Review: lignin conversion by manganese peroxidase (MnP)

White rot fungal impact on the evolution of simple phenols during decay of silver fir wood by UHPLC-HQOMS

INTRODUCTION

Silver fir (Abies alba Mill.) is one of the most valuable conifer wood species in Europe. Among the main opportunistic pathogens that cause root and butt rot on silver fir are Armillaria ostoyae and Heterobasidion abietinum. Due to the different enzymatic pools of these wood-decay fungi, different strategies in metabolizing the phenols were available.

OBJECTIVE

This work explores the changes in phenolic compounds during silver fir wood degradation.

METHODOLOGY

Phenols were analyzed before and after fungus inoculation in silver fir macerated wood after 2, 4 and 6 months. All samples were analyzed using high-performance liquid chromatography coupled to a hybrid quadrupole-orbitrap mass spectrometer.

RESULTS

Thirteen compounds, including simple phenols, alkylphenyl alcohols, hydroxybenzoketones, hydroxycinnamaldehydes, hydroxybenzaldehydes, hydroxyphenylacetic acids, hydroxycinnamic acids, hydroxybenzoic acids and hydroxycoumarins, were detected. Pyrocatechol, coniferyl alcohol, acetovanillone, vanillin, benzoic acid, 4-hydroxybenzoic acid and vanillic acid contents decreased during the degradation process. Methyl vanillate, ferulic acid and p-coumaric were initially produced and then degraded. Scopoletin was accumulated. Pyrocatechol, acetovanillone and methyl vanillate were found for the first time in both degrading and non-degrading wood of silver fir.

CONCLUSIONS

Despite differences in the enzymatic pool, both fungi caused a significant decrease in the amounts of phenolic compounds with the accumulation of the only scopoletin. Principal component analysis revealed an initial differentiation between the degradation activity of the two fungal species during degradation, but similar phenolic contents at the end of wood degradation.

Food-Grade Expression of Manganese Peroxidases in Recombinant Kluyveromyces lactis and Degradation of Aflatoxin B1 Using Fermentation Supernatants

Aflatoxins are naturally occurring high-toxic secondary metabolites, which cause worldwide environmental contaminations and wastes of food and feed resources and severely threaten human health. Thus, the highly efficient methods and technologies for detoxification of aflatoxins are urgently needed in a long term. In this work, we report the construction of recombinant Kluyveromyces lactis strains GG799(pKLAC1-Phsmnp), GG799(pKLAC1-Plomnp), GG799(pKLAC1-Phcmnp), and then the food-grade expression of the three manganese peroxidases in these strains, followed by the degradation of aflatoxin B1 (AFB1) using the fermentation supernatants. The expression of the manganese peroxidases was achieved in a food-grade manner since Kluyveromyces lactis is food-safe and suitable for application in food or feed industries. The inducible expression process of the optimal recombinant strain GG799(pKLAC1-Phcmnp) and the aflatoxin B1 degradation process were both optimized in detail. After optimization, the degradation ratio reached 75.71%, which was an increase of 49.86% compared to the unoptimized results. The degradation product was analyzed and determined to be AFB1-8,9-dihydrodiol. The recombinant strain GG799(pKLAC1-Phcmnp) supernatants degraded more than 90% of AFB1 in the peanut samples after twice treatments. The structural computational analysis for further mutagenesis of the enzyme PhcMnp was also conducted in this work. The food-grade recombinant yeast strain and the enzyme PhcMnp have potential to be applied in food or feed industries.

Ligninolytic enzymes in Basidiomycetes and their application in xenobiotics degradation

Variety of microorganisms have already proven their capabilities for degradation of wide range of wastes with anthropogenic nature. These pollutants, both liquid and solids, also include so called xenobiotics like phenol and its derivatives, PAHs, dyes, pesticides, pharmaceuticals, etc. Xenobiotics as bisphenol A (BPA), chlorhexidine (CHX), octenidine (OCT), other disinfectants and antiseptics have high ecotoxicological impact. Moreover, they can also impair our quality of life and our health interfering different metabolic and hormone receptors pathways in human body. Chemical treatment of such wastes is not a viable option because of its poor socio-economics and environmental merits. Therefore, applying effective, ecofriendly and cheap treatment methods is of great importance. Basidiomycetes are extensively investigated for their abilities to degrade numerous pollutants and xenobiotics. Through their extracellular ligninolytic enzymes they are capable of reducing or completely removing wide range of hazardous compounds. These enzymes can be categorized in two groups: oxidases (laccase) and peroxidases (manganese peroxidase, lignin peroxidase, versatile peroxidase). Due to the broad substrate specificity of the secreted enzymes Basidiomycetes can be applied as a powerful tool for bioremediation of diverse xenobiotics and recalcitrant compounds.

Bundling the removal of emerging contaminants with the production of ligninolytic enzymes from residual streams

Abstract

Enzymes offer interesting features as biological catalysts for industry: high specificity, activity under mild conditions, accessibility, and environmental friendliness. Being able to produce enzymes in large quantities and having them available in a stable and reusable form reduces the production costs of any enzyme-based process. Agricultural residues have recently demonstrated their potential as substrates to produce ligninolytic enzymes by different white rot fungi. In this study, the biotechnological production of a manganese peroxidase (MnP) by Irpex lacteus was conducted through solid-state fermentation (SSF) with wheat straw as substrate and submerged fermentation (SmF) employing wheat straw extract (WSE). The obtained enzyme cocktail also showed manganese-independent activity (MiP), related to the presence of a short MnP and a dye-decolorizing peroxidase (DyP) which was confirmed by shotgun proteomic analyses. In view of the enhanced production of ligninolytic enzymes in SmF, different parameters such as WSE concentration and nitrogen source were evaluated. The highest enzyme titers were obtained with a medium formulated with glucose and peptone (339 U/L MnP and 15 U/L MiP). The scale-up to a 30 L reactor achieved similar activities, demonstrating the feasibility of enzyme production from the residual substrate at different production scales. Degradation of five emerging pollutants was performed to demonstrate the high oxidative capacity of the enzyme. Complete removal of hormones and bisphenol A was achieved in less than 1 h, whereas almost 30% degradation of carbamazepine was achieved in 24 h, which is a significant improvement compared to previous enzymatic treatments of this compound.

Key points

• Wheat straw extract is suitable for the growth of I. lacteus.

• The enzyme cocktail obtained allows the degradation of emerging contaminants.

• Mn-dependent and Mn-independent activities increases the catalytic potential.

Graphical abstract

Supplementary Information

The online version contains supplementary material available at 10.1007/s00253-022-11776-7.

Long-Term Effects of Climate and Litter Chemistry on Rates and Stable Fractions of Decomposing Scots Pine and Norway Spruce Needle Litter—A Synthesis

We have reviewed information on early-, late- and limit-value decomposition stages for litter of Norway spruce (Picea abies) and Scots pine (Pinus silvestris). This synthesis covers c 16 studies/papers made along a climatic gradient; range in mean annual temperature (MAT) from −1 to +7 °C and mean annual precipitation (MAP) from 425 to 1070 mm. Scots pine has an early stage dominated by carbohydrate decomposition and a late stage dominated by decomposition of lignin; Norway spruce has just one stage dominated by lignin decomposition. We used data for annual mass loss to identify rate-regulating factors in both stages; climate data, namely, MAT and MAP, as well as substrate properties, namely, nitrogen (N), acid unhydrolyzable residue (AUR), manganese (Mn). Early-stage decomposition for Scots pine litter was dominated positively by MAT; the late stage was dominated negatively by MAT, N, and AUR, changing with decomposition stage; there was no effect of Mn. Norway spruce litter had no early stage; decomposition in the lignin-dominated stage was mainly negative to MAP, a negative relationship to AUR and non-significant relationships to N and MAT. Mn had a positive relationship. Limit values for decomposition, namely, the accumulated mass loss at which decomposition is calculated to be zero, were related positively to Mn and AUR for Scots pine litter and negatively to AUR for Norway spruce litter. With different sets of rate-regulating factors as well as different compounds/elements related to the limit values, the decomposition patterns or pathways are different.

Wood degradation by Fomitiporia mediterranea M. Fischer: Physiologic, metabolomic and proteomic approaches

Fomitiporia mediterranea (Fmed) is one of the main fungal species found in grapevine wood rot, also called "amadou," one of the most typical symptoms of grapevine trunk disease Esca. This fungus is functionally classified as a white-rot, able to degrade all wood structure polymers, i.e., hemicelluloses, cellulose, and the most recalcitrant component, lignin. Specific enzymes are secreted by the fungus to degrade those components, namely carbohydrate active enzymes for hemicelluloses and cellulose, which can be highly specific for given polysaccharide, and peroxidases, which enable white-rot to degrade lignin, with specificities relating to lignin composition as well. Furthermore, besides polymers, a highly diverse set of metabolites often associated with antifungal activities is found in wood, this set differing among the various wood species. Wood decayers possess the ability to detoxify these specific extractives and this ability could reflect the adaptation of these fungi to their specific environment. The aim of this study is to better understand the molecular mechanisms used by Fmed to degrade wood structure, and in particular its potential adaptation to grapevine wood. To do so, Fmed was cultivated on sawdust from different origins: grapevine, beech, and spruce. Carbon mineralization rate, mass loss, wood structure polymers contents, targeted metabolites (extractives) and secreted proteins were measured. We used the well-known white-rot model Trametes versicolor for comparison. Whereas no significant degradation was observed with spruce, a higher mass loss was measured on Fmed grapevine culture compared to beech culture. Moreover, on both substrates, a simultaneous degradation pattern was demonstrated, and proteomic analysis identified a relative overproduction of oxidoreductases involved in lignin and extractive degradation on grapevine cultures, and only few differences in carbohydrate active enzymes. These results could explain at least partially the adaptation of Fmed to grapevine wood structural composition compared to other wood species, and suggest that other biotic and abiotic factors should be considered to fully understand the potential adaptation of Fmed to its ecological niche. Proteomics data are available via ProteomeXchange with identifier PXD036889.

Lignocellulose biomass bioconversion during composting: Mechanism of action of lignocellulase, pretreatment methods and future perspectives

Composting is a biodegradation and transformation process that converts lignocellulosic biomass into value-added products, such as humic substances (HSs). However, the recalcitrant nature of lignocellulose hinders the utilization of cellulose and hemicellulose, decreasing the bioconversion efficiency of lignocellulose. Pretreatment is an essential step to disrupt the structure of lignocellulosic biomass. Many pretreatment methods for composting may cause microbial inactivation and death. Thus, the pretreatment methods suitable for composting can promote the degradation and transformation of lignocellulosic biomass. Therefore, this review summarizes the pretreatment methods suitable for composting. Microbial consortium pretreatment, Fenton pretreatment and surfactant-assisted pretreatment for composting may improve the bioconversion process. Microbial consortium pretreatment is a cost-effective pretreatment method to enhance HSs yields during composting. On the other hand, the efficiency of enzyme production during composting is very important for the degradation of lignocellulose, whose action mechanism is unknown. Therefore, this review describes the mechanism of action of lignocellulase, the predominant microbes producing lignocellulase and their related genes. Finally, optimizing pretreatment conditions and increasing enzymatic hydrolysis to improve the quality of composts by controlling suitable microenvironmental factors and core target microbial activities as a research focus in the bioconversion of lignocellulose during composting in the future.

Effect of manganese peroxidase on the decomposition of cellulosic components: Direct cellulolytic activity and synergistic effect with cellulase

Herein, it was unearthed that manganese peroxidase (MnP) from Phanerochaete chrysosporium, a lignin-degrading enzyme, is capable of not only directly decomposing cellulosic components but also boosting cellulase activity. MnP decomposes various cellulosic substrates (carboxymethyl cellulose, cellobiose [CMC], and Avicel®) and produces reducing sugars rather than oxidized sugars such as lactone and ketoaldolase. MnP with Mn^II in acetate buffer evolves the Mn^III-acetate complex functioning as a strong oxidant, and the non-specificity of Mn^III-acetate enables cellulose-decomposition. The catalytic mechanism was proposed by analyzing catalytic products derived from MnP-treated cellopentaose. Notably, MnP also boosts cellulase activity on CMC and Avicel®, even considering the cellulolytic activity of MnP itself. To the best of the authors' knowledge, this is the first report demonstrating a previously unknown fungal MnP activity in cellulose-decomposition in addition to a known delignification activity. Consequently, the results provide a promising insight for further investigation of the versatility of lignin-degrading biocatalysts.

Engineering the Oleaginous Yeast Rhodosporidium toruloides for Improved Resistance Against Inhibitors in Biomass Hydrolysates

Conversion of lignocellulosic biomass into lipids and related chemicals has attracted much attention in the past two decades, and the oleaginous yeast Rhodosporidiumtoruloides has been widely used in this area. While R. toruloides species naturally have physiological advantages in terms of substrate utilization, lipid accumulation, and inhibitor resistance, reduced lipid production and cell growth are noticed when biomass hydrolysates are used as feedstocks. To improve the robustness of R. toruloides, here, we devised engineered strains by overexpressing genes responsible for phenolic compound degradation. Specifically, gene expression cassettes of the manganese peroxidase gene (MNP) and versatile peroxidase gene (VP) were constructed and integrated into the genome of R. toruloides NP11. A series of engineered strains were evaluated for lipid production in the presence of typical phenolic inhibitors. The results showed that R. toruloides strains with proper expression of MNP or VP indeed grew faster in the presence of vanillin and 5-hydroxymethylfurfural than the parental strain. When cultivated in concentrated mode biomass hydrolysates, the strain VP18 had improved performance as the cell mass and lipid content increased by 30% and 25%, respectively. This study provides more robust oleaginous yeast strains for microbial lipid production from lignocellulosic biomass, and similar efforts may be used to devise more advanced lipid producers.

Lignin degradation by microorganisms: A review

Lignin is an abundant plant-based biopolymer that has found applications in a variety of industries from construction to bioethanol production. This recalcitrant branched polymer is naturally degraded by many different species of microorganisms, including fungi and bacteria. These microbial lignin degradation mechanisms provide a host of possibilities to overcome the challenges of using harmful chemicals to degrade lignin biowaste in many industries. The classes and mechanisms of different microbial lignin degradation options available in nature form the primary focus of the present review. This review first discusses the chemical building blocks of lignin and the industrial sources and applications of this multifaceted polymer. The review further places emphasis on the degradation of lignin by natural means, discussing in detail the lignin degradation activities of various fungal and bacterial species. The lignin-degrading enzymes produced by various microbial species, specifically white-rot fungi, brown-rot fungi, and bacteria, are described. In the end, possible directions for future lignin biodegradation applications and research investigations have been provided.

Fungal-mediated electrochemical system: Prospects, applications and challenges

Microbial fuel cells (MFCs) that generate bioelectricity from biodegradable waste have received considerable attention from biologists. Fungi play a significant role as both anodic and cathodic catalysts in MFCs. Saccharomyces cerevisiae is a fungus with an ability to transfer electrons through mediators such as methylene blue (MB), neutral red (NR) or even without a mediator. This unique role of fungal cells in exocellular electron transfer (EET) and their interactions with electrodes hold a lot of promise in areas such as wastewater treatment where yeast cell-based MFCs can be used. The present article highlights the physico-chemical factors affecting the performance of fungal-mediated MFCs in terms of power output and degradation of organic pollutants, along with the challenges associated with fungal MFCs. In addition, to this comparative assessment of fungal-mediated bio-electrochemical systems, their development, possible applications and potential challenges are also discussed.

Myco-remediation: A mechanistic understanding of contaminants alleviation from natural environment and future prospect

Industrialization and modernization of agricultural systems contaminated lithosphere, hydrosphere, and biosphere of the Earth. Sustainable remediation of contamination is essential for environmental sustainability. Myco-remediation is proposed to be a green, economical, and efficient technology over conventional remediation technologies to combat escalating pollution problems at a global scale. Fungi can perform remediation of pollutants through several mechanisms like biosorption, precipitation, biotransformation, and sequestration. Myco-remediation significantly removes or degrades metal metals, persistent organic pollutants, and other emerging pollutants. The current review highlights the species-specific remediation potential, influencing factors, genetic and molecular control mechanism, applicability merits to enhance the bioremediation efficiency. Structure and composition of fungal cell wall is crucial for immobilization of toxic pollutants and a subtle change on fungal cell wall structure may significantly affect the immobilization efficiency. The utilization protocol and applicability of enzyme engineering and myco-nanotechnology to enhance the bioremediation efficiency of any potential fungus was proposed. It is advocated that the association of hyper-accumulator plants with plant growth-promoting fungi could help in an effective cleanup strategy for the alleviation of persistent soil pollutants. The functions, activity, and regulation of fungal enzymes in myco-remediation practices required further research to enhance the myco-remediation potential. Study of the biotransformation mechanisms and risk assessment of the products formed are required to minimize environmental pollution. Recent advancements in molecular "Omic techniques"and biotechnological tools can further upgrade myco-remediation efficiency in polluted soils and water.

Factors Influencing Decolourization and Detoxification of Remazol Brilliant Blue R Dye by Aspergillus flavus

<b>Background and Objectives:</b> Anthraquinone synthetic dyes are widely used in textile, dyeing and paper painting. The discharge of these dyes into the environment causes detriment. The removal of physiochemical dyes is sometimes unsuccessful and expensive. Biological removal is inexpensive, eco-friendly and may break down organic contaminants. In the current work, a fungal technique was applied to decolorize and detoxify dye. <b>Materials and Methods:</b> Dye decolorizing fungi isolation, selection and identification of the most effective isolate and dye decolorization optimization based on carbon and nitrogen sources. In addition, the product's cytotoxicity and metabolites were tested. The enzyme activities were measured to determine dye decolorization. <b>Results:</b> Decolorization of reactive blue 19 dye by the most effective fungal strain isolate (5BF) isolated from industrial effluents were studied. This isolate was identified as <i>Aspergillus flavus</i> based on phenotypic characteristics and confirmed using 18S rRNA gene sequencing. Thin-layer chromatography indicated that this strain is aflatoxins free. Furthermore, metabolites produced from dye treatment with <i>A. flavus</i> were assessed using gas chromatography-mass spectrometry. Toxicity data revealed that <i>A. flavus</i> metabolites were not toxic to plants. Using a one-factor-at-a-time optimization technique, a maximum decolorization percentage (99%) was obtained after 72 hrs in the presence of mannitol and NH<sub>4</sub>NO<sub>3</sub> or NH<sub>4</sub>Cl as carbon and nitrogen sources. Two enzymes (laccase and manganese peroxidase) were shown to be active during dye decolorization by <i>A. flavus</i>. <b>Conclusion:</b> The <i>A. flavus</i> strain was shown to be safe when it came to removing dye from a synthetic medium with high efficiency and their metabolites had no negative influence on the environment. As a result, this strain will be used in the future for dye wastewater bioremediation.

Decay by ectomycorrhizal fungi couples soil organic matter to nitrogen availability

Interactions between soil nitrogen (N) availability, fungal community composition, and soil organic matter (SOM) regulate soil carbon (C) dynamics in many forest ecosystems, but context dependency in these relationships has precluded general predictive theory. We found that ectomycorrhizal (ECM) fungi with peroxidases decreased with increasing inorganic N availability across a natural inorganic N gradient in northern temperate forests, whereas ligninolytic fungal saprotrophs exhibited no response. Lignin-derived SOM and soil C were negatively correlated with ECM fungi with peroxidases and were positively correlated with inorganic N availability, suggesting decay of lignin-derived SOM by these ECM fungi reduced soil C storage. The correlations we observed link SOM decay in temperate forests to tradeoffs in tree N nutrition and ECM composition, and we propose SOM varies along a single continuum across temperate and boreal ecosystems depending upon how tree allocation to functionally distinct ECM taxa and environmental stress covary with soil N availability.

Enzymatic bioconversion process of lignin: mechanisms, reactions and kinetics

Lignin is a wasted renewable source of biomass-derived value-added chemicals. However, due to its material resistance to degradation, it remains highly underutilized. In order to develop new, catalysed and more environment friendly reaction processes for lignin valorization, science has turned a selective concentrated attention to microbial enzymes. This present work looks at the enzymes involved with the main reference focus on the different elementary mechanisms of action/conversion rate kinetics. Pathways, like with laccases/peroxidases, employ radicals, which more readily result in polymerization than de-polymerization. The β-etherase system interaction of proteins targets β-O-4 ether covalent bond, which targets lower molecular weight product species. Enzymatic activity is influenced by a wide variety of different factors which need to be considered in order to obtain the best functionality and synthesis yields.

Simultaneous Biological Pretreatment and Saccharification of Rice Straw by Ligninolytic Enzymes from Panus neostrigosus I9 and Commercial Cellulase

The utilization of rice straw for biofuel production is limited by its composition. The pretreatment process is required to improve the enzymatic accessibility of polysaccharides in the biomass prior to enzymatic saccharification. In this study, simultaneous biological pretreatment and saccharification (SPS) of rice straw starting from laccase production by Panus neostrigosus I9 was operated in a 2-L fermenter. It was found that fungal physiology was strongly influenced by the agitation, and that the highest laccase production was obtained at an agitation speed of 750 rpm (209.96 ± 0.34 U/L). The dilution rate of 0.05 h-1 was set in continuous fermentation which resulted in laccase activity of 678.49 ± 20.39 U/L, approximately three times higher than that in batch culture. Response surface methodology (RSM) was applied to achieve the condition for maximum percentage of delignification. The maximum percentage of delignification of 45.55% was accomplished after pretreatment of rice straw with laccase enzyme 39.40 U/g rice straw at 43.70 °C for 11.19 h. Reducing sugar of 3.85 ± 0.15 g/L was obtained from the digested rice straw in a SPS reactor, while non-pretreated rice straw gave only 1.13 ± 0.10 g/L within 12 h of incubation. The results indicated that simultaneous biological pretreatment and saccharification (SPS) of rice straw by laccase helped to improve the accessibility of cellulose by cellulolytic enzymes.

A Critical Review on the Multiple Roles of Manganese in Stabilizing and Destabilizing Soil Organic Matter

Manganese (Mn) is a biologically important and redox-active metal that may exert a poorly recognized control on carbon (C) cycling in terrestrial ecosystems. Manganese influences ecosystem C dynamics by mediating biochemical pathways that include photosynthesis, serving as a reactive intermediate in the breakdown of organic molecules, and binding and/or oxidizing organic molecules through organo-mineral associations. However, the potential for Mn to influence ecosystem C storage remains unresolved. Although substantial research has demonstrated the ability of Fe- and Al-oxides to stabilize organic matter, there is a scarcity of similar information regarding Mn-oxides. Furthermore, Mn-mediated reactions regulate important litter decomposition pathways, but these processes are poorly constrained across diverse ecosystems. Here, we discuss the ecological roles of Mn in terrestrial environments and synthesize existing knowledge on the multiple pathways by which biogeochemical Mn and C cycling intersect. We demonstrate that Mn has a high potential to degrade organic molecules through abiotic and microbially mediated oxidation and to stabilize organic molecules, at least temporarily, through organo-mineral associations. We outline research priorities needed to advance understanding of Mn-C interactions, highlighting knowledge gaps that may address key uncertainties in soil C predictions.

First Dye-Decolorizing Peroxidase from an Ascomycetous Fungus Secreted by Xylaria grammica

Background: Fungal DyP-type peroxidases have so far been described exclusively for basidiomycetes. Moreover, peroxidases from ascomycetes that oxidize Mn²⁺ ions are yet not known. Methods: We describe here the physicochemical, biocatalytic, and molecular characterization of a DyP-type peroxidase (DyP, EC 1.11.1.19) from an ascomycetous fungus. Results: The enzyme oxidizes classic peroxidase substrates such as 2,6-DMP but also veratryl alcohol and notably Mn²⁺ to Mn³⁺ ions, suggesting a physiological function of this DyP in lignin modification. The K_M value (49 µM) indicates that Mn²⁺ ions bind with high affinity to the XgrDyP protein but their subsequent oxidation into reactive Mn³⁺ proceeds with moderate efficiency compared to MnPs and VPs. Mn²⁺ oxidation was most effective at an acidic pH (between 4.0 and 5.0) and a hypothetical surface exposed an Mn²⁺ binding site comprising three acidic amino acids (two aspartates and one glutamate) could be localized within the hypothetical XgrDyP structure. The oxidation of Mn²⁺ ions is seemingly supported by four aromatic amino acids that mediate an electron transfer from the surface to the heme center. Conclusions: Our findings shed new light on the possible involvement of DyP-type peroxidases in lignocellulose degradation, especially by fungi that lack prototypical ligninolytic class II peroxidases.

Functions of elements in soil microorganisms

The soil microbial community fulfils various functions, such as nutrient cycling and carbon (C) sequestration, therefore contributing to maintenance of soil fertility and mitigation of global warming. In this context, a major focus of research has been on C, nitrogen (N) and phosphorus (P) cycling. However, from aquatic and other environments, it is well known that other elements beyond C, N, and P are essential for microbial functioning. Nonetheless, for soil microorganisms this knowledge has not yet been synthesised. To gain a better mechanistic understanding of microbial processes in soil systems, we aimed at summarising the current knowledge on the function of a range of essential or beneficial elements, which may affect the efficiency of microbial processes in soil. This knowledge is discussed in the context of microbial driven nutrient and C cycling. Our findings may support future investigations and data evaluation, where other elements than C, N, and P affect microbial processes.

Manganese promoted wheat straw decomposition by regulating microbial communities and enzyme activities

AIMS

This study investigated the dose-effect of manganese (Mn) addition on wheat straw (WS) decomposition, and explored the potential mechanisms of Mn involved in the acceleration of WS decomposition in regards to the soil microbial communities and enzyme activities.

METHODS AND RESULTS

A 180-day incubation experiment was performed to examine the decomposition of WS under four Mn levels, that is, 0, 0.25, 1 and 2 mg g^-1 . The effects of microbial communities and enzyme activities were evaluated using control (0 mg g^-1 ) and Mn (0.25 mg g^-1 ) treatments. Our results revealed that Mn (0.25 mg g^-1 ) addition significantly increased WS decomposition, and enhanced the release of carbon and nitrogen. Optimal Mn addition (0.25 mg g^-1 ) also caused significant increases in the activity of neutral xylanase (NEX), laccase (Lac), manganese peroxidase (MnP) and lignin peroxidase (LiP) within the incubation period. Mn (0.25 mg g^-1 ) addition also enriched some operational taxonomic units (OTUs) that, in turn, had the potential ability to decompose crop straw, such as secreting lignocellulolytic enzymes.

CONCLUSIONS

Mn (0.25 mg g^-1 ) could promote WS decomposition through enrichment of the microbial species involved in biomass decomposition, which enhanced the lignocellulose-degrading enzyme activity.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study provides evidence for Mn to promote WS biodegradation after Mn application, opening new windows to improve the utilization efficiency of crop residues.

Pectin and Xylan Biosynthesis in Poplar: Implications and Opportunities for Biofuels Production

A potential method by which society's reliance on fossil fuels can be lessened is via the large-scale utilization of biofuels derived from the secondary cell walls of woody plants; however, there remain a number of technical challenges to the large-scale production of biofuels. Many of these challenges emerge from the underlying complexity of the secondary cell wall. The challenges associated with lignin have been well explored elsewhere, but the dicot cell wall components of hemicellulose and pectin also present a number of difficulties. Here, we provide an overview of the research wherein pectin and xylan biosynthesis has been altered, along with investigations on the function of irregular xylem 8 (IRX8) and glycosyltransferase 8D (GT8D), genes putatively involved in xylan and pectin synthesis. Additionally, we provide an analysis of the evidence in support of two hypotheses regarding GT8D and conclude that while there is evidence to lend credence to these hypotheses, there are still questions that require further research and examination.

Manganese peroxidase mediated oxidation of sulfamethoxazole: Integrating the computational analysis to reveal the reaction kinetics, mechanistic insights, and oxidation pathway

In this study, manganese peroxidase (MnP) was applied to induce the in vitro oxidation of sulfamethoxazole (SMX). The results indicated that 87.04% of the SMX was transformed and followed first-order kinetics (k_obs=0.438 h^-1) within 6 h when 40 U L^-1 of MnP was added. The reaction kinetics were investigated under different conditions, including pH, MnP activity, and H₂O₂ concentration. The active species Mn³⁺ was responsible for the oxidation of SMX, and the Mn³⁺ production rate was monitored to reveal the interaction among MnP, Mn³⁺, and SMX. By integrating the characterizations analysis of the MnP/H₂O₂ system with the density functional theory (DFT) calculations, the proton-coupled electron transfer (PCET) process dominated the catalytic circle of MnP and the transformation of Mn³⁺. Additionally, possible oxidation pathways of SMX were proposed based on single-electron transfer mechanism, which primarily included the S-N bond cleavage, the C-S bond cleavage, and one electron loss without bond breakage. It was then transformed to hydrolysis, N-H oxidation, self-coupling, and carboxylic acid coupling products. This study provides insights into the atomic-level mechanism of MnP and the transformation pathways of sulfamethoxazole, which lays a significant foundation for the potential of MnP in wastewater treatment applications.

Textile Dye Biodecolorization by Manganese Peroxidase: A Review

Wastewater emissions from textile factories cause serious environmental problems. Manganese peroxidase (MnP) is an oxidoreductase with ligninolytic activity and is a promising biocatalyst for the biodegradation of hazardous environmental contaminants, and especially for dye wastewater decolorization. This article first summarizes the origin, crystal structure, and catalytic cycle of MnP, and then reviews the recent literature on its application to dye wastewater decolorization. In addition, the application of new technologies such as enzyme immobilization and genetic engineering that could improve the stability, durability, adaptability, and operating costs of the enzyme are highlighted. Finally, we discuss and propose future strategies to improve the performance of MnP-assisted dye decolorization in industrial applications.

A comprehensive insight into the application of white rot fungi and their lignocellulolytic enzymes in the removal of organic pollutants

Environmental problems resultant from organic pollutants are a major current challenge for modern societies. White rot fungi (WRF) are well known for their extensive organic compound degradation abilities. The unique oxidative and extracellular ligninolytic systems of WRF that exhibit low substrate specificity, enable them to display a considerable ability to transform or degrade different environmental contaminants. In recent decades, WRF and their ligninolytic enzymes have been widely applied in the removal of polycyclic aromatic hydrocarbons (PAHs), pharmaceutically active compounds (PhACs), endocrine disruptor compounds (EDCs), pesticides, synthetic dyes, and other environmental pollutants, wherein promising results have been achieved. This review focuses on advances in WRF-based bioremediation of organic pollutants over the last 10 years. We comprehensively document the application of WRF and their lignocellulolytic enzymes for removing organic pollutants. Moreover, potential problems and intriguing observations that are worthy of additional research attention are highlighted. Lastly, we discuss trends in WRF-remediation system development and avenues that should be considered to advance research in the field.

Mushroom Ligninolytic Enzymes―Features and Application of Potential Enzymes for Conversion of Lignin into Bio-Based Chemicals and Materials

Mushroom ligninolytic enzymes are attractive biocatalysts that can degrade lignin through oxido-reduction. Laccase, lignin peroxidase, manganese peroxidase, and versatile peroxidase are the main enzymes that depolymerize highly complex lignin structures containing aromatic or aliphatic moieties and oxidize the subunits of monolignol associated with oxidizing agents. Among these enzymes, mushroom laccases are secreted glycoproteins, belonging to a polyphenol oxidase family, which have a powerful oxidizing capability that catalyzes the modification of lignin using synthetic or natural mediators by radical mechanisms via lignin bond cleavage. The high redox potential laccase within mediators can catalyze the oxidation of a wide range of substrates and the polymerization of lignin derivatives for value-added chemicals and materials. The chemoenzymatic process using mushroom laccases has been applied effectively for lignin utilization and the degradation of recalcitrant chemicals as an eco-friendly technology. Laccase-mediated grafting has also been employed to modify lignin and other polymers to obtain novel functional groups able to conjugate small and macro-biomolecules. In this review, the biochemical features of mushroom ligninolytic enzymes and their potential applications in catalytic reactions involving lignin and its derivatives to obtain value-added chemicals and novel materials in lignin valorization are discussed.

Chemo-metric engineering designs for deciphering the biodegradation of polycyclic aromatic hydrocarbons

Polycyclic aromatic hydrocarbons (PAHs) are non-polar organic compounds that are omnipresent in the environment and released due to anthropogenic activities through emissions and discharges. PAHs, being xenobiotic and exerts health impacts, thus they attract serious concern by the environmentalists. The stringent regulations and the need of sustainable development urges the hunt for a technically feasible and cost-effective wastewater treatment. Although the conventional physico-chemical treatment are widely preferred, they cause secondary pollution problems and demand subsequent treatment options. This comprehensive review intends to address the (a) different PAHs and their associated toxicity, (b) the remedial strategies, particularly biodegradation. The biological wastewater treatment techniques that involve microbial systems are highly influenced by the different physio-chemical and environmental parameters. Therefore, suitable optimization techniques are prerequisite for effective functioning of the biological treatment that sustains judiciously and interpreted in a lesser time. Here we have aimed to discuss (a) different chemo-metric tools involved in the design of experiments (DoE), (b) design equations and models, (c) tools for evaluating the model's adequacy and (d) plots for graphically interpreting the chemo-metric designs. However, to best of our knowledge, this is a first review to discuss the PAHs biodegradation that are tailored by chemo-metric designs. The associated challenges, available opportunities and techno-economic aspects of PAHs degradation using chemo-metric engineering designs are explained. Additionally, the review highlights how well these DoE tools can be suited for the sustainable socio-industrial sectors. Concomitantly, the futuristic scope and prospects to undertake new areas of research exploration were emphasized to unravel the least explored chemo-metric designs.

Degradation of conventional plastic wastes in the environment: A review on current status of knowledge and future perspectives of disposal

Accumulation of plastic wastes has been recently recognized as one of the most critical environmental challenges, affecting all life forms, natural ecosystems and economy, worldwide. Under this threat, finding alternative environmentally-friendly solutions, such as biodegradation instead of traditional disposal, is of utmost importance. However, up to date, there is limited knowledge on plastic biodegradation mechanisms and efficiency. From this point of view, the purpose of this review is to highlight the negative effects of the accumulation of the most conventional plastic waste (polyethylene, polypropylene, polystyrene, polyvinylchloride, polyethylene terephthalate and polyurethane) on the environment and to present their degradability potential through abiotic and biotic processes. Furthermore, the ability of different microbial species for degradation of these polymers is thoroughly discussed. The present review also addresses the contribution of invertebrates, such as insects, in plastic degradation process, highlighting the vital role that they could play in the future. In total, a schematic pathway of an innovative approach to improve the disposal of plastic wastes is proposed, with view to establishing an effective and sustainable practice for plastic waste management.

Enhancement of Laccase Production by Optimizing the Cultural Conditions for Pleurotus sajor-caju in Solid-State Fermentation

Nowadays, a lot of interest has been given to the development of cost-effective and efficient enzyme production technologies. Laccase enzymes are widely used in biotechnological, environmental and industrial sectors. Due to the cost-effectiveness of the solid-state fermentation (SSF) process, it is widely used to produce a broad range of biological products. In this study, optimization of moisture content, temperature, pH, and inoculum size were studied to enhance laccase production ability of Pleurotus sajor-caju in SSF by using One Factor At Time (OFAT) and Response Surface Methodology (RSM). OFAT was used as a baseline study for deducing the experimental design of RSM. The highest production of laccase enzyme (1450 U/g) by Pleurotus sajor-caju on wheat straw was observed at 26°C, 6.0 pH, 72.5 % moisture content, 7.5% inoculum size, 1% fructose and 0.5 % peptone. Unlike the conventional inoculum preparation method, here the inoculum was generated by the spawning method for SSF. The molecular weight of partially purified laccase from Pleurotus sajor-caju was estimated to be around 62 K Da using SDS PAGE. The activity staining of laccase was observed as a zymogram on Native PAGE using ABTS as a substrate. Lignin degradation of wheat straw and its structural disruption due to laccase was observed by Scanning Electron Microscopy (SEM).

Improvement of saccharide yield from wood by simultaneous enzymatic delignification and saccharification using a ligninolytic enzyme and cellulase

White-rot fungi are thought to hold promise for development of a delignification pretreatment process for wood biorefinery that is less energy-consuming than current processes. However, the reaction must take place over weeks and consumes non-neglectable amounts of saccharides. To establish a biological process for wood biorefinery would first require establishment of an enzymatic approach to delignification. Such an approach has the potential to lower costs and reduce saccharide loss. Here, we attempted enzymatic delignification reactions using manganese peroxidases (MnP), a lignin-degrading enzyme, under several reaction conditions. The delignification rate from beech wood meal (particle size <45 μm) of up to 11.0% in 48 h was reached in a MnP reaction supplemented with multiple co-oxidants, glucose, glucose oxidase (GOD) and commercial cellulase. An additional 48-h reaction using fresh MnP/co-oxidants increased the delignification rate to 14.2%. Simultaneous enzymatic delignification and saccharification, which occurs without a need for glucose supplementation, successfully improved the glucose yield to 160% of the reaction without MnP. Development of a more accurate imitation of the mechanisms of delignification that occurs in white-rot fungi has the potential to improve the monosaccharide yield resulting from simultaneous delignification and saccharification.

Elucidating fungal Rigidoporus species FMD21 lignin-modifying enzyme genes and 2,3,7,8-tetrachlorodibenzo-p-dioxin degradation by laccase isozymes

White-rot fungus Rigidoporus sp. FMD21 is a lignin-modifying enzyme producing fungus that can degrade dioxin. Extracellular enzymes from FMD21 include laccase and manganese peroxidase which are promising enzymes for myco-remediation because of their wide substrate specificity and mild catalysis conditions. The FMD21 genome was sequenced using Ion Torrent technology and consists of 38.98 Mbps with a GC content of 47.4 %. Gene prediction using Augustus with Basidiomycota reference setting resulted in 8245 genes. Functional gene annotations were carried out by using several programs and databases. We focused on laccase and ligninolytic peroxidase genes, which are most likely involved in the degradation of aromatic pollutants. The genome of FMD21 contains 12 predicted laccase genes (10 out of 12 predicted as full length) and 13 putative ligninolytic peroxidases which were annotated as MnP or versatile peroxidases. Four predicted laccases showed a higher than 65 % binding chance to 2,3,7,8-TCDD with the highest at 72 % in in silico docking analysis. Heterologous expressed laccases showed activity towards three tested substrates included ABTS, guaiacol and 2,6-DMP. ABTS displayed two-stage oxidation which differed from natural FMD21 laccases. 2,3,7,8-TCDD was degraded by 50 % after two weeks of enzymatic treatment by three out of five laccase isozymes which were natural laccases secreted by FMD21. In this study, we provide direct evidence for the 2,3,7,8-TCDD biodegradation capability of fungal laccases.

Depolymerization and conversion of lignin to value-added bioproducts by microbial and enzymatic catalysis

Lignin, the most abundant renewable aromatic compound in nature, is an excellent feedstock for value-added bioproducts manufacturing; while the intrinsic heterogeneity and recalcitrance of which hindered the efficient lignin biorefinery and utilization. Compared with chemical processing, bioprocessing with microbial and enzymatic catalysis is a clean and efficient method for lignin depolymerization and conversion. Generally, lignin bioprocessing involves lignin decomposition to lignin-based aromatics via extracellular microbial enzymes and further converted to value-added bioproducts through microbial metabolism. In the review, the most recent advances in degradation and conversion of lignin to value-added bioproducts catalyzed by microbes and enzymes were summarized. The lignin-degrading microorganisms of white-rot fungi, brown-rot fungi, soft-rot fungi, and bacteria under aerobic and anaerobic conditions were comparatively analyzed. The catalytic metabolism of the microbial lignin-degrading enzymes of laccase, lignin peroxidase, manganese peroxidase, biphenyl bond cleavage enzyme, versatile peroxidase, and β-etherize was discussed. The microbial metabolic process of H-lignin, G-lignin, S-lignin based derivatives, protocatechuic acid, and catechol was reviewed. Lignin was depolymerized to lignin-derived aromatic compounds by the secreted enzymes of fungi and bacteria, and the aromatics were converted to value-added compounds through microbial catalysis and metabolic engineering. The review also proposes new insights for future work to overcome the recalcitrance of lignin and convert it to value-added bioproducts by microbial and enzymatic catalysis.

Contribution of the Fenton reaction and ligninolytic enzymes to soil organic matter mineralisation under anoxic conditions

Mechanisms of carbon dioxide (CO₂) release from soil in the absence of oxygen were studied considering the Fenton process, which encompasses the reaction of H₂O₂ with Fe(II) yielding a hydroxyl radical (OH), in combination with manganese peroxidase (MnP) and lignin peroxidase (LiP). This study aimed to explain the high rate of soil organic matter (SOM) mineralisation and CO₂ release from humid temperate rainforest soils under oxygen-limited conditions. The investigated mechanisms challenge the traditional view that SOM mineralisation in rainforest is slow due to anaerobic (micro)environments under high precipitation and explain intensive CO₂ release even under oxygen limitation. We hypothesised that the Fenton reaction (FR) greatly contributes to the CO₂ released from SOM mineralised under anaerobic conditions especially in the presence of ligninolytic enzymes. We used a novel technique that combines labelled H₂¹⁸O₂ and Fe(II) to induce the FR and measured CO¹⁸O, Fe(II) solubilisation, and peroxide consumption in a closed gas circulation system for 6 h. Maximal CO₂ amount was released when the FR was induced in combination with LiP addition. The CO₂ efflux with LiP was 10-fold that of abiotic FR reactions without enzymes, or in soils amended with MnP. This was consistent with i) the contribution of ¹⁸O from peroxide to CO₂ release, ii) peroxide consumption, and iii) Fe(II) solubilisation by FR. The amount of consumed peroxide was closely correlated with the CO¹⁸O derived from soil without enzyme addition or with LiP addition. Concluding, abiotic Fenton Reaction coupled with oxidative enzymes, such as LiP, are crucial for SOM oxidation under anaerobic conditions, e.g. in temperate rainforest soils.

The Influence of Forest Management and Changed Hydrology on Soil Biochemical Properties in a Central-European Floodplain Forest

Anthropogenic modifications to water regimes are one of the main factors threatening the stability and existence of floodplain forests. This study presents an analysis of topsoil biogeochemistry within three floodplain forest stands with different levels of human alteration. Decreasing contents of soil organic carbon (OC) and microbial biomass were observed along the gradient from natural to plantation forest. High annual variations were observed in soil N contents and in microbial biomass, while comparable spatial variations were observed within the natural forest. High ground-water levels resulted in increased accumulation of available Na+ and SO42− in the natural forest soil, yet the concentrations of ions were at sub-saline levels. The increasing contents of available Mn, SO42− or Cl− had mostly positive effects on soil microbial activity across the sites, though the results indicate the existence of a certain ecological limit for soil microorganisms. Reintroduction of surface-water flooding should be considered in future forest and water management to promote the dilution of ions accumulated in soils and natural deposition of sediments rich in organic matter (OM) at the sites.

Mechanisms of Manganese(II) Oxidation by Filamentous Ascomycete Fungi Vary With Species and Time as a Function of Secretome Composition

Manganese (Mn) oxides are among the strongest oxidants and sorbents in the environment, and Mn(II) oxidation to Mn(III/IV) (hydr)oxides includes both abiotic and microbially-mediated processes. While white-rot Basidiomycete fungi oxidize Mn(II) using laccases and manganese peroxidases in association with lignocellulose degradation, the mechanisms by which filamentous Ascomycete fungi oxidize Mn(II) and a physiological role for Mn(II) oxidation in these organisms remain poorly understood. Here we use a combination of chemical and in-gel assays and bulk mass spectrometry to demonstrate secretome-based Mn(II) oxidation in three phylogenetically diverse Ascomycetes that is mechanistically distinct from hyphal-associated Mn(II) oxidation on solid substrates. We show that Mn(II) oxidative capacity of these fungi is dictated by species-specific secreted enzymes and varies with secretome age, and we reveal the presence of both Cu-based and FAD-based Mn(II) oxidation mechanisms in all 3 species, demonstrating mechanistic redundancy. Specifically, we identify candidate Mn(II)-oxidizing enzymes as tyrosinase and glyoxal oxidase in Stagonospora sp. SRC1lsM3a, bilirubin oxidase in Stagonospora sp. and Paraconiothyrium sporulosum AP3s5-JAC2a, and GMC oxidoreductase in all 3 species, including Pyrenochaeta sp. DS3sAY3a. The diversity of the candidate Mn(II)-oxidizing enzymes identified in this study suggests that the ability of fungal secretomes to oxidize Mn(II) may be more widespread than previously thought.

Natural attenuation of lead by microbial manganese oxides in a karst aquifer

Lead is a toxic environmental contaminant associated with current and historic mine sites. Here we studied the natural attenuation of Pb in a limestone cave system that receives drainage from the ancient Priddy Mineries, UK. Extensive deposits of manganese oxides were observed to be forming on the cave walls and as coatings in the stream beds. Analysis of these deposits identified them as birnessite (δ-MnO₂), with some extremely high concentrations of sorbed Pb (up to 56 wt%) also present. We hypothesised that these cave crusts were actively being formed by microbial Mn(II)-oxidation, and to investigate this the microbial communities were characterised by DNA sequencing, enrichment and isolation experiments. The birnessite deposits contained abundant and diverse prokaryotes and fungi, with ~5% of prokaryotes and ~ 10% of fungi closely related to known heterotrophic Mn(II)-oxidisers. A substantial proportion (up to 17%) of prokaryote sequences were assigned to groups known as autotrophic ammonia and nitrite oxidisers, suggesting that nitrogen cycling may play an important role in contributing energy and carbon to the cave crust microbial communities and consequently the formation of Mn(IV) oxides and Pb attenuation. Enrichment and isolation experiments showed that the birnessite deposits contained Mn(II)-oxidising microorganisms, and two isolates (Streptomyces sp. and Phyllobacterium sp.) could oxidise Mn(II) in the presence of 0.1 mM Pb. Supplying the enrichment cultures with acetate as a source of energy and carbon stimulated Mn(II)-oxidation, but excess organics in the form of glucose generated aqueous Mn(II), likely via microbial Mn(IV)-reduction. In this karst cave, microbial Mn(II)-oxidation contributes to the active sequestration and natural attenuation of Pb from contaminated waters, and therefore may be considered a natural analogue for the design of wastewater remediation systems and for understanding the geochemical controls on karst groundwater quality, a resource relied upon by billions of people across the globe.

The Potential of Peroxidases Extracted from the Spent Mushroom (Flammulina velutipes) Substrate Significantly Degrade Mycotoxin Deoxynivalenol

Little is known about the degradability of mycotoxin deoxynivalenol (DON) by the spent mushroom substrate (SMS)-derived manganese peroxidase (MnP) and lignin peroxidase (LiP) and its potential. The present study investigated the growth inhibition of Fusarium graminearum KR1 and the degradation of DON by MnP and LiP extracted from SMS. The results from the 7-day treatment period showed that mycelium inhibition of F. graminearum KR1 by MnP and LiP were 23.7% and 74.7%, respectively. Deoxynivalenol production in the mycelium of F. graminearum KR1 was undetectable after treatment with 50 U/mL of MnP or LiP for 7 days. N-acetyl-D-glucosamine (GlcNAc) content and chitinase activity both increased in the hyphae of F. graminearum KR1 after treatment with MnP and LiP for 1, 3, and 6 h, respectively. At 12 h, only the LiP-treated group had higher chitinase activity and GlcNAc content than those of the control group (p < 0.05). However, more than 60% of DON degradabilities (0.5 mg/kg, 1 h) were observed under various pH values (2.5, 4.5, and 6.5) in both MnP (50 U/g) and LiP (50 U/g) groups, while DON degradability at 1 mg/kg was 85.5% after 50 U/g of LiP treatment for 7 h in simulated pig gastrointestinal tracts. Similarly, DON degradability at 5 mg/kg was 67.1% after LiP treatment for 4.5 h in simulated poultry gastrointestinal tracts. The present study demonstrated that SMS-extracted peroxidases, particularly LiP, could effectively degrade DON and inhibit the mycelium growth of F. graminearum KR1.

Amplicon Sequencing-Based Bipartite Network Analysis Confirms a High Degree of Specialization and Modularity for Fungi and Prokaryotes in Deadwood

Deadwood is important for our forest ecosystems. It feeds and houses many organisms, e.g., fungi and prokaryotes, with many different species contributing to its decomposition and nutrient cycling.

Fungi and prokaryotes are dominant colonizers of wood and mediate its decomposition. Much progress has been achieved to unravel these communities and link them to specific wood properties. However, comparative studies considering both groups of organisms and assessing their relationships to wood resources are largely missing. Bipartite interaction networks provide an opportunity to investigate this colonizer-resource relationship more in detail and aim to directly compare results between different biotic groups. The main questions were as follows. Are network structures reflecting the trophic relationship between fungal and prokaryotic colonizers and their resources? If so, do they reflect the critical role of these groups, especially that of fungi, during decomposition? We used amplicon sequencing data to analyze fungal and prokaryotic interaction networks from deadwood of 13 temperate tree species at an early to middle stage of decomposition. Several diversity- and specialization-related indices were determined and the observed network structures were related to intrinsic wood traits. We hypothesized nonrandom bipartite networks for both groups and a higher degree of specialization for fungi, as they are the key players in wood decomposition. The results reveal highly modular and specialized interaction networks for both groups of organisms, demonstrating that many fungi and prokaryotes are resource-specific colonizers. However, as the level of specialization of fungi significantly surpassed that of prokaryotes, our findings reflect the strong association between fungi and their host. Our novel approach shows that the application of bipartite interaction networks is a useful tool to explore, quantify, and compare the deadwood-colonizers relationship based on sequencing data.

IMPORTANCE Deadwood is important for our forest ecosystems. It feeds and houses many organisms, e.g., fungi and prokaryotes, with many different species contributing to its decomposition and nutrient cycling. The aim of this study was to explore and quantify the relationship between these two main wood-inhabiting organism groups and their corresponding host trees. Two independent DNA-based amplicon sequencing data sets (fungi and prokaryotes) were analyzed via bipartite interaction networks. The links in the networks represent the interactions between the deadwood colonizers and their deadwood hosts. The networks allowed us to analyze whether many colonizing species interact mostly with a restricted number of deadwood tree species, so-called specialization. Our results demonstrate that many prokaryotes and fungi are resource-specific colonizers. The direct comparison between both groups revealed significantly higher specialization values for fungi, emphasizing their strong association to respective host trees, which reflects their dominant role in exploiting this resource.

Batch Mode Reactor for 3,5-Dinitrosalicylic Acid Degradation by Phanerochaete chrysosporium

A new batch mode reactor was constructed to conduct continuous biodegradation of 3,5-dinitrosalicylic acid. Various types of matrices with immobilized Phanerochaete chrysosporium were immersed in a solution containing pollutant and mineral nutrients. Three parameters were chosen to optimize the process. The nitrate and nitrite ions concentrations and HPLC analysis were used to prove the biodegradation of 3,5-dinitrosalicylic acid, and the mixed effects model using one-factor ANOVA was used for statistical calculations. The results showed the correlation between the initial pH, a medium composition, and the process time. In pH = 6.5, the degradation effectiveness was estimated at 99% decrease in the substrate within 14 days, while an 80% decrease of acid concentration was indicated in pH = 3.5 after 28 days of the process duration.

Cycling in degradation of organic polymers and uptake of nutrients by a litter-degrading fungus

Wood and litter degrading fungi are the main decomposers of lignocellulose and thus play a key role in carbon cycling in nature. Here, we provide evidence for a novel lignocellulose degradation strategy employed by the litter degrading fungus Agaricus bisporus (known as the white button mushroom). Fusion of hyphae allows this fungus to synchronize the activity of its mycelium over large distances (50 cm). The synchronized activity has a 13-h interval that increases to 20 h before becoming irregular and it is associated with a 3.5-fold increase in respiration, while compost temperature increases up to 2°C. Transcriptomic analysis of this burst-like phenomenon supports a cyclic degradation of lignin, deconstruction of (hemi-) cellulose and microbial cell wall polymers, and uptake of degradation products during vegetative growth of A. bisporus. Cycling in expression of the ligninolytic system, of enzymes involved in saccharification, and of proteins involved in nutrient uptake is proposed to provide an efficient way for degradation of substrates such as litter.

Microbial polyhydroxyalkanoate production from lignin by Pseudomonas putida NX-1

Biological approaches play an important role in lignin valorization, whereas many issues in this area remain unclear. Herein, ligninolytic enzymes in Pseudomonas putida NX-1 were systematically unraveled based on genome sequence technology. Particularly, a dye-decolorizing peroxidase was systematically studied by heterologous expression, enzyme purification, and enzymatic characterization, which suggested it possessed activities on both synthetic dyes and lignin-derived aromatics. Moreover, a complete pathway for polyhydroxyalkanoate biosynthesis was annotated, and the polyhydroxyalkanoate biosynthesis capability of P. putida NX-1 was experimentally confirmed with lignin as the sole carbon source. Furthermore, the monomer compositions, molecular weights, and thermal properties of polyhydroxyalkanoate from glucose and lignin-derived aromatics were comprehensively determined by gas chromatography-mass spectrometry, gel permeation chromatography, differential scanning calorimetry, and thermogravimetric analysis. The results indicated that physical properties of polyhydroxyalkanoate prepared from glucose and lignin-derived aromatics were similar, which suggested lignin could be an alternative feedstock for polyhydroxyalkanoate production without compromising its quality.

Increasing rates of long-term nitrogen deposition consistently increased litter decomposition in a semi-arid grassland

The continuing nitrogen (N) deposition observed worldwide alters ecosystem nutrient cycling and ecosystem functioning. Litter decomposition is a key process contributing to these changes, but the numerous mechanisms for altered decomposition remain poorly identified. We assessed these different mechanisms with a decomposition experiment using litter from four abundant species (Achnatherum sibiricum, Agropyron cristatum, Leymus chinensis and Stipa grandis) and litter mixtures representing treatment-specific community composition in a semi-arid grassland under long-term simulation of six different rates of N deposition. Decomposition increased consistently with increasing rates of N addition in all litter types. Higher soil manganese (Mn) availability, which apparently was a consequence of N addition-induced lower soil pH, was the most important factor for faster decomposition. Soil C : N ratios were lower with N addition that subsequently led to markedly higher bacterial to fungal ratios, which also stimulated litter decomposition. Several factors contributed jointly to higher rates of litter decomposition in response to N deposition. Shifts in plant species composition and litter quality played a minor role compared to N-driven reductions in soil pH and C : N, which increased soil Mn availability and altered microbial community structure. The soil-driven effect on decomposition reported here may have long-lasting impacts on nutrient cycling, soil organic matter dynamics and ecosystem functioning.

Effects of surface charge and chemical forms of manganese(II) on rice roots on manganese absorption by different rice varieties

The roots of 4 japonica, 4 indica, and 7 hybrid rice varieties were obtained by hydroponic experiment and used to explore the relationship between charge characteristics and exchangeable manganese(II) (Mn(II)) on rice roots and Mn(II) absorption in roots and shoots of the rice. Results indicated Mn(II) adsorbed on rice roots mainly existed as exchangeable Mn(II) after 2 h. The roots of indica and hybrid rice carried more negative charges than the roots of japonica rice. Accordingly, this led to more exchangeable Mn(II) to be adsorbed on roots of indica and hybrid rice after 2 h and more Mn(II) absorbed in the roots of the same varieties after 48 h. However, this was contrary to the result of Mn(II) absorption in rice shoots after 48 h. Coexisting cations of K⁺, Na⁺, Ca²⁺, and Mg²⁺ reduced the exchangeable Mn(II) on rice roots through their competition with Mn(II) for sorption sites on rice roots, which led to the decrease in Mn(II) absorption in rice roots and shoots. Ca²⁺ and Mg²⁺ showed a greater decrease in the Mn(II) absorbed in roots and shoots than K⁺ and Na⁺. The reduction of Mn(II) absorption in the roots of indica rice and hybrid rice induced by Ca²⁺ and Mg²⁺ was more than that of japonica rice. This was attributed to more negative charges on the roots of the former than the latter. Therefore, the absorption of Mn(II) by rice roots was determined by surface charge properties and exchangeable Mn(II) on the rice roots. The results suggested that Ca²⁺ and Mg²⁺ have potential to alleviate Mn(II) toxicity to rice.

Ideal Feedstock and Fermentation Process Improvements for the Production of Lignocellulolytic Enzymes

The usage of lignocellulosic biomass in energy production for biofuels and other value-added products can extensively decrease the carbon footprint of current and future energy sectors. However, the infrastructure in the processing of lignocellulosic biomass is not well-established as compared to the fossil fuel industry. One of the bottlenecks is the production of the lignocellulolytic enzymes. These enzymes are produced by different fungal and bacterial species for degradation of the lignocellulosic biomass into its reactive fibers, which can then be converted to biofuel. The selection of an ideal feedstock for the lignocellulolytic enzyme production is one of the most studied aspects of lignocellulolytic enzyme production. Similarly, the fermentation enhancement strategies for different fermentation variables and modes are also the focuses of researchers. The implementation of fermentation enhancement strategies such as optimization of culture parameters (pH, temperature, agitation, incubation time, etc.) and the media nutrient amendment can increase the lignocellulolytic enzyme production significantly. Therefore, this review paper summarized these strategies and feedstock characteristics required for hydrolytic enzyme production with a special focus on the characteristics of an ideal feedstock to be utilized for the production of such enzymes on industrial scales.

Enzymes, Manganese, or Iron? Drivers of Oxidative Organic Matter Decomposition in Soils

Oxidative decomposition of soil organic matter determines the proportion of carbon that is either stored or emitted to the atmosphere as CO₂. Full conversion of organic matter to CO₂ requires oxidative mechanisms that depolymerize complex molecules into smaller, soluble monomers that can be respired by microbes. Current models attribute oxidative depolymerization largely to the activity of extracellular enzymes. Here we show that reactive manganese (Mn) and iron (Fe) intermediates, rather than other measured soil characteristics, best predict oxidative activity in temperate forest soils. Combining bioassays, spectroscopy, and wet-chemical analysis, we found that oxidative activity in surface litters was most significantly correlated to the abundance of reactive Mn(III) species. In contrast, oxidative activity in underlying mineral soils was most significantly correlated to the abundance of reactive Fe(II/III) species. Positive controls showed that both Mn(III) and Fe(II/III) species are equally potent in generating oxidative activity, but imply conventional bioassays have a systematic bias toward Fe. Combined, our results highlight the coupled biotic-abiotic nature of oxidative mechanisms, with Mn-mediated oxidation dominating within Mn-rich organic soils and Fe-mediated oxidation dominating Fe-rich mineral soils. These findings suggest microbes rely on different oxidative strategies depending on the relative availability of Fe and Mn in a given soil environment.