ABSTRACT Lignocellulosic biomass represents a promising renewable feedstock for sustainable biorefinery applications, yet efficient enzymatic saccharification remains challenging due to the recalcitrant structure of plant cell walls. This study presents a comprehensive comparative analysis of enzymatic activities, saccharification performance, and secretome composition of six fungal species cultivated under solid-state fermentation (SSF) and submerged fermentation (SmF) conditions using untreated flax shives as substrate. While SmF yielded approximately 4-fold higher total protein concentrations (0.38 ± 0.13 g.L -1 vs. 0.08 ± 0.02 g.L -1 ), SSF-derived enzymes demonstrated superior specific enzymatic activities, particularly for endo-xylanase and endo-cellulase, resulting in more efficient biomass saccharification. Proteomics analysis revealed distinct secretome profiles between fermentation modes, with SSF showing higher proportions of polysaccharide metabolism proteins (71.0%) compared to SmF (49.3%), while SmF exhibited greater enzyme diversity including more lytic polysaccharide monooxygenases (LPMOs) and auxiliary activity enzymes. Trichoderma species consistently demonstrated the highest saccharification efficiency, with glucose yields reaching 2.37 mM under SSF conditions. A Scheffé simplex-lattice mixture design comprising 65 enzyme cocktail combinations revealed significant synergistic interactions between several cocktails, with the binary mixture of Trichoderma 2SA21 and P. chrysogenum achieving 54% synergy - in terms of higher sugar release above expectations - and the highest total monosaccharide release (1.80 mM). These findings provide practical guidance for developing cost-effective enzyme cocktails for lignocellulosic biorefinery applications, emphasizing the importance of fermentation mode selection and strategic strain combination over enzyme supplementation complexity. The methodology established here, combining systematic screening, comparative proteomics, and statistical mixture design, offers a robust framework for optimizing fungal enzyme systems across diverse biomass substrates. BULLET POINTS Superior enzymatic activity (xylanase, cellulase) and saccharification in solid-state fermentation Superior total protein content and diversity in submerged fermentation Specific enzyme cocktails combination can lead to synergistic effects, justifying a combinatorial approach GRAPHICAL ABSTRACT

The enhancement of polymer depolymerization represents a significant challenge to reduce the environmental impact of plastic pollution and the utilization of raw materials. Recently, there has been a demand to optimize degradation analysis approaches, which have been observed to be sometimes used inappropriately or incompletely. This article proposes an analysis strategy for monitoring the depolymerization of poly(bisphenol A carbonate) (PBPAC), using methanolysis as model method. It is based on five analytical methods, which our study attempts to combine and compare according to their ideal use case: size exclusion chromatography, liquid chromatography and FT-IR, NMR and MALDI-TOF spectroscopy. This strategy allows for both a qualitative approach to be taken, whereby the depolymerization products can be identified, along with a quantitative one, whereby the percentages of polymer degradation can be determined. As a result, the range of applications for each method is assessed, and a guide to the minimum methods to be used to qualify and quantify degradation is proposed, in relation to the progress of degradation and the yields obtained. This has enabled us to characterize and propose a new quantitative FT-IR based methodology, compatible with high-throughput screening, to the degradation of PBPAC, allowing to quantify degradation from 10 % onwards.

Abstract Background. Short-chain carboxylic acids are interesting building blocks that can be synthesized from biogenic residues with the so-called dark fermentation. One challenge though is the hydrolysis of lignocellulosic residues to make them accessible for whole cell biotransformation. Accessibility can be achieved through conversion of lignocellulose through microbial exoenzymes. In this study, bacteria and fungi were isolated from different lignocellulose-containing feedstock. A workflow of an automated screening with the isolated strains for their ability to accumulate short-chain carboxylic acids in fermentation was elaborated. The screening was performed with and without addition of fungal enzymes. Results. Results show a three-fold increase in acetic acid concentration and nearly a six-fold increase in succinic acid concentration if the feedstock was pre-treated in comparison to untreated feedstock. When adding the enzyme-containing supernatant to a continuous dark fermentation with wood barks as feedstock, the acid concentration increased remarkably from 1 to 2.6 g⋅L− 1. Conclusion. The methodology, thus, is suitable to identify strains and enzyme mixtures for improving hydrolysis of complex lignocellulosic feedstock.

Two extraction approaches were compared, ultrasound-assisted extraction (UAE) and conventional extraction (CE), for the recovery of natural antioxidant phenolic compounds from spent coffee grounds (SCG), which could be used as cosmetics additives or nutritional supplements. Two factorial designs were used to investigate the effect of the varied process parameters on performances of UAE and CE processes, which were evaluated and compared regarding total polyphenols recovery, antioxidant activity of the obtained extracts and energy con-sumption. Polyphenols recovery was influenced mostly by ethanol content in the solvent, then ultrasound power for UAE and heating temperature for CE. Optimal operating conditions were identified as 400 W ultrasound power, 50% (v/v) ethanol in the solvent and 40 mL/g dm (dry matter) liquid to solid ratio for UAE, and about 50 degrees C heating temperature and 50% (v/v) ethanol in the solvent for CE. Under these optimal conditions for each process, more than 83% and 64% of available polyphenols in SCG were recovered with UAE and CE, respectively. Ultrasound assistance thus allowed about 33% enhancement of polyphenols recovery, while dividing energy consumption by more than 2. Hence, UAE process was demonstrated to be an efficient and sustainable method to recover antioxidant polyphenols from spent coffee grounds.

Today, plant production is increasing, but most industrial processes generate a lot of waste and by-products for which, in the current context, it is a priority to recycle or valorize them. One of the cheapest valorization routes is fermentation, in particular lactic fermentation by Lactobacillus species, which produces lactic acid and other molecules of industrial interest such as bioactive compounds such as anthocyanin, organic acid, peptides, or phenol, which are widely found in the plant matrix, mainly in cereals, grass, fruits, and vegetables. Bioactive compounds may exert beneficial health effects, such as antioxidant, anti-inflammatory, antimicrobial, or prebiotic activities. In addition, lactic acid fermentation can improve existing products and lead to new applications in food, livestock feeding and biotechnology, such as the production of lactic acid, protein, or silage. This chapter reviews the use of Lactobacillus strains in the fermentation process of many plant bioresources or by-products through their different bioactivities, active molecules, and applications.

Cocultures have been widely explored for their use in deciphering microbial interaction and its impact on the metabolisms of the interacting microorganisms. In this work, we investigate, in different liquid coculture conditions, the compatibility of two microorganisms with the potential for the biocontrol of plant diseases: the fungus Trichoderma harzianum IHEM5437 and the bacterium Bacillus velezensis GA1 (a strong antifungal lipopeptide producing strain). While the Bacillus overgrew the Trichoderma in a rich medium due to its antifungal lipopeptide production, a drastically different trend was observed in a medium in which a nitrogen nutritional dependency was imposed. Indeed, in this minimum medium containing nitrate as the sole nitrogen source, cooperation between the bacterium and the fungus was established. This is reflected by the growth of both species as well as the inhibition of the expression of Bacillus genes encoding lipopeptide synthetases. Interestingly, the growth of the bacterium in the minimum medium was enabled by the amendment of the culture by the fungal supernatant, which, in this case, ensures a high production yield of lipopeptides. These results highlight, for the first time, that Trichoderma harzianum and Bacillus velezensis are able, in specific environmental conditions, to adapt their metabolisms in order to grow together.

PURPOSE:In this study, a combinatory approach was undertaken to assay the efficiency of fungal enzymatic cocktails from different fermentation conditions to degrade different lignocellulosic biomasses with the aim of finely characterizing fungal enzymatic cocktails.METHODS:Enzymatic assays (AZO and pNP-linked substrates and ABTS) were used to assess the composition of the fungal enzymatic cocktails for cellulase, xylanase and laccase activities. Comparisons were made with a new range of chromogenic substrates based on complex biomass (CBS substrates). The saccharification efficiency of the cocktails was evaluated as a quantification of the sugar monomers released from the different biomasses after incubation with the enzymatic cocktails.RESULTS:The results obtained showed striking differences between the AZO and pNP-linked substrates and the CBS substrates for the same enzymatic cocktails. On AZO and pNP-linked substrates, different hydrolysis profiles were observed between the different fungi species with Aspergillus oryzae being the most efficient. However, the results on CBS substrates were more contrasted depending on the biomass tested. Altogether, the results highlighted that assessing laccase activities and taking into account the complexity of the biomass to degrade were key in order to provide the best enzymatic cocktails.CONCLUSION:The complementary experiments performed in this study showed that different approaches needed to be taken in order to accurately assess the ability of an enzymatic cocktail to be efficient when it comes to lignocellulosic biomass degradation. The saccharification assay proved to be essential to validate the data obtained from both simple and complex substrates.

The bioproduction of high-value chemicals such as itaconic and fumaric acids (IA and FA, respectively) from renewable resources via solid-state fermentation (SSF) represents an alternative to the current bioprocesses of submerged fermentation using refined sugars. Both acids are excellent platform chemicals with a wide range of applications in different market, such as plastics, coating, or cosmetics. The use of lignocellulosic biomass instead of food resources (starch or grains) in the frame of a sustainable development for IA and FA bioproduction is of prime importance. Filamentous fungi, especially belonging to the Aspergillus genus, have shown a great capacity to produce these organic dicarboxylic acids. This study attempts to develop and optimize the SSF conditions with lignocellulosic biomasses using A. terreus and A. oryzae to produce IA and FA. First, a kinetic study of SSF was performed with non-food resources (wheat bran and corn cobs) and a panel of pH and moisture conditions was studied during fermentation. Next, a new process using an enzymatic cocktail simultaneously with SSF was investigated in order to facilitate the use of the biomass as microbial substrate. Finally, a large-scale fermentation process was developed for SSF using corn cobs with A. oryzae; this specific condition showed the best yield in acid production. The yields achieved were 0.05 mg of IA and 0.16 mg of FA per gram of biomass after 48 h. These values currently represent the highest reported productions for SSF from raw lignocellulosic biomass.

Polyurethanes (PU) are a family of versatile synthetic polymers intended for diverse applications. Biological degradation of PU is a blooming research domain as it contributes to the design of eco-friendly materials sensitive to biodegradation phenomena and the development of green recycling processes. In this field, an increasing number of studies deal with the discovery and characterization of enzymes and microorganisms able to degrade PU chains. The synthesis of short lifespan PU material sensitive to biological degradation is also of growing interest. Measurement of PU degradation can be performed by a wide range of analytical tools depending on the architecture of the materials and the biological entities. Recent developments of these analytical techniques allowed for a better understanding of the mechanisms involved in PU biodegradation. Here, we reviewed the evaluation of biological PU degradation, including the required analytics. Advantages, drawbacks, specific uses, and results of these analytics are largely discussed to provide a critical overview and support future studies.

This study aimed at developing a complete miniaturized high-throughput screening workflow for the evaluation of the Cell Wall-Degrading Enzyme (CWDE) activities produced by any fungal strain directly cultivated on raw feedstock in a submerged manner. In this study, wheat straw was selected as model substrate as it represents an important carbon source but yet poorly valorised to yield high added value products. Fungi were grown in a microbioreactor in a high-throughput (HT) way to replace the fastidious shaking flask cultivations. Both approaches were compared in order to validate our new methodology. The range of CWDE activities produced from the cultures was assayed using AZO-died and pNP-linked substrates in an SBS plate format using a Biomek FXp pipetting platform. As highlighted in this study, it was shown that the CWDE activities gathered from the microbioreactor cultivations were similar or higher to those obtained from shake flasks cultures, with a lower standard deviation on the measured values, making this new method much faster than the traditional one and suitable for HT CWDE production thanks to its pipetting platform compatibility. Also, the results showed that the enzymatic activities measured were the same when doing the assay manually or using the automated method.

Biological recycling of polyurethanes (PU) is a huge challenge to take up in order to reduce a large part of the environmental pollution from these materials. However, enzymatic depolymerization of PU still needs to be improved to propose valuable and green solutions. The present study aims to identify efficient PU degrading enzymes among a collection of 50 hydrolases. Screenings based on model molecules were performed leading to the selection of an efficient amidase (E4143) able to hydrolyze the urethane bond of a low molar mass molecule and an esterase (E3576) able to hydrolyze a waterborne polyester polyurethane dispersion. Degradation activities of the amidase, the esterase and a mix of these enzymes were then evaluated on four thermoplastic polyurethanes (TPU) specifically designed for this assay. The highest degradation was obtained on a polycaprolactone polyol-based polyurethane with weight loss of 33% after 51 days measured for the esterase. Deep cracks on the polymer surface observed by scanning electron microscopy and the presence of oligomers on the remaining TPU detected by size exclusion chromatography evidenced the polymer degradation. Mixing both enzymes led to an increased amount of urethane bonds hydrolysis of the polymer. 6-hydroxycaproic acid and 4,4'-methylene dianiline were recovered after depolymerization as hydrolysis products. Such building blocks could get a second life with the synthesis of new macromolecular architectures. (C) 2018 The Authors. Published by Elsevier Ltd.

Crop improvement is essential to meet the demands of a changing world (eg, increased population, climate change, and decreasing land base). Plant breeding programs are continuously striving to increase crop yield, enhance crop quality, and improve crop tolerance to diseases and pests. It takes approximately 10 years to develop a new crop variety, although this depends on the species. The traditional plant breeding methods involve the time-consuming process of self-fertilization or back-crossing in order to produce homozygous lines. Doubled haploid (DH) production is the quickest method for developing homozygous breeding lines (as reviewed in Ferrie and Möllers, 2011). The production of DH lines from microspores or ovules makes it possible to obtain stable homozygous lines in a single step. This chapter provides an overview of in vitro DH methods for improving oilseeds intended for industrial purposes. The focus will be on Brassica, other cruciferous, Apiaceae, and Compositae species, because little or no DH work has been done on other potential industrial oilseeds.

Lipopeptides, such as surfactins are important biosurfactants produced by Bacillus sp. that find applications in many areas (environment, medicine, and food industries). Giving their importance, the use of simple detection methods will facilitate screening and quantification. In the present work, the authors describe a completely automated workflow for the screening of lipopeptide-producing strains, including quantification. First, isolated colonies from environmental samples are automatically picked and inoculated in 96 wells growth plate. After overnight incubation, surfactin produced in the broth is quantified, using a new sensitive fluorescent method. The method uses fluorescein (FL), which is an anionic dye at neutral to alkaline pH and forms a stable complex with the cationic surfactant cetylpiridinium chloride (CPC), quenching fluorescence. Upon addition of surfactin or other lipopeptides, fluorescein is released from the CPC-FL complex and quantified. The robustness of this method is assessed by comparing the quantification results to those conventionally measured by RP-UPLC and the results of strain screening are confirmed by MALDI-ToF analysis. The authors report for the first time the successful application of this analytical method for high-throughput screening of novel lipopeptide-producing strains.

This study presents a miniaturized 3-methyl-2-benzothiazolinone hydrazone hydrochloride-assay (MBTH-assay)1, optimized for high-throughput measurement of shrimp phenol oxidase activities and the screening of potential inhibitors of post-mortem melanosis. To validate this approach, assay parameters, including limit of detection and dynamic range, were compared to values obtained for DOPAchrome-assay, used here as a reference method. A reliable high-throughput automatized analysis was also performed, under standardized parameters, in order to compare and characterize 40 potential inhibitors of phenol oxidase activities. Among the selected molecules, twenty showed inhibitory action. Enzyme-inhibitor dissociation constant (Ki), median inhibitor concentration (IC50) and inhibition modes could be determined for nine of them. 4-Hexylresorcinol, n-phenylthiourea l-cystein and glutathione displayed Ki values lower than sulfite salts (Na2S2O5 and Na2SO3) used as positive controls.

As a highly resistant polymer family, polyurethanes (PU) are responsible for increasing environmental issues. Then, PU biodegradation is a challenging way to develop sustainable waste management processes based on biological recycling. Since the metabolic diversity of fungi is a major asset for polymer degradation, nearly thirty strains were isolated from sampling on six different PU wastes-containing environments. A screening of the fungi on four thermoplastic PU (TPU) with different macromolecular architectures led to the selection of three strains able to use two polyester PU as sole carbon source: Alternaria sp., Penicillium section Lanata-Divaricata and Aspergillus section flavi. Weight loss, FT-IR, Scanning Electron Microscopy and Size Exclusion Chromatography analyses revealed that these three fungi degrade slightly and similarly a fatty acid dimer-based TPU while variability of degradation was noticed on a polycaprolactone-based TPU. On this last TPU, robust analysis of the degraded polymers showed that the Penicillium strain was the best degrading microorganism. Membrane enzymes seemed to be involved in this degradation. It is the first time that a strain of Penicillium of the section Lanata-Divaricata displaying PU biodegradation ability is isolated. These newly discovered fungi are promising for the development of polyester PU waste management process.

Innovations in novel enzyme discoveries impact upon a wide range of industries for which biocatalysis and biotransformations represent a great challenge, i.e., food industry, polymers and chemical industry. Key tools and technologies, such as bioinformatics tools to guide mutant library design, molecular biology tools to create mutants library, microfluidics/microplates, parallel miniscale bioreactors and mass spectrometry technologies to create high-throughput screening methods and experimental design tools for screening and optimization, allow to evolve the discovery, development and implementation of enzymes and whole cells in (bio)processes. These technological innovations are also accompanied by the development and implementation of clean and sustainable integrated processes to meet the growing needs of chemical, pharmaceutical, environmental and biorefinery industries. This review gives an overview of the benefits of high-throughput screening approach from the discovery and engineering of biocatalysts to cell culture for optimizing their production in integrated processes and their extraction/purification.

The production of high-value chemicals from natural resources as an alternative for petroleum-based products is currently expanding in parallel with biorefinery. The use of lignocellulosic biomass as raw material is promising to achieve economic and environmental sustainability. Filamentous fungi, particularly Aspergillus species, are already used industrially to produce organic acid as well as many enzymes. The production of lignocellulose-degrading enzymes opens the possibility for direct fungal fermentation towards organic acids such as itaconic acid (IA) and fumaric acid (FA). These acids have wide-range applications and potentially addressable markets as platform chemicals. However, current technologies for the production of these compounds are mostly based on submerged fermentation. This work showed the capacity of two Aspergillus species (A. terreus and A. oryzae) to yield both acids by solid-state fermentation and simultaneous saccharification and fermentation. FA was optimally produced at by A. oryzae in simultaneous saccharification and fermentation (0.54mg/g wheat bran). The yield of 0.11mg IA/g biomass by A. oryzae is the highest reported in the literature for simultaneous solid-state fermentation without sugar supplements.

The immobilization of Candida antarctica lipase B (CALB) was performed by physical adsorption on both neat and organo-modified forms of sepiolite and montmorillonite. The influence of different parameters, e.g., solvent, enzyme loading, cross-linking, and type of clay support, on immobilization efficiency and catalyst hydrolytic activity has been investigated. The highest hydrolytic activities were obtained for CALB immobilized on organo-modified clay minerals, highlighting the beneficial effect of organo-modification. The esterification activity of these CALB/organoclay catalysts was also tested in the ring-opening polymerization of ε-caprolactone. The polymerization kinetics observed for clay-immobilized catalysts confirmed that CALB adsorbed on organo-modified montmorillonite (CALB/MMTMOD) was the highest-performing catalytic system.

Itaconic acid (IA) is a dicarboxylic acid included in the US Department of Energy's (DOE) 2004 list of the most promising chemical platforms derived from sugars. IA is produced industrially using liquid-state fermentation (LSF) by Aspergillus terreus with glucose as the carbon source. To utilize IA production in renewable resource-based biorefinery, the present study investigated the use of lignocellulosic biomass as a carbon source for LSF. We also investigated the production of fumaric acid (FA), which is also on the DOE's list. FA is a primary metabolite, whereas IA is a secondary metabolite and requires the enzyme cis-aconitate decarboxylase for its production. Two lignocellulosic biomasses (wheat bran and corn cobs) were tested for fungal fermentation. Liquid hydrolysates obtained after acid or enzymatic treatment were used in LSF. We show that each treatment resulted in different concentrations of sugars, metals, or inhibitors. Furthermore, different acid yields (IA and FA) were obtained depending on which of the four Aspergillus strains tested were employed. The maximum FA yield was obtained when A. terreus was used for LSF of corn cob hydrolysate (1.9% total glucose); whereas an IA yield of 0.14% was obtained by LSF of corn cob hydrolysates by A. oryzae.