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Cili (Rosa sterilis D. shi) fruit is appealing to consumers due to its sensorial and nutritional characteristics. However, postharvest lignification leads to the loss of acceptance and edible quality of the fruit. In this study, the effects of postharvest treatment with 1.0 μL L−1 1-methylcyclopropene (1-MCP) and 100 μL L−1 ethylene on lignification and the postharvest quality of Cili fruit were investigated by analysing lignin metabolism, sucrose metabolism, and cell wall enzyme activities. The results showed that ethylene facilitated an increase in the respiration rate and weight loss of the fruit, promoted the activities of cell wall-related enzymes, including cellulase, sucrose synthase, β-galactosidase, phenylalanine ammonialyase and peroxidase, and accelerated the accumulation of total polyphenols and lignin. By contrast, 1-MCP had the opposite effects. Together, these findings show that 1-MCP can maintain the quality of Cili fruit by inhibiting lignification, while ethylene may play an important role in the lignification process. [ABSTRACT FROM AUTHOR]

Moderate deficit irrigation can improve lignin metabolism, thereby increasing wheat yield and lodging resistance. The moisture-sensitive variety Xinchun 22 (XC22) and drought-resistant variety Xinchun 6 (XC6) were used as experimental materials. We set mild drought (T1, J1 and 60–65% FC, where FC is the field capacity) and moderate drought (T2, J2 and 45–50% FC) during the tillering stage (T) and the jointing stage (J). We used conventional drip irrigation as a control (CK and 75–80% FC). The results show that the activity of lignin synthesis-related enzymes decreased with the growth process, while the accumulation and monomer content of lignin increased under different water treatments. The lignin metabolism and morphological characteristics of XC6 were higher than those of XC22. Under the same processing conditions, the indicators of XC22 showed more significant changes and were more sensitive to changes in the moisture content. Compared with other treatments, the stem thickness and wall thickness of the J1 treatment increased by 0.86–23.49% and 1.72–23.58%. The yield of the T1 treatment was the highest, increasing by 3.05–44.06% compared to other treatments. In addition, by improving PAL, H-type lignin monomers, S-type lignin monomers, stem thickness and lignin metabolism, grain yield can be increased. After mild drought during the jointing stage, J1 significantly improved the lignin metabolism capacity of the stem, increased stem thickness and wall thickness, and was beneficial for improving lodging resistance. The T1 treatment favored the improvement of the production capacity of assimilates, thus promoting a high yield of spring wheat. [ABSTRACT FROM AUTHOR]

BACKGROUND: Detoxifying enzymes are likely involved in lignin feeding and immune defense mechanisms within termites, rendering them potential targets for biological control. However, investigations into the dual functionality of termite detoxification enzymes in vivo have not been documented. RESULTS: In this study, the complete cDNA of the catalase gene (Cfcat) derived from Coptotermes formosanus Shiraki was amplified. CFCAT comprises an open reading frame spanning 1527 bp, encoding a 508‐amino acid sequence. The highest expression was observed in the epidermal tissues (including the fat body and hemolymph) followed by the foregut/salivary gland. Furthermore, we confirmed the catalase activity of the recombinant Cfcat protein. Using RNA interference (RNAi) technology, the importance of Cfcat in the lignin‐feeding of C. formosanus was demonstrated, and the role of Cfcat in innate immunity was investigated. Survival assays showed that Cfcat RNAi significantly increased the susceptibility of C. formosanus to Metarhizium anisopliae. Irrespective of the infection status, Cfcat inhibition had a significant impact on multiple factors of humoral and intestinal immunity in C. formosanus. Notably, Cfcat RNAi exhibited a more pronounced immunosuppressive effect on humoral immunity than on intestinal immunity. CONCLUSION: Cfcat plays an important role in the regulation of innate immunity and lignin feeding in C. formosanus. Cfcat RNAi can weaken the immune response of termites against M. anisopliae, which may aid the biocontrol efficiency of M. anisopliae against C. formosanus. This study provides a theoretical basis and technical reference for the development of a novel biocontrol strategy targeting detoxifying enzymes of termites. © 2024 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

To improve light harvest and plant structural support under low light intensity, it is useful to investigate the effects of different ratios of blue light on petiole and stem growth. Two true leaves of soybean seedlings were exposed to a total light intensity of 200 µmol m-2 s-1, presented as either white light or three levels of blue light (40 µmol m-2 s-1, 67 µ mol m-2 s-1 and 100 µmol m-2 s-1) for 15 days. Soybean petioles under the low blue light treatment upregulated expression of genes relating to lignin metabolism, enhancing lignin content compared with the white light treatment. The low blue light treatment had high petiole length, increased plant height and improved petiole strength arising from high lignin content, thus significantly increasing leaf dry weight relative to the white light treatment. Compared with white light, the treatment with the highest blue light ratio reduced plant height and enhanced plant support through increased cellulose and hemicellulose content in the stem. Under low light intensity, 20% blue light enhanced petiole length and strength to improve photosynthate biomass; whereas 50% blue light lowered plants' centre of gravity, preventing lodging and conserving carbohydrate allocation. [ABSTRACT FROM AUTHOR]

Increasing storage root number is a pivotal approach to enhance both storage root (SR) yield and appearance quality of sweet potato. Here, 2-year field experiments were conducted to investigate the effect of 0 (K0), 120 (K1), 240 (K2), and 360 (K3) kg ha-1 potassium fertilizer (K2O) on lignin metabolism, root growth, storage root yield, and uniformity. The results demonstrated that potassium (K) application led to a decrease in the activities of key enzymes involved in lignin biosynthesis, including phenylalanine deaminase (PAL), 4-coumarate coenzyme A ligase (4-CL), cinnamic acid dehydrogenase (CAD), polyphenol oxidase (PPO), and peroxidase (POD). This resulted in a significant reduction in lignin and G-type lignin contents in potential SRs compared to K0 treatment within 10-30 days after planting (DAP). BJ553 exhibited a significant decrease in PAL activity, as well as lignin and G-type contents at 10 DAP, whereas YS25 showed delayed effects until 20 DAP. However, the number and distribution of secondary xylem conduits as well as the mid-column diameter area in roots were increased in K2 treatment. Interestingly, K2 treatment exhibited significantly larger potential SR diameter than other treatments at 15, 20, and 25 DAP. At harvest, K2 treatment increased the SR number, the single SR weight, and overall yield greatly compared with K0 treatment, with an average increase of 19.12%, 16.54%, and 16.92% respectively. The increase of SR number in BJ553 was higher than that of YS25. Furthermore, K2 treatment exhibited the lowest coefficient of variation for both SR length and diameter, indicating a higher yield of middle-sized SRs. In general, appropriate potassium application could effectively suppress lignin biosynthesis, leading to a reduction in the degree of pericycle lignification in potential SRs. This promotes an increase in the number of storage roots and ultimately enhances both yield and appearance quality of sweet potato. The effect of potassium fertilizer on lignin metabolism in BJ553 roots was earlier and resulted in a greater increase in the SR number compared to YS25. [ABSTRACT FROM AUTHOR]

Pear (Pyrus L.) is one of the most important fruits in the world. Fruit dots are an important trait that affects pear quality. Abnormal fruit dots usually reduce the merchantability of pears. In this research, during cold storage, 'Danxiahong' pear fruit exhibited protrudent fruit dots on the peels. Microscopy system measurement showed that fruit dots size and height on the abnormal fruit peel were bigger and higher than the normal ones. Likewise, scanning electron microscopy observations indicated that the abnormal fruit peel, in contrast to the normal pear peel, exhibited an abnormal cell structure and fruit dots. Physiological analysis showed that the lignin content in abnormal fruit peel was significantly higher than in normal fruit peel. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis revealed that the top-enriched pathways were mainly associated with lignin synthesis and metabolism. The transcripts of lignin biosynthesis-associated genes were analyzed, and the results showed that the expression of a cascade of structural genes, including PpyPAL, PpyCCR, PpyC3H, PpyC4H, PpyHCT, PpyCAD, PpyLAC, and PpyPOD, was significantly induced in the protrudent peels. Furthermore, the expression of regulatory genes involved in lignin biosynthesis, especially the NAC-MYB-based gene regulatory network, was significantly upregulated in the abnormal peels. Real-time quantitative PCR (RT-qPCR) analysis confirmed the induction of lignin biosynthesis genes. Overall, this research revealed that the abnormal fruit surface was caused by fruit dots disorder during cold storage. This research provides insights into the fine regulation pathways in the prevention of fruit dots protrusion, especially in modulating lignin synthesis and metabolism during postharvest storage. [ABSTRACT FROM AUTHOR]

Root-knot nematodes (RKN) cause significant damage to sweetpotato plants and cause significant losses in yield and quality. Reactive oxygen species (ROS) play an important role in plant defenses, with levels of ROS-detoxifying antioxidant enzymes tightly regulated during pathogen infection. In this study, ROS metabolism was examined in three RKN-resistant and three RKN-susceptible sweetpotato cultivars. The antioxidant enzymes superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD) were assessed, as was lignin-related metabolism. In RKN-infected roots, both resistant and susceptible cultivars increased SOD activity to produce higher levels of hydrogen peroxide (H2O2). However, H2O2 removal by CAT activity differed between cultivars, with susceptible cultivars having higher CAT activity and lower overall H2O2 levels. In addition, the expression of phenylpropanoid-related phenylalanine ammonia-lyase and cinnamyl alcohol dehydrogenase genes, which encode enzymes involved in lignin metabolism, were higher in resistant cultivars, as were total phenolic and lignin contents. Enzyme activities and H2O2 levels were examined during the early (7 days) and late (28 days) phases of infection in representative susceptible and resistant cultivars, revealing contrasting changes in ROS levels and antioxidant responses in the different stages of infection. This study suggests that differences in antioxidant enzyme activities and ROS regulation in resistant and susceptible cultivars might explain reduced RKN infection in resistant cultivars, resulting in smaller RKN populations and overall higher resistance to infection and infestation by RKNs. [ABSTRACT FROM AUTHOR]

The plastic elongation of mesocotyl (MES) and coleoptile (COL), which can be repressed by light exposure, plays a vital role in maize seedling emergence and establishment under adverse environmental conditions. Understanding the molecular mechanisms of light-mediated repression of MES and COL elongation in maize will allow us to develop new strategies for genetic improvement of these two crucial traits in maize. A maize variety, Zheng58, was used to monitor the transcriptome and physiological changes in MES and COL in response to darkness, as well as red, blue, and white light. The elongation of MES and COL was significantly inhibited by light spectral quality in this order: blue light > red light > white light. Physiological analyses revealed that light-mediated inhibition of maize MES and COL elongation was closely related to the dynamics of phytohormones accumulation and lignin deposition in these tissues. In response to light exposure, the levels of indole-3-acetic acid, trans-zeatin, gibberellin 3, and abscisic acid levels significantly decreased in MES and COL; by contrast, the levels of jasmonic acid, salicylic acid, lignin, phenylalanine ammonia-lyase, and peroxidase enzyme activity significantly increased. Transcriptome analysis revealed multiple differentially expressed genes (DEGs) involved in circadian rhythm, phytohormone biosynthesis and signal transduction, cytoskeleton and cell wall organization, lignin biosynthesis, and starch and sucrose metabolism. These DEGs exhibited synergistic and antagonistic interactions, forming a complex network that regulated the light-mediated inhibition of MES and COL elongation. Additionally, gene co-expression network analysis revealed that 49 hub genes in one and 19 hub genes in two modules were significantly associated with the elongation plasticity of COL and MES, respectively. These findings enhance our knowledge of the light-regulated elongation mechanisms of MES and COL, and provide a theoretical foundation for developing elitemaize varieties with improved abiotic stress resistance. [ABSTRACT FROM AUTHOR]

Copper (Cu) pollution is one of environmental problems that adversely affects the growth and development of plants. However, knowledge of lignin metabolism associated with Cu-induced phytotoxicity mechanism is insufficient. The objective of this study was to reveal the mechanisms underlying Cu-induced phytotoxicity by evaluating changes in the photosynthetic characteristics and lignin metabolism in the seedlings of wheat cultivar ‘Longchun 30′. Treatment with varying concentrations of Cu clearly retarded seedling growth, as demonstrated by a reduction in the growth parameters. Cu exposure reduced the photosynthetic pigment content, gas exchange parameters, and chlorophyll fluorescence parameters, including the maximum photosynthetic efficiency, potential efficiency of photosystem II (PS II), photochemical efficiency of PS II in light, photochemical quenching, actual photochemical efficiency, quantum yield of PS II electron transport, and electron transport rate, but notably increased the nonphotochemical quenching and quantum yield of regulatory energy dissipation. Additionally, a significant increase was observed in the amount of cell wall lignin in wheat leaves and roots under Cu exposure. This increase was positively associated with the up-regulation of enzymes related to lignin synthesis, such as phenylalanine ammonia-lyase, 4-coumarate:CoA ligase, cinnamyl alcohol dehydrogenase, laccase, cell wall bound (CW-bound) guaiacol peroxidase, and CW-bound conifer alcohol peroxidase, and TaPAL, Ta4CL, TaCAD, and TaLAC expression. Correlation analysis revealed that lignin levels in the cell wall were negatively correlated with the growth of wheat leaves and roots. Taken together, Cu exposure inhibited photosynthesis in wheat seedlings, resulting from a reduction in photosynthetic pigment content, light energy conversion, and photosynthetic electron transport in the leaves of Cu-stressed seedlings, and the Cu-inhibitory effect on seedling growth was related to the inhibition of photosynthesis and an increase in cell wall lignification.

Composting converts organic agricultural wastes into value-added products, yet the presence of significant non-biodegradable lignocelluloses hinders its efficiency. The introduction of various exogenous microbial agents has been shown to effectively addresses this challenge. In this context, basing on the microbial enzymatic mechanism for lignocellulose degradation, this paper synthesizes the latest research advancements and practical applications of exogenous microbial agents in agricultural waste composting. Given that the effectiveness of lignocellulose degradation is highly dependent on the waste's inherent characteristics, it is crucial to carefully consider the composition of fungi and bacteria, the dosage of microbial agents, and the composting process operation, tailored to the specific type of agricultural waste. Moreover, the combination of additives with exogenous microbial agents can further enhance the degradation of lignocelluloses and the humification of organic matters. Furthermore, insights into the future research and application trends of exogenous microbial agents in agricultural waste composting was prospected., Competing Interests: Declarations. Conflict of interest: The authors have no relevant financial or non-financial interests to disclose. Ethical approval: This article does not contain any studies with human participants or animals performed by any of the authors., (© 2025. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Lignocellulose, an abundant renewable resource, presents a promising alternative for sustainable energy and industrial applications. However, large-scale adoption of lignocellulosic feedstocks faces considerable obstacles, including scalability, bioprocessing efficiency, and resilience to climate change. This Review examines current efforts and future opportunities for leveraging lignocellulosic feedstocks in bio-based energy and products, with a focus on enhancing conversion efficiency and scalability. It also explores emerging biotechnologies such as CRISPR-based genome editing informed by machine learning, aimed at improving feedstock traits and reducing the environmental impact of fossil fuel dependence., Competing Interests: Competing interests: The authors declare no competing interests., (© 2025. The Author(s).)

The lignocellulosic biomass (LCB) is an attractive, sustainable, and environmentally friendly alternative to fossil sources to produce biofuel, biomaterials, and biochemicals. However, its recalcitrant and heterogenous structure challenges its biodegradation and valorization. The gut microbiome of soil invertebrate species has emerged as a rich source of LCB-degrading bacteria and enzymes in terrestrial ecosystems. The primary objective of this investigation was to identify the bacterial communities within the Porcellio dilatatus gut (Crustacea: Isopods), to obtain enriched cultures, and to identify bacterial isolates with LCB-degrading activity. A total of 112 enriched cultures were screened, all exhibiting xylanolytic activity. Among them, 94 displayed cellulolytic activity, 30 showed chitinolytic activity, and 21 demonstrated ligninolytic activity. Four enriched cultures were selected, and 128 bacteria with cellulolytic, xylanolytic, chitinolytic, or ligninolytic activity were isolated and taxonomically classified. The obtained results reinforce the potential of bacterial communities within the digestive tract of soil invertebrates as a valuable source of lignocellulose-degrading microorganisms. Thirty-one isolates underwent in-depth enzymatic characterization, and five were selected and functionally evaluated. An artificial bacterial consortium was constructed to assess the potential benefits of using consortia to achieve enhanced LCB degradation. The positive results of this proof-of-concept artificial consortium (PdG-AC) can be used in future applications and is a valuable tool for enzymatic and microbial consortia engineering by, e.g., changing growth conditions for enhanced LCB-degrading abilities. KEY POINTS: • The gut microbiome of Porcellio dilatatus was characterized. • Porcellio dilatatus gut hosts many lignocellulose-degrading bacteria. • Developed an artificial bacterial consortium for lignocellulose degradation., Competing Interests: Declarations. Ethics approval and consent to participate: This article contains no studies with human participants or animals performed by any authors. Consent for publication: All the authors read and agree with the content of this paper and its publications. Competing interests: The authors declare no competing interests., (© 2025. The Author(s).)

As an evolutionary achievement of almost all terrestrial plants, lignin biosynthesis is essential for various mechanical and physiological processes. Possible effects of plant cell wall lignification on large-scale vegetation distribution are, however, not yet fully understood. Here, we present double-stained, wood anatomical stem measurements of 207 perennial herbs (Potentilla pamirica Wolf), which were collected between 5550 and 5850 m asl on the north-western Tibetan Plateau in Ladakh, India. We also measured changes in situ root zone and surface air temperatures along the sampling gradient and applied piecewise structural equation models to assess direct and indirect relationships between the age and size of plants, the degree of cell wall lignification in their stems, and the elevation at which they were growing. Based on the world's highest-occurring vascular plants, the Pamir Cinquefoils, we demonstrate that the amount of lignin in the secondary cell walls decreases significantly with increasing elevation (r = -0.73; p < 0.01). Since elevation is a proxy for temperature, our findings suggest a thermal constrain on lignin biosynthesis at the cold range limit of woody plant growth., (© 2024 The Author(s). Plant, Cell & Environment published by John Wiley & Sons Ltd.)

Effective hydrolysis of lignocelluloses for producing reducing sugar is impeded by the covalent binding of hemicellulose and cellulose through lignin, which could be eliminated by laccases. This study identified a novel thermostable laccase from Bacillus safensis TCCC 111022 and created an iterative mutant E231D/Y441H, exhibiting 1.59-fold greater specific activity and a 183 % greater half-life at 80°C than the wild-type enzyme. Computational analysis revealed that the stability and activity of the E231D/Y441H could be simultaneously enhanced by increasing the flexibility of the ring around the substrate binding pocket. Additionally, the saccharification efficiency of sugarcane bagasse and corn stalks were both enhanced by 235 % in the system adding E231D/Y441H, mixed-cellulases, and mediator (1-hydroxybenzotriazole) compared to the samples treated with mixed-cellulases. The findings of this research provide a reference for the degradation of lignocellulosic substrates and contribute to the sustainable development of biomass-based industries., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Cotton stalk, an important by-product of cotton farming, is challenging in lignocellulosic feedstock application due to the limited understanding of their compositional and lignin structural characteristics. This study elucidates the composition of lignocellulose components and fundamental lignin structural features of cotton stalk. Lignocellulosic hydrolysates were prepared from various cotton stalk parts and used for single-cell protein production. As a proof of concept, cotton stalk hydrolysates were successfully converted into single-cell protein using the superior microbial host, Candida utilis ACCC20060, owing to its favorable sugar consumption efficiency and high protein quality. The highest SCP concentration of 5.74 g/L was obtained, yielding 0.23 g/g from the lignocellulose-derived sugars released from cotton stalk roots. This study provides valuable references for cotton stalk utilization toward lignocellulosic feedstock application and introduces a promising microbial host for single-cell protein production from such feedstocks., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Feruloyl esterase (FAE) has been extensively studied for its crucial auxiliary effect in the biodegradation of lignocellulose. In this study, a FAE database including 15,293 amino acid sequences was established to gain a better understanding of rumen FAEs through multi-omics analysis. The higher expression level of rumen fungal FAEs over bacterial FAEs suggests that rumen fungi may have more important role in the lignocellulose degradation. Analyses of the information acquired through the database showed that the rumen FAEs are mainly derived from anaerobic fungi. One special candidate harboring both feruloyl esterase and endoxylanase modules (Fae00416) from anaerobic fungus Pecoramyces ruminantium F1 was found to have intramolecular synergy between the esterase and xylanase domains, which underpins the importance of this enzymes in heteropolysaccharide degradation. The discovery of novel and efficient FAEs in rumen could contribute to enhancing the production of biofuels and bioproducts., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Lignin, a major wood component, is the key limiting factor for wood conversion efficiency. Its biosynthesis is controlled by transcriptional regulatory networks involving transcription factor (TF)-DNA interactions. However, the epigenetic mechanisms underlying these interactions in lignin biosynthesis remain largely unknown. Here, using yeast one-hybrid, chromatin immunoprecipitation, and electrophoretic mobility shift assays, we identified that PtrbZIP44-A1, a key wood-forming TF, directly interacts with the promoters of PtrCCoAOMT2 and PtrCCR2, genes involved in the monolignol biosynthetic pathway. We used yeast two-hybrid, bimolecular fluorescence complementation, biochemical analyses, transient and CRISPR-mediated transgenesis in Populus trichocarpa to demonstrate that PtrHDA15, a histone deacetylase, acts as an epigenetic inhibitor and is recruited by PtrbZIP44-A1 for chromatin histone modifications to repress PtrCCoAOMT2 and PtrCCR2, leading to reduced lignin deposition. In transgenic lines overexpressing PtrbZIP44-A1 or PtrHDA15, histone acetylation at the promoters of PtrCCoAOMT2 and PtrCCR2 decreased, reducing their expression and lignin content. Conversely, in loss-of-function ptrbzip44-a1 and ptrhda15 mutants, histone acetylation levels at PtrCCoAOMT2 and PtrCCR2 promoters increased, enhancing target gene expression and lignin content. Our study uncovered an epigenetic mechanism that suppresses lignin biosynthesis. This finding may help fill a knowledge gap between epigenetic regulation and lignin biosynthesis during wood formation in Populus., (© 2024 The Author(s). New Phytologist © 2024 New Phytologist Foundation.)

Background: The potential for the efficient conversion of lignocellulosic biomass has been extensively explored to produce a wide range of bioproducts. Many approaches have been sought for the deep conversion of lignin to generate products that are toxin-free and beneficial for processing into high-value-added components., Results: This study reported a fungus isolated from the deep sea with strong synthesis of multiple lignocellulases, conversion of lignin and guaiacol (0.1%) by 71.6% and 86.1% within 9 days at 30 °C respectively, and outstanding environmental adaptability (20-50 °C and pH 3-8). Metabolic pathway profiling showed that this fungus utilized lignin to rapidly activate multiple ring-opening reactions including the 2,3- and 3,4-cleavage pathways, with the 2,3-cleavage pathway predominating after 5 days. Conversion of metabolic intermediates confirmed the superb potential of this strain for lignin treatment. Meanwhile, its shikimic acid pathway was metabolically active under lignin., Conclusion: This further expands the potential to produce valuable bioproducts during lignin treatment, especially under ambient conditions, which can significantly enhance high-value precursor compound production. © 2024 Society of Chemical Industry., (© 2024 Society of Chemical Industry.)

Lignocellulose is the most abundant, sustainable, and comparatively economical renewable biomass containing ample fermentable sugars for bio-based chemical production, such as lactic acid (LA). LA is a versatile chemical with substantial global demand. However, the concurrent utilization of mixed sugars derived from lignocellulose, including glucose, xylose, and arabinose, remains a formidable challenge because of the metabolic regulation of carbon catabolite repression (CCR), in which glucose is preferentially utilized over non-glucose sugars, resulting in the loss of carbon resources and a decrease in biorefinery efficacy. Most current studies on CCR have concentrated on elucidating the principles and their impact on specific bacterial species using mixed carbon sources. However, there remains a notable dearth of comprehensive reviews summarizing the underlying principles and corresponding mitigation strategies across other bacterial strains encountering similar challenges. In light of this, this article delineates the possible factors that lead to CCR, including signal transduction and metabolic pathways. Additionally, the fermentation conditions and nutrients are described. Finally, this study proposes appropriate mitigation strategies to overcome the aforementioned obstacles and presents new insights into the rapid and simultaneous consumption of mixed sugars to bolster the production yields of biofuels and chemicals in the future., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Nowadays, the rapid growth of population has led to a substantial increase in kitchen waste and wasted sludge. Kitchen waste is rich in organic matter, including lignocellulose. Synergistic treatment involving kitchen waste and wasted sludge can enhance treatment process. Vermicomposting can facilitate microbial activities on organic matter. Nevertheless, the underlying mechanisms remain unclear. In this study, metagenomics was used to analyze microbial functional genes in vermicomposting. Redundancy analysis found that TOC, TN and DTN adversely affect earthworm growth and reproduction. The relative abundance of Bacteroidetes and Firmicutes increased with earthworms, thereby potentially augmenting lignocellulose degradation. The predominant functional genes included amino acid, carbohydrate, and inorganic ion conversion and metabolism. Metagenomics analysis demonstrated that GH1, GH3, GH5, GH6, GH9, GH12, GH44, GH48 and GH74, GT41, GT4, GT2, and GT51 were dominant. Furthermore, there was higher abundance of carbohydrate-active enzymes in the vermicomposting, particularly during the later phases (30-45 days). Co-occurrence network revealed that Cellvibrio in the vermicomposting exhibited a relatively dense positive correlation with other microbial groups. The findings elucidated the mechanism of vermicomposting as a promising approach for managing kitchen waste and wasted sludge., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

In this study, 15 plant species representing plant evolution were selected, and distinct lignocellulose compositions for largely varied biomass enzymatic saccharification were detected. By comparison, the acid-pretreated lignocellulose of rice mutant was of the highest Congo-red adsorption (298 mg/g) accounting for cellulose accessibility, leading to complete cellulose hydrolysis and high bioethanol production. By conducting oxidative-catalysis with the acid-pretreated lignocellulose of moss plant, the optimal biosorbent was generated with maximum Cd/Pb adsorption (54/118 mg/g), mainly due to half-reduced cellulose polymerization degree and raised functional groups accountable for multiple physical and chemical interactions. Furthermore, the acid-pretreated lignocellulose of eucalyptus was of large and small pores for much higher adsorption capacities with direct-yellow and direct-blue than those of the previously-reported. Therefore, this study raises a mechanism model about how distinct lignocelluloses of plant evolution are selective for complete biomass saccharification and optimal biosorbents assembly, providing insights into lignocellulose biosynthesis and biomass conversion., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Wood-fall micro-ecosystems contribute to biogeochemical processes in the oligotrophic deep ocean. However, the community assembly processes and biogeochemical functions of microbiomes in wood fall remain unclear. This study investigated the diversity, community structure, assembly processes, and functional profiles of bacteria and fungi in a deep-sea wood fall from the South China Sea using physicochemical indices, amplicon sequencing, and metagenomics. The results showed that distinct wood-fall contact surfaces exhibit habitat heterogeneity. The bacterial community of all contact surfaces and the fungal community of seawater contact surface (SWCS) were affected by homogeneous selection. In SWCS and transition region (TR), bacterial communities were influenced by dispersal limitation, whereas fungal communities were affected by homogenizing dispersal. The Venn diagram visualization revealed that the shared fungal community between SWCS and TR was dominated by Aspergillaceae. Additionally, the bacterial community demonstrated a higher genetic potential for sulfur, nitrogen, and methane metabolism than fungi. The sediment contact surface enriched modules were associated with dissimilatory sulfate reduction and methanogenesis, whereas the modules related to nitrate reduction exhibited enrichment characteristics in TR. Moreover, fungi showed a stronger potential for lignocellulase production compared to bacteria, with Microascaceae and Nectriaceae identified as potential contributors to lignocellulose degradation. These results indicate that environmental filtering and organism exchange levels regulated the microbial community assembly of wood fall. The biogeochemical cycling of sulfur, nitrogen, and methane was mainly driven by the bacterial community. Nevertheless, the terrestrial fungi Microascaceae and Nectriaceae might degrade lignocellulose via the combined action of multiple lignocellulases.IMPORTANCEThe presence and activity of microbial communities may play a crucial role in the biogeochemical cycle of deep-sea wood-fall micro-ecosystems. Previous studies on wood falls have focused on the microbiome diversity, community composition, and environmental impact, while few have investigated wood-fall micro-ecosystems by distinguishing among distinct contact surfaces. Our study investigated the microbiome dynamics and functional profiles of bacteria and fungi among distinct wood-fall contact surfaces. We found that the microbiome community assembly was regulated by environmental filtering and organism exchange levels. Bacteria drive the biogeochemical cycling of sulfur, nitrogen, and methane in wood fall through diverse metabolic pathways, whereas fungi are crucial for lignocellulose degradation. Ultimately, this study provides new insights into the driving pattern of community assembly, biogeochemical processes, and lignocellulose degradation in the microbiomes of deep-sea wood-fall micro-ecosystems, enhancing our comprehension of the ecological impacts of organic falls on deep-sea oligotrophic environments., Competing Interests: The authors declare no conflict of interest.

Lignin degradation by biocatalysts is a key strategy to develop a plant-based sustainable carbon economy and thus alleviate global climate change. This process involves synergy between ligninases and auxiliary enzymes. However, auxiliary enzymes within secretomes, which are composed of thousands of enzymes, remain enigmatic, although several ligninolytic enzymes have been well characterized. Moreover, it is a challenge to understand synergistic lignin degradation via a diverse array of enzymes, especially in bacterial systems. In this study, the coexpression network of the periplasmic proteome uncovers potential accessory enzymes for B-type dye-decolorizing peroxidases (DypBs) in Pseudomonas putida A514. The catalytic network of the DypBs-based multienzyme complex is characterized. DypBs couple with quinone reductases and nitroreductase to participate in quinone redox cycling. They work with superoxide dismutase to induce Fenton reaction for lignin oxidation. A synthetic enzyme cocktail (SEC), recruiting 15 enzymes, was consequently designed with four functions. It overcomes the limitation of lignin repolymerization, exhibiting a capacity comparable to that of the native periplasmic secretome. Importantly, we reveal the synergistic mechanism of a SEC-A514 cell system, which incorporates the advantages of in vitro enzyme catalysis and in vivo microbial catabolism. Chemical analysis shows that this system significantly reduces the molecular weight of lignin, substantially extends the degradation spectra for lignin functional groups, and efficiently metabolizes lignin derivatives. As a result, 25% of lignin is utilized, and its average molecular weight is reduced by 27%. Our study advances the knowledge of bacterial lignin-degrading multienzymes and provides a viable lignin degradation strategy., Competing Interests: Competing interests statement:The authors declare no competing interest.

Microbial chemotaxis plays a key role in a diversity of biological and ecological processes. Although microfluidics-based assays have been applied to investigate bacterial chemotaxis, retrieving chemotactic cells off-chip based on their dynamic chemotactic responses remains limited. Here, we present a simple three-dimensional microfluidic platform capable of programmable delivery of solutions, maintaining static, stable gradients for over 20 hours, followed by active sorting and retrieval of bacteria based on their chemotactic phenotypes. Using this platform, we revealed the swimming features of individual E. coli cells in response to chemoattractant and observed rapid bacterial adaptation to the gradients. Furthermore, the robust performance of the platform allowed us to investigate complex natural microbial communities. Exemplified by sorting bacteria towards soluble cellulose and lignin compounds, we found only a small percentage (<20%) of chemotactic bacteria from a leaf mould microbiota exhibited cellulolytic or lignin-degradation abilities. These findings highlight that chemotaxis does not always align with degradation abilities. Interestingly, a new Erwinia aphidicola strain was discovered with substantial cellulose degradation capabilities. These results illustrate the strong potential of this microfluidic platform for investigating broad processes involving bacterial chemotaxis and for discovering functional microbes.

Efficient degradation of lignocellulosic biomass is key for the production of value-added products, contributing to sustainable and renewable solutions. This study employs a two-step approach to evaluate lignocellulolytic enzymes of Ceratocystis paradoxa, Colletotrichum falcatum, and Sporisorium scitamineum. First, an in silico genomic analysis was conducted to predict the potential enzyme groups produced by these fungi. Second, a 2³ full factorial design of solid-state cultivation was employed to investigate the cultivation conditions that optimize enzyme activity. In silico analysis of phytopathogen genomes identified proteins with the potential for biomass degradation. Cellulase and phenoloxidase activities were assessed in culture medium and solid-state cultivation. A 2³ full factorial design was employed for solid-state cultivation to evaluate the cellulose, endoglucanase, and laccase activities. In silico analysis shows that C. falcatum has the most diverse enzyme set for lignocellulosic biomass degradation. In vitro assays corroborate this, demonstrating that C. falcatum produces the highest enzyme quantities, except for cellulase, where C. paradoxa outperforms it. Both C. paradoxa and C. falcatum exhibit cellulase and phenoloxidase activities, but only C. falcatum shows laccase activity. Most favorable enzyme production in solid-state cultivation occurred with 85-95 g 100 g - 1 bagasse moisture and 5 g 100 g - 1 yeast extract, with four-day cultivation period needed for cellulase and endoglucanase in C. paradoxa and 12 days for endoglucanase and laccase in C. falcatum. The in silico and in vitro assays demonstrated that C. falcatum can produce a diverse enzyme set, including laccase, cellulase, and endoglucanase, making it a promising candidate for enzymatic industrial applications., Competing Interests: Declarations. Competing interests: The authors declare no competing interests. Conflict of interest: No potential conflict of interest was reported by the authors., (© 2024. The Author(s), under exclusive licence to Springer Nature B.V.)

Lignin, the most abundant renewable source of aromatic compounds on earth, remains underexploited in traditional biorefining. Fraxetin, a naturally occurring flavonoid, has garnered considerable attention in the scientific community due to its diverse and potent biological activities such as antimicrobial, anticancer, antioxidant, anti-inflammatory, and neurological protective actions. To enhance the green and value-added utilization of lignin, Saccharomyces cerevisiae was engineered as a cell factory to transform lignin derivatives to produce fraxetin. The expression of scopoletin 8-hydroxylase (S8H) and coumarin synthase (COSY) enabled S. cerevisiae to produce fraxetin from ferulic acid, one of the three principal monomers. The optimized fermentation strategies produced 19.1 mg/L fraxetin from ferulic acid by engineered S. cerevisiae. Additionally, the engineered cell factory achieved a fraxetin titer of 7.7 mg/L in lignin hydrolysate. This study successfully demonstrates the biotransformation of lignin monomers and lignin hydrolysate into fraxetin using a S. cerevisiae cell factory, thereby providing a viable strategy for the valorization of lignin. KEY POINTS: • AtS8H showed substance specificity in the hydroxylation of scopoletin. • AtCOSY and AtS8H were key enzymes for converting ferulic acid into fraxetin. • Yeast was engineered to produce fraxetin from lignin hydrolysate., Competing Interests: Declarations. Ethical approval: This article does not contain any studies with human participants or animals performed by any of the authors. Conflict of interest: The authors declare no competing interests., (© 2025. The Author(s).)

Second-generation (2G) bioethanol production, derived from lignocellulosic biomass, has emerged as a sustainable alternative to fossil fuels by addressing growing energy demands and environmental concerns. Fungal sugar transporters (STs) play a critical role in this process, enabling the uptake of monosaccharides such as glucose and xylose, which are released during the enzymatic hydrolysis of biomass. This mini-review explores recent advances in the structural and functional characterization of STs in filamentous fungi and yeasts, highlighting their roles in processes such as cellulase induction, carbon catabolite repression, and sugar signaling pathways. The review also emphasizes the potential of genetic engineering to enhance the specificity and efficiency of these transporters, overcoming challenges such as substrate competition and limited pentose metabolism in industrial strains. By integrating the latest research findings, this work underscores the pivotal role of fungal STs in optimizing lignocellulosic bioethanol production and advancing the bioeconomy. Future prospects for engineering transport systems and their implications for industrial biotechnology are also discussed. KEY POINTS: STs present a conserved structure with different sugar affinities STs are involved in the signaling and transport of sugars derived from plant biomass Genetic engineering of STs can improve 2G bioethanol production., Competing Interests: Declarations. Ethical approval: This article does not contain any studies with human participants or animals performed by any of the authors. Conflict of interest: The authors declare no competing interests., (© 2025. The Author(s).)

This study emphasized the synergistic production of bioprocessible lignin and carbohydrates during a sequential liquid hot water and alkali pretreatment of lignocellulose, facilitating their subsequent individual fermentation. Increasing the dose of alkaline lignin from 0 to 8 g/L inhibited cell growth in anaerobic digestion, with varying levels of inhibition observed in the following order: hydrolytic bacteria < acidogens < acetogens. Alkali pretreatment was adapted to maximize yields of bioprocessible lignin liquor without compromising utilization of the carbohydrates. Increasing the NaOH dose from 50 to 200 mg/g-feedstock monotonically improved lignin yields, but further increases in alkali loading led to a decline in lignin recovery. Volatile fatty acids production from anaerobic digestion of the carbohydrate moiety consistently increased with higher NaOH doses. The optimal conditions for maximizing lignin yields were determined to be 105 °C for 30 min, with NaOH loading in the range of 150-200 mg/g-feedstock, resulting in approximately 80 % lignin recovery, of which 35 % was biologically utilizable. Liquid hot water treatment prior to alkali pretreatment was confirmed as necessary to preserve carbohydrates of 0.1 g/g-feedstock at a low temperature of 70 °C. These findings are crucial for economically producing bioprocessible lignin without carbohydrate loss, a key step towards achieving full lignocellulose valorization., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Sugarcane has the most complex polyploid genome in the world, and sugar-related traits are one of the most important aims in sugarcane breeding. It is essential to construct a representative pan-transcriptome that contains all transcripts of a species for studies on genetic diversity, population expression, and omics analyses in sugarcane. In this study, we constructed the first comprehensive pan-transcriptome for sugarcane, and 8434 highly reliable open reading frames were found, which were not aligned with any published sugarcane genome. The core and dispensable gene clusters, as well as high- and low-expression gene clusters of the pan-transcriptome, were identified and analyzed. The integration of two sugar content differential transcriptome data revealed nine key candidate genes, including the ScHCT gene, encoding a crucial enzyme for lignin synthesis. Furthermore, the function of the ScHCT gene was validated in Arabidopsis , which was negatively correlated with sugar content and positively correlated with lignin content. The interaction protein of ScHCT, ScABH, was screened via a yeast two-hybrid assay and further validated by point-to-point Y2H and bimolecular fluorescence complementation assays. The phenotype of the Arabidopsis abh mutant line revealed that loss of function of ABH resulted in a decrease of sucrose content in stem tissue. This study provides important reference information and genetic resources for sugarcane research and varietal improvement.

Lignin, as the abundant carbon polymer, is essential for carbon cycle and biorefinery. Microorganisms interact to form communities for lignin biodegradation, yet it is a challenge to understand such complex interactions. Here, we develop a coastal lignin-degrading bacterial consortium (LD), through "top-down" enrichment. Sequencing and physiological analyses reveal that LD is dominated by the lignin degrader Pluralibacter gergoviae (>98%), with additional rare non-degraders. Interestingly, LD, cultured in lignin-MB medium, significantly enhances cell growth and lignin degradation as compared to P. gergoviae alone, implying a role of additional outliers. Using genome-scale metabolic models, metabolic profiling and culture experiments, modeling of inter-species interactions between P. gergoviae, Vibrio alginolyticus, Aeromonas hydrophila and Shewanella putrefaciens, unravels cross-feeding of amino acids, organic acids and alcohols between the degrader and non-degraders. Furthermore, the sub-population ratio is essential to enforce the synergy. Our study highlights the unrecognized role of outliers in lignin degradation., Competing Interests: Competing interests: The authors declare no competing interests., (© 2025. The Author(s).)

Background: The main application of cork is the production of stoppers for wine bottles. Cork sometimes contains 2,4,6-trichloroanisole, a compound that, at a concentration of ng/L, produces an unpleasant musty odor that destroys the organoleptic properties of wine and results in enormous economic losses for wineries and cork industries. Cork can exhibit a defect known as yellow stain, which is associated with high levels of 2,4,6-trichloroanisole. We describe how the microbiota of cork and yellow stain define a novel mechanism that explains the formation of chlorophenols and chloroanisoles (including 2,4,6-trichloroanisole) from p-hydroxybenzoate produced during lignin and/or suberin breakdown., Results: Electron microscopy revealed that cork affected by yellow stain exhibited significant structural degradation. This deterioration was attributed to the presence of higher microbial populations compared to those found in standard cork. Cork microbiota is rich in filamentous fungi able to metabolize lignin. A metataxonomic analysis confirmed that yellow stain contained significantly greater populations of fungal species belonging to Absidia, Geomyces, Mortierella, Mucor, Penicillium, Pseudogymnoascus, Talaromyces, and Umbelopsis. It also contained significantly greater amounts of bacteria belonging to Enterobacterales, Streptosporangiales, Tepidisphaerales, Pseudomonas, and several members of Burkholderiaceae, particularly species of the Burkholderia-Caballeronia-Paraburkholderia group. The extraction of aromatic compounds from cork samples allowed the identification of several compounds typically observed following lignin depolymerization. Notably, p-hydroxybenzoic acid and phenol were detected. Two strains of the genus Streptomyces isolated from yellow stain were able to biotransform p-hydroxybenzoate into phenol in resting cell assays. Phenol could be efficiently chlorinated in vitro to produce 2,4,6-trichlorophenol by a fungal chloroperoxidase, an enzymatic activity commonly found in filamentous fungi isolated from cork. Finally, as has been widely demonstrated before, 2,4,6-trichlorophenol can be efficiently O-methylated to 2,4,6-trichloroanisole by many of fungi that inhabit cork., Conclusions: Chlorophenols and chloroanisoles can be produced de novo in cork from p-hydroxybenzoate generated by the microbial biodegradation of lignin and/or suberin through the participation of different types of microorganisms present in cork. The natural origin of these compounds, which are of great interest for the chlorine cycle and represent a new source of environmental contamination that differs from that caused by human activity, is described. Video Abstract., Competing Interests: Declarations. Ethics approval and consent to participate: Not applicable. Consent for publication: Not applicable. Competing interests: The authors declare no competing interests., (© 2025. The Author(s).)

Main Conclusion: This study seeks to improve the biomass extractability of Sorghum bicolor by targeting a critical enzyme, 4CL, through metabolic engineering of the lignin biosynthetic pathway at the post-transcriptional level. Sorghum bicolor L., a significant forage crop, offers a potential source of carbohydrate components for biofuel production. The high lignin content in sorghum stems often impedes the extractability of desired carbohydrate components for industrial use. Thus, the present study aimed to develop an improved variety of S. bicolor with reduced lignin through RNA interference of the endogenous 4-coumarate:CoA ligase (4CL) gene involved in the lignin biosynthetic pathway. The S. bicolor gene was isolated, characterized, and used to construct the RNAi-inducing hpRNA gene-silencing construct. Two independent transgenic sorghum lines were produced by introducing an hpRNA-induced gene-silencing cassette of the Sb4CL through Agrobacterium-mediated transformation in the shoot tips of S. bicolor. This was confirmed by PCR amplification of the hygromycin-resistance gene and Southern hybridization. The Sb4CL gene transcript and its enzymatic activity were found to reduce to varying degrees, as shown by northern hybridization and enzyme activity in the independent transgenic samples. Endogenous Sb4CL downregulation in sorghum stem tissue correlates with reduced lignin content to a maximum range of 25%. The transfer of the transgene in the second generation was also analyzed. Decreased lignin content in the transgenic lines was compensated by increased total cell wall carbohydrates such as cellulose (36.56%) and soluble sugars (59.72%) compared to untransformed plants. The study suggests that suppressing the Sb4CL gene effectively develops better sorghum varieties with lower lignin content. This can be useful for industrial purposes, as the enhanced carbohydrate content and favorable alteration of lignin content can lead to economic benefits., Competing Interests: Declarations. Conflict of interest: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this manuscript., (© 2025. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Lignin is a crucial defense phytochemical against phytophagous insects. Cinnamoyl-CoA reductase (CCR) is a key enzyme in lignin biosynthesis. In this study, transgenic Populus davidiana × P. bolleana overexpressing the PdbCCR gene were generated via Agrobacterium-mediated transformation. Successful integration of PdbCCR into the poplar genome was confirmed by PCR amplification and quantitative reverse transcription PCR (qRT-PCR). The lignin content in the transgenic poplar leaves was significantly higher than that in the wild poplar, and after L. dispar larvae fed on the transgenic poplar, the CCR activity was clearly induced. The L. dispar larvae grew slowly after feeding on transgenic poplar and the laccase, cellulase and three detoxifying enzymes were induced compared with larvae after feeding on wild-type poplar. The bioassay further revealed that transgenic poplar plants overexpressing PdbCCR showed a high level of resistance to L. dispar larvae. These results confirmed that PdbCCR is a candidate gene for breeding insect resistant poplar., Competing Interests: Declarations. Conflicts of interest: The authors declare no competing interests., (© 2025. The Author(s), under exclusive licence to Springer Nature Switzerland AG.)

In arid and semi-arid climates, native plants have developed unique strategies to survive challenging conditions. These adaptations often rely on molecular pathways that shape plant architecture to enhance their resilience. Date palms (Phoenix dactylifera) and mangroves (Avicennia marina) endure extreme heat and high salinity, yet the metabolic pathways underlying this resilience remain underexplored. Here, we integrate tissue imaging with spatial metabolomics to uncover shared and distinct adaptive features in these species. We found that mangrove roots accumulate suberin and lignin in meristematic tissues, this is unlike other plant species, where only the differentiation zones contain these compounds. Our metabolomic analysis shows that date palm roots are enriched in metabolites involved in amino acid biosynthesis, whereas compounds involved in lignin and suberin production were more abundant in mangrove roots. Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) revealed tissue- and species-specific metabolite distributions in root tissues. We identified common osmoprotectants accumulating in the exodermis/epidermis of date palm and mangrove root meristems, along with a unique metabolite highly abundant in the inner cortex of date palm roots. These findings provide valuable insights into stress adaptation pathways and highlight key tissue types involved in root stress response., Competing Interests: Declarations. Competing interests: The authors declare no competing interests., (© 2025. The Author(s).)

Switchgrass ( Panicum virgatum L.) is considered a sustainable biofuel feedstock, given its fast-impact growth, low input requirements, and high biomass yields. Improvements in bioenergy conversion efficiency of switchgrass could be made by reducing its lignin content. Engineered switchgrass that expresses a bacterial 3-dehydroshikimate dehydratase (QsuB) has reduced lignin content and improved biomass saccharification due to the rerouting of the shikimate pathway towards the simple aromatic protocatechuate at the expense of lignin biosynthesis. However, the impacts of this QsuB trait on switchgrass microbiome structure and function remain unclear. To address this, wild-type and QsuB-engineered switchgrass were grown in switchgrass field soils, and samples were collected from inflorescences, leaves, roots, rhizospheres, and bulk soils for microbiome analysis. We investigated how QsuB expression influenced switchgrass-associated fungal and bacterial communities using high-throughput Illumina MiSeq amplicon sequencing of ITS and 16S rDNA. Compared to wild-type, QsuB-engineered switchgrass hosted different microbial communities in roots, rhizosphere, and leaves. Specifically, QsuB-engineered plants had a lower relative abundance of arbuscular mycorrhizal fungi (AMF). Additionally, QsuB-engineered plants had fewer Actinobacteriota in root and rhizosphere samples. These findings may indicate that changes in the plant metabolism impact both AMF and Actinobacteriota similarly or potential interactions between AMF and the bacterial community. This study enhances understanding of plant-microbiome interactions by providing baseline microbial data for developing beneficial bioengineering strategies and by assessing nontarget impacts of engineered plant traits on the plant microbiome., Importance: Bioenergy crops provide an important strategy for mitigating climate change. Reducing the lignin in bioenergy crops could improve fermentable sugar yields for more efficient conversion into bioenergy and bioproducts. In this study, we assessed how switchgrass engineered for low lignin impacted aboveground and belowground switchgrass microbiome. Our results show unexpected reductions in mycorrhizas and actinobacteria in belowground tissues, raising questions on the resilience and function of genetically engineered plants in agricultural systems., Competing Interests: The authors declare no conflict of interest.

Plants mount induced resistance and adult-plant resistance against different pathogens throughout the whole growth period. Rice production faces threats from multiple major diseases, including rice blast, sheath blight, and bacterial leaf blight. Here, we report that the miR172a-SNB-MYB30 module regulates both induced and adult-plant resistance to these three major diseases via lignification in rice. Mechanistically, pathogen infections induce the expression of miR172a, which downregulates the transcription factor SNB to release its suppression of MYB30, leading to an increase in lignin biosynthesis and disease resistance throughout the whole growth period. Moreover, expression levels of miR172a and MYB30 gradually increase and are consistently correlated with lignin contents and disease resistance during rice development, reaching a peak at full maturity, whereas SNB RNA levels are negatively correlated with lignin contents and disease resistance, indicating the involvement of the miR172a-SNB-MYB30 module in adult-plant resistance. The functional domain of SNB protein and its binding sites in the MYB30 promoter are highly conserved among more than 4000 rice accessions, while abnormal expression of miR172a, SNB, or MYB30 compromises yield traits, suggesting artificial selection of the miR172a-SNB-MYB30 module during rice domestication. Taken together, these results reveal a novel role for a conserved miRNA-regulated module that contributes significantly to induced and adult-plant resistance against multiple pathogens by increasing lignin accumulation, deepening our understanding of broad-spectrum resistance and adult-plant resistance., (Copyright © 2024 The Author. Published by Elsevier Inc. All rights reserved.)

Mangrove ecosystems are globally recognized for their blue carbon (C) sequestration capacity. Lignocellulosic detritus constitutes the primary C input to mangrove sediments, but the microbial processes involved in its bioprocessing remain unclear. Using lignocellulosic analysis and metagenomic sequencing across five 100-cm sediment cores, we found a high proportion of lignin (95.0-97.7%) within sediments' lignocellulosic detritus, with a small fraction of lignin-degrading genes (1.24-1.98%) of lignin-degrading genes within the carbohydrate-active enzyme coding genes. Depth stratification was observed in genes and microbial communities involved in lignin depolymerization and mineralization of lignin monomer derivatives. Further microbe-centered analyses of biomass production rates and adaptive metabolism revealed diminished microbial C use efficiency potential and augmented "enzyme latch" with increasing sediment depths. These findings enhance our understanding of sedimentary organic C cycling and storage in coastal blue C ecosystems., Competing Interests: Competing interests: The authors declare no competing interests., (© 2025. The Author(s).)

Using maize plants expressing an apoplast targeted Aspergillus niger ferulic acid esterase (FAEA), with FAEA driven by a Lolium multiflorum senescence enhanced promoter (LmSee1), we extended measurements of FAEA activity to late-stage senescing plants and measured the stability of FAEA activity following stover storage. The impact of FAEA expression on cell wall hydroxycinnamic acid levels and arabinoxylan (AX) cross-links, and on the levels of cell wall sugars, acetyl bromide lignin and sugar release following saccharification by a cocktail of cellulases and xylanases, was assessed during plant development to full leaf senescence. These were determined in both individual internodes and in combined leaves and combined internodes of FAEA expressing and control partner plants. FAEA expression was found to increase with plant growth up to the reproductive stage (R) of development in both stems and leaves but decreased as the leaves entered full senescence at R+ (18-20 d after R) stage. Moreover, FAEA activity was shown to be relatively stable over a six-month period following stover storage at 4°C. This FAEA expression resulted in significantly reduced levels of cell wall ferulates and diferulates in internodes. The internodes of late stage and senescing FAEA-expressing plants exhibited significantly improved saccharification with a cocktail of cellulase and xylanase enzymes at both the R and R+ stages of development., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2025 Buanafina et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Stone cells are one of the limiting factors affecting pear fruit quality and commodity value. The formation of stone cell is highly correlated with lignin deposition. However, the molecular mechanism of stone cell formation and regulation is still unclear. Here, we observed that exogenous application of GA significantly inhibited the formation of stone cells and also decreased the content of lignin in 'Nanguo' (Pyrus ussuriensis) pear fruits. The key gene PuPRX73 involved in the lignin synthesis pathway was further identified using RT-PCR, and GA-treatment significantly inhibited the expression of PuPRX73. Overexpression or silencing of PuPRX73 in pear fruits significantly increases or decreases the content of stone cells and lignin. We identified the transcription factors PuMYB91 and PuERF023 using mRNA-seq and their expression was significantly decreased after GA-treatment. Transient overexpression of PuMYB91 and PuERF023 promotes lignin and stone cells content in pear fruits, while silencing of PuMYB91 and PuERF023 led to the opposite results and inhibited the expression of PuPRX73. Yeast one-hybrid (Y1H) and GUS activity analysis revealed that PuMYB91 and PuERF023 directly bind and activate the PuPRX73 promoter, and co-transfection of PuMYB91 and PuERF023 in Nicotiana benthamiana leaves further promoted the promoter activity of PuPRX73. Furthermore, we found that PuMYB91 interacted with PuERF023 in vitro by using Yeast two-hybrid assays (Y2H). In conclusion, our results revealed that exogenous GA-treatment inhibits stone cell production by suppressing the expression of PuMYB91 and PuERF023 in pear fruits., (© 2025 Scandinavian Plant Physiology Society.)

Rac/Rop proteins, a kind of unique small GTPases in plants, play crucial roles in plant growth and development and in response to abiotic and biotic stresses. However, it is poorly understood whether cotton Rac/Rop protein genes are involved in mediating cotton resistance to Verticillium dahliae. Here, we focused on the function and mechanism of cotton Rac/Rop gene GhRac9 in the defense response to Verticillium dahliae infection. The expression level of GhRac9 peaked at 24 h after V. dahliae infection and remained consistently elevated from 24 to 48 h upon SA treatment. Furthermore, silencing GhRac9 using VIGS (Virus-induced gene silence) method attenuated cotton defense response to V. dahliae by reducing ROS (Reactive Oxygen Species) burst, peroxidase activity and lignin content in cotton plants. On the contrary, heterologous overexpression of GhRac9 enhanced Arabidopsis resistance to V. dahliae and significantly increased ROS production in Arabidopsis plants. Furthemore, transient overexpressing of GhRac9 significantly enhanced ROS burst and POD activity in cotton plants. In addition, GhRac9 positively regulated the expression levels of the genes related to SA signaling pathway in cotton plants. In conclusion, GhRac9 functioned as a positive regulator in the cotton defense response to V. dahliae, which provided important insights for breeding new cotton varieties resistant to V. dahliae., (© 2025 Scandinavian Plant Physiology Society.)

Poplar plantations are often established on nitrogen-poor land, and poplar growth and wood formation are constrained by low nitrogen (LN) availability. However, the molecular mechanisms by which specific genes regulate wood formation in acclimation to LN availability remain unclear. Here, we report a previously unrecognized module, basic region/leucine zipper 55 (PtobZIP55)-PtoMYB170, which regulates the wood formation of Populus tomentosa in acclimation to LN availability. PtobZIP55 was highly expressed in poplar wood and induced by LN. Altered wood anatomical properties and increased lignification were detected in PtobZIP55-overexpressing poplars, whereas the opposite results were detected in PtobZIP55-knockout poplars. Molecular and transgenic analyses revealed that PtobZIP55 directly binds to the promoter sequence of PtoMYB170 to activate its transcription. The phenotypes of PtoMYB170 transgenic poplars were similar to those of PtobZIP55 transgenic poplars under LN conditions. Further molecular analyses revealed that PtoMYB170 directly bound the promoter sequences of lignin biosynthetic genes to activate their transcription to increase lignin concentrations in LN-treated poplar wood. These results suggest that PtobZIP55 activates PtoMYB170 transcription, which in turn positively regulates lignin biosynthetic genes, increasing lignin deposition in the wood of P. tomentosa in the context of acclimation to LN availability., (© 2024 Institute of Botany, Chinese Academy of Sciences.)

This study investigates the effects of composite electric field pretreatment (CEP) on hydrogen production from corn stover enzymatic hydrolysates in dark fermentation. The findings reveal that under optimal conditions, the CEP group achieved a cumulative hydrogen yield of 77.3  ±  2.6 mL/g TS, marking a 55.3 % increase compared to the control group without the electric field. CEP significantly enhances the fermentation capacity of enzymatic hydrolysates during the acid-stage of dark fermentation by disrupting the lignin structure and optimizing cellulase hydrolysis efficiency. Additionally, pH self-regulation is facilitated through the interaction between volatile fatty acids (VFAs) and ammonia nitrogen. Microbial community analysis revealed that CEP shifts the metabolic balance between Clostridium&#95;sensu&#95;stricto&#95;1 and Lactococcus, leading to increased hydrogen yield and concentration during acid fermentation. Notably, Terrisporobacter exhibited a superior acid-producing capability compared to Bacteroides during the dark fermentation of enzymatic hydrolysates. This study provides a new perspective for the practical application of corn stover., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier Ltd.)

Because of the association with other complex polysaccharides, extracting and utilizing cellulose from lignocellulosic materials requires the combined action of a broad range of carbohydrate-active enzymes, including multiple glycoside hydrolases (GHs) and lytic polysaccharide monooxygenases (LPMOs). The interplay between these enzymes and the way in which Nature orchestrates their co-existence and combined action are topics of great scientific and industrial interest. To gain more insight into these issues, we have studied the lignocellulose-degrading abilities of an enzyme from Caldibacillus cellulovorans (CcLPMO10-Man5), comprising an LPMO domain, a GH5 mannanase domain and two family 3 carbohydrate-binding modules (CBM3). Using a natural softwood substrate, we show that this enzyme promotes cellulase activity, i.e., saccharification of cellulose, both by removing mannan covering the cellulose and by oxidatively breaking up the cellulose structure. Synergy with CcLPMO10-Man5 was most pronounced for two tested cellobiohydrolases, whereas effects were smaller for a tested endoglucanase, which is in line with the notion that cellobiohydrolases and LPMOs attack the same crystalline regions of the cellulose, whereas endoglucanases attack semi-crystalline and amorphous regions. Importantly, the LPMO domain of CcLPMO10-Man5 is incapable of accessing the softwood cellulose in absence of the mannanase domain. Considering that LPMOs not bound to a substrate are sensitive to autocatalytic inactivation, this intramolecular synergy provides a perfect rationale for the evolution of modular enzymes such as CcLPMO10-Man5. The intramolecular coupling of the LPMO with a mannanase and two CBMs ensures that the LPMO is directed to areas where mannans are removed and cellulose thus becomes available., (© 2024 The Author(s). The FEBS Journal published by John Wiley & Sons Ltd on behalf of Federation of European Biochemical Societies.)

Biochar and SiO 2 NPs are effective soil conditioners, but the impacts and mechanisms of combined application in oilseed rape are not yet clear. Therefore, an experiment was designed to investigate oilseed rape growth, physiological indexes, and transcriptome sequencing under four treatments: control (CK), Platanus orientalis L. leaf biochar (B), SiO 2 NPs (S), and BS. Our results showed that B, S and BS treatments all promoted the root growth, root activity and biomass of oilseed rape, especially the root length and fresh weight in BS, which were increased by 77.48% and 279.07%, respectively. Moreover, the three-dimensional fluorescence spectra of B and BS were similar, and the tyrosine-like substance proportion in B, S and BS increased from 7.8 to 9.4%, 10.2% and 19.5%, respectively. In transcriptome analysis, there were 10,280 differentially expressed genes (DEGs) shared in B and BS, 3431 DEGs shared in S and BS, and 2815 DEGs shared in B, S and BS. We also found that B, S and BS all regulated oilseed rape growth by inducing the lignin biosynthesis and the relevant genes encoding BBE-like, BGL, UDP in the phenylpropanoid biosynthesis pathway. The results provide gene regulation associated with the phenylpropanoid biosynthesis applying the biochar and SiO 2 NPs, which can be used to increase biomass., Competing Interests: Declarations. Competing interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2024. The Author(s) under exclusive licence to The Botanical Society of Japan.)

R2R3-MYB transcription factors function as the master regulators of the phenylpropanoid pathway in which both lignin and anthocyanin are produced. In poplar, R2R3-MYB transcription factor PdMYB118 positively regulates anthocyanin production to change leaf color. However, the molecular mechanism by which it controls different branches of the phenylpropanoid pathway still remains poorly understood. Here, we reported that in addition to anthocyanin synthesis, lignin deposition and xylem differentiation were regulated by PdMYB118 through inhibiting PagKNAT2/6b gene expression. The transgenic poplar plants overexpressing PdMYB118 accumulated more xylem, lignin and anthocyanin. Transcriptome and reverse transcription quantitative PCR analyses revealed that the expression of PagKNAT2/6b gene which inhibited lignin deposition and xylem differentiation was significantly down-regulated in transgenic poplar plants. Subsequent dual-luciferase reporter and yeast-one-hybrid assays demonstrated that PdMYB118 directly inhibited the transcription of PagKNAT2/6b by binding to the AC elements in its promoter region. Further experiments with transgenic poplar plants overexpressing PagKNAT2/6b demonstrated that overexpression of PagKNAT2/6b in the PdMYB118 overexpression background rescued lignin accumulation and xylem width to the same level of wild type plants. The findings in this work suggest that PdMYB118 is involved in the lignin deposition and xylem differentiation via modulating the expression of PagKNAT2/6b, and the PdMYB118- PagKNAT2/6b model can be used for the genetic breeding of new woody tree with high lignin production., Competing Interests: Declaration of Competing Interest The authors declare no conflict of interest., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Plants have evolved sophisticated defense mechanisms against insect herbivores, including cell wall fortification through lignin biosynthesis. Insect attack primes systemic acquired resistance in plants, preparing them to respond more swiftly and vigorously to subsequent insect assaults. Here, we found that Beauveria bassiana-exposed maize plants can emit phytol upon infestation by Spodoptera frugiperda, inducing plant-to-plant (PTP) communication of alert signals for neighboring plants, and revealed the expansin protein EXP-A20 as a pivotal node mediating maize defense responses in neighboring plants against the destructive pest Ostrinia furnacalis via stimulation of ethylene (ET) synthesis and lignin production. Through virus-induced gene silencing, we showed that EXP-A20 is essential for maize resistance, while downregulating ET and lignin pathways. Critically, protein-protein interactions determined via luciferase complementation and yeast two-hybrid assays demonstrated that EXP-A20 binds to and likely activates the ET-forming enzyme gene ACO31 to initiate defense signaling cascades, representing a novel signaling modality for expansins. Treatment with the plant volatile phytol has known insecticidal/priming activity, but we found that its effectiveness requires EXP-A20. This finding highlights the importance of EXP-A20 upstream of hormone-cell wall crosstalk in defense activation by volatiles. Overall, our multifaceted dissection of EXP-A20 revealed key molecular intersections underlying inducible maize immunity against herbivores. Furthermore, we provide functional evidence that extensive cell growth processes directly stimulate defense programs in plants. Our work opens new avenues for enhancing durable, broad-spectrum pest resistance in maize through the use of volatile organic compounds and PTP interactions., (© 2024 Society for Experimental Biology and John Wiley & Sons Ltd.)