A PCR-based method to quantify fungal growth during pretreatment of lignocellulosic biomass

Morphological growth pattern of Phanerochaete chrysosporium cultivated on different Miscanthus x giganteus biomass fractions

BACKGROUND

Solid-state fermentation is a fungal culture technique used to produce compounds and products of industrial interest. The growth behaviour of filamentous fungi on solid media is challenging to study due to the intermixity of the substrate and the growing organism. Several strategies are available to measure indirectly the fungal biomass during the fermentation such as following the biochemical production of mycelium-specific components or microscopic observation. The microscopic observation of the development of the mycelium, on lignocellulosic substrate, has not been reported. In this study, we set up an experimental protocol based on microscopy and image processing through which we investigated the growth pattern of Phanerochaete chrysosporium on different Miscanthus x giganteus biomass fractions.

RESULTS

Object coalescence, the occupied surface area, and radial expansion of the colony were measured in time. The substrate was sterilized by autoclaving, which could be considered a type of pre-treatment. The fastest growth rate was measured on the unfractionated biomass, followed by the soluble fraction of the biomass, then the residual solid fractions. The growth rate on the different fractions of the substrate was additive, suggesting that both the solid and soluble fractions were used by the fungus. Based on the FTIR analysis, there were differences in composition between the solid and soluble fractions of the substrate, but the main components for growth were always present. We propose using this novel method for measuring the very initial fungal growth by following the variation of the number of objects over time. Once growth is established, the growth can be followed by measurement of the occupied surface by the mycelium.

CONCLUSION

Our data showed that the growth was affected from the very beginning by the nature of the substrate. The most extensive colonization of the surface was observed with the unfractionated substrate containing both soluble and solid components. The methodology was practical and may be applied to investigate the growth of other fungi, including the influence of environmental parameters on the fungal growth.

A Putative Lignin Copper Oxidase from Trichoderma reesei

The ability of Trichoderma reesei, a fungus widely used for the commercial production of hemicellulases and cellulases, to grow and modify technical soda lignin was investigated. By quantifying fungal genomic DNA, T. reesei showed growth and sporulation in solid and liquid cultures containing lignin alone. The analysis of released soluble lignin and residual insoluble lignin was indicative of enzymatic oxidative conversion of phenolic lignin side chains and the modification of lignin structure by cleaving the β-O-4 linkages. The results also showed that polymerization reactions were taking place. A proteomic analysis conducted to investigate secreted proteins at days 3, 7, and 14 of growth revealed the presence of five auxiliary activity (AA) enzymes in the secretome: AA6, AA9, two AA3 enzymes), and the only copper radical oxidase encoded in the genome of T. reesei. This enzyme was heterologously produced and characterized, and its activity on lignin-derived molecules was investigated. Phylogenetic characterization demonstrated that this enzyme belonged to the AA5_1 family, which includes characterized glyoxal oxidases. However, the enzyme displayed overlapping physicochemical and catalytic properties across the AA5 family. The enzyme was remarkably stable at high pH and oxidized both, alcohols and aldehydes with preference to the alcohol group. It was also active on lignin-derived phenolic molecules as well as simple carbohydrates. HPSEC and LC-MS analyses on the reactions of the produced protein on lignin dimers (SS ββ, SS βO4 and GG β5) uncovered the polymerizing activity of this enzyme, which was accordingly named lignin copper oxidase (TrLOx). Polymers of up 10 units were formed by hydroxy group oxidation and radical formation. The activations of lignin molecules by TrLOx along with the co-secretion of this enzyme with reductases and FAD flavoproteins oxidoreductases during growth on lignin suggest a synergistic mechanism for lignin breakdown.

Fungal Treatment for the Valorization of Technical Soda Lignin

Technical lignins produced as a by-product in biorefinery processes represent a potential source of renewable carbon. In consideration of the possibilities of the industrial transformation of this substrate into various valuable bio-based molecules, the biological deconstruction of a technical soda lignin by filamentous fungi was investigated. The ability of three basidiomycetes (Polyporus brumalis, Pycnoporus sanguineus and Leiotrametes menziesii) to modify this material, the resultant structural and chemical changes, and the secreted proteins during growth on this substrate were investigated. The three fungi could grow on the technical lignin alone, and the growth rate increased when the media were supplemented with glucose or maltose. The proteomic analysis of the culture supernatants after three days of growth revealed the secretion of numerous Carbohydrate-Active Enzymes (CAZymes). The secretomic profiles varied widely between the strains and the presence of technical lignin alone triggered the early secretion of many lignin-acting oxidoreductases. The secretomes were notably rich in glycoside hydrolases and H₂O₂-producing auxiliary activity enzymes with copper radical oxidases being induced on lignin for all strains. The lignin treatment by fungi modified both the soluble and insoluble lignin fractions. A significant decrease in the amount of soluble higher molar mass compounds was observed in the case of P. sanguineus. This strain was also responsible for the modification of the lower molar mass compounds of the lignin insoluble fraction and a 40% decrease in the thioacidolysis yield. The similarity in the activities of P. sanguineus and P. brumalis in modifying the functional groups of the technical lignin were observed, the results suggest that the lignin has undergone structural changes, or at least changes in its composition, and pave the route for the utilization of filamentous fungi to functionalize technical lignins and produce the enzymes of interest for biorefinery applications.

Systematic Review and Study of S Curves for Biomass Quantification in Solid-state Fermentation (SSF) and Digital Image Processing (DIP) Applied to Biomass Measurement in Food Processes

BACKGROUND

There are several methods for the quantification of biomass in SSF, such as glucosamine measurement, ergosterol content, protein concentration, change in dry weight or evolution of CO2 production. However, all have drawbacks when obtaining accurate data on the progress of the SSF due to the dispersion in cell growth on the solid substrate, and the difficulty encountered in separating the biomass. Studying the disadvantages associated with the process of biomass quantification in SSF, the monitoring of the growth of biomass by a technique known as digital image processing (DIP), consists of obtaining information on the production of different compounds during fermentation, using colorimetric methods based on the pixels that are obtained from photographs.

OBJECTIVE

The purpose of this study was to know about the state of the technology and the advantages of DIP.

METHODS

The methodology employed four phases; the first describes the search equations for the SSF and the DIP. A search for patents related to SSF and DIP carried out in the Free Patents Online and Patent inspiration databases. Then there is the selection of the most relevant articles in each of the technologies. As a third step, modifications for obtaining the best adjustments were also carried out. Finally, the analysis of the results was done and the inflection years were determined by means of six mathematical models widely studied.

RESULTS

For these models, the inflection years were 2018 and 2019 for both the SSF and the DIP. Additionally, the main methods for the measurement of biomass in SSF were found, and are also indicated in the review, as DIP measurement processes have already been carried out using the same technology.

CONCLUSION

In addition, the DIP has shown satisfactory results and could be an interesting alternative for biomass measurement in SSF, due to its ease and versatility.

Investigating a non-destructive alternative for a preliminary evaluation of fungal growth in solid state fermentations

Solid state fermentation (SSF) is an ancient technique which keeps attracting the attention of the food and biotechnology industries; however, a direct quantification of microbial biomass is still a fundamental challenge in this type of processes. Typically, growth is measured using indirect and destructive methods which do not allow a continuous evaluation of the evolution of microbial biomass within a single system. This article presents a non-destructive, quick and simple technique, based on digital imaging analysis (DIA) for the evaluation of growth in SSF laboratory experiments. DIA uses computational analysis of images from a SSF to measure areas and colour changes on a surface. The method can then be used to monitor microbial growth by assigning quantitative values for the growth of filamentous fungi. Firstly, studies on agar plates are used for the description of the method and to illustrate how it can be used to monitor fungal colony areas and densities. Following that, agro-industrial residues are used to demonstrate the application of the technique. DIA proved to be a practical and inexpensive tool to measure colony areas and densities. Furthermore, it is a non-destructive and non-intrusive method, which means that the evaluation of growth can be achieved within a single system.

Integrative visual omics of the white-rot fungus Polyporus brumalis exposes the biotechnological potential of its oxidative enzymes for delignifying raw plant biomass

BACKGROUND

Plant biomass conversion for green chemistry and bio-energy is a current challenge for a modern sustainable bioeconomy. The complex polyaromatic lignin polymers in raw biomass feedstocks (i.e., agriculture and forestry by-products) are major obstacles for biomass conversions. White-rot fungi are wood decayers able to degrade all polymers from lignocellulosic biomass including cellulose, hemicelluloses, and lignin. The white-rot fungus Polyporus brumalis efficiently breaks down lignin and is regarded as having a high potential for the initial treatment of plant biomass in its conversion to bio-energy. Here, we describe the extraordinary ability of P. brumalis for lignin degradation using its enzymatic arsenal to break down wheat straw, a lignocellulosic substrate that is considered as a biomass feedstock worldwide.

RESULTS

We performed integrative multi-omics analyses by combining data from the fungal genome, transcriptomes, and secretomes. We found that the fungus possessed an unexpectedly large set of genes coding for Class II peroxidases involved in lignin degradation (19 genes) and GMC oxidoreductases/dehydrogenases involved in generating the hydrogen peroxide required for lignin peroxidase activity and promoting redox cycling of the fungal enzymes involved in oxidative cleavage of lignocellulose polymers (36 genes). The examination of interrelated multi-omics patterns revealed that eleven Class II Peroxidases were secreted by the fungus during fermentation and eight of them where tightly co-regulated with redox cycling enzymatic partners.

CONCLUSION

As a peculiar feature of P. brumalis, we observed gene family extension, up-regulation and secretion of an abundant set of versatile peroxidases and manganese peroxidases, compared with other Polyporales species. The orchestrated secretion of an abundant set of these delignifying enzymes and redox cycling enzymatic partners could contribute to the delignification capabilities of the fungus. Our findings highlight the diversity of wood decay mechanisms present in Polyporales and the potentiality of further exploring this taxonomic order for enzymatic functions of biotechnological interest.