence of CTW. Degradation of various creosote-constituting polycyclic aromatic hydrocarbons by this strain was evaluated by GC-MS and the ecotoxicity of treated and untreated CTW was compared by Microtox test.

Enzymatic properties of two β-glucosidases from Ceriporiopsis subvermispora produced in biopulping conditions

AIMS

Ceriporiopsis subvermispora produces endoglucanase and beta-glucosidase when cultivated on cellulose or wood, but biodegradation of cellulose during biopulping by C. subvermispora is low even after long periods. To resolve this discrepancy, we grew C. subvermispora on Pinus taeda wood chips and purified the major beta-glucosidases it produced. Kinetic parameters were determined to clear if this fungus produces enzymes capable of yielding assimilable glucose from wood.

METHODS AND RESULTS

Ceriporiopsis subvermispora was grown on P. taeda wood chips under solid-state fermentation. After 30 days, the crude extract obtained from enzyme extraction with sodium acetate buffer 50 mmol l(-1), pH 5.4, was filtrated in membranes with a molecular mass exclusion limit of 100 kDa. Enzyme purification was carried out using successively Sephacryl S-300 gel filtration. The retained fraction attained 76% of beta-glucosidase activity with 3.7-fold purification. Two beta-glucosidases were detected with molecular mass of 110 and 53 kDa. We have performed a characterization of the enzymatic properties of the beta-glucosidase of 110 kDa. The optimum pH and temperature were 3.5 and 60 degrees C, respectively. The K(m) and V(max) values were respectively 3.29 mmol l(-1) and 0.113 micromol min(-1) for the hydrolysis of p-nitrophenyl-beta-glucopyranoside (pNPG) and 2.63 mmol l(-1) and 0.103 micromol min(-1), towards cellobiose. beta-Glucosidase activity was strongly increased by Mn(2+) and Fe(3+), while Cu(2+) severely inhibited it.

CONCLUSIONS

Ceriporiopsis subvermispora produces small amounts of beta-glucosidase when grown on wood. The gel filtration and polyacrylamide gel electrophoresis data revealed the existence of two beta-glucosidases with 110 and 53 kDa. The 110 kDa beta-glucosidase from C. subvermispora can be efficiently purified in a single step by gel filtration chromatography. The enzyme has an acid pH optimum with similar activity on pNPG and cellobiose and is thus typical beta-glucosidase.

SIGNIFICANCE AND IMPACT OF THE STUDY

Ceriporiopsis subvermispora produces beta-glucosidase with limited action during wood decay making able its use for the production of biomechanical and biochemical pulps. The results presented in this paper show the importance of studying the behaviour of beta-glucosidases during biopulping.

Involvement of lignocellulolytic enzymes in the decomposition of leaf litter in a subtropical forest

The involvement of ligninolytic and cellulolytic enzymes, such as laccase, lignin peroxidase, manganese peroxidase, carboxymethylcellulase (CMCase), and filter paper activity (FPA), in the decomposition process of leaf litter driven by 6 soil-inhabiting fungi imperfecti was studied under solid-state fermentations. All the tested fungi exhibited varied production profiles of lignocellulolytic enzymes and each caused different losses in total organic matter (TOM) during decomposition. Based on the results, the 6 fungi could be divided into 2 functional groups: Group 1 includes Alternaria sp., Penicillium sp., Acremonium sp., and Trichoderma sp., and Group 2 includes Pestalotiopsis sp. and Aspergillus fumigatus. Group 1, with higher CMCase and FPA activities, showed a higher decomposition rate than the fungi of Group 2 over the first 16 d, and thereafter the cellulolytic activities and decomposition rate slowed down. Group 2 showed the maximum and significantly higher CMCase and FPA activities than those of the Group 1 fungi during the later days. This, combined with the much higher laccase activity, produced a synergistic reaction that led to a much faster average mass loss rate. These results suggest that the fungi of Group 1 are efficient decomposers of cellulose and that the fungi of Group 2 are efficient decomposers of lignocellulose. During cultivation, Pestalotiopsis sp. produced an appreciable amount of laccase activity (0.56+/-0.09 U/ml) without the addition of inducers and caused a loss in TOM of 38.2%+/-3.0%, suggesting that it has high potential to be a new efficient laccase-producing fungus.

Purification and properties of a xylanase from Ceriporiopsis subvermispora cultivated on Pinus taeda

The production of hemicellulose and cellulose degrading enzymes by the white-rot fungus Ceriporiopsis subvermispora was determined while growing in Pinus taeda wood chips. Enzymes produced by the fungus were extracted after 30 days of cultivation and at least two different xylanases were secreted. An endo-(1,4)-beta-xylanase was purified by means of ultrafiltration, anion exchange chromatography and gel filtration. Its molecular mass was 29 kDa and the pH and temperature optima were 5.0 and 60 degrees C, respectively. The endo-xylanase was able to hydrolyze xylan to principally xylotriose and xylotetraose and it has different activities against different xylans. With birchwood xylan as substrate, the enzyme showed a K(m) of 1.93 mg/ml and specific activity of 538 units/mg protein at 50 degrees C.