Search Results (65)

Cottonseed hull is an abundant and low-cost cotton processing byproduct, but its feed application is severely limited by free gossypol. This study screened a gossypol-degrading fungal strain from naturally fermented cottonseed hulls and soy sauce koji, and evaluated its detoxification and feed improvement effects via solid-state fermentation. Strain TM-2 was identified as Aspergillus oryzae. It degraded over 60% of gossypol in liquid fermentation and 69.54% in cottonseed hull solid-state fermentation. Genome annotation revealed 409 CAZyme genes and key pathways for naphthalene and aromatic compound degradation. After fermentation, crude protein and acid-soluble protein were significantly increased, while cellulose, hemicellulose, lignin, neutral detergent fiber, and acid detergent fiber were notably reduced. Antioxidant activity was also greatly enhanced. Secretomic analysis identified 92 extracellular proteins, including hemicellulases, cellulases, proteases, and peptidases that jointly promoted detoxification and quality improvement. A. oryzae TM-2 efficiently degrades gossypol and improves feed quality, showing high value in fermented feed development and agricultural byproduct utilization. Full article

To identify efficient cellulose-degrading microbes suitable for the animal intestinal environment and to address the low utilization of crude fiber in feed, eight cellulolytic strains were isolated from the ileum of Yangzhou geese. Among them, strain A2 showed the highest cellulolytic activity (D/d = 1.48) via the CMC (carboxymethyl cellulose) agar transparent zone method. Based on whole-genome-based identification, strain A2 was identified as Bacillus subtilis. Whole-genome sequencing revealed a circular chromosome of 4.02 Mb with a GC content of 43.72%, containing 4083 protein-coding sequences, of which 7.40% were involved in carbohydrate transport and metabolism. CAZyme annotation identified 167 carbohydrate-active enzyme genes, including 64 glycoside hydrolase genes, along with 60 hemicellulase and 3 lignin-degrading enzyme genes, forming a complete lignocellulose-degrading system. The cellulase from A2 exhibited optimal activity at 55 °C and pH 7.0, with good stability at 50–65 °C and pH 5–7, and was significantly inhibited by Cu²⁺, Mn²⁺, and Zn²⁺. Notably, its degradation efficiency toward microcrystalline cellulose reached 197% of that toward CMC. In conclusion, B. subtilis A2, with its excellent enzymatic properties and robust genetic foundation, is a promising candidate for developing feed enzymes and enhancing lignocellulose utilization. Full article

Biological control fungi play an important role in the management of plant-parasitic nematodes; however, the molecular basis underlying their diverse biocontrol strategies remains incompletely understood. In this study, a comparative genomic analysis was performed on four representative biocontrol fungi: Purpureocillium lilacinum PLFJ-1, Trichoderma harzianum CBS 226.95, Pochonia chlamydosporia 170, and Aspergillus niger CBS 513.88. Genome comparison revealed substantial variation: genome size ranged from 34.0 Mb (A. niger) to 44.2 Mb (P. chlamydosporia), GC content from 47.5% (T. harzianum) to 58.5% (P. lilacinum), and predicted gene models also differed markedly among the four fungi. Phylogenetic analysis based on the Internal Transcribed Spacer divided these fungi into two major clades corresponding to distinct evolutionary lineages. Orthogroup analysis identified both a conserved core gene set and species-specific gene repertoires. Functional annotation using KEGG, KOG, and GO indicated a high degree of conservation across core metabolic processes, catalytic activities, and cellular components, with distinct differences within specific functional categories. Further comparative analyses demonstrated pronounced variation in the composition and abundance of carbohydrate-active enzymes (CAZymes) and peptidases, as well as a notable expansion and enrichment of S8 subtilisin-like serine peptidases in the nematode-parasitic fungi P. lilacinum and P. chlamydosporia. Secondary metabolite analysis revealed lineage-specific biosynthetic gene clusters (BGCs). Notably, P. lilacinum and P. chlamydosporia carried PKS/NRPS clusters potentially linked to nematicidal activity, while A. niger and T. harzianum displayed broader but less infection-specific metabolic profiles. Together, these findings suggest that distinct enzymatic and metabolic gene repertoires, particularly expansions of S8 serine peptidases and specific CAZyme families, may contribute to the biocontrol potential of these fungi. Full article

Nigrospora musae ST1 is a newly identified pathogen responsible for leaf spot disease in Idesia polycarpa. In order to further advance our understanding of this strain and improve management strategies for the leaf spot disease, the PacBio Sequel II platform was used to perform whole-genome sequencing of N. musae ST1. The assembled genome comprised 42 contigs, with a total length of 49,259,803 bp and an average GC content of 56.23%. Functional annotation identified 12,063 protein-coding genes, including 125 Transporter Classification Database (TCDB)-related genes, 3600 pathogen host interaction (PHI) genes, 2503 Virulence Factor Database (DFVF)-related genes, and 722 genes encoding carbohydrate-active enzymes (CAZymes). Integrated analyses of the secretome, PHI, and DFVF databases revealed six secreted carbohydrate-active enzymes implicated in plant pathogenicity, including three glycoside hydrolases, two pectinate lyases, and one cutinase, potentially playing important roles in pathogenicity. A total of 77 secondary metabolite gene clusters were predicted. Comparative genomic analysis between N. musae ST1 and other Nigrospora species revealed differences in genome rearrangements in Nigrospora fungi. In conclusion, this study has clarified the whole-genome structural characteristics and evolutionary relationships of the newly reported pathogenic fungus, N. musae ST1. It provides a theoretical foundation for future investigations into the pathogenic mechanisms of N. musae ST1 infection in I. polycarpa, as well as potential targets for disease control. Full article

Atrazine persistence poses serious environmental threats. This study used metagenomics and qPCR to elucidate the remediation mechanism of vermicompost in atrazine degradation pathways. Seven treatments were established: unsterilized soil (CKn); sterilized soil amended with 45 (SsV1), 60 (SsV2), and 75 (SsV3) days of vermicompost; and unsterilized soil with the same vermicompost (SnV1, SnV2 and SnV3). Vermicompost significantly restructured soil microbial communities. SsV1 exhibited the highest Proteobacteria abundance (51.38%), while SsV3 markedly increased Bacteroidetes abundance (10.34%). Functional annotation revealed that vermicompost enriched carbohydrate metabolism-related COG units and upregulated CAZymes (e.g., CE1 and CE10 families), providing energy support for degrading microbial communities. Regarding metabolic pathways, SnV2 exhibited the highest atrazine degradation abundance (2.94%), significantly enriching Bauldia (4.84 RPKM) for dechlorination. During cyanuric acid ring-opening, SnV3 significantly enriched Pseudorhodoplanes (12.14 RPKM). During terminal mineralization, SsV2 increased Caenimonas abundance (15.25 RPKM) and introduced the exogenous genus Pseudorhodoplanes (7.78 RPKM). qPCR confirmed SnV2’s trzN (day 20) and atzB (day 40) reached 9.03 × 10⁴ and 6.95 × 10⁷ copies/g, respectively. These findings indicate vermicompost accelerated atrazine mineralization by enriching degradative microbial communities and promoting key functional gene expression, with 60-day vermicompost demonstrating superior performance. This study provides a robust theoretical framework for remediating atrazine-contaminated soil by vermicompost. Full article

Floccularia luteovirens is a rare and edible fungus endemic to the Qinghai–Tibet Plateau. Traditional viewpoints have inferred it to be a mycorrhizal fungus based on its spatial association with Kobresia, yet direct morphological evidence (e.g., Hartig net) and molecular evidence is lacking. Through a systematic review of the existing literature, this study found that all current evidence supporting a mycorrhizal relationship is merely indirect inference. In contrast, experiments conducted by our research team demonstrated that this fungus colonizes well on sawdust-based substrates, which is compatible with saprobic growth capacity and does not exclude the possibility of conditional mycorrhizal symbiosis in natural environments. Based on these findings, we propose that F. luteovirens may adopt a facultative nutritional mode to adapt to the alpine environment. Genomic analysis revealed that the CAZyme repertoire of F. luteovirens (including key enzyme families such as GH6, GH7, and AA1) shows high similarity to that of the saprobic fungus Agaricus bisporus and appears to be more comprehensive than that of the ectomycorrhizal fungus Boletus edulis, based on current annotation data. This pattern suggests its potential capacity for lignocellulose degradation. The successful cultivation of its closely related species Lepista sordida on various lignocellulosic substrates further supports this functional potential. This study proposes that F. luteovirens employs a ‘facultative nutrition’ strategy, which presents an alternative perspective to the traditional view of obligate dependence on mycorrhizal symbiosis. These findings contribute to our understanding of fungal adaptation in alpine environments and may inform strategies for artificial domestication of this valuable species. Full article

Bifidobacterium animalis subsp. lactis is a widely used probiotic, yet its efficacy is highly strain-specific, and growing antibiotic resistance necessitates rigorous safety evaluations. We used whole-genome sequencing and in vitro assays to characterize the safety and probiotic traits of infant feces-sourced strain BD1, which shows preliminary mood-modulating and anti-inflammatory potential. The BD1 genome showed a favorable safety profile. VFDB analysis identified 139 low-similarity homologs, with no major toxins detected. Only four chromosomally encoded antibiotic resistance genes were found; phenotypic testing confirmed resistance solely to tetracycline and mupirocin. Although the tetracycline resistance gene tet(W) was identified in genomic island GI01, the absence of associated mobile genetic elements results in a negligible risk of its mobilization. Functional annotation highlighted a dominant metabolic capacity for carbohydrate and amino acid metabolism. BD1 is rich in CAZymes, enabling superior utilization of diverse substrates (starch, sucrose, galactose). Enrichment in lipid metabolism pathways (glycerolipid, sphingolipid) further suggests potential for enhancing fermented product flavor. In vitro assessment demonstrated moderate gastrointestinal tolerance and strong bile salt tolerance. Surface properties showed pronounced cell surface hydrophobicity and confirmed biofilm-forming potential. In conclusion, BD1 exhibits robust safety, metabolic versatility, and strong probiotic characteristics, supporting its development as a functional probiotic strain. Full article

Low-density polyethylene (LDPE) and poly (butylene adipate-co-terephthalate) (PBAT) agricultural films are major components of microplastics (MPs) and their contamination in agriculture due to their difficulty to recycle. However, potential degradation mechanisms of MPs from LDPE and PBAT in agricultural soils are still unclear. Here, we isolated a strain of Bacillus cereus L6 from long-term agricultural MP-contaminated soil and analyzed its potential biochemical pathways involved in LDPE and PBAT turnover through functional prediction from shotgun genome sequencing. After 28 days of incubation with MPs, Bacillus cereus L6 caused a net mass loss of 0.99% LDPE-MPs/28 days and 3.58% PBAT-MPs/28 days. The surfaces of LDPE and PBAT degraded in bioassays added with Bacillus cereus L6 showed wrinkles, cracks, and pits, accompanied by an increase in roughness. The crystallinity and thermal stability of both LDPE- and PBAT-MPs were decreased and the hydrophobicity of PBAT-MPs was reduced. Whole-genome sequencing analysis showed that Bacillus cereus L6 potentially encoded genes for enzymes related to the biodeterioration of additives in LDPE and PBAT. Moreover, genomic CAZymes predictive analysis showed that genes related to oxygenases and lyases were annotated in the strain L6 Auxiliary Activities family. These findings offer a theoretical foundation for deeper exploration into the degradation and metabolic processes of MPs from discarded agricultural plastics in the environment. Full article

The recently described genus Candolleomyces (Basidiomycota, Agaricales, Psathyrellaceae) is now recognized as a distinct taxonomic group separate from Psathyrella. Currently, no fully assembled and accurately annotated genomes of Candolleomyces species are available, limiting our understanding of their physiological traits and biotechnological potential. Numerous tools exist for fungal genome assembly and annotation, each using different algorithms, resulting in substantial variation in gene content and distribution within the same genome. In this work, a hybrid assembly and annotation of the genome of strain CMU-8613 were performed using pipelines that combine different assembly and annotation tools. Phylogenetic analysis showed that the analyzed strain CMU-8613 belongs to Candolleomyces candolleanus. The assembled genome size ranged from 46.8 Mb (NECAT + Racon) to 59.3 Mb (Canu + Coprinellus micaceus genome assembly), depending on the assembly and polishing strategy. The analysis identified 15–25 secondary metabolite gene clusters (BGCs), depending on the genome assembly and the tools used for BGC prediction. In strain CMU-8613, CAZyme-encoding genes varied across assemblies: 494 genes were detected in the Flye assembly and 453 in NECAT; in both cases, the AA (Auxiliary Activities) and GH (Glycoside Hydrolases) families were the most represented. The diversity of CAZymes observed among Candolleomyces species suggests differences in their saprophytic capacities. Analysis of the MAT-A/MAT-B loci revealed that C. candolleanus possesses a tetrapolar mating system. This study provides the first annotated genome of C. candolleanus, highlighting its enzymatic potential to degrade plant biomass and its capacity to synthesize diverse secondary metabolites. The combination of assembly and annotation tools employed here offers robust alternative strategies for characterizing non-model fungi or species lacking high-quality reference genomes. Full article

Ganoderma tsugae is a typical white-rot fungus capable of decaying both coniferous and broad-leaved trees and is also used in traditional Chinese medicine for its immunomodulatory and anticancer properties. To elucidate the molecular basis of its broad substrate adaptability, we performed integrated genomic and transcriptomic analyses of two G. tsugae strains (collected from Xingjiang on Betula and Jilin on Larix). The high-quality genomes of G. tsugae Wu 2022 from Xinjiang (40.8 Mb, 12,496 genes) and G. tsugae Cui 14110 from Jilin (45.6 Mb, 13,450 genes) were obtained. There are enriched gene families related to carbohydrate-active enzymes (CAZymes) in two G. tsugae strains. Notably, specific CAZyme families implicated in hemicellulose (GH16), chitin metabolism (GH18), and ester bond cleavage (CE10) were prominently expanded. Transcriptome analyses under the induction of Betula and Larix sawdust revealed a core adaptive response. A total of 5558 genes were differentially expressed, including 2094 up-regulated and 3464 down-regulated genes. Most differentially expressed genes (DEGs) were annotated as “catalytic activity”, “metabolic processes” and specific functions such as nutrient transport (“MFS transporter”), and lipid metabolism (“3-oxoacyl-[acyl-carrier protein] reductase”). In addition, a conserved suite of the eleven shared DEGs were annotated as “Heat shock protein 9/12”, “alcohol dehydrogenase”, and “Cytochrome p450” related to secondary metabolites biosynthesis, transport, and catabolism. Based on the annotation results, the wood degradation mechanism of G. tsugae can be described as synthesizing and secreting degradation enzyme system to obtain energy, using protective enzyme systems to ensure its own health, and employing a transport enzyme system to recycle metabolic capacity. This progress ensures the environmental adaptability and high degradation efficiency of G. tsugae during wood degradation. Full article

Weissella viridescens has been proposed as a probiotic candidate, but strain-level multi-omics evidence remains limited. The complete genome of the human-derived W. viridescens strain Wv2365 was sequenced through a hybrid assembly of Illumina and PacBio sequencing reads and compared with eight publicly available W. viridescens genomes. Pangenome analysis and functional annotation were performed, and metabolites were profiled by broadly targeted metabolomic analysis. In addition, the acid and bile tolerance, auto-aggregation and cell surface hydrophobicity, and antioxidant activity of the strain, as well as both in silico and phenotypic safety, were assessed. Wv2365 carries a single chromosome of 1.57 Mb with 41.3% G+C content. The species has an open pangenome with 803 core genes. Genomic and metabolomic features converged on carbohydrate and amino acid metabolism, including glycolysis/tricarboxylic acid (TCA) cycle and arginine pathways, and a carbohydrate-active enzyme (CAZyme) repertoire dominated by glycosyltransferases. In vitro, Wv2365 tolerated pH 3.0 and 0.3% bile, showed auto-aggregation, surface hydrophobicity, and 2,2-diphenyl-1-picrylhydrazyl (DPPH) and hydroxyl radical scavenging. The strain was susceptible to 10 antibiotics tested except for its intrinsic vancomycin non-susceptibility and was non-hemolytic and gelatinase negative. No acquired antimicrobial resistance or virulence genes were found in the genome. These findings indicate that W. viridescens Wv2365 is safe with probiotic traits relevant to gastrointestinal survival, colonization, and redox balance. 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

A pathogenic fungus was isolated from the leaves of strawberry black spot in Zhengzhou China. Based on morphological and phylogenetic analysis, the isolate was identified as Alternaria alstroemeriae. Hybrid sequencing and assembly yielded a high-quality 38.7 Mb genome with 12,781 predicted genes and 99.6% Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness. Functional annotation revealed enrichment in carbohydrate metabolism, secondary metabolite biosynthesis, and virulence-associated genes. Strain L6 harbored 45 biosynthetic gene clusters(BGCs), including 12 clusters for terpenes, 7 for non-ribosomal peptide synthetases, and 7 for polyketide synthases. Six BGCs showed high similarity to known pathways producing alternariol (phytotoxic/mycotoxic compound), alternapyrone (phytotoxin), choline (osmoprotectant), terpestacin (anti-angiogenic agent), clavaric acid (anticancer terpenoid), and betaenone derivatives (phytotoxins). CAZyme analysis identified 596 carbohydrate-active enzymes, aligning with L6’s biotrophic lifestyle. Additionally, 996 secreted proteins were predicted, of which five candidate effectors contained the conserved RxLx [EDQ] host-targeting motif, suggesting potential roles in virulence. This genome resource highlights L6’s exceptional secondary metabolites (SMs) diversity, featuring both plant-pathogenic toxins and pharmacologically valuable compounds, indicating that this endophytic fungus is a potential producer of metabolites meriting further exploration and development. Full article

Viruses play a regulatory role in microbial ecology. Traditional fermented foods have complex fermentation environments with abundant viral participation, yet current research on viral communities in fermented foods remains insufficient. Traditional, manually produced solid-state fermented vinegar serves as an excellent model for studying the role of viral communities in fermented foods. Using metagenomic approaches, this study investigates the structure and dynamics of viral communities during the acetic acid fermentation process of Shanxi aged vinegar. All identified viruses were bacteriophages, and the dominant families were identified as Herelleviridae, Autographiviridae, and Stanwilliamsviridae. The richness and diversity of viral communities exhibited significant variations during acetic acid fermentation. Furthermore, correlation analysis revealed a strong association (p < 0.01) between core bacteria and core viruses. Functional annotation revealed the presence of viral genes associated with amino acid and carbohydrate metabolism. Notably, abundant auxiliary carbohydrate-active enzyme (CAZyme) genes were identified in viruses, with glycoside hydrolases (GHs), glycosyltransferases (GTs), and carbohydrate-binding modules (CBMs) demonstrating particularly high abundance. Additionally, several antibiotic resistance genes were detected in viruses. This study elucidates the impact of viral communities on microbial dynamics during food fermentation, advancing our understanding of viral roles in traditional fermented food ecosystems. Full article

Gerronema lapidescens (Lei Wan), a valued medicinal basidiomycete traditionally employed for antiparasitic and digestive ailments, faces severe conservation threats due to unsustainable wild harvesting and the absence of reliable cultivation protocols. To address this crisis and unlock its pharmacotherapeutic potential, we present the first chromosome-scale genome assembly and comprehensive methylome profile for the wild strain G. lapidescens QL01, domesticated from the Qinling Mountains. A multi-platform sequencing strategy (Illumina and PacBio HiFi) yielded a high-quality 82.23 Mb assembly anchored to 11 chromosomes, exhibiting high completeness (98.4% BUSCO) and 46.03% GC content. Annotation predicted 15,847 protein-coding genes, with 81.12% functionally assigned. Genome-wide analysis identified 8.46 million high-confidence single-nucleotide polymorphisms (SNPs). Notably, methylation profiling revealed 3.25 million methylation events, with elevated densities on chromosomes 4, 9, and 10, suggesting roles in gene silencing and environmental adaptation. Phylogenomic analyses clarified the evolutionary status of G. lapidescens, whilst gene family evolution indicated moderate dynamics reflecting niche adaptation. Carbohydrate-Active enzymes (CAZymes) analysis identified 521 enzymes, including 211 Glycoside Hydrolases (GHs), consistent with organic matter degradation. Additionally, 3279 SSRs were catalogued as molecular markers. This foundational resource elucidates G. lapidescens’s genetic architecture, epigenetic regulation, evolutionary history, and enzymatic toolkit, underpinning future research into medicinal compound biosynthesis, environmental adaptation, germplasm conservation, and sustainable cultivation. Full article