Search Results (1,054)

The prized wild mushroom Tricholoma matsutake maintains distinctive microbiota within its dominant zone; however, the spatial and seasonal reorganization of microbiota from taxonomic and functional perspectives remain poorly understood. High-throughput amplicon sequencing was performed in warming (March–June) and cooling (September–December) seasons to compare microbial communities among T. matsutake-dominant (present, visible mycelium) and -nondominant soils (transition, adjacent with present; control, distant from fairy ring). Fungal and bacterial community structures in T. matsutake-dominant soils were obviously distinct (ANOSIM, R > 0.6, p = 0.001), and bacterial communities exhibited clear seasonal separation. The relative abundances of Ascomycota and Mortierellomycota significantly reduced, whereas mycorrhiza-helper bacteria, including Paenibacillus, Bacillus, and Cohnella, were enriched. Functional predictions suggested that the potential expression of cofactor and vitamin biosynthesis, nutrient degradation, and inorganic nutrient metabolism pathways may be enriched in T. matsutake-dominant soil. During the fruiting period, the expression of the predicted amino acid biosynthesis pathway may be reduced, whereas that of the cofactor/carrier/vitamin biosynthesis pathway may be enriched. Our findings suggest that T. matsutake dominance could be associated with the spatial and seasonal restructuring of soil microbial communities, potentially leading to the formation of functionally interconnected microbial networks. Therefore, this study predicts hidden ecological insights that, once biochemically validated, may be used to develop important strategies for the sustainable conservation and artificial cultivation of T. matsutake. Full article

High-quality genomic DNA extraction remains a major bottleneck for fungal genomics, particularly for worldwide aerobic and non-photosynthetic mushroom species that rely on their rigid cell walls, interference between metabolites, polysaccharides, etc., and complex genomes. This study systematically compares five DNA extraction protocols involving four distinct sample preparation procedures (fresh (A), filtered (B), frozen (C) and cryogenic mycelium (D)) across mycelial cultures of eight Tunisian fungal strains representing Ascomycota and Basidiomycota to identify the optimal combination for genomic DNA extraction from mycelium. The eight phylogenetically diverse fungal species were analyzed using short-read (MiSeq and NextSeq550) and/or long-read (MinION Mk1C) sequencing technologies, giving a depth coverage between 3.7× and 83×. The generation and quality of the assemblies were assessed within the Galaxy platform, which revealed a gap percentage of 0–0.509%. Taxonomic characterization and phylogenetic inference were performed with SANGER technology using the Internal Transcribed Spacer (ITS) and D1/D2 region of the 26S rRNA gene, assigning the species to our eight different strains: Clitopilus baronii (BS6), Porostereum spadiceum (BS200), Trametes versicolor (BS22-9), Schizophyllum commune (BS23-13), Gloeophyllum abietinum (BS23-14), Irpex laceratus (BS100), Trichoderma asperellum (GC9) and Trichoderma harzianum (S3). The optimized DNeasy Plant Pro Kit protocol with cryogenic biomass treatment presents a safe and cost-effective method for fungal genome sequencing and taxonomic resolution. This integrated comparative evaluation of extraction for sequencing identifies an optimal Qiagen-based extraction strategy combined with cryogenic treatment for eight diverse Tunisian fungal species, guiding method selection based on specific cell wall characteristics rather than proposing a universal protocol limited by unequal replication and strain numbers. Full article

Alpine treeline and shrubline ecotones are climatically sensitive transition zones where vegetation shifts strongly influence belowground microbial processes. Soil bacteria and fungi, as core component of the soil microbiome, play vital roles in nutrient cycling and plant–soil interactions within these fragile ecosystems. However, the structure and diversity of soil microbial communities across the treeline–shrubline transition remain poorly understood. Here, we investigated soil bacterial and fungal communities across treeline and shrubline ecotones in two mountain on the eastern Tibetan Plateau. We further examined how soil physicochemical properties shaped microbial community assembly. Our results demonstrated that the community composition of both bacteria and fungi differed significantly between the treeline and shrubline ecotones, while the Shannon index showed no significant variation. At the phylum level, Proteobacteria, Actinobacteriota, and Acidobacteriota dominated bacterial communities, while Ascomycota and Basidiomycota were the predominant fungal phyla. Both the network complexity of soil bacterial and fungal communities changed significantly across ecotones. Specifically, bacterial network complexity increased significantly toward the shrubline, whereas fungal network complexity declined. Bacterial community compositions were co-regulated by both environmental and vegetation factors, while fungal community compositions were only regulated by soil pH. Redundancy analysis revealed that soil organic carbon, pH, and moisture were the primary drivers of bacterial community (38.17%), whereas vegetation cover, soil organic carbon, and moisture explained the largest proportion of fungal community (44.79%). Our findings reveal the distribution patterns and underlying shift mechanisms of microbial communities between the treeline and shrubline ecotone. These insights are crucial for mountain biodiversity conservation and for improving predictions of forest responses to climate change. Full article

Aiming to clarify the spatial distribution characteristics of soil microbial assemblages and the environmental factors shaping them across a narrow altitudinal transect, this investigation concentrated on the surface soil layer within naturally occurring mixed forests of Picea crassifolia and Betula platyphylla, situated in the elevation band from 2400 to 2800 m along the southern flank of the Qilian Mountains. Leveraging the Illumina NextSeq 2000 high-throughput sequencing platform, integrated with α- and β-diversity analyses and redundancy analysis (RDA), we systematically characterized the composition and diversity traits of soil bacterial and fungal communities, as well as their associations with environmental factors. Notably, the bacterial communities were dominated by Pseudomonadota, Actinomycetota, and Acidobacteria with the abundance of Pseudomonadota decreasing with increasing altitude and that of Acidobacteria increasing with increasing altitude. Furthermore, Ascomycota and Basidiomycota were the dominant phyla in the fungal community. In contrast, bacterial α-diversity—as estimated by the Ace index—showed no significant variation across altitudes. Yet, the fungal alpha diversity metrics—namely Ace and Chao1—were markedly elevated at the 2800 m elevation relative to those observed at both intermediate and lower-altitude locations. Importantly, fungal diversity and community composition showed stronger altitudinal differentiation than bacterial communities in this dataset. Moreover, soil pH, total phosphorus, organic carbon, litter C:N:P stoichiometric ratios, and microbial biomass C:N:P stoichiometric ratios were strongly associated with soil microbial community variation along the altitude gradient, suggesting that they may act as important environmental filters. In conclusion, altitude-driven variations in litter characteristics and soil physicochemical properties jointly shape the assembly processes and spatial distribution patterns of soil microbial communities in this region. Full article

The potential of Trichoderma nordicum (Hypocreales, Ascomycota), a recently described species, for antagonism and use in the biocontrol of oomycete-caused plant diseases is unknown. Trichoderma is a well-known genus for containing microbial antagonists and biocontrol agents. The T. nordicum in this study was isolated from decomposing wood, and rpb2 and tef1 barcode sequencing demonstrated that the isolates were a match to the reference T. nordicum and T. nigricans strains. Since T. nordicum was described before T. nigricans, the isolates were assigned to T. nordicum, although taxonomic uncertainty between these species requires future clarification. In dual-culture confrontation assays, T. nordicum overgrew five economically important oomycete plant pathogens (Phytophthora capsici, P. sojae, Pythium aphanidermatum, P. myriotylum, and Globisporangium ultimum). The inability to recover viable P. aphanidermatum and P. capsici from the parts of the plate overgrown by T. nordicum, coupled with protease and endo-cellulase activities, correlates with T. nordicum having antagonistic abilities. Inoculation with T. nordicum preventively reduced the levels of cucumber seedling damping-off caused by P. aphanidermatum by up to 70%. The T. nordicum biocontrol effects against pepper blight caused by P. capsici were greater than 80%, compared to an autoclaved T. nordicum spore control. T. nordicum could also significantly promote the growth of pepper, with plant weight increased by up to 40%, compared to an autoclaved-spore control. In contrast, T. nordicum could not be used to control Pythium soft rot of ginger caused by P. myriotylum, even though P. myriotylum was overgrown by T. nordicum, suggesting host- or pathosystem-specific factors influence biocontrol efficacy. In summary, T. nordicum is a promising biocontrol agent for use in the control of pepper blight caused by P. capsici, and also has potential for use in the control of other oomycete-caused plant diseases in vegetable production systems. Full article

The Ningxia Yellow River Irrigation District in China has long been influenced by flood irrigation and intensive fertilizer input under its particular geological and climatic constraints, and this region is characterized by low soil organic matter, poor nutrient status, low permeability, high pH, and widespread salinization. This cross-sectional field study compared the soil physicochemical properties and microbial communities among saline–alkali soil (SAS), straw-returning farmland (SR), and traditionally managed farmland (FM). EC was higher in SAS (approximately 4.21 dS·m⁻¹) than in SR and FM (approximately 0.23 and 0.30 dS·m⁻¹, respectively), whereas TOC and C/N were higher in SR (approximately 1.00% and 10.58, respectively) than in FM (approximately 0.78% and 8.69) and SAS (approximately 0.43% and 8.81). Bacterial and fungal communities showed different distribution patterns among the three farmland types. Compared with fungi, bacterial community structure and richness varied more clearly across soils differing in salinity and organic matter status. Variations in microbial community composition were accompanied by differences in soil salinity and carbon- and nitrogen-related properties. Acidobacteriota was positively correlated with soil carbon and nitrogen variables and negatively correlated with pH and EC, while Ascomycota was positively correlated with total carbon (TC) and TOC. These results show that straw-returning farmland differed from saline–alkali soil and traditionally managed farmland in both soil properties and microbial community characteristics, highlighting potential soil–microbe associations in saline-affected agricultural systems. Full article

Nitrogen addition significantly affects soil aggregate stability by altering the aggregate microenvironment. Although the ecological effects of nitrogen addition on soil aggregates have been extensively investigated, studies specifically focusing on the responses of soil aggregate stability in Larix olgensis forest understories remain scarce. The effects of different forms of nitrogen addition (urea (CO(NH₂)₂), ammonium chloride (NH₄Cl), and sodium nitrate (NaNO₃)) were investigated at 20 kg N·ha⁻¹·yr⁻¹ across all treatments, and the physicochemical properties, stability, and microbial community composition of soil aggregates were determined to analyze soil aggregate stability. NaNO₃ significantly increased soil nutrient contents, promoted the formation of macroaggregates, and significantly enhanced soil aggregate stability. NH₄Cl significantly decreased bacterial diversity in microaggregates, while NaNO₃ significantly elevated fungal diversity in macroaggregates. CO(NH₂)₂ and NH₄Cl increased the relative abundances of Ascomycota and Proteobacteria in microaggregates, whereas NaNO₃ elevated the relative abundances of Mortierellomycota and Gemmatimonadetes in soil aggregates of all particle sizes. These results indicated that NaNO₃ was more effective in improving soil aggregate stability and exerted regulatory effects on microbial community structure compared to the other nitrogen forms. These findings can provide a theoretical basis for an in-depth understanding of the microecological processes of forest soil aggregates under the context of nitrogen deposition. Full article

The genomic basis underlying the remarkable ecological flexibility of endophytic fungi (EF), particularly their potential to transition between symbiotic, saprophytic, and pathogenic lifestyles, remains poorly understood. Through comparative genomics of 75 Ascomycota and a validation set of 36 Fusarium genomes, we uncovered a distinct pattern of genome evolution in EF, contrasting with the well-known “gene loss” model in obligate symbionts. Our analysis reveals that EF genomes are significantly expanded, primarily driven by the accumulation of DNA transposable elements (TEs). Crucially, this TE-mediated genomic plasticity is coupled with the retention and significant expansion of gene families for both saprotrophy and potential pathogenesis. We propose a novel “dual-trophic potential” model: TE-driven genomic expansion and plasticity provide the genetic raw material for EF to maintain a versatile repertoire of ecological tools, facilitating adaptive shifts across the endophytic–saprophytic–pathogenic continuum. This study reframes our understanding of fungal endophytism from a static symbiotic state to a dynamic, genetically enabled ecological strategy. Full article

Background: The nasopharyngeal microbiome is crucial for respiratory health in mammals, yet it remains poorly characterized in the endangered forest musk deer (Moschus berezovskii), particularly in the context of disease. Methods: We compared the bacterial (16S rRNA) and fungal (ITS2) communities in the nasopharynx of healthy (n = 6) and clinically diseased (n = 6) individuals. Results: Although alpha diversity did not differ significantly, beta diversity (PCoA) analysis revealed distinct bacterial (PERMANOVA, R² = 0.165, p = 0.014) and fungal (R² = 0.577, p = 0.003) community structures between groups. The diseased group exhibited a significant increase in the bacterial phylum Proteobacteria (70.97% vs. 46.27%), primarily driven by the genera Bibersteinia and Pseudomonas. Fungal communities in the diseased group were dominated by a higher relative abundance of Ascomycota and Basidiomycota, with significant enrichment of Wallemia and Aspergillus. LEfSe analysis identified Pseudomonas and multiple fungal taxa (e.g., Wallemia, Aspergillus) as biomarkers for the diseased group. PICRUSt2 prediction indicated enrichment of pathways related to carotenoid biosynthesis and sphingolipid metabolism in the diseased state, while FUNGuild analysis suggested a higher abundance of animal/plant pathogen-related fungi. Conclusions: Symptomatic respiratory infections in forest musk deer are associated with significant dysbiosis of the nasopharyngeal microbiome, characterized by the marked enrichment of potential bacterial opportunists (e.g., Pseudomonas) and specific fungal taxa (e.g., Wallemia, Aspergillus), alongside distinct functional shifts in the microbiome. These findings provide the first integrated bacterial–fungal profile of the nasopharyngeal microbiome in this endangered species, and highlight potential microbial biomarkers associated with respiratory disease. Full article

Marine fungi are pivotal components of coastal ecosystems, facilitating essential biogeochemical cycling and trophic dynamics. However, the complex mechanisms governing their spatiotemporal community patterns in tropical–subtropical coasts remain largely unexplored. In this study, we characterized marine fungal diversity across a comprehensive seasonal cycle (spring (March), summer (June), autumn (August), and winter (December)) at 21 representative sites along the Leizhou Peninsula, China. These sites were strategically selected to encompass a broad range of dissolved inorganic nitrogen (DIN) gradients. Fungal community composition was characterized via high-throughput sequencing of the internal transcribed spacer 2 (ITS2) region, followed by functional guild profiling using the FUNGuild database. A total of 8777 amplicon sequence variants (ASVs) were identified, encompassing a broad taxonomic breadth of 10 phyla and 358 genera. Ascomycota, Basidiomycota, and Chytridiomycota emerged as the predominant phyla across all samples. Our results revealed significant spatiotemporal heterogeneities: seasonal succession fundamentally reshaped community composition, with DIN exerting its most pronounced influence during the winter. Furthermore, fungal functional structures exhibited distinctive clustering across regions defined by DIN enrichment levels. Co-occurrence network analysis revealed a highly modular and robust architecture, characterized by predominantly positive interactions and dense inter-taxon connectivity. These findings underscore the synergistic influence of temporal dynamics and DIN enrichment in shaping marine fungal community assembly and functional compositions. Our study provides critical baseline insights into the ecological resilience of coastal mycobiota in the South China Sea. Full article

Soil- and plant-associated fungi and bacteria are an important part of many ecosystems as they can affect plant health, growth and stress tolerance. However, it remains poorly understood whether the microbiomes differ between conifer species growing in the same site conditions and between tree ecosystem compartments. The main aim of the study was to describe and compare the microbiomes of Scots pine (Pinus sylvestris L.) and Norway spruce (Picea abies (L.) H. Karst.), growing in a boreal forest common garden experiment on adjacent forest plots, to analyse the tree species effect on the composition of the needle and surface soil organic-mineral horizon microbiomes. The needle and surface soil organic-mineral horizon bacterial and fungal microbiomes were simultaneously analysed by full-length 16S and ITS sequencing on a long-read sequencing platform; however, the bacterial analysis was restricted to soil samples. The highly abundant bacterial phyla in both pine and spruce soil were Actinomycetota, Pseudomonadota, Planctomycetota and Acidobacteriota. The dominant fungal phyla in pine and spruce surface organic-mineral soil was Basidiomycota, while the needles were dominated by Ascomycota. The results showed an effect of tree species on the soil bacterial and fungal microbiomes and needle fungal microbiomes based on alpha diversity, which was higher for Norway spruce compared to Scots pine. The results indicated that Norway spruce might be able to support higher microbial diversity, which could potentially be due to differences in needle longevity, root exudates, litter input and its degradation, between pine and spruce. Furthermore, the results indicated distinct microbiomes between the soil and needle compartments. Full article

To investigate the main drivers of rhizosphere soil microbial community structure and diversity in Camellia reticulata, this study collected rhizosphere soil samples from six regions at two soil depths (0–30 cm and 30–60 cm). Using high-throughput sequencing, we systematically analyzed the effects of soil environmental factors on microbial communities. The results showed that the dominant bacterial phyla were Proteobacteria, Acidobacteriota, Chloroflexi, Actinobacteriota, and Bacteroidota, while the dominant fungal phyla were Ascomycota, Basidiomycota, and Mortierellomycota. Alpha diversity of both bacterial and fungal communities was higher in surface soils (0–30 cm) than in deeper layers (30–60 cm), although the differences were not statistically significant (p > 0.05). Soil pH, potassium content (K), and catalase activity (S-CAT) were identified as the main environmental factors significantly correlated with microbial community structure. Network analysis identified Acidobacteriota and Ascomycota as highly connected taxa within microbial networks, suggesting their potential importance in maintaining network structure. This study reveals the vertical differentiation characteristics of rhizosphere microbial communities in C. reticulata and their responses to environmental factors, providing a theoretical basis for cultivation management and rhizosphere microecological regulation. Full article

This study investigated how fertilization regimes and ridge furrow planting patterns influence the soil nutrient conditions and microbial taxonomic composition and function in the rhizosphere of spring maize in Northeast China. Three treatments were compared: CK (compound fertilizer, small ridge), KF (formula fertilization, small ridge), and BMP (formula fertilization, large double-row ridge). High-throughput sequencing was used to characterize the soil bacterial and fungal community composition and diversity. The results showed that the combination of formula fertilizer and wide-ridge cultivation synergistically improved soil physicochemical properties and significantly increased maize yield (p < 0.05). Compared with CK, both BMP and KF significantly improved the composition and diversity of microbial communities. Notably, the BMP treatment increased the relative abundances of Ascomycota and Basidiomycota—key decomposers of soil organic matter, lignin, and cellulose—which suggested enhanced nutrient cycling potential under this integrated management practice. Among the three treatments, BMP (N:P₂O₅:K₂O = 1:2:1, 130 cm wide-ridge double-row planting) achieved the highest maize yield (859 ± 14 kg ha⁻¹), representing an 11.0% increase over conventional practices (CK, 774 ± 13 kg ha⁻¹). We propose that integrating optimized fertilization with ridge configuration is an effective strategy for improving soil quality, microbial functionality, and crop productivity in Northeast China’s black soil region. Full article

This study aimed to investigate the effects of different aerobic exposure durations on mycotoxin accumulation, nutritional quality changes, and microbial community dynamics of corncob silage. The experiment was divided into four groups: T0 (corncob silage fermented for 45 days without aerobic exposure), T4 (corncob silage exposed to air for 4 days), T8 (corncob silage exposed to air for 8 days), and T12 (corncob silage exposed to air for 12 days). The results showed that after aerobic exposure, the contents of dry matter (DM), crude protein (CP), water-soluble carbohydrates (WSC), Crude Ash, lactic acid (LA), and ammonia nitrogen (NH₃-N) in all exposed groups (T4, T8, T12) were significantly lower than those in the T0 group, whereas the contents of neutral detergent fiber (NDF), acid detergent fiber (ADF), propionic acid (PA), and butyric acid (BA) were significantly higher than those in the T0 group. Exposure to aerobic conditions for 12 days resulted in the four mycotoxins exhibiting levels significantly higher than those in the other groups, and notably, zearalenone (ZEN) and ochratoxin (OT) exhibited a continuous increase in concentration with the extension of aerobic exposure. Aerobic exposure increased bacterial diversity and fungal relative abundance, and significant separations were observed in both bacterial and fungal communities between the T0 group and the aerobic exposure groups. At the phylum level, Firmicutes was the dominant bacterial phylum in the T0 group, while Pseudomonadota became the dominant phylum after aerobic exposure. At the genus level, Lacticaseibacillus was the dominant bacterial genus in the T0 group, whereas Variovorax, Vibrionimonas, and Mycobacterium dominated the bacterial communities in the aerobic exposure groups. The relative abundance of the fungal phylum Ascomycota increased from 30% in the T0 group to 80~90% in the aerobic exposure groups; the dominant fungal genera shifted from Zygosaccharomyces to Albifimbria and Pichia. In conclusion, prolonged aerobic exposure elevates the concentrations of mycotoxins in corncob silage, reduces the nutritional quality, and induces significant shifts in both bacterial and fungal community compositions. Full article

The integration of appropriate tillage practices with straw returning can effectively mitigate soil degradation in Northeast China. However, limited research has explored the impacts of different tillage practices combined with varying straw incorporation depths on the structure and diversity of soil microbial communities. In 2016, a field experiment was initiated using a two-factor split-plot design, featuring six treatments: two tillage depths of 10 cm (D10) and 30 cm (D30) combined with three straw management practices—straw mixing incorporation (SM), straw deep burial (SB), and straw removal (SR). Soil samples collected in 2019 were analyzed for multiple soil properties and microbial indices. Results indicated that both straw returning and tillage depth significantly influenced soil organic carbon (SOC), soil total nitrogen (STN), total phosphorus (TP), and total potassium (TK), with the D30 treatment combined with straw returning optimizing soil nutrient contents most effectively. Under straw returning, D10 significantly increased urease activity in the 0–10 cm soil layer, whereas D30 enhanced this enzyme activity in the 10–30 cm soil layer, while β-glucosidase activity was less responsive to tillage depth. For the D10 treatment with straw returning, acid phosphatase activity was markedly higher than that in the straw removal treatment, whereas N-acetyl-β-D-glucosaminidase activity exhibited the opposite trend. Straw-returning methods had no significant effects on the bacterial and fungal Chao1 indices, while the Shannon index was positively correlated with key soil properties. Redundancy analysis (RDA) of microbial community composition at the phylum level and soil environmental factors revealed that soil nutrients in the 0–10 cm soil layer were positively correlated with Actinobacteriota, Ascomycota, and Basidiomycota, whereas the explanatory power of soil nutrients for microbial community variation decreased in the 10–30 cm soil layer. Our results highlight that tillage depth and straw returning can regulate soil microbial community composition and enhance soil nutrient cycling, thereby providing a theoretical basis for optimizing the combined application mode of tillage and straw-returning practices in Northeast China. Full article