An Enzymatic and Proteomic Analysis of Panus lecomtei during Biodegradation of Gossypol in Cottonseed.

Cotton is an important plant-based protein. Cottonseed cake, a byproduct of the biodiesel industry, offers potential in animal supplementation, although the presence of the antinutritional sesquiterpenoid gossypol limits utilization. The macrofungus Panus lecomtei offers potential in detoxification of antinutritional factors. Through an enzymatic and proteomic analysis of P. lecomtei strain BRM044603, grown on crushed whole cottonseed contrasting in the presence of free gossypol (FG), this study investigated FG biodegradation over a 15-day cultivation period. Fungal growth reduced FG to levels at 100 µg/g, with a complex adaptive response observed, involving primary metabolism and activation of oxidative enzymes for metabolism of xenobiotics. Increasing activity of secreted laccases correlated with a reduction in FG, with enzyme fractions degrading synthetic gossypol to trace levels. A total of 143 and 49 differentially abundant proteins were observed across the two contrasting growth conditions after 6 and 12 days of cultivation, respectively, revealing a dynamic protein profile during FG degradation, initially related to constitutive metabolism, then later associated with responses to oxidative stress. The findings advance our understanding of the mechanisms involved in gossypol degradation and highlight the potential of P. lecomtei BRM044603 in cotton waste biotreatment, relevant for animal supplementation, sustainable resource utilization, and bioremediation.

Decoding the chromosome-scale genome of the nutrient-rich Agaricus subrufescens: a resource for fungal biology and biotechnology.

Agaricus subrufescens, also known as the "sun mushroom," has significant nutritional and medicinal value. However, its short shelf life due to the browning process results in post-harvest losses unless it's quickly dehydrated. This restricts its availability to consumers in the form of capsules. A genome sequence of A. subrufescens may lead to new cultivation alternatives or the application of gene editing strategies to delay the browning process. We assembled a chromosome-scale genome using a hybrid approach combining Illumina and Nanopore sequencing. The genome was assembled into 13 chromosomes and 31 unplaced scaffolds, totaling 44.5 Mb with 96.5% completeness and 47.24% GC content. 14,332 protein-coding genes were identified, with 64.6% of the genome covered by genes and 23.41% transposable elements. The mitogenome was circularized and encoded fourteen typical mitochondrial genes. Four polyphenol oxidase (PPO) genes and the Mating-type locus were identified. Phylogenomic analysis supports the placement of A. subrufescens in the Agaricomycetes clade. This is the first available genome sequence of a strain of the "sun mushroom." Results are available through a Genome Browser (https://plantgenomics.ncc.unesp.br/gen.php?id=Asub) and can support further fungal biological and genomic studies.

Aqueous Extracts of Fermented Macrofungi Cultivated in Oilseed Cakes as a Carbon Source for Probiotic Bacteria and Potential Antibacterial Activity.

Plant biomass colonized by macrofungi can contain molecules with bioactive properties with applications to human/animal health. This work aimed to verify antibacterial activities from aqueous extracts from oil seed cakes of Jatropha curcas (JSC) and cottonseed (CSC), fermented by macrofungi for probiotic bacteria cultivation. Coriolopsis sp., Tyromyces sp., Panus lecomtei, and Pleurotus pulmonarius were cultivated in solid and submerged media. The aqueous extract of unfermented JSC was more efficient than glucose for the growth of all probiotic bacteria. Extracts from four macrofungi fermented in CSC favored Lactobacillus acidophilus growth. In solid fermentation, macrofungi extracts cultivated in JSC favored Bifidobacterium lactis growth. All fungi extracts showed more significant growth than carbohydrates among the four probiotic bacteria evaluated. Regarding antimicrobial activities, no fungal extract or bacterial supernatant showed a more significant inhibition halo for enteropathogenic bacteria than ampicillin (control). Extracts from P. lecomtei and Coriolopsis sp. in CSC showed inhibition halos for Salmonella enterica. Supernatants from L. acidophilus, B. lactis, and Lactobacillus rhamnosus resulted in more significant inhibition of Staphylococcus aureus than the control, which indicates possible antimicrobial activity. Unfermented JSC supernatant showed better results for bacterial growth, while supernatants and aqueous extracts from CSC fermentation can be used for probiotic bacteria culture.

Development of reference genes for RT-qPCR analysis of gene expression in Pleurotus pulmonarius for biotechnological applications.

Jatropha curcas is an oilseed crop with biorefinery applications. Whilst cake generated following oil extraction offers potential as a protein source for animal feed, inactivation of toxic phorbol esters present in the material is necessary. Pleurotus pulmonarius is a detoxifying agent for jatropha cake with additional potential as animal feed, edible mushroom and for enzyme production. For the characterization of fungal genes involved in phorbol ester degradation, together with other industrial applications, reverse transcription-quantitative PCR (RT-qPCR) is a tool that enables accurate quantification of gene expression. For this, reliable analysis requires reference genes for normalization of mRNA levels validated under conditions employed for target genes. The stability of potential reference genes ß-TUB, ACTIN, GAPDH, PHOS, EF1α, TRPHO, LAC, MNP3, MYP and VP were evaluated following growth of P. pulmonarius on toxic, non-toxic jatropha cake and a combined treatment, respectively. NormFinder and geNorm algorithms for expression stability analysis identified PHOS, EF1α and MNP3 as appropriate for normalizing gene expression. Reference gene combinations contrasting in ranking were compared following normalization of relative expression of the CHU_2040 gene, encoding an esterase enzyme potentially involved in phorbol ester degradation. The reference genes for P. pulmonarius will facilitate the elucidation of mechanisms involved in detoxification of phorbol esters as well as analysis of target genes for application in biorefinery models.

Bioactives and Extracellular Enzymes Obtained from Fermented Macrofungi Cultivated in Cotton and Jatropha Seed Cakes.

This work focused on obtaining fermented oil cake (cotton or Jatropha) via macrofungi growth with potential characteristics for animal feed formulations, such as the presence of extracellular enzymes, bioactive (ergosterol and antioxidants), and detoxification of antinutritional compounds. The concentration of phorbol esters was reduced by four macrofungi in Jatropha seed cake (JSC) to non-toxic levels. At least two macrofungi efficiently degraded free gossypol in cottonseed cake (CSC). Fermentation with Coriolopsis sp. INPA1646 and Tyromyces sp. INPA1696 resulted in increased ergosterol concentrations, antioxidant activity reduction, and high activity of laccases and proteases. Bromatological analysis indicated high crude protein concentrations, with partial solubilization by fungal proteases. Fermented products from Coriolopsis sp. and Tyromyces sp. in JSC or CSC can be considered important biological inputs for monogastric and polygastric animal feed.

A new circular economy approach for integrated production of tomatoes and mushrooms.

Spent mushroom Substrate is the by-product generated at the end of the mushroom growing cycle. It can be used in agriculture for different purposes, including seedling production, soil conditioning or application as an organic fertilizer. Tomato is one of the world́s most important crops, requiring considerable care, in terms of both nutrition and disease control. The objective of this study was to investigate the viability of spent mushroom substrate as a nutrient source for tomato seedlings and develop an integrated tomato and mushroom co-production system. For seedling production, different compositions were evaluated with spent mushroom substrate from Pleurotus ostreatus or substrate colonized with Agaricus bisporus. The parameters evaluated comprised germination rate, seedling quality and physicochemical analysis. A tomato and mushroom integrated production system was developed using a 40-liter pot divided into upper (spent mushroom substrate and soil), middle (spent mushroom substrate from P. ostreatus) and lower (gravel) layers. For seedlings production, plants treated with the substrate colonized with A. bisporus presented a superior root length (10.1 cm) and aerial part length (6.6 cm). Co-production of tomato and mushrooms was also shown to be viable. In this co-cultivation system between tomato and mushroom, the treatment with the substrate colonized with A. bisporus differed from others, with this treatment presenting high yields of tomato (2.35 kg/plant pot) and mushrooms (1.33 kg/plant pot) within the same bucket. With this co-production system, the tomato production time was reduced by 60 days and prolonged continuous mushroom production by 120 days. These findings show a sustainable approach to manage different agroindustrial residues, encouraging the use of these residues for olericulture and fungiculture production.

Outdoor versus indoor cultivation: Effects on the metabolite profile of Agaricus subrufescens strains analyzed by untargeted metabolomics.

Agaricus subrufescens has emerged as an important culinary-medicinal mushroom over the last decades. Efforts have been dedicated to upgrade the A. subrufescens productive process via strain selection and cultivation scaling-up. However, little is known on the influence of those variables on the metabolite profiles and nutraceutical properties of this mushroom. In this work, the effects of outdoor versus indoor cultivation on the metabolite profiles of five commercial strains of A. subrufescens were investigated by untargeted metabolomics. UHPLC-MS coupled to multivariate data analysis revealed that the concentration of several metabolites with reported health-related properties as well as related to taste and browning varied significantly between strains and were affected by the cultivation system in a strain-dependent manner. Data suggest that increasing the production scale by means of indoor cultivation may decrease the nutraceutical quality of some A. subrufescens strains while also affecting taste and browning susceptibility to different extents.

Characterization of extracellular secondary metabolites in Oudemansiella canarii BRM-044600 displaying antifungal activity against the phytopathogen Sclerotinia sclerotiorum.

White mold disease, caused by the phytopathogen Sclerotinia sclerotiorum, provokes severe productivity losses in several economically important crops. Biocontrol agents, especially antagonist filamentous fungi, are environmentally friendly alternatives to the chemical fungicides used in white mold management. The objective of this study was to screen for basidiomycete fungi capable of inhibiting S. sclerotiorum and investigate their bioactive metabolites responsible for antifungal activities. Two out of 17 tested basidiomycete isolates inhibited the mycelial growth of S. sclerotiorum in pair culture experiments on agar plates, namely Oudemansiella canarii BRM-044600 and Laetisaria arvalis ATCC52088. O. canarii BRM-044600 liquid culture filtrate exhibited the greatest antifungal activity and was selected for further investigation. UHPLC-MS analysis suggests that six putative strobilurins, including strobilurin A and/or stereoisomers of this compound (m/z 259.1299, [M + H]+) and three putative strobilurins with m/z 257.1184 ([M + H]+) are likely responsible for the antifungal activity observed in the culture filtrate. For the first time, this work demonstrated the potential of O. canarii for white mold biocontrol and strobilurin production.

Biomass of unconventional plants from Brazilian semiarid as substrate for hydrolytic enzymes production by Aspergillus niger under solid and submerged fermentation

Aspergillus niger KIJH was grown in solid and submerged fermentation using leaves and roots (with and without bark) of plants typically from Brazilian semiarid as substrate to produce a multienzymatic extract, which was characterised for its potential biotechnological applications. Solid-state fermentation (SSF) was applied to select the most promising plants biomass as induction substrates for the production of hydrolytic enzymes by fungus. The best biomasses were used as substrate in submerged fermentation (SmF) assays at two scales. Samples of up scale fermented culture were partially purified by ultrafiltration and activity and pH and temperature stability of CMCase and xylanase were evaluated. A. niger KIJH produced hydrolytic enzymes under SSF containing unconventional plants biomass from Brazilian semiarid. In SmF conditions, maximum CMCase (0.264 U mL-1) and xylanase (1.163 U mL-1) activities were induced by Jacaratia corumbensis. Scaling up the SmF to 500 mL of medium was able to maintain constant the production of CMCase (0.346 U mL-1) and xylanase (1.273 U mL-1) on the fermented culture. Ultrafiltered and concentrated extract presented CMCase activities practically constant in all temperature ranges (30-80°C) and pH (3.0-9.0), while xylanase optimum activity temperature was 50°C and pH in the range of 3.0 to 5.0. CMCase activity remained stable for 24 hours at 50°C

Biomass of unconventional plants from Brazilian semiarid as substrate for hydrolytic enzymes production by Aspergillus niger under solid and submerged fermentation

Aspergillus niger KIJH was grown in solid and submerged fermentation using leaves and roots (with and without bark) of plants typically from Brazilian semiarid as substrate to produce a multienzymatic extract, which was characterised for its potential biotechnological applications. Solid-state fermentation (SSF) was applied to select the most promising plants biomass as induction substrates for the production of hydrolytic enzymes by fungus. The best biomasses were used as substrate in submerged fermentation (SmF) assays at two scales. Samples of up scale fermented culture were partially purified by ultrafiltration and activity and pH and temperature stability of CMCase and xylanase were evaluated. A. niger KIJH produced hydrolytic enzymes under SSF containing unconventional plants biomass from Brazilian semiarid. In SmF conditions, maximum CMCase (0.264 U mL-1) and xylanase (1.163 U mL-1) activities were induced by Jacaratia corumbensis. Scaling up the SmF to 500 mL of medium was able to maintain constant the production of CMCase (0.346 U mL-1) and xylanase (1.273 U mL-1) on the fermented culture. Ultrafiltered and concentrated extract presented CMCase activities practically constant in all temperature ranges (30-80°C) and pH (3.0-9.0), while xylanase optimum activity temperature was 50°C and pH in the range of 3.0 to 5.0. CMCase activity remained stable for 24 hours at 50°C a

Pigment production by Fusarium solani BRM054066 and determination of antioxidant and anti-inflammatory properties.

The fungal kingdom has been widely studied as a source of bioactive compounds of interest to the pharmaceutical and food industry. This paper studies the production of natural red pigments by Fusarium solani BRM054066 in the submerged fermentation system, using Doehlert experimental design to determine optimal cultivation conditions. The chemical composition of the red pigment was determined by Nuclear Magnetic Resonance spectroscopy (NMR) and Ultra-Performance Liquid Chromatography coupled to Mass Spectrometry (UPLC-MS). Antioxidant activity was assessed by the ability to sequester of free radical DPPH. In the analysis of anti-inflammatory activity, murine peritoneal macrophages activated by LPS were used, and the gene expression of TNF-α, IL-1ß, IL-6, IL-10 and IL-17 was determined using qPCR. As a result, it was found that agitation at 200 rpm and glucose concentration ≥ 20 g/L promote the best results in the production of red pigment. The chemical compounds identified were two naphthoquinones, fusarubin and dihydrofusarubin, and an anthraquinone, a bostrycoidin, being fusarubin the majority compound. The red pigment showed antioxidant activity by scavenge 50% of the DPPH radical, in a concentration of 24 µg/mL. The pigment also showed an effective anti-inflammatory capacity by reducing the overexpression of the pro-inflammatory cytokines TNF-α, IL-1ß and IL-6 and promoting the production of anti-inflammatory IL-10 and IL-17, in murine macrophages activated by LPS (p < 0.05). According to the results, the fungus F. solani BRM054066, under optimized conditions of cultivation, proved to be a promising source of biologically active natural pigments with wide industrial applicability.

Chemical features and antioxidant profile by Schizophyllum commune produced on different agroindustrial wastes and byproducts of biodiesel production.

Schizophyllum commune VE_07 was produced in different culture media containing pine sawdust (PS), grape residue (GR), cotton cake (CC) and jatropha seed cake (JC). The content of phenolics and antioxidant activity were determined for the substrates and mushrooms produced. The content of ß-glucans and the composition of S. commune were also evaluated. The medium formulated with 94% grape residue enabled the highest values of yield, biological efficiency, and productivity. Mushrooms grown in this condition showed the highest value (13.14%) of ß-glucans. The contents of proteins and dietary fibre were 16.59% and 59.61%, respectively. Mushrooms grown in cotton cake showed the highest phenolic content (291.51 ± 1.83 mg GAE/ 100 g mushroom) and antioxidant activity (58.15 ± 0.86 DPPH % scavenging). The results obtained indicate that substrate composition affected the production of S. commune and its chemical composition.

Chemical features and bioactivity of grain flours colonized by macrofungi as a strategy for nutritional enrichment.

Agaricus blazei, Auricularia fuscosuccinea and Pleurotus albidus mycelia were obtained in solid-state cultivation (SSC), using grains (brown rice, canjica corn and wheat) as raw material. Colonized grain flours were analysed for their nutritional, physical and physico-chemical characteristics and biological activity in vitro. Wheat flour with P. albidus showed higher values for protein (18.34 g/100 g), ergosterol (0.60 mg/g), mycelial biomass (183 mg/g) and total amino acids (58.34 mg/g). Corn flour with A. fuscosuccinea showed the highest total phenolic content (2.38 mg GAE/g), antioxidant activity in the 1,1-diphenyl-2-picrylhydrazyl (DPPH) (8.90 µmol TEAC/g) and 2,2'-Azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) (16.52 µmol TEAC/g) assay. Wheat flour with P. albidus were more effective at inhibiting of pancreatic lipase (74.5%) and of α-glucosidase (98.2%). In conclusion, grains colonized by macrofungi mycelia through SSC can enrich the nutritional value and the biological activity of the flours, which presents a potential for functional foods.

Upscale and characterization of lignin-modifying enzymes from Marasmiellus palmivorus VE111 in a bioreactor under parameter optimization and the effect of inducers.

Testing different pHs, dissolved oxygen concentrations and temperatures, plus the addition of inducers, to optimize ligninolytic enzyme activity, resulted in increased production of laccases, total peroxidases and manganese peroxidases on the order of 2.1-fold, 4.6-fold and 10-fold, respectively; laccases reached 6588 U/mL, total peroxidases reached 3533 U/mL and manganese peroxidase achieved 60 U/mL. Furthermore, an increase in laccase volumetric productivity and in its specific activity was verified. The addition of inducers, such as copper sulphate and manganese sulphate, improved enzymatic activity. In addition, a new previously unidentified laccase isoform was documented by zymography. The present work successfully increased the production of ligninolytic enzymes.

Development of an RP-UHPLC-PDA method for quantification of free gossypol in cottonseed cake and fungal-treated cottonseed cake.

Cottonseed cake biomass, which is a residue of oil extraction, is potentially appropriate for use as animal feed, given the high mineral, fibre and protein content. The presence of free gossypol, however, a toxic pigment in the glands of the cotton plant, limits use of this biomass for monogastric livestock. A promising method to detoxify cottonseed cake relies on fermentation by fungi, which can eliminate up to 100% of gossypol. In order to quantify trace levels of free gossypol in different cotton materials, including cottonseed cake treated with macrofungi, a simple and rapid chromatographic detection method was developed and validated. Under optimized conditions, extraction was performed using 70% acetone. The extract was then analysed by Ultra High-Performance Liquid Chromatography (UHPLC), with gradient elution on a C18 reverse phase column KINETEX® (100 x 2.10 mm, 2.6 µm). Methanol-0.1% TFA aqueous solution was employed as mobile phase and PDA detection conducted at 254 nm. The optimized method was validated by analysis of specificity, linearity and range, limit of detection, limit of quantification, precision and accuracy. Detection and quantification limits were observed at 0.2 and 0.5 µg/mL, respectively. With good reproducibility, with precision (RSD)<10% and recovery greater than 94%, the developed assay was appropriate for quantification of low quantities of free gossypol. The validated method was successfully applied to determine trace levels of free gossypol cottonseed treated with a macrofungus.

Current Strategies for the Detoxification of Jatropha curcas Seed Cake: A Review.

Jatropha curcas is an important oilseed plant, with considerable potential in the development of biodiesel. Although Jatropha seed cake, the byproduct of oil extraction, is a residue rich in nitrogen, phosphorus, potassium, and carbon, with high protein content suitable for application in animal feed, the presence of toxic phorbol esters limits its application in feed supplements and fertilizers. This review summarizes the current methods available for detoxification of this residue, based upon chemical, physical, biological, or combined processes. The advantages and disadvantages of each process are discussed, and future directions involving genomic and proteomic approaches for advancing our understanding of biodegradation processes involving microorganisms are highlighted.

Production, purification and characterization of an aspartic protease from Aspergillus foetidus.

An acidic thermostable protease was extracellularly produced either in shake flask or in stirred tank bioreactor by an Aspergillus foetidus strain isolated from the Brazilian savanna soil using different nitrogen sources. Its maximum activity (63.7 U mL-1) was obtained in a medium containing 2% (w/v) peptone. A cultivation carried out in a 5.0 L stirred-tank bioreactor provided a maximum protease activity 9% lower than that observed in Erlenmeyer flasks, which was obtained after a significantly shorter (by 16-29%) time. Protease purification by a combination of gel-filtration chromatography resulted in a 16.9-fold increase in specific activity (248.1 U g-1). The estimated molecular weight of the purified enzyme was 50.6 kDa, and the optimal pH and temperature were 5.0 and 55 °C, respectively. The enzyme was completely inhibited by pepstatin A, and its activity enhanced by some metals. According to the inhibition profiles, it was confirmed that the purified acid protease belongs to the aspartic protease type. These results are quite promising for future development of large-scale production of such protease, which can be useful in biotechnological applications requiring high enzyme activity and stability under acidic conditions.

Microalgae cultivation in sugarcane vinasse: Selection, growth and biochemical characterization.

Sugarcane ethanol is produced at large scale generating wastes that could be used for microalgae biomass production in a biorefinery strategy. In this study, forty microalgae strains were screened for growth in sugarcane vinasse at different concentrations. Two microalgae strains, Micractinium sp. Embrapa|LBA32 and C. biconvexa Embrapa|LBA40, presented vigorous growth in a light-dependent manner even in undiluted vinasse under non-axenic conditions. Microalgae strains presented higher biomass productivity in vinasse-based media compared to standard Bold's Basal Medium in cultures performed using 15L airlift flat plate photobioreactors. Chemical composition analyses showed that proteins and carbohydrates comprise the major fractions of algal biomass. Glucose was the main monosaccharide detected, ranging from 46% to 76% of the total carbohydrates content according to the strain and culture media used. This research highlights the potential of using residues derived from ethanol plants to cultivate microalgae for the production of energy and bioproducts.

The hydrolysis of agro-industrial residues by holocellulose-degrading enzymes

Holocellulose structures from agro-industrial residues rely on main and side chain attacking enzymes with different specificities for complete hydrolysis. Combinations of crude enzymatic extracts from different fungal species, including Aspergillus terreus, Aspergillus oryzae, Aspergillus niger and Trichoderma longibrachiatum, were applied to sugar cane bagasse, banana stem and dirty cotton residue to investigate the hydrolysis of holocellulose structures. A. terreus and A. oryzae were the best producers of FPase and xylanase activities. A combination of A. terreus and A. oryzae extracts in a 50% proportion provided optimal hydrolysis of dirty cotton residue and banana stem. For the hydrolysis of sugar cane bagasse, the best results were obtained with samples only containing A. terreus crude extract.

The hydrolysis of agro-industrial residues by holocellulose-degrading enzymes.

Holocellulose structures from agro-industrial residues rely on main and side chain attacking enzymes with different specificities for complete hydrolysis. Combinations of crude enzymatic extracts from different fungal species, including Aspergillus terreus, Aspergillus oryzae, Aspergillus niger and Trichoderma longibrachiatum, were applied to sugar cane bagasse, banana stem and dirty cotton residue to investigate the hydrolysis of holocellulose structures. A. terreus and A. oryzae were the best producers of FPase and xylanase activities. A combination of A. terreus and A. oryzae extracts in a 50% proportion provided optimal hydrolysis of dirty cotton residue and banana stem. For the hydrolysis of sugar cane bagasse, the best results were obtained with samples only containing A. terreus crude extract.