Decomposition of spruce wood and release of volatile organic compounds depend on decay type, fungal interactions and enzyme production patterns

Journey of lignin from a roadblock to bridge for lignocellulose biorefineries: A comprehensive review

The grave concerns arisen as a result of environmental pollution and diminishing fossil fuel reserves in the 21st century have shifted the focus on the use of sustainable and environment friendly alternative resources. Lignocellulosic biomass constituted by cellulose, hemicellulose and lignin is an abundantly available natural bioresource. Lignin, a natural biopolymer has over the years gained much importance as a high value material with commercial importance. The present review provides an in-depth knowledge on the journey of lignin from being considered a roadblock to a bridge connecting diverse industries with widescale applications. The successful valorization of lignin for the production of bio-based platform chemicals and fuels has been the subject of intensive investigation. A deeper understanding of lignin characteristics and factors governing the biomass conversion into valuable products can support improved biomass consumption. The components of lignocellulosic biomass might be totally transformed into a variety of value-added products with the improvements in bioprocess techniques that valorize lignin. In this review, the recent advances in the lignin extraction and depolymerization methods that may help in achieving the cost-economics of the bioprocess are summarized and compared. The industrial potential of lignin-derived products such as aromatics, biopolymers, biofuels and agrochemicals are also outlined. Additionally, assessment of the recent research trends in lignin valorization into value-added chemicals has been done and present scenario of technological-industrial applications of lignin with economic perspectives is highlighted.

The Necrobiome of Deadwood: The Life after Death

In recent decades, sustainable forest management has been increasingly recognized, promoting the diffusion of silvicultural practices aimed at considering all components of the forest system. Deadwood is an important component of the forest ecosystem. It plays a fundamental role in providing nutrients and habitats for a wide variety of saprotrophic and heterotrophic organisms and significantly contributes to soil formation and carbon storage. Deadwood is inhabited by a plethora of organisms from various kingdoms that have evolved the ability to utilize decaying organic matter. This community, consisting of both eukaryotic and prokaryotic species, can be defined as “necrobiome”. Through the interactions between its various members, the necrobiome influences the decay rates of deadwood and plays a crucial role in the balance between organic matter decomposition, carbon sequestration, and gas exchanges (e.g., CO2) with the atmosphere. The present work aims to provide an overview of the biodiversity and role of the microbial communities that inhabit deadwood and their possible involvement in greenhouse gas (CO2, N2O, and CH4) emissions.

Metabolomics Highlights Different Life History Strategies of White and Brown Rot Wood-Degrading Fungi

White and brown rot fungi efficiently deconstruct lignocellulose in wood, Earth's largest pool of aboveground biotic carbon and an important natural resource. Despite its vital importance, little is known about the metabolomic signatures among fungal species and nutritional modes (rot types). In this study, we used GC-MS metabolomics in solid wood substrates (in planta) to compare brown rot fungi (Rhodonia placenta and Gloeophylum trabeum) and white rot fungi (Trametes versicolor and Pleurotus ostreatus) at two decay stages (earlier and later), finding identifiable patterns for brown rot fungi at later decay stages. These patterns occurred in highly reducing environments that were not observed in white rot fungi. Metabolomes measured among the two white rot fungi were notably different, but we found a potential biomarker compound, galactitol, that was characteristic to white rot taxa. In addition, we found that white rot fungi were more efficient at catabolizing phenolic compounds that were originally present in wood. Collectively, white rot fungi were characterized by measured sugar release relative to higher carbohydrate solubilization by brown rot fungi, a distinction in soluble sugar availability that might shape success in the face of "cheater" competitors. This need to protect excess free sugars may explain the differentially high brown rot fungal production of pyranones and furanones, likely linked to an expansion of polyketide synthase genes. IMPORTANCE Despite the ecological and economic importance of wood-degrading fungi, little is known about the array of metabolites that fungi produce during wood decomposition. This study provides an in-depth insight into the wood decomposition process by analyzing and comparing the changes of >100 compounds produced by fungi with metabolic distinct nutritional modes (white and brown rot fungi) at different decay stages. We found a unique pattern of metabolites that correlated well with brown rot (carbohydrate selective mode) in later decay. These compounds were in line with some of the physiochemical and genetic features previously seen in these fungi such as a faster sugar release, lower pH, and the expansion of polyketide-synthase genes compared to white rot fungi (lignin-degrading mode). This study provides spatiotemporally resolved mechanism insights as well as critical groundwork that will be valuable for studies in basic biology and ecology, as well as applied biomass deconstruction and bioremediation.

Microbial valorization of lignin: Prospects and challenges

Lignin is the world's second most prevalent biomaterial, but its effective value-added product valorization methods are still being developed. The most common preparation processes for converting lignin to platform chemicals and biofuels are fragmentation and depolymerization. Due to its structural diversity, fragmentation generally produces a variety of products, necessitating tedious separation and purifying methods to isolate the desired products. Bacterial-based techniques are commonly utilized for lignin fragmentation due to their high metabolitic activity. Recent advancements in lignin valorization utilizing bacteria, such as lignin decomposing microbes and major pathways involved that can breakdown lignin into various valuable products namely lipids, furfural, vanillin, polyhydroxybutyrate, poly lactic acid blends were discussed in this review. This review also covers the genetic and fermentation methodologies to enhance lignin decomposition, challenges and future trends of microbe based lignin valorization.

Coprinopsis cinerea uses laccase Lcc9 as a defense strategy to eliminate oxidative stress during fungal-fungal interactions

Frequently, laccases are triggered during fungal cocultivation for overexpression. The function of these activated laccases during coculture has not been clarified. Previously, we reported that Gongronella sp. w5 (w5) (Mucoromycota, Mucoromycetes) specifically triggered the laccase Lcc9 overexpression in Coprinopsis cinerea (Basidiomycota, Agaricomycetes). To systematically analyze the function of the overexpressed laccase during fungal interaction, C. cinerea mycelia before and after the initial Lcc9 overexpression were chosen for transcriptome analysis. Results showed that accompanied by specific utilization of fructose as carbohydrate substrate, oxidative stress derived from antagonistic compounds secreted by w5 appears to be a signal critical for laccase production in C. cinerea. Reactive oxygen species (ROS) decrease in the C. cinerea wild-type strain followed the increase in laccase production and then, lcc9 transcription and laccase activity stopped. By comparison, increased H₂O₂ content and mycelial ROS levels were observed during the entire cocultivation in lcc9 silenced C. cinerea strains. Moreover, lcc9 silencing slowed down the C. cinerea mycelial growth, affected hyphal morphology, and decreased the asexual sporulation in coculture. Our results showed that intracellular ROS acted as signal molecules to stimulate defense responses by C. cinerea with the expression of oxidative stress response regulator Skn7 and various detoxification proteins. Lcc9 takes part as a defense strategy to eliminate oxidative stress during the interspecific interaction with w5. Importance: The overproduction of laccase during interspecific fungal interactions is notoriously known. However, the exact role of the up-regulated laccases remains underexplored. Based on comparative transcriptomic analysis of C. cinerea and gene silencing of laccase Lcc9, here we show that oxidative stress derived from antagonistic compounds secreted by Gongronella sp. w5 was a signal critical for laccase Lcc9 production in Coprinopsis cinerea. Intracellular ROS acted as signal molecules to stimulate defense responses by C. cinerea with the expression of oxidative stress response regulator Skn7 and various detoxification proteins. Ultimately, Lcc9 takes part as a defense strategy to eliminate oxidative stress and help cell growth and development during the interspecific interaction with Gongronella sp. w5. These findings deepened our understanding of fungal interactions in their natural population and communities.

A biorefinery approach for enzymatic complex production for the synthesis of xylooligosaccharides from sugarcane bagasse

The use of low-cost feedstock for enzyme production is an environmental and economic solution. Sugarcane bagasse and soybean meal are employed in this study for optimised xylanase production with the concomitant synthesis of proteases. The enzymatic complex is produced by submerged fermentation by Aspergillus niger. Optimisation steps lead to a 2.16-fold increase in enzymatic activity. The fermentation kinetics are studied in Erlenmeyer flasks, a stirred tank reactor and a bubble column reactor, with the xylanase activities reaching 52.9; 33.7 and 60.5 U.mL^-1, respectively. The protease production profile is also better in the bubble column reactor, exceeding 7 U.mL^-1. The enzyme complex is then evaluated for the synthesis of xylooligosaccharides from sugarcane extracted xylan with a production of 3.1 g.L^-1 where xylotriose is the main product. Excellent perspectives are observed for the developed process with potential applications in the animal feed, prebiotics and paper industries.

Volatilome of Aleppo Pine litter over decomposition process

Biogenic Volatile Organic Compounds (BVOC) are largely accepted to contribute to both atmospheric chemistry and ecosystem functioning. While the forest canopy is recognized as a major source of BVOC, emissions from plant litter have scarcely been explored with just a couple of studies being focused on emission patterns over litter decomposition process. The aim of this study was to quantitatively and qualitatively characterize BVOC emissions (C1-C15) from Pinus halepensis litter, one of the major Mediterranean conifer species, over a 15-month litter decomposition experiment. Senescent needles of P. halepensis were collected and placed in 42 litterbags where they underwent in situ decomposition. Litterbags were collected every 3 months and litter BVOC emissions were studied in vitro using both online (PTR-ToF-MS) and offline analyses (GC-MS). Results showed a large diversity of BVOC (58 compounds detected), with a strong variation over time. Maximum total BVOC emissions were observed after 3 months of decomposition with 9.18 µg gDM -1 hr-1 mainly composed by terpene emissions (e.g., α-pinene, terpinolene, β-caryophyllene). At this stage, methanol, acetone, and acetic acid were the most important nonterpenic volatiles representing, respectively, up to 26%, 10%, and 26% of total emissions. This study gives an overview of the evolution of BVOC emissions from litter along with decomposition process and will thus contribute to better understand the dynamics and sources of BVOC emission in Mediterranean pine forests.

Enhanced Lignocellulolytic Enzyme Activities on Hardwood and Softwood during Interspecific Interactions of White- and Brown-Rot Fungi

Wood decomposition is a sophisticated process where various biocatalysts act simultaneously and synergistically on biopolymers to efficiently break down plant cell walls. In nature, this process depends on the activities of the wood-inhabiting fungal communities that co-exist and interact during wood decay. Wood-decaying fungal species have traditionally been classified as white-rot and brown-rot fungi, which differ in their decay mechanism and enzyme repertoire. To mimic the species interaction during wood decomposition, we have cultivated the white-rot fungus, Bjerkandera adusta, and two brown-rot fungi, Gloeophyllum sepiarium and Antrodia sinuosa, in single and co-cultivations on softwood and hardwood. We compared their extracellular hydrolytic carbohydrate-active and oxidative lignin-degrading enzyme activities and production profiles. The interaction of white-rot and brown-rot species showed enhanced (hemi)cellulase activities on birch and spruce-supplemented cultivations. Based on the enzyme activity profiles, the combination of B. adusta and G. sepiarium facilitated birch wood degradation, whereas B. adusta and A. sinuosa is a promising combination for efficient degradation of spruce wood, showing synergy in β-glucosidase (BGL) and α-galactosidase (AGL) activity. Synergistic BGL and AGL activity was also detected on birch during the interaction of brown-rot species. Our findings indicate that fungal interaction on different woody substrates have an impact on both simultaneous and sequential biocatalytic activities.

Comparison of the Decay Behavior of Two White-Rot Fungi in Relation to Wood Type and Exposure Conditions

Fungal wood decay strategies are influenced by several factors, such as wood species, moisture content, and temperature. This study aims to evaluate wood degradation characteristics of spruce, beech, and oak after exposure to the white-rot fungi Pleurotusostreatus and Trametesversicolor. Both fungi caused high mass losses in beech wood, while spruce and oak wood were more resistant to decay. The moisture content values of the decayed wood correlated with the mass losses for all three wood species and incubation periods. Combined microscopic and chemical studies indicated that the two fungi differed in their decay behavior. While T. versicolor produced a decay pattern (cell wall erosion) typical of white-rot fungi in all wood species, P. ostreatus caused cell wall erosion in spruce and beech and soft-rot type I (cavity formation) decay in oak wood. These observations suggest that P. ostreatus may have the capacity to produce a wider range of enzymes/radicals triggered by the chemical composition of wood cell walls and/or local compositional variability within the cell wall.

Wood construction more strongly shapes deadwood microbial communities than spatial location over 5 years of decay

Diverse communities of fungi and bacteria in deadwood mediate wood decay. While rates of decomposition vary greatly among woody species and spatially distinct habitats, the relative importance of these factors in structuring microbial communities and whether these shift over time remains largely unknown. We characterized fungal and bacterial diversity within pieces of deadwood that experienced 6.3-98.8% mass loss while decaying in common garden 'rotplots' in a temperate oak-hickory forest in the Ozark Highlands, MO, USA. Communities were isolated from 21 woody species that had been decomposing for 1-5 years in spatially distinct habitats at the landscape scale (top and bottom of watersheds) and within stems (top and bottom of stems). Microbial community structure varied more strongly with wood traits than with spatial locations, mirroring the relative role of these factors on decay rates on the same pieces of wood even after 5 years. Co-occurring fungal and bacterial communities persistently influenced one another independently from their shared environmental conditions. However, the relative influence of wood construction versus spatial locations differed between fungi and bacteria, suggesting that life history characteristics of these clades structure diversity differently across space and time in decomposing wood.

Enzyme Activity Profiles Produced on Wood and Straw by Four Fungi of Different Decay Strategies

Four well-studied saprotrophic Basidiomycota Agaricomycetes species with different decay strategies were cultivated on solid lignocellulose substrates to compare their extracellular decomposing carbohydrate-active and lignin-attacking enzyme production profiles. Two Polyporales species, the white rot fungus Phlebia radiata and brown rot fungus Fomitopsis pinicola, as well as one Agaricales species, the intermediate "grey" rot fungus Schizophyllum commune, were cultivated on birch wood pieces for 12 weeks, whereas the second Agaricales species, the litter-decomposing fungus Coprinopsis cinerea was cultivated on barley straw for 6 weeks under laboratory conditions. During 3 months of growth on birch wood, only the white rot fungus P. radiata produced high laccase and MnP activities. The brown rot fungus F. pinicola demonstrated notable production of xylanase activity up to 43 nkat/mL on birch wood, together with moderate β-glucosidase and endoglucanase cellulolytic activities. The intermediate rot fungus S. commune was the strongest producer of β-glucosidase with activities up to 54 nkat/mL, and a notable producer of xylanase activity, even up to 620 nkat/mL, on birch wood. Low lignin-attacking but moderate activities against cellulose and hemicellulose were observed with the litter-decomposer C. cinerea on barley straw. Overall, our results imply that plant cell wall decomposition ability of taxonomically and ecologically divergent fungi is in line with their enzymatic decay strategy, which is fundamental in understanding their physiology and potential for biotechnological applications.