Selection of a pH- and temperature-stable laccase from Ganoderma australe and its application for bioremediation of textile dyes

Valorization of sugarcane bagasse for high-yield production of laccase through Aspergillus terreus for effective azo dye decolourization

Synthetic dyes such as azo dyes are significant pollutants in the wastewater released from various textile industries. The low biodegradability and production from synthetic sources with high shelf life make azo dyes a challenging material for degradation. This study used chemically mutated Aspergillus terrus in the laccase production under solid-state fermentation using sugarcane bagasse. Initially, the wild-type strain produced a laccase activity of 4.12 U/mL. Later, the alkaline pretreatment of sugarcane bagasse showed a significant increase in laccase activity by 38.9%. Further, random mutagenesis treatment with 100 mM EMS generated a hyper laccase-producing strain with a 2.3-fold increment in laccase activity compared to the wild-type strain. The enzyme displayed optimal activity at pH 6.5 and 35 °C. The metal ions such as Fe3+ (29.4 U/mL), Fe2+ (20.8 U/mL) and Cu2+ (18.05 U/mL) showed positive effects on laccase activity. The crude laccase was used to bioremediate Congo red, a prominent azo dye used in textile and pharmaceutical industries. The preliminary studies with a crude enzyme displayed 68.86% dye decolourization after 24 h of incubation. Additionally, with Taguchi orthogonal array optimization experiments, the maximal dye decolorization of 78.24% was achieved by maintaining crude enzyme concentration (20 U), dye concentration (25 mg/L) and pH 4.5.

Enhanced degradation of phenolic pollutants by a novel cold-adapted laccase from Peribacillus simplex

Laccase (EC 1.10.3.2), as eco-friendly biocatalysts, holds immense potential for sustainable applications across various environmental and industrial sectors. Despite the growing interest, the exploration of cold-adapted laccases, especially their unique properties and applicability, remains limited. In this study, we have isolated, cloned, expressed, and purified a novel laccase from Peribacillus simplex (GenBank: PP430751), which was derived from permafrost layer. The recombinant laccase (PsLac) exhibited optimal activity at 30 °C and a pH optimum of 3.5. Remarkably, PsLac exhibited remarkable stability in the presence of organic solvents, with its enzyme activity increasing by 20 % after being incubated in a 30 % trichloromethane solution for 12 h, compared to its initial activity. Furthermore, the enzyme preserved 100 % of its activity after undergoing eight freeze-thaw cycles. Notably, the catalytic center of PsLac contains Zn2+ instead of the typically observed Cu2+ found in other laccases, and metal-ion substitution experiments raised the catalytic efficiency to 3-fold when Zn2+ was replaced with Fe2+. Additionally, PsLac has demonstrated a proficient ability to degrade phenolic pollutants, such as hydroquinone, even at a low temperature of 16 °C, positioning it as a promising candidate for environmental bioremediation and contributing to cleaner production processes.

Selective pressure leads to an improved synthetic consortium fit for dye degradation

Microorganisms have great potential for bioremediation as they have powerful enzymes and machineries that can transform xenobiotics. The use of a microbial consortium provides more advantages in application point of view than pure cultures due to cross-feeding, adaptations, functional redundancies, and positive interactions among the organisms. In this study, we screened about 107 isolates for their ability to degrade dyes in aerobic conditions and without additional carbon source. From our screening results, we finally limited our synthetic consortium to Gordonia and Rhodococcus isolates. The synthetic consortium was trained and optimized for azo dye degradation using sequential treatment of small aromatic compounds such as phenols that act as selective pressure agents. After four rounds of optimization with different aims for each round, the consortium was able to decolorize and degrade various dyes after 48 h (80%-100% for brilliant black bn, methyl orange, and chromotrop 2b; 50-70% for orange II and reactive orange 16; 15-30% for chlorazol black e, reactive red 120, and allura red ac). Through rational approaches, we can show that treatment with phenolic compounds at micromolar dosages can significantly improve the degradation of bulky dyes and increase its substrate scope. Moreover, our selective pressure approach led to the production of various dye-degrading enzymes as azoreductase, laccase-like, and peroxidase-like activities were detected from the phenol-treated consortium. Evidence of degradation was also shown as metabolites arising from the degradation of methyl red and brilliant black bn were detected using HPLC and LC-MS analysis. Therefore, this study establishes the importance of rational and systematic screening and optimization of a consortium. Not only can this approach be applied to dye degradation, but this study also offers insights into how we can fully maximize microbial consortium activity for other applications, especially in biodegradation and biotransformation.

Efficient degradation and detoxification of structurally different dyes and mixed dyes by LAC-4 laccase purified from white-rot fungi Ganoderma lucidum

The purpose of this study is to evaluate the decolorization ability and detoxification effect of LAC-4 laccase on various types of single and mixed dyes, and lay a good foundation for better application of laccase in the efficient treatment of dye pollutants. The reaction system of the LAC-4 decolorizing single dyes (azo, anthraquinone, triphenylmethane, and indigo dyes, 17 dyes in total) were established. To explore the decolorization effect of the dye mixture by LAC-4, two dyes of the same type or different types were mixed at the same concentration (100 mg/L) in the reaction system containing 0.5 U laccase, and time-course decolorization were performed on the dye mixture. The combined dye mixtures consisted of azo + azo, azo + anthraquinone, azo + indigo, azo + triphenylmethane, indigo + triphenylmethane, and triphenylmethane + triphenylmethane. The results obtained in this study were as follows. Under optimal conditions of 30 °C and pH 5.0, LAC-4 (0.5 U) can efficiently decolorize four different types of dyes. The 24-hour decolorization efficiencies of LAC-4 for 800 mg/L Orange G and Acid Orange 7 (azo), Remazol Brilliant Blue R (anthraquinone), Bromophenol Blue and Methyl Green (triphenylmethane), and Indigo Carmine (indigo) were 75.94%, 93.30%, 96.56%, 99.94%, 96.37%, and 37.23%, respectively. LAC-4 could also efficiently decolorize mixed dyes with different structures. LAC-4 can achieve a decolorization efficiency of over 80% for various dye mixtures such as Orange G + Indigo Carmine (100 mg/L+100 mg/L), Reactive Orange 16 + Methyl Green (100 mg/L+100 mg/L), and Remazol Brilliant Blue R + Methyl Green (100 mg/L+100 mg/L). During the decolorization process of the mixed dyes by laccase, four different interaction relationships were observed between the dyes. Decolorization efficiencies and rates of the dyes that were difficult to be degraded by laccase could be greatly improved when mixed with other dyes. Degradable dyes could greatly enhance the ability of LAC-4 to decolorize extremely difficult-to-degrade dyes. It was also found that the decolorization efficiencies of the two dyes significantly increased after mixing. The possible mechanisms underlying the different interaction relationships were further discussed. Free, but not immobilized, LAC-4 showed a strong continuous batch decolorization ability for single dyes, two-dye mixtures, and four-dye mixtures with different structures. LAC-4 exhibited high stability, sustainable degradability, and good reusability in the continuous batch decolorization. The LAC-4-catalyzed decolorization markedly reduced or fully abolished the toxic effects of single dyes (azo, anthraquinone, and indigo dye) and mix dyes (nine dye mixtures containing four structural types of dyes) on plants. Our findings indicated that LAC-4 laccase had significant potential for use in bioremediation due to its efficient degradation and detoxification of single and mixed dyes with different structural types.

Study on biodegradation mechanism of Fusarium solani NK-NH1 on the hull wood of the Nanhai No. 1 shipwreck

The Nanhai No. 1 shipwreck is an ancient wooden ship in the Southern Song Dynasty. Currently, serious challenges of microbial diseases exist on the hull wood. This study aimed to obtain microbial samples from the ship hull in December 2021 and analyze the microbial diseases through scanning electron microscopy and high-throughput sequencing to preserve the Nanhai No. 1 shipwreck. The biodegradation mechanism of diseased microorganisms was explored through whole genome sequencing and the detection of enzyme activity and gene expression levels of diseased microorganisms under different conditions. The results showed that there was obvious fungal colonization on the surface of the hull wood and Fusarium solani NK-NH1 was the dominant disease fungus on the surface. NK-NH1 has strong cellulose and lignin degradation ability. Its whole genome size is 52,389,955 bp, and it contains 17,402 genes. It has a variety of key enzyme genes involved in cellulose and lignin degradation. The NK-NH1 dominant degrading enzyme lignin peroxidase has the highest enzyme activity at pH = 4, NaCl concentration of 30%, and FeSO4 concentration of 50 mg/L, while laccase has the highest enzyme activity at pH = 4, NaCl concentration of 10%, and FeSO4 concentration of 100 mg/L. The above research results prove that NK-NH1 is a key fungus to the biodegradation of ship hull wood when it is exposed to air, low pH, high salt, and rich in sulfur iron compounds. This study provides a theoretical basis for the preservation of the Nanhai No. 1 shipwreck.

Laccase immobilization and its degradation of emerging pollutants: A comprehensive review

The chronic lack of effective disposal of pollutants has resulted in the detection of a wide variety of EPs in the environment, with concentrations high enough to affect ecological health. Laccase, as a versatile oxidase capable of catalyzing a wide range of substrates and without producing toxic by-products, is a potential candidate for the biodegradation of pollutants. Immobilization can provide favorable protection for free laccase, improve the stability of laccase in complex environments, and greatly enhance the reusability of laccase, which is significant in reducing the cost of industrial applications. This study introduces the properties of laccase and subsequently elaborate on the different support materials for laccase immobilization. The research advances in the degradation of EDs, PPCPs, and PAHs by immobilized laccase are then reviewed. This review provides a comprehensive understanding of laccase immobilization, as well as the advantages of various support materials, facilitating the development of more economical and efficient immobilization systems that can be put into practice to achieve the green degradation of EPs.

Recovery and partial purification of fibrinolytic protease from Pleurotus ostreatus and P. eryngii and cytotoxic and antioxidant activity of their extracts

Mushrooms are a source of primary and secondary metabolites. Little is known about the most suitable conditions for production of mushrooms by submerged fermentation. This article reports antioxidant and cytotoxic assays, in addition to quantitatively evaluating the content of proteases with fibrinolytic action in the crude extracts of two species of edible mushrooms produced in different formulations, as well as evaluating the recovery of these enzymes by aqueous two-phase systems (ATPS). The mushrooms Pleurotus ostreatus and Pleurotus eryngii, at concentration of 100 µg/mL, displayed inhibition of DPPH and ABTS radicals below 50%. In the cytotoxicity test, the cells human fibroblast cell lines (MRC-5) showed cell viability greater than 80%. Concerning fibrinolytic activity, P. eryngii presented 226.47 ± 7.26 U/mL, therefore being more efficient than P. ostreatus (71.5 ± 0.56 U/mL). In the recovery of the P. eryngii extract by ATPS, the fibrinolytic protease was partitioned in the salt phase (30.25 U/mL). The molecular mass of the proteases was between 75 and 100 kDa. These results prove the low cytotoxicity of the extracts produced and that fermentation in supplemented malt broth favored the excretion of fibrinolytic proteases compared to the other evaluated media.

Optimization and purification of laccase activity from Mammaliicoccus sciuri isolated from the soils of Similipal, Odisha, India: a kinetics study of crystal violet dye decolorization

Four laccase-producing bacteria were found in soil samples from the Similipal Biosphere Reserve in Odisha, according to the current study. The isolates (SLCB1 to SLCB4) were evaluated for their laccase-producing ability in LB broth supplemented with guaiacol. The ABTS assay was performed to assess the laccase activity. The bacterium Mammaliicoccus sciuri shows the highest laccase activity i.e., 0.5125 U/L at the optimized conditions of pH 5.5, temperature 32.5 °C, ABTS concentration of 0.75 μl with an incubation time of 9 d. Laccase activity of M. sciuri grown in Sawdust was significantly increased in comparison to that in other agro wastes. The partially purified laccase enzyme after ammonium sulfate precipitation and dialysis showed a molecular weight of ∼58.5 kDa as determined by SDS-PAGE. A decolorization efficiency of 66.67% was recorded for the dye crystal violet after 1 h treatment with dialyzed laccase enzyme compared with phenol red, brilliant blue, and methylene blue.

Whole genome sequencing and annotation of Daedaleopsis sinensis, a wood-decaying fungus significantly degrading lignocellulose

Daedaleopsis sinensis is a fungus that grows on wood and secretes a series of enzymes to degrade cellulose, hemicellulose, and lignin and cause wood rot decay. Wood-decaying fungi have ecological, economic, edible, and medicinal functions. Furthermore, the use of microorganisms to biodegrade lignocellulose has high application value. Genome sequencing has allowed microorganisms to be analyzed from the aspects of genome characteristics, genome function annotation, metabolic pathways, and comparative genomics. Subsequently, the relevant information regarding lignocellulosic degradation has been mined by bioinformatics. Here, we sequenced and analyzed the genome of D. sinensis for the first time. A 51.67-Mb genome sequence was assembled to 24 contigs, which led to the prediction of 12,153 protein-coding genes. Kyoto Encyclopedia of Genes and Genomes database analysis of the D. sinensis data revealed that 3,831 genes are involved in almost 120 metabolic pathways. According to the Carbohydrate-Active Enzyme database, 481 enzymes are found in D. sinensis, of which glycoside hydrolases are the most abundant. The genome sequence of D. sinensis provides insights into its lignocellulosic degradation and subsequent applications.

Immobilization of commercial horseradish peroxidase in calcium alginate-starch hybrid support and its application in the biodegradation of phenol red dye

In this study, horseradish peroxidase (HRP) was immobilized for the first time on Ca alginate-starch hybrid beads and employed for the biodegradation of phenol red dye. The optimal protein loading was 50 mg/g of support. Immobilized HRP demonstrated improved thermal stability and maximum catalytic activity at 50 °C and pH 6.0, with an increase in half-life (t1/2) and enzymatic deactivation energy (Ed) compared to free HRP. After 30 days of storage at 4 °C, immobilized HRP retained 109% of its initial activity. Compared to free HRP, the immobilized enzyme exhibited higher potential for phenol red dye degradation, as evidenced by the removal of 55.87% of initial phenol red after 90 min, which was 11.5 times greater than free HRP. In sequential batch reactions, the immobilized HRP demonstrated good potential efficiency for the biodegradation of phenol red dye. The immobilized HRP was used for a total of 15 cycles, degrading 18.99% after 10 cycles and 11.69% after 15 cycles, with a residual enzymatic activity of 19.40% and 12.34%, respectively. Overall, the results suggest that HRP immobilized on Ca alginate-starch hybrid supports shows promise as a biocatalyst for industrial and biotechnological applications, particularly for the biodegradation of recalcitrant compounds such as phenol red dye.

An Inferred Ancestral CotA Laccase with Improved Expression and Kinetic Efficiency

Laccases are widely used in industrial production due to their broad substrate availability and environmentally friendly nature. However, the pursuit of laccases with superior stability and increased heterogeneous expression to meet industry demands appears to be an ongoing challenge. To address this challenge, we resurrected five ancestral sequences of laccase BsCotA and their homologues. All five variants were successfully expressed in soluble and functional forms with improved expression levels in Escherichia coli. Among the five variants, three exhibited higher catalytic rates, thermal stabilities, and acidic stabilities. Notably, AncCotA2, the best-performing variant, displayed a k_cat/K_M of 7.5 × 10⁵ M^-1·s^-1, 5.2-fold higher than that of the wild-type BsCotA, an improved thermo- and acidic stability, and better dye decolorization ability. This study provides a laccase variant with high application potential and presents a new starting point for future enzyme engineering.

Laccase Production from Agrocybe pediades: Purification and Functional Characterization of a Consistent Laccase Isoenzyme in Liquid Culture

Laccases are valuable enzymes as an excellent ecological alternative for bioremediation issues because they can oxidize persistent xenobiotic compounds. The production and characterization of extracellular laccases from saprotrophic fungi from disturbed environments have been scarcely explored, even though this could diversify their functional characteristics and expand the conditions in which they carry out their catalysis. Agrocybe pediades, isolated from a disturbed forest, produces an extracellular laccase in liquid culture. The enzyme was purified, identified and characterized. Copper and hexachlorobenzene do not function as inducers for the laccase produced. Partial amino acid sequences were obtained by LC-MS/MS that share similarity with laccases from other fungi. Purified laccase is a monomer with a molecular mass between 55-60 kDa and had an optimum activity at pH 5.0 and the optimum temperature at 45 °C using 2,6-dimethoxyphenol (2,6-DMP) as substrate. The K_m and V_max also determined with 2,6-DMP were 100 μM and 285 μmol∙min^-1∙mg^-1, respectively, showing that the laccase of A. pediades has a higher affinity for this substrate than that of other Agaricales. These features could provide a potential catalyst for different toxic substrates and in the future laccase could be used in environmental recovery processes.

Purification and characterization of a fungal laccase expressed in Kluyveromyces lactis suitable for baking

Laccase enzyme can replace chemical additives to improve texture properties and the volume of bread. Laccase encoding gene from Phlebia brevispora, a native fungus from Misiones, Argentina, was expressed in the generally recognized as safe yeast Kluyveromyces lactis. To improve laccase activity, medium conditions were optimized. The use of iron sulfate at a concentration of 1 mM led to optimum laccase activity (1289 U·L^-1 ) on the fourth day of incubation. SDS-PAGE analysis revealed that the molecular mass of purified laccase was about 180 kDa. Optimum pH for the enzyme was 4 and optimum temperature was 40°C. Laccase exhibited high stability at low pH and high temperature. The application of recombinant laccase to bread decreased hardness, gumminess, and chewiness and increased bread volume. Based on these results, recombinant laccase from P. brevispora with improved yield is a good option for application as an improver of the physicochemical quality of bread at the industrial level. Besides, it will allow us to advance toward our goal of developing healthy alternatives for the bakery industry. No previous work has been reported concerning the heterologous expression of the laccase gene native to the province of Misiones, Argentina, with an aim for application in baking. PRACTICAL APPLICATION: Healthy bakeries became a trend in recent years. The use of the laccase enzyme increases the specific volume and decreases the hardness of bread, being thus an alternative for the replacement of chemical additives in the bakery industry.

Bacterial-derived surfactants: an update on general aspects and forthcoming applications

The search for sustainable alternatives to the production of chemicals using renewable substrates and natural processes has been widely encouraged. Microbial surfactants or biosurfactants are surface-active compounds synthesized by fungi, yeasts, and bacteria. Due to their great metabolic versatility, bacteria are the most traditional and well-known microbial surfactant producers, being Bacillus and Pseudomonas species their typical representatives. To be successfully applied in industry, surfactants need to maintain stability under the harsh environmental conditions present in manufacturing processes; thus, the prospection of biosurfactants derived from extremophiles is a promising strategy to the discovery of novel and useful molecules. Bacterial surfactants show interesting properties suitable for a range of applications in the oil industry, food, agriculture, pharmaceuticals, cosmetics, bioremediation, and more recently, nanotechnology. In addition, they can be synthesized using renewable resources as substrates, contributing to the circular economy and sustainability. The article presents a general and updated review of bacterial-derived biosurfactants, focusing on the potential of some groups that are still underexploited, as well as, recent trends and contributions of these versatile biomolecules to circular bioeconomy and nanotechnology.

Comprehensive analysis of codon bias in 13 Ganoderma mitochondrial genomes

Introduction

Codon usage bias is a prevalent phenomenon observed across various species and genes. However, the specific attributes of codon usage in the mitochondrial genome of Ganoderma species remain unknown.

Methods

In this study, we investigated the codon bias of 12 mitochondrial core protein-coding genes (PCGs) in 9 Ganoderma species, including 13 Ganoderma strains.

Results

The codons of all Ganoderma strains showed a preference for ending in A/T. Additionally, correlations between codon base composition and the codon adaptation index (CAI), codon bias index (CBI) and frequency of optimal codons (FOP) were identified, demonstrating the impact of base composition on codon bias. Various base bias indicators were found to vary between or within Ganoderma strains, including GC3s, the CAI, the CBI, and the FOP. The results also revealed that the mitochondrial core PCGs of Ganoderma have an average effective number of codons (ENC) lower than 35, indicating strong bias toward certain codons. Evidence from neutrality plot and PR2-bias plot analysis indicates that natural selection is a major factor affecting codon bias in Ganoderma. Additionally, 11 to 22 optimal codons (ΔRSCU>0.08 and RSCU>1) were identified in 13 Ganoderma strains, with GCA, AUC, and UUC being the most widely used optimal codons in Ganoderma. By analyzing the combined mitochondrial sequences and relative synonymous codon usage (RSCU) values, the genetic relationships between or within Ganoderma strains were determined, indicating variations between them. Nevertheless, RSCU-based analysis illustrated the intra- and interspecies relationships of certain Ganoderma species.

Discussion

This study deepens our insight into the synonymous codon usage characteristics, genetics, and evolution of this important fungal group.

Taxonomy and phylogeny of Sanguinoderma rugosum complex with descriptions of a new species and a new combination

Sanguinoderma is distributed in tropical and subtropical areas as a member of Amauroderma s. lat., and the economic values of Sanguinoderma led to high attention in the taxonomic studies. Previously, 16 species have been developed into Sanguinoderma. In this study, the taxonomic system of Sanguinoderma was reconducted based on morphological and multi-gene phylogenetic analyses, especially making a distinction for Sanguinoderma rugosum complex. Morphological analysis was based on the notes of macro- and micro morphological observations. Multi-gene phylogenetic analyses were used maximum likelihood (ML) and Bayesian inference (BI) analyses inferred from combined dataset of ITS, nLSU, rpb2, tef1, mtSSU, and nSSU. Combined with morphological characters and phylogenetic evidence, the results demonstrated that S. rugosum complex consists of five taxa, in which Sanguinoderma leucomarginatum was described as a new species, and it is characterized by the orbicular pilei with white to buff margin when fresh and clavate apical cells of pileipellis with septa. In addition, Amauroderma preussii was transferred to Sanguinoderma as a new combination due to its blood-red color-changed pore surface; it is characterized by the funnel-shaped, greyish brown, and glabrous pilei with strongly incurved margin. Detailed descriptions and photographs of the two species were provided. With the extension of this study, 18 species were accepted in Sanguinoderma, and 12 species among them were distributed in China. A key to accepted species of Sanguinoderma was also provided.

Phylogenomics and Comparative Genomics Highlight Specific Genetic Features in Ganoderma Species

The Ganoderma species in Polyporales are ecologically and economically relevant wood decayers used in traditional medicine, but their genomic traits are still poorly documented. In the present study, we carried out a phylogenomic and comparative genomic analyses to better understand the genetic blueprint of this fungal lineage. We investigated seven Ganoderma genomes, including three new genomes, G. australe, G. leucocontextum, and G. lingzhi. The size of the newly sequenced genomes ranged from 60.34 to 84.27 Mb and they encoded 15,007 to 20,460 genes. A total of 58 species, including 40 white-rot fungi, 11 brown-rot fungi, four ectomycorrhizal fungi, one endophyte fungus, and two pathogens in Basidiomycota, were used for phylogenomic analyses based on 143 single-copy genes. It confirmed that Ganoderma species belong to the core polyporoid clade. Comparing to the other selected species, the genomes of the Ganoderma species encoded a larger set of genes involved in terpene metabolism and coding for secreted proteins (CAZymes, lipases, proteases and SSPs). Of note, G. australe has the largest genome size with no obvious genome wide duplication, but showed transposable elements (TEs) expansion and the largest set of terpene gene clusters, suggesting a high ability to produce terpenoids for medicinal treatment. G. australe also encoded the largest set of proteins containing domains for cytochrome P450s, heterokaryon incompatibility and major facilitator families. Besides, the size of G. australe secretome is the largest, including CAZymes (AA9, GH18, A01A), proteases G01, and lipases GGGX, which may enhance the catabolism of cell wall carbohydrates, proteins, and fats during hosts colonization. The current genomic resource will be used to develop further biotechnology and medicinal applications, together with ecological studies of the Ganoderma species.