Search Results (109)

Lignin is a complex aromatic polymer that constitutes a major fraction of plant biomass and represents a valuable renewable carbon resource. Naturally decaying wood serves as an environmental reservoir of microorganisms capable of degrading lignin. In this study, we isolated and characterized sixteen bacterial strains from decaying Tilia cordata wood using an enrichment culture technique with lignin as the sole carbon source. Taxonomic identification via 16S rRNA gene sequencing revealed microbial diversity spanning the genera Bacillus, Pseudomonas, Stenotrophomonas, and several members of the Enterobacteriaceae family, including Raoultella terrigena isolates. Metagenomic sequencing of the wood substrate revealed an exceptionally rich and balanced bacterial community (Shannon index H′ = 5.07), dominated by Streptomyces, Bradyrhizobium, Bacillus, and Pseudomonas, likely reflecting a specialized consortium adapted to lignin rich late-stage decay. Functional phenotyping demonstrated that all isolates possess ligninolytic potential, evidenced by peroxidase/laccase-type activity through methylene blue decolorization. Dynamic Light Scattering (DLS) and HPLC analyses showed that some isolates, such as Raoultella terrigena MGMM806, effectively depolymerized lignosulfonate into low molecular weight fragments (1.23 nm), while others accumulated intermediate metabolites or completely mineralized the substrate. Growth profiling on monolignol substrates revealed a broad spectrum of catabolic specialization in lignin monomer degradation. The results demonstrate a complex system of metabolic partitioning within a natural bacterial consortium. This collection represents a foundational genetic resource for developing engineered biocatalysts and synthetic microbial communities aimed at the efficient conversion of lignin into valuable aromatic compounds. Full article

Forest type strongly influences soil microbial community composition and associated carbon cycling, yet its influence on microbial functional traits remains poorly understood. In this study, metagenomics sequencing was used to investigate soil microbial communities and carbon metabolism genes across three forest types: deciduous broadleaf (DBF), mixed coniferous–broadleaf (CBMF), and coniferous forest (CF) at two soil depths (0–20 cm and 20–40 cm) on Lushan Mountain in subtropical China. The results showed that CF exhibited higher bacterial diversity and a distinct microbial composition, with an increase in Actinomycetota and Bacteroidota and a decrease in Acidobacteriota and Pseudomonadota. The Calvin cycle was the dominant carbon fixation pathway in all forests, while the relative abundance of secondary pathways (i.e., the 3-hydroxypropionate bi-cycle and reductive citrate cycle) varied significantly with forest type. Key carbon fixation genes (sucD, pckA) were more abundant in CF and CBMF, with higher levels of rpiA/B and ackA in DBF. Functional profiling further indicated that CF soils, especially in the surface layer, were enriched in glycoside hydrolases (GHs) and carbohydrate esterases (CEs), while CBMF showed a greater potential for starch and lignin degradation. Multivariate statistical analyses identified soil available phosphorus (AP) and pH as primary factors shaping microbial community variation, with AP emerging as being the dominant regulator of carbon-related functional gene abundance. Overall, the prevalence of these distinct genetic potentials across forest types underscores how vegetation composition may shape microbial functional traits, thereby influencing the stability and dynamics of the soil carbon pool in forest ecosystem. Full article

Carbon (C) is crucial for nutrient cycling and the assembly of microbial populations in the soil. However, it is still unclear how the C-source utilization characteristics of microbes in distinct types of soils respond to changes in soil phosphorus (P) activity. This study investigated how the addition of different C sources with different decomposition rates (glucose, hemicellulose, and lignin) affects P transformation in two distinct agricultural soils (i.e., Mollisols and Fluvo-aquic soil). Results revealed that the short-term glucose addition to soil induced rapid acidification and microbial biomass accumulation, thereby significantly increasing labile P (NaHCO₃-P_i, NaOH-P_o) content in Fluvo-aquic soil. Lignin amendment promoted gradual HCl-P release in Mollisols, reflecting differential microbial utilization strategies. Glucose stimulated phosphatase activity (2.5–3.0× control) and phoD gene abundance (4.8×) in Fluvo-aquic soil in the early stage, favoring the growth of Pseudomonas and Burkholderia, whereas lignin sustained the mineralization of fungal-associated P in Mollisols (1.8–2.3× phosphatase activity) by enhancing the abundance of Streptomyces and Bradyrhizobium. Soil type dictated P mobilization efficiency. The Fluvo-aquic soil exhibited rapid but transient P release via bacterial dominance, while Mollisols retained slower yet persistent P availability through specialized microbial consortia. Notably, glucose enhanced organic P mineralization by stimulating C decomposition by microbes, particularly in C-rich Mollisols. Lignin increased P availability in Mollisols via Fe/Al-P desorption. However, in Fluvo-aquic soil, lignin reduced the availability of P through microbial immobilization. These findings highlight that C source degradability and soil properties interactively govern microbial-mediated P cycling in soil. Therefore, organic amendments in contrasting agroecosystems need to be optimized. Full article

Lignin is one of the primary biomass resources in nature; however, its highly stable structure makes it difficult to degrade and utilise. As efficient decomposers of lignocellulosic biomass, termites rely on their gut microbiota for digestion. Consequently, termite guts harbour abundant and specialized lignin-degrading microorganisms. In this study, we isolated a bacterium from the termite gut and identified it as Bacillus cereus BC-8. The laccase activity of B. cereus BC-8 reached the maximum of 87.8 U/L at 72 h, and the lignin degradation rate reached 33.66% within 7 days. Furthermore, we analyzed the structural changes in lignin after treatment with this bacterial strain. Field emission scanning electron microscopy observations revealed that the surface structural integrity of lignin was significantly disrupted after treatment. Fourier transform infrared spectroscopy analysis indicated that B. cereus BC-8 affected the side chains and aromatic skeleton structures of lignin. Thermogravimetric analysis further revealed that B. cereus BC-8 disrupted the primary inter-unit β-O-4 ether bonds of lignin. Whole-genome sequencing of B. cereus BC-8 revealed a genome length of 5,374,773 bp and a GC content of 35.34%. Functional gene annotation revealed that the B. cereus BC-8 genome contains genes encoding various lignin-degrading enzymes (laccase, cytochrome P450, and vanillin oxidase) and their auxiliary factors, along with the phenylalanine and benzoic acid metabolic pathways, which are associated with lignin degradation. In conclusion, B. cereus BC-8 can break down the side chains, aromatic skeletons, and β-O-4 ether bonds of lignin molecules, demonstrating excellent lignin degradation ability. At the molecular level, this study elucidates the key genes and metabolic pathways related to lignin degradation in the genome of B. cereus BC-8. Full article

The white-rot fungus Irpex lacteus is recognized for its strong ligninolytic and polysaccharide-degrading capacity, but the key advantages in degrading lignocellulose and the regulation of its enzyme systems remain poorly understood. In this study, we identified a rich repertoire of carbohydrate-active enzymes in the genome of I. lacteus QJ. Relative to other white-rot fungi, an expanded glycoside hydrolase gene family in I. lacteus QJ suggesting strong potential for lignocellulose degradation. When I. lacteus QJ was cultivated on glucose or wheat straw for 4 and 8 days, wheat straw strongly induced carbohydrate-active enzyme genes on day 4, while ligninolytic enzyme genes exhibited delayed upregulation on day 8. The cellobiose dehydrogenase plays an important role in the degradation processes. Its expression pattern is consistent with that of cellulase, and it can support peroxidase activity by providing H₂O₂. These findings reveal temporal coordination between polysaccharide- and lignin-degrading enzymes, providing new theoretical ideas for the application of I. lacteus during the degradation process. Our results not only improve the mechanistic understanding of fungal lignocellulose deconstruction but also inform strategies to enhance biological pretreatment of agricultural residues for biorefinery applications. Full article

Plant cell wall polysaccharides (PCWPs) serve as an abundant but recalcitrant carbon source for many microbes living in the gut of humans and animals. An adhesion to PCWPs is common in gut bacteria and can even be observed in the lactobacilli, which are supposed to promote the growth competence of these non-PCWP degraders because of the facilitated acquisition of newly released oligosaccharides. Nevertheless, the binding of molecules of lactobacilli to PCWPs and the underlying mechanisms remain largely unknown. By analyzing the transcriptome of Lactobacillus brevis grown in xylan supplemented with a xylanase, a gene was identified to encode a putative S-layer PCWP-binding protein (Lb1145). Lb1145 was predicted to have four domains, among which domains 1 and 2 were responsible for binding PCWPs. The binding was nonspecific, since structurally distinct PCWPs, e.g., cellulose, xylan, mannan, and chitin, and even lignin, were all bound by Lb1145. Both of the two N-terminal domains have a high pI, and we demonstrated that a non-enzymatic glycosylation-like process plays an important role in binding. Compared with another L. brevis surface protein, i.e., the WxL protein Lb630, Lb1145 displayed a binding preference for the phloem sieve tube in the wheat stem section. Moreover, Lb1145 could bind ten strains within the Lactobacillus, Enterococcus, Pediococcus, and Bacillus genera among the seventeen selected gut bacterial species. An analysis of the reported S-layer proteins from the Gram-positive bacteria (lactobacilli and bifidobacteria) and outer membrane proteins from the Gram-negative (Bacteroides fragilis and Prevotella intermedia) indicated that bacterial cell surface proteins with high pI values are not rare. The high pI-based and non-enzymatic glycosylation-like process-mediated binding represents a new paradigm and may be popular in gut bacterial surface proteins binding to PCWPs, with important physiological implications in growth competition in the gut microbiota. Full article

Fruit peel cracking significantly reduces the commercial value of melons (Cucumis melo). To elucidate the underlying mechanisms of peel cracking, we conducted integrated investigations including morphological, physiological, metabolomic and transcriptomic analyses of cracked and non-cracked peels from the crack-resistant ‘Xizhoumi 17’ and crack-susceptible ‘Xizhoumi 25’ cultivars. The parenchyma cells in ‘Xizhoumi 17’ exhibited a compact and well-organized arrangement, whereas those in ‘Xizhoumi 25’ displayed a loosely packed and disordered structure. Notably, cracked peels exhibited significantly higher levels of water-soluble pectin and lignin, along with increased cellulase, polygalacturonase, catalase, superoxide dismutase, and peroxidase activities. In contrast, protopectin, cellulose, and hemicellulose contents, as well as polyphenol oxidase activity, were markedly reduced compared to non-cracked peels. Metabolomic analysis revealed that the phenylpropanoid biosynthesis pathway is positively correlated with the progression of peel cracking. RNA-seq analysis revealed 119 and 82 differentially expressed genes associated with cell wall metabolism and lignin biosynthesis pathways, respectively. Collectively, these findings underscore the involvement of genes related to cell wall synthesis and degradation, as well as lignin synthesis, in modulating peel cracking through alterations in cell wall composition and structural stability, thereby offering practical implications for reducing melon peel cracking incidence via targeted molecular breeding of key genes regulating cell wall composition and the phenylpropanoid pathway. Full article

The sustainable utilization of rice straw is challenged by its recalcitrant lignocellulosic structure, especially under low-to-moderate field temperatures. In this study, a novel microbial consortium (SXJG15) mainly containing Sphingobacterium, Azospirillum, and Pseudomonas was enriched from overwintering rice stubble in Zhejiang, China, and evaluated for its rice straw degradation efficiency at 25 °C. Over an 18-day cultivation period, SXJG15 achieved a 52.5% degradation of total rice straw, including 60.2% cellulose, 76.3% hemicellulose, and 40.7% lignin. High extracellular enzymatic activities, including cellulases (up to 80.3 U/mL) and xylanases (up to 324.8 U/mL), were observed during the biodegradation process. 16S rRNA gene sequencing and metagenomics analyses revealed a succession of dominant taxa, including Sphingobacterium, Azospirillum, and Cellulomonas. Further, CAZy annotation indicated that the SXJG15 enzyme system was rich in glycoside hydrolases (42.7%) and glycosyltransferases (34.2%), demonstrating its high potential for lignocellulose degradation. This study uniquely demonstrates the mesophilic (moderate temperature 25 °C) efficiency of SXJG15 in lignocellulose breakdown, provides new insights into the microbial mechanisms of straw decomposition, and lays a foundation for bioenergy and soil fertility applications for developing a sustainable agriculture system. Full article

The pathogenic fungus Mycocentrospora acerina, responsible for Panax notoginseng round spot disease, poses a serious threat to the development of the P. notoginseng industry. To investigate its genetic information and potential pathogenic mechanisms, this study employed nanopore third-generation sequencing technology to conduct de novo genome sequencing and analysis of M. acerina, followed by an assessment of its plant cell wall-degrading enzyme activities. The sequencing results revealed that the M. acerina genome has a total length of 37.03 Mb, a GC content of 47.68%, an N50 value of 1.66 Mb, and a repeat sequence proportion of 9.37%. A total of 9989 protein-coding genes were predicted. Genome annotation identified 499 carbohydrate-active enzyme (CAZyme) family genes—more than those found in Botrytis cinerea (469), Phanerochaete chrysosporium (381), and Erysiphe necator (136). Moreover, M. acerina harbors a relatively large number of genes encoding plant cell wall-degrading enzymes. Experimental measurements of cell wall-degrading enzyme activities were consistent with the genomic predictions, demonstrating that M. acerina exhibits strong abilities to degrade cellulose, pectin, and lignin. This study provides new insights into the pathogenic mechanisms of M. acerina and establishes a theoretical foundation for developing potential control strategies for P. notoginseng round spot disease. Full article

Gut microbiota enable wood-feeding insects to digest recalcitrant diets. Two DNA-based analyses were performed. Amplicon sequencing of gut microbiota samples from Cryptocercus punctulatus showed inter-individual heterogeneity with visually distinct ordination patterns; however, no statistically significant differences were detected. Shotgun metagenomics was used to compare the taxonomic and functional profiles of C. punctulatus gut microbiota with those of other xylophagous Dictyoptera. Despite taxonomic differences, C. punctulatus microbiota revealed functional convergence with termites (Mastotermes darwiniensis and Nasutitermes sp.). Carbohydrate metabolism was performed by different bacterial phyla across all insects. All insect species possessed metabolic potential for cellulose, hemicellulose, pectin, and starch digestion, but lignin degradation capabilities were not detected. Termites showed higher abundance of chitin and xylan degradation pathways and nitrogen fixation genes, though nitrogen fixation was also present in Cryptocercus cockroaches. Genes for oxidative stress tolerance were present across all species but were most abundant in cockroaches, particularly, Cryptocercus. All insects harbored antibiotic resistance genes, with highest levels found in cockroaches. These findings indicate that metabolic requirements for wood digestion shape gut microbial community assembly across xylophagous insects, with distinct microbial taxa contributing to cellulose and hemicellulose breakdown. Moreover, the widespread presence of antibiotic resistance genes raises concerns about the potential transmission of antibiotic resistance within insect-associated microbiomes. Full article

To achieve synchronous regulation of growth and lignocellulose degradation in Pleurotus ostreatus (PO-01) during fungal residue biorefining, we systematically evaluated O₂ gradients (5%, 20%, 40%) and N₂/CO₂ regarding mycelial development, lignocellulose degradation, and bioethanol potential. A total of 20% O₂ emerged as the critical threshold, balancing mycelial growth (which was faster than that under 5% O₂) and lignocellulose degradation (with lignin degradation rate reaching 15.29%). Metabolomics identified 53 aromatic derivatives related to lignin degradation, with their abundance correlating with actual lignin degradation rates. Meanwhile, it clarified the synergistic degradation mechanism and bioinformatics characteristics of key lignin-degrading enzymes and confirmed the AA9 gene associated with cellulose degradation at the molecular level. Measurements of polysaccharide content and ethanol yield revealed that the 20% O₂ environment led to a remarkably high ethanol yield of 101.90 L·ha⁻¹. In contrast, 5% and 40% O₂ concentrations not only reduced the polysaccharide content but also inhibited bioethanol production, highlighting O₂ as a crucial factor in regulating the synergy between growth and degradation. After comprehensive analysis, this study designated 20% O₂ as the optimal parameter for the integrated biorefining of fungal residues, offering a gas-phase solution to overcome industrial bottlenecks in biofuel production. Full article

Stalk lodging constitutes a primary constraint on achieving consistently high yields in maize. Genetic improvement of lodging resistance requires the identification of stable quantitative trait loci (QTL) to facilitate the application of genomics-assisted breeding for improving selection efficiency in breeding programs. In this study, we performed a meta-analysis to identify consensus loci and functionally characterized candidate genes associated with stalk lodging-related traits. Through meta-analysis integrating 889 reported lodging-related QTLs using the IBM2 2008 Neighbors high-density genetic map, we identified 67 meta-QTLs (MQTLs), of which 32 were determined as core MQTLs. Among them, 67% were validated by co-localized marker–trait associations from genome-wide association studies (GWAS). Comparative genomics further revealed 40 evolutionarily conserved orthologs via protein alignment with rice lodging genes, while screening of core MQTL regions detected 802 candidate genes with KEGG enrichment implicating galactose degradation II in cell wall reinforcement, supported by transcriptomic evidence of their roles in lignin biosynthesis pathways modulating mechanical strength. In conclusion, the MQTL identified and validated in our study have significant scope in marker-assisted selection (MAS) breeding and map-based cloning programs for improving maize stalk lodging. Full article

Aromatic compounds are vital in both natural and synthetic chemistry, and they are traditionally sourced from non-renewable petrochemicals. However, plant biomass, particularly lignin, offers a renewable alternative source of aromatic compounds. Lignin, a complex polymer found in plant cell walls, is the largest renewable source of aromatic compounds, though its degradation remains challenging. Lignin can be chemically degraded through oxidation, acid hydrolysis or solvolysis. As an alternative, microorganisms, including fungi, could offer a sustainable alternative for breaking down lignin. The aromatic compounds released from lignin, by either microbial, chemical or enzymatic degradation, can be used by microorganisms to produce valuable compounds. Fungi possess unique enzymes capable of converting aromatic compounds derived from lignin or other sources into chemical building blocks that can be used in several industries. However, their aromatic metabolic pathways are poorly studied compared to bacterial systems. In the past, only a handful of genes and enzymes involved in the aromatic metabolic pathways had been identified. Recent advances in genomics, proteomics, and metabolic engineering are helping to reveal these metabolic pathways and identify the involved genes. This review highlights recent progress in understanding fungal aromatic metabolism, focusing on how Aspergillus niger converts plant-derived aromatic compounds into potentially useful products and the versatility of aromatic metabolism within the Aspergillus genus. Addressing the current knowledge gaps in terms of fungal pathways could unlock their potential for use in sustainable technologies, promoting eco-friendly production of chemical building blocks from renewable resources or bioremediation. Full article

Biodegradation is a green and efficient method for lignin depolymerization and conversion. In order to screen potential bacterial strains for efficient lignin degradation, composts of cow dung and wheat straw were prepared, and the dynamic changes in the predicted bacterial community structure and function in different periods of the composts were investigated. Then, bacteria with an efficient lignin degradation ability were finally screened out from the compost samples. Based on the monitoring results of the physicochemical indexes of the composting process, it was found that the temperature and pH of the compost firstly increased and then decreased with the extension of time, and the water content and C/N gradually decreased. High-throughput sequencing of compost samples from the initial (DA), high-temperature (DB), and cooling (DC) periods revealed that the number of OTUs increased sharply then stabilized around 2000, and the alpha diversity of the bacterial community decreased firstly and then increased. The predominant phyla identified included Proteobacteria, Firmicutes, Chloroflexi, and Bacteroidetes, determined by the relative abundance of beta-diversity-associated species. Functional gene analysis conducted using Tax4Fun revealed that the genes were primarily categorized into Metabolism, Genetic Information Processing, Environmental Information Processing, and Cellular Processes. Based on the decolorization of aniline blue and the degradation efficiency of alkali lignin, eight bacterial strains were isolated from compost samples at the three stages. Cupriavidus sp. F1 showed the highest degradation of alkali lignin with 66.01%. Cupriavidus sp. D8 showed the highest lignin degradation potential with all three enzyme activities significantly higher than the other strains. The results provide a strategy for the lignin degradation and utilization of biomass resources. Full article

Swine wastewater (SW) has a high chemical oxygen demand (COD) content and is difficult to degrade; an effective strategy to address this issue is through biodegradation, which poses negligible secondary pollution risks and ensures cost-efficiency. The objectives of this study were to isolate an effective COD-degrading strain of SW, characterize (at the molecular level) its transformation of SW, and apply it to practical production. A strain of Corynebacterium xerosis H1 was isolated and had a 27.93% ± 0.68% (mean ± SD) degradation rate of COD in SW. This strain precipitated growth in liquids, which has the advantage of not needing to be immobilized, unlike other wastewater-degrading bacteria. Based on analysis by Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS), this bacterium removed nitrogen-containing compounds in SW, with proteins and lipids decreasing from 41 to 10% and lignins increasing from 51 to 82%. Furthermore, the enhancement of the sequencing batch reactor (SBR) with strain H1 improved COD removal in effluent, with reductions in the fluorescence intensity of aromatic protein I, aromatic protein II, humic-like acids, and fulvic acid regions. In addition, based on 16S rRNA gene sequencing analysis, SBR_H1 successfully colonized some H1 bacteria and had a higher abundance of functional microbiota than SBR_C. This study confirms that Corynebacterium xerosis H1, as a carrier-free efficient strain, can be directly applied to swine wastewater treatment, reducing carrier costs and the risk of secondary pollution. The discovery of this strain enriches the microbial resource pool for SW COD degradation and provides a new scheme with both economic and environmental friendliness for large-scale treatment. Full article