Ethanol production from high cellulose concentration by the basidiomycete fungus Flammulina velutipes

Screening of Fusarium moniliforme as Potential Fungus for Integrated Biodelignification and Consolidated Bioprocessing of Napier Grass for Bioethanol Production

A fungus capable of producing ethanol from various carbon substrates was screened for direct ethanol production from lignocellulose. Fusarium moniliforme BIOTECH 3170 produced ethanol from glucose, xylose, and cellobiose after three days with theoretical yields of 86.4%, 68.6%, and 45.4%, respectively. The coculture of glucose and xylose progressed sequentially at 79.2% of the theoretical yield, with both sugars completely consumed in five days. The solid-state consolidated bioprocessing of cellulose produced 25.2 g/L of ethanol after 20 days. After 28 days of the integrated biodelignification and consolidated bioprocessing of Napier grass at solid-state conditions, up to 10.5 g/L of ethanol was produced, corresponding to an ethanol yield of 0.032 g/g biomass. Given a sufficient carbon source, the screened fungus could produce up to 42.06 g/L ethanol. F. moniliforme BIOTECH 3170 demonstrated the characteristics of a fungus for potential ethanol production from cellulose, mixed sugars, and lignocellulosic materials.

Effect of Zinc-Calcium on Xylose Consumption by Mucor circinelloides (MN128960): Xylitol and Ethanol Yield Optimization

Xylose is the second most abundant monomeric sugar on earth. Nevertheless, metabolizing xylose into ethanol is a complex process due to several biochemical reactions. Some microorganisms of the genus Mucor are suitable for this bioprocess. Using metal ions, such as zinc and calcium, allows some fungal species to increase their ethanol yield. In this work, the wild strain Mucor spp. (C1502) was molecularly identified via internal transcribed spacer (ITS) sequencing. Secondly, an optimization using response surface methodology (RSM) with a central composite experimental design (CCD) was carried out. The independent variables (X) were ZnSO4·7H2O (X1, 0.0–1.5 g/L) and CaCl2 (X2, 0.0–2.5 g/L) concentration in the fermentation broth in order to demonstrate the effect of these ions, xylose was used as the only carbon source. The dependent variables (Y) measured were ethanol yield (Y1, g ethanol/g xylose) and xylitol yield (Y2, g xylitol/g xylose). The identified strain, Mucor circinelloides, was given the accession number MN128960 by the NCBI. Once the optimal concentrations of zinc and calcium were calculated, experimental validation was performed, with the highest ethanol and xylitol yields reaching 0.36 g ethanol/g xylose and 0.35 g xylitol/g xylose, respectively. This study demonstrated that increasing the xylitol yield using the effect of the ions, zinc and calcium, increases the ethanol yield. Furthermore, M. circinelloides (C1502) can produce metabolites, such as ethanol and xylitol, from the xylose obtained from hemicellulose biomasses, which can be used as a carbon source at low cost and with great availability.

Fermentation Dynamics and Benzylic Derivative Production in Ischnoderma resinosum Isolates

Fermentation dynamics and benzylic derivative production were evaluated in the fermentation broth of six different Ischnoderma resinosum (P. Karst) isolates over a period of 30 days to understand their potential applications in bioreactor optimization for natural flavor compound production. d-Glucose and d-fructose levels decreased from 20.4 ± 0.4 to 7.1 ± 1.4 g/L and 1.0 ± 0.1 to <0.1 g/L, respectively, in all fermentations. Isolate I₂ produced the highest concentration of ethanol (546. 4 ± 0.4 mg/L). l-Lactic acid production varied between 4.3 ± 0.6 and 3.7 ± 0.2 mg/L, whereas acetic acid concentrations decreased from 81.0 ± 3.3 to <40.0 mg/L. pH decreased from 4.9 ± 0.0 to 3.6 ± 0.4 at the end of 30 days in all fermentations. Isolate I₃ was the highest producer of benzaldehyde (BA) (12.0 ± 0.2 mg/kg) and 4-methoxybenzaldehyde (4-MBA) (239.6 ± 3.9 mg/kg), while isolate I₄ was the highest producer of 3,4-dimethoxybenzaldehyde (3,4-DMBA) (27.8 ± 0.2 mg/18 kg). Identification of isolate I₃ as a high BA and 4-MBA producer and isolate I₄ as a high 3,4-DMBA producer suggested differential benzylic derivative production among I. resinosum isolates. This study lays the foundation for future investigations evaluating additional I. resinosum isolates for benzylic derivative production as well as studies aimed at bioreactor optimization with potential commercial application.

Genome Sequence Analysis of Auricularia heimuer Combined with Genetic Linkage Map

Auricularia heimuer is one of the most popular edible fungi in China. In this study, the whole genome of A. heimuer was sequenced on the Illumina HiSeq X system and compared with other mushrooms genomes. As a wood-rotting fungus, a total of 509 carbohydrate-active enzymes (CAZymes) were annotated in order to explore its potential capabilities on wood degradation. The glycoside hydrolases (GH) family genes in the A. heimuer genome were more abundant than the genes in the other 11 mushrooms genomes. The A. heimuer genome contained 102 genes encoding class III, IV, and V ethanol dehydrogenases. Evolutionary analysis based on 562 orthologous single-copy genes from 15 mushrooms showed that Auricularia formed an early independent branch of Agaricomycetes. The mating-type locus of A. heimuer was located on linkage group 8 by genetic linkage analysis. By combining the genome sequence analysis with the genetic linkage map, the mating-type locus of A. heimuer was located on scaffold45 and consisted of two subunits, α and β. Each subunit consisted of a pair of homeodomain mating-type protein genes HD1 and HD2. The mapping revealed conserved synteny at the whole mating-type loci and mirror symmetry relations near the β subunit between A. heimuer and Exidia glandulosa. This study proposed the potential for the bioethanol production by consolidated bioprocessing of A. heimuer. It will promote understanding of the lignocellulose degradation system and facilitate more efficient conversion of the agricultural wastes used for mushroom cultivation. It also will advance the research on the fruiting body development and evolution of A. heimuer.

Efficient hydrolysis of wine and grape juice anthocyanins by Malbranchea pulchella β-glucosidase immobilized on MANAE-agarose and ConA-Sepharose supports

β-glucosidases (BGLs) hydrolyze short-chain cellulooligosaccharides. Some BGLs can hydrolyze anthocyanins and be applied in the clarification process of food industries, especially grape juice and wine. Enzyme immobilization is a valuable tool to increase enzyme stabilization. In this work, Malbranchea pulchella BGL was immobilized on Monoaminoethyl-N-ethyl-agarose ionic support, MANAE-agarose, and Concanavalin A-Sepharose affinity support, Con-A-Sepharose. The formed biocatalysts, denominated BLG-MANAE and BLG-ConA, were applied in the grape juice and red wine clarification. BGL-MANAE and BGL-ConA hyperactivated M. pulchella BGL 10- and 3-fold, respectively. Both biocatalysts showed at least 70% activity at pH range 2-11, until 24 h incubation. BGL-MANAE and BGL-ConA showed activity of 60% and 100%, respectively, at 50 °C, up to 24 h. Both biocatalysts were efficiently reused 20-fold. They were stable in the presence of up to 0.1 M glucose for 24 h incubation, and with 5%, 10% and 15% ethanol kept up to 70% activity. BGL-MANAE biocatalyst was 11% and 25% more efficient than BGL-ConA in clarification of concentrate and diluted wines, respectively. Likewise, BGL-MANAE biocatalysts were 14% and 33% more efficient than the BGL-ConA in clarification of diluted and concentrated juices, respectively. Therefore, the BGL-MANAE biocatalyst was especially effective in red wine and grape juice clarification.

Direct Ethanol Production from Lignocellulosic Materials by Mixed Culture of Wood Rot Fungi Schizophyllum commune, Bjerkandera adusta, and Fomitopsis palustris

The cost of bioethanol production from lignocellulosic materials is relatively high because the additional processes of delignification and saccharification are required. Consolidated bioprocessing (CBP) simultaneously uses the multiple processes of delignification, saccharification, and fermentation in a single reactor and has the potential to solve the problem of cost. Some wood-degrading basidiomycetes have lignin- and cellulose-degrading abilities as well as ethanol fermentation ability. The white rot fungus Schizophyllum commune NBRC 4928 was selected as a strong fermenter from a previous study. The lignin-degrading fungus Bjerkandera adusta and polysaccharide-degrading fungus Fomitopsis palustris were respectively added to S. commune ethanol fermentations to help degrade lignocellulosic materials. Bjerkandera adusta produced more ligninase under aerobic conditions, so a switching aeration condition was adopted. The mixed culture of S. commune and B. adusta promoted direct ethanol production from cedar wood. Fomitopsis palustris produced enzymes that released glucose from both carboxymethylcellulose and microcrystalline cellulose. The mixed culture of S. commune and F. palustris did not enhance ethanol production from cedar. The combination of S. commune and cellulase significantly increased the rate of ethanol production. The results suggest that CBP for ethanol production from cellulosic material can be achieved by using multiple fungi in one reactor.

Second Generation Bioethanol Production: On the Use of Pulp and Paper Industry Wastes as Feedstock

Due to the health and environment impacts of fossil fuels utilization, biofuels have been investigated as a potential alternative renewable source of energy. Bioethanol is currently the most produced biofuel, mainly of first generation, resulting in food-fuel competition. Second generation bioethanol is produced from lignocellulosic biomass, but a costly and difficult pretreatment is required. The pulp and paper industry has the biggest income of biomass for non-food-chain production, and, simultaneously generates a high amount of residues. According to the circular economy model, these residues, rich in monosaccharides, or even in polysaccharides besides lignin, can be utilized as a proper feedstock for second generation bioethanol production. Biorefineries can be integrated in the existing pulp and paper industrial plants by exploiting the high level of technology and also the infrastructures and logistics that are required to fractionate and handle woody biomass. This would contribute to the diversification of products and the increase of profitability of pulp and paper industry with additional environmental benefits. This work reviews the literature supporting the feasibility of producing ethanol from Kraft pulp, spent sulfite liquor, and pulp and paper sludge, presenting and discussing the practical attempt of biorefineries implementation in pulp and paper mills for bioethanol production.

Cellulases and beyond: the first 70 years of the enzyme producer Trichoderma reesei

More than 70 years ago, the filamentous ascomycete Trichoderma reesei was isolated on the Solomon Islands due to its ability to degrade and thrive on cellulose containing fabrics. This trait that relies on its secreted cellulases is nowadays exploited by several industries. Most prominently in biorefineries which use T. reesei enzymes to saccharify lignocellulose from renewable plant biomass in order to produce biobased fuels and chemicals. In this review we summarize important milestones of the development of T. reesei as the leading production host for biorefinery enzymes, and discuss emerging trends in strain engineering. Trichoderma reesei has very recently also been proposed as a consolidated bioprocessing organism capable of direct conversion of biopolymeric substrates to desired products. We therefore cover this topic by reviewing novel approaches in metabolic engineering of T. reesei.

Destructuring plant biomass: focus on fungal and extremophilic cell wall hydrolases

The use of plant biomass as feedstock for biomaterial and biofuel production is relevant in the current bio-based economy scenario of valorizing renewable resources. Fungi, which degrade complex and recalcitrant plant polymers, secrete different enzymes that hydrolyze plant cell wall polysaccharides. The present review discusses the current research trends on fungal, as well as extremophilic cell wall hydrolases that can withstand extreme physico-chemical conditions required in efficient industrial processes. Secretomes of fungi from the phyla Ascomycota, Basidiomycota, Zygomycota and Neocallimastigomycota are presented along with metabolic cues (nutrient sensing, coordination of carbon and nitrogen metabolism) affecting their composition. We conclude the review by suggesting further research avenues focused on the one hand on a comprehensive analysis of the physiology and epigenetics underlying cell wall degrading enzyme production in fungi and on the other hand on the analysis of proteins with unknown function and metagenomics of extremophilic consortia. The current advances in consolidated bioprocessing, altered secretory pathways and creation of designer plants are also examined. Furthermore, recent developments in enhancing the activity, stability and reusability of enzymes based on synergistic, proximity and entropic effects, fusion enzymes, structure-guided recombination between homologous enzymes and magnetic enzymes are considered with a view to improving saccharification.

RNA-sequencing reveals the complexities of the transcriptional response to lignocellulosic biofuel substrates in Aspergillus niger

Background

Filamentous fungi are well known for their ability to degrade lignocellulosic biomass and have a natural ability to convert certain products of biomass degradation, for example glucose, into various organic acids. Organic acids are suggested to give a competitive advantage to filamentous fungi over other organisms by decreasing the ambient pH. They also have an impact on the ecosystem by enhancing weathering and metal detoxification. Commercially, organic acids can be used as chemical intermediates or as synthons for the production of biodegradable polymers which could replace petroleum-based or synthetic chemicals. One of the advantages of filamentous fungi as biotechnological production platforms for synthetic biology is their ability to degrade vegetal biomass, which is a promising feedstock for the biotechnological production of organic acids. The Fungal Culture Collection of the International Centre of Microbial Resources (CIRM-CF), curated by our laboratory, contains more than 1600 strains of filamentous fungi, mainly Basidiomycetes and Ascomycetes. The natural biodiversity found in this collection is wide, with strains collected from around the world in different climatic conditions. This collection is mainly studied to unravel the arsenal of secreted lignocellulolytic enzymes available to the fungi in order to enhance biomass degradation. While the fungal biodiversity is a tremendous reservoir for “green” molecules production, its potentiality for organic acids production is not completely known.

Results

In this study, we screened 40 strains of Ascomycota and 26 strains of Basidiomycota, representing the distribution of fungal diversity of the CIRM-CF collection, in order to evaluate their potential for organic acid and ethanol production, in a glucose liquid medium. We observed that most of the filamentous fungi are able to grow and acidify the medium. We were also able to discriminate two groups of filamentous fungi considering their organic acid production at day 6 of incubation. This first group represented fungi co-producing a wide variety of organic acids and ethanol at concentrations up to 4 g.L⁻¹ and was composed of all the Aspergilli and only 3 other Ascomycota. The second group was composed of the remaining Ascomycota and all the Basidiomycota which produced mainly ethanol. Among the Basidiomycota, two strains produced oxalic acid and one strain produced gluconic and formic acid. Six strains of Aspergillus producing high concentrations of oxalic, citric and gluconic acids, and ethanol were selected for metabolism analysis.

Conclusion

These results illustrate the versatility in metabolites production among the fungal kingdom. Moreover, we found that some of the studied strains have good predispositions to produce valuable molecules. These strains could be of great interest in the study of metabolism and may represent new models for synthetic biology or consolidated bioprocessing of biomass.

Electronic supplementary material

The online version of this article (doi:10.1186/s40694-014-0001-z) contains supplementary material, which is available to authorized users.

Whole genome and global gene expression analyses of the model mushroom Flammulina velutipes reveal a high capacity for lignocellulose degradation

Flammulina velutipes is a fungus with health and medicinal benefits that has been used for consumption and cultivation in East Asia. F. velutipes is also known to degrade lignocellulose and produce ethanol. The overlapping interests of mushroom production and wood bioconversion make F. velutipes an attractive new model for fungal wood related studies. Here, we present the complete sequence of the F. velutipes genome. This is the first sequenced genome for a commercially produced edible mushroom that also degrades wood. The 35.6-Mb genome contained 12,218 predicted protein-encoding genes and 287 tRNA genes assembled into 11 scaffolds corresponding with the 11 chromosomes of strain KACC42780. The 88.4-kb mitochondrial genome contained 35 genes. Well-developed wood degrading machinery with strong potential for lignin degradation (69 auxiliary activities, formerly FOLymes) and carbohydrate degradation (392 CAZymes), along with 58 alcohol dehydrogenase genes were highly expressed in the mycelium, demonstrating the potential application of this organism to bioethanol production. Thus, the newly uncovered wood degrading capacity and sequential nature of this process in F. velutipes, offer interesting possibilities for more detailed studies on either lignin or (hemi-) cellulose degradation in complex wood substrates. The mutual interest in wood degradation by the mushroom industry and (ligno-)cellulose biomass related industries further increase the significance of F. velutipes as a new model.