Novel Synergistic Mechanism for Lignocellulose Degradation by a Thermophilic Filamentous Fungus and a Thermophilic Actinobacterium Based on Functional Proteomics

Straw degradation enhanced in Thermomyces lanuginosus by transferring AgCMCase from Aspergillus glaucus

Fungi play a crucial role in straw composting due to the synergistic degradation effects of their secreted lignocellulose hydrolases. An efficient straw-composting system relies on thermophilic fungi and their lignocellulose hydrolases. Thermomyces lanuginosus, a typical thermophilic fungus in compost, lacks cellulase genes. A versatile Thermomyces strain capable of degrading cellulose, T. lanuginosus M85, which grows at 67 °C, was developed and transformed using the AgCMCase of Aspergillus glaucus. The R6 transformant exhibited high-level expression of the AgCMCase. Significant quantities of active cellulase produced by R6 were detected in the cellulose fermentation broth, peaking within 6-8 days. Compost analysis indicated that R6 increased the internal compost temperatures and prolonged high-temperature durations. Correspondingly, more reducing sugars and humus were released, which could promote plants growth. In summary, a cellulase-producing strain of T. lanuginosus capable of efficiently converting straws into organic fertilizers was engineered. This innovation holds considerable promise for sustainable and circular agricultural practices.

An insight into omics analysis and metabolic pathway engineering of lignin-degrading enzymes for enhanced lignin valorization

Lignin, a highly heterogeneous polymer of lignocellulosic biomass, is intricately associated with cellulose and hemicellulose, responsible for its strength and rigidity. Lignin decomposition is carried out through certain enzymes derived from microorganisms to promote the hydrolysis of lignin. Analyzing multi-omics data helps to emphasize the probable value of fungal-produced enzymes to degrade the lignocellulosic material, which provides them an advantage in their ecological niches. This review focuses on lignin biodegrading microorganisms and associated ligninolytic enzymes, including lignin peroxidase, manganese peroxidase, versatile peroxidase, laccase, and dye-decolorizing peroxidase. Further, enzymatic catalysis, lignin biodegradation mechanisms, vital factors responsible for lignin modification and degradation, and the design and selection of practical metabolic pathways are also discussed. Highlights were made on metabolic pathway engineering, different aspects of omics analyses, and its scope and applications to ligninase enzymes. Finally, the advantages and essential steps of successfully applying metabolic engineering and its path forward have been addressed.

Interkingdom interaction: the soil isopod Porcellio scaber stimulates the methane-driven bacterial and fungal interaction

Porcellio scaber (woodlice) are (sub-)surface-dwelling isopods, widely recognized as "soil bioengineers", modifying the edaphic properties of their habitat, and affecting carbon and nitrogen mineralization that leads to greenhouse gas emissions. Yet, the impact of soil isopods on methane-cycling processes remains unknown. Using P. scaber as a model macroinvertebrate in a microcosm study, we determined how the isopod influences methane uptake and the associated interaction network in an agricultural soil. Stable isotope probing (SIP) with 13C-methane was combined to a co-occurrence network analysis to directly link activity to the methane-oxidizing community (bacteria and fungus) involved in the trophic interaction. Compared to microcosms without the isopod, P. scaber significantly induced methane uptake, associated to a more complex bacteria-bacteria and bacteria-fungi interaction, and modified the soil nutritional status. Interestingly, 13C was transferred via the methanotrophs into the fungi, concomitant to significantly higher fungal abundance in the P. scaber-impacted soil, indicating that the fungal community utilized methane-derived substrates in the food web along with bacteria. Taken together, results showed the relevance of P. scaber in modulating methanotrophic activity with implications for bacteria-fungus interaction.

Degradation of poly(butylene adipate-co-terephthalate) films by Thermobifida fusca FXJ-1 isolated from compost

In recent years, Poly(butylene adipate-co-terephthalate) (PBAT) films were wildly used due to its biodegradable properties. However, there are few reports of strains that can high efficiently degrade PBAT. Thermobifida fusca FXJ-1, a thermophilic actinomycete, was screened and identified from compost. FXJ-1 can efficiently degrade PBAT at 55 °C in MSM medium. The degradation rates of the pure PBAT film (PF), PBAT film used for mulching on agricultural fields (PAF), and PBAT-PLA-ST film (PPSF) were 82.87 ± 1.01%, 87.83 ± 2.00% and 52.53 ± 0.54%, respectively, after nine days of incubation in MSM medium. Cracking areas were monitored uniformly distributed on the surfaces of three kinds of PBAT-based films after treatment with FXJ-1 using scanning electron microscopy. The LC-MS results showed that PBAT might be degraded into adipic acid, terephthalic acid, butylene adipate, butylene terephthalate and butylene adipate-co-terephthalate, and these products are involved in the cleavage of ester bonds. We also found that amylase produced by FXJ-1 played an important role in the degradation of PPSF. FXJ-1 also showed an efficient PBAT-based films degradation ability in simulating compost environment, which implied its potential application in PBAT and starch-based film degradation by industrial composting.

Potential of indigenous ligno-cellulolytic microbial consortium to accelerate degradation of heterogenous crop residues

Indigenous microbial diversity has potential for rapid decomposition of residue through enzyme activities that is alternative, effective, and environment friendly strategy to accelerate degradation of lignocellulose in agricultural residues and make composting process economically viable. Keeping this view, the main objective of the present study was isolation and characterization of lignocellulosic degrading microbial diversity from long-term residue management practice experiments and to develop potential microbial consortium for rapid degradation of lignocellulosic biomass. In this study, twenty-five bacteria, nine fungi, and four actinomycetes isolates were obtained from the soil samples of different residue management fields from Ludhiana, Punjab, India. All isolates were qualitatively and quantitatively screened for enzyme activities, i.e., cellulase, xylanase, laccase, and lignin peroxidase. On the basis of quantitative estimation of enzyme activities, 3 fungal (S1F1, S2F4, and S6F9), 2 actinomycetes (S1A1 and S6A4), and 2 bacterial strains (S6B16 and S6B17) were further selected for in vitro bio-compatibility assay. Selected bio-compatible microbial strains were identified as Streptomyces flavomacrosporus (S6A4), Aspergillus terreus (S2F4), and Bacillus altitudinis (S6B16) through 16S rRNA and 18S rRNA sequencing. Furthermore, single and developed microbial consortium (S6B16 + S6A4 + S2F4) were screened for quantitative estimation of cellulase, xylanase, laccase, and lignin peroxidase enzymes with 23 biochemically different cereal, legume, and oil seed crop residues for optimization of enzyme activities at different time intervals. Results revealed that Vigna radiata followed by Cajanus cajan and Arachis hypogaea straw residue powder @ 1% in culture broth are a promising carbon source for B. altitudinis, S. flavomacrosporus, and A. terreus to produce higher ligno-cellulolytic microbial degrading enzymes due to variable range of carbon (C):nitrogen (N) ratio and higher ligno-cellulolytic content in the studied crop residues. Thus, the application of indigenous microbial consortium with efficient lignocellulose hydrolysis enzyme machinery might be an attractive alternative for ex situ crop residue management practices under sustainable manners.

A thermostable and CBM2-linked GH10 xylanase from Thermobifida fusca for paper bleaching

Xylanases have the potential to be used as bio-deinking and bio-bleaching materials and their application will decrease the consumption of the chlorine-based chemicals currently used for this purpose. However, xylanases with specific properties could act effectively, such as having significant thermostability and alkali resistance, etc. In this study, we found that TfXyl10A, a xylanase from Thermobifida fusca, was greatly induced to transcript by microcrystalline cellulose (MCC) substrate. Biochemical characterization showed that TfXyl10A is optimally effective at temperature of 80 °C and pH of 9.0. After removing the carbohydrate-binding module (CBM) and linker regions, the optimum temperature of TfXyl10A-CD was reduced by 10°C (to 70°C), at which the enzyme’s temperature tolerance was also weakened. While truncating only the CBM domain (TfXyl10AdC) had no significant effect on its thermostability. Importantly, polysaccharide-binding experiment showed that the auxiliary domain CBM2 could specifically bind to cellulose substrates, which endowed xylanase TfXyl10A with the ability to degrade xylan surrounding cellulose. These results indicated that TfXyl10A might be an excellent candidate in bio-bleaching processes of paper industry. In addition, the features of active-site architecture of TfXyl10A in GH10 family were further analyzed. By mutating each residue at the -2 and -1 subsites to alanine, the binding force and enzyme activity of mutants were observably decreased. Interestingly, the mutant E51A, locating at the distal -3 subsite, exhibited 90% increase in relative activity compared with wild-type (WT) enzyme TfXyl10A-CD (the catalytic domain of TfXyl110A). This study explored the function of a GH10 xylanase containing a CBM2 domain and the contribution of amino acids in active-site architecture to catalytic activity. The results obtained provide guidance for the rational design of xylanases for industrial applications under high heat and alkali-based operating conditions, such as paper bleaching.

Pretreatment of rice straw by newly isolated fungal consortium enhanced lignocellulose degradation and humification during composting

The slow decomposition rate of the reluctant structure of lignocellulose in agricultural waste is the great limitation of composting processes, which can be averted by pretreatment-strategies. This study focused on the impacts of pretreating rice straw using a consortium of newly isolated fungal species on lignocellulose degradation and humic substances during composting. Fungal pretreatment had a significant impact on lignocellulose degradation (84%) of rice straw by producing higher lignocellulytic enzymes than chemical pretreatments (79%) or the control (61%). The compost with fungal pretreated rice straw (FPT) showed significantly high composting temperature in the late mesophilic stage, which enhanced the degradation of lignocellulose. The fluorescence excitation emission spectroscopy revealed that significantly more humic acid-like compounds were formed in FPT. These findings suggest that fungal pretreatment is a feasible method to accelerate straw degradation and humification.

Lignocellulosic Materials for the Production of Biofuels, Biochemicals and Biomaterials and Applications of Lignocellulose-Based Polyurethanes: A Review

The present review is devoted to the description of the state-of-the-art techniques and procedures concerning treatments and modifications of lignocellulosic materials in order to use them as precursors for biomaterials, biochemicals and biofuels, with particular focus on lignin and lignin-based products. Four different main pretreatment types are outlined, i.e., thermal, mechanical, chemical and biological, with special emphasis on the biological action of fungi and bacteria. Therefore, by selecting a determined type of fungi or bacteria, some of the fractions may remain unaltered, while others may be decomposed. In this sense, the possibilities to obtain different final products are massive, depending on the type of microorganism and the biomass selected. Biofuels, biochemicals and biomaterials derived from lignocellulose are extensively described, covering those obtained from the lignocellulose as a whole, but also from the main biopolymers that comprise its structure, i.e., cellulose, hemicellulose and lignin. In addition, special attention has been paid to the formulation of bio-polyurethanes from lignocellulosic materials, focusing more specifically on their applications in the lubricant, adhesive and cushioning material fields. High-performance alternatives to petroleum-derived products have been reported, such as adhesives that substantially exceed the adhesion performance of those commercially available in different surfaces, lubricating greases with tribological behaviour superior to those in lithium and calcium soap and elastomers with excellent static and dynamic performance.

Contemporary proteomic research on lignocellulosic enzymes and enzymolysis: A review

This review overviewed the current researches on the isolation of novel strains, the development of novel identification protocols, the key enzymes and their synergistic interactions with other functional enzyme systems, and the strategies for enhancing enzymolysis efficiencies. The main obstacle for realizing biorefinery of lignocellulosic biomass to biofuels or biochemicals is the high cost of enzymolysis stage. Therefore, research prospects to reduce the costs for lignocellulose hydrolysis were outlined.

Phylogenetic and Functional Diversity of Saprolegniales and Fungi Isolated from Temperate Lakes in Northeast Germany

The contribution of fungi to the degradation of plant litter and transformation of dissolved organic matter (humic substances, in particular) in freshwater ecosystems has received increasing attention recently. However, the role of Saprolegniales as one of the most common eukaryotic organisms is rarely studied. In this study, we isolated and phylogenetically placed 51 fungal and 62 Saprolegniales strains from 12 German lakes. We studied the cellulo-, lignino-, and chitinolytic activity of the strains using plate assays. Furthermore, we determined the capacity of 10 selected strains to utilize 95 different labile compounds, using Biolog FF MicroPlates™. Finally, the ability of three selected strains to utilize maltose and degrade/produce humic substances was measured. Cladosporium and Penicillium were amongst the most prevalent fungal strains, while Saprolegnia, Achlya, and Leptolegnia were the most frequent Saprolegniales strains. Although the isolated strains assigned to genera were phylogenetically similar, their enzymatic activity and physiological profiling were quite diverse. Our results indicate that Saprolegniales, in contrast to fungi, lack ligninolytic activity and are not involved in the production/transformation of humic substances. We hypothesize that Saprolegniales and fungi might have complementary roles in interacting with dissolved organic matter, which has ecological implications for carbon cycling in freshwater ecosystems.

Planifilum fulgidum Is the Dominant Functional Microorganism in Compost Containing Spent Mushroom Substrate

The extensive accumulation of spent mushroom substrate (SMS) owing to the large-scale production of edible fungi is causing environmental problems that cannot be ignored. Co-composting is a promising method for agricultural and animal husbandry waste disposal. In this study, the composition and function of microbial communities in the process of cattle manure–maize straw composting with SMS addition were compared through an integrated meta-omics approach. The results showed that irrespective of SMS addition, the predominant fungi were Ascomycota, while the dominant bacteria were Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes. High temperature promoted the evolution from Gram-negative bacteria (Bacteroides, Proteobacteria) to Gram-positive bacteria (Firmicutes, Actinomycetes). The composting process was accelerated by SMS addition, and the substrate was effectively degraded in 14 days. Metaproteomics results showed that the dominant microorganism, Planifilum fulgidum, secreted large amounts of S8, M17, and M32 proteases that could degrade macromolecular protein substrates in the presence of SMS. Planifilum fulgidum, along with Thermobifida fusca and Melanocarpus albomyces, synergistically degraded hemicellulose, cellulose, and protein. In addition, the dominant microorganisms related to the initial raw materials such as Pichia, Lactobacillus in the microbial agent and Hypsizygus in SMS could not adapt to the high-temperature environment (>60 °C) and were replaced by thermophilic bacteria after 5 days of composting.

Harnessing microbial wealth for lignocellulose biomass valorization through secretomics: a review

The recalcitrance of lignocellulosic biomass is a major constraint to its high-value use at industrial scale. In nature, microbes play a crucial role in biomass degradation, nutrient recycling and ecosystem functioning. Therefore, the use of microbes is an attractive way to transform biomass to produce clean energy and high-value compounds. The microbial degradation of lignocelluloses is a complex process which is dependent upon multiple secreted enzymes and their synergistic activities. The availability of the cutting edge proteomics and highly sensitive mass spectrometry tools make possible for researchers to probe the secretome of microbes and microbial consortia grown on different lignocelluloses for the identification of hydrolytic enzymes of industrial interest and their substrate-dependent expression. This review summarizes the role of secretomics in identifying enzymes involved in lignocelluloses deconstruction, the development of enzyme cocktails and the construction of synthetic microbial consortia for biomass valorization, providing our perspectives to address the current challenges.