Search Results (1,047)

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

Despite the importance of surface microbiota in postharvest quality, the effects of mechanical damage on microbial succession in Hypsizygus marmoreus during refrigerated storage remain insufficiently understood. In this study, 16S rRNA gene and ITS amplicon sequencing were used to characterize the bacterial and fungal communities on intact and mechanically damaged H. marmoreus during 15 days of storage at 4 °C. Storage time, rather than mechanical damage, was the main driver of whole-community variation, although mechanical damage accelerated visible spoilage assessed qualitatively. Bacterial communities showed pronounced temporal turnover, shifting from early Firmicutes-rich assemblages to late-stage Proteobacteria-dominated communities, especially Pseudomonas. In contrast, fungal communities remained largely dominated by Ascomycota throughout storage, although mechanically damaged mushrooms showed a greater late-stage occurrence of opportunistic yeasts such as Candida. Predicted functional and phenotypic analyses further suggested late-stage increases in Gram-negative, aerobic, biofilm-forming, stress-tolerant, and potentially pathogenic bacterial traits. Because these traits were inferred from 16S rRNA gene-based prediction rather than measured directly, they should be interpreted cautiously. Overall, the results suggest that maintaining the physical integrity of H. marmoreus during postharvest handling may help preserve quality and delay the emergence of spoilage-associated microbial traits during refrigerated storage. Full article

Substances derived from the combustion of Carpinus betulus and Salix viminalis wood may have the potential to selectively modulate the structure and diversity of soil fungi. Therefore, the aim of this study was to evaluate their effects on the structure and diversity of the mycobiome, the physicochemical and thermodynamic properties of proteins, and the biomass of Zea mays. The pot experiment was conducted for 60 days on Eutric Cambisols soil developed from sandy loam (pH_KCl = 4.37). Changes in the taxonomic profile of fungi were analyzed using the ITS region sequencing. Ascomycota dominated the control soil, while the addition of substances from the combustion of S. viminalis reduced their relative abundance, and C. betulus increased it. The growth of fungi of the genera Penicillium, Fusarium, Fusicolla, Chaetomium, and Mortierella was inhibited, whereas Iodophanus was stimulated by both additives. The abundance of Vishniacozyma spp. decreased after the addition of C. betulus and increased after the addition of S. viminalis. The most thermodynamically stable proteins were observed in the genera Fusarium and Penicillium, and the least stable in Mortierella and Vishniacozyma. Substances derived from tree biomass combustion significantly altered the diversity and evenness of fungal communities and exerted an inhibitory effect on both above-ground and root biomass of plants. These results suggest that the presence of these substances in the soil influences the structure and functional activity of fungi. Full article

The genus Xylaria comprises numerous species, particularly prevalent in tropical ecosystems such as those of Ecuador. Despite its ecological importance, the taxonomy of the genus remains challenging, and much of its diversity in the Neotropics remains under-documented. This study provides a preliminary characterization of the Xylaria diversity at the Estación Científica San Francisco, an Andean biodiversity hotspot in Southern Ecuador. Through an integrated approach including detailed macro- and micro-morphological descriptions and nuclear ribosomal DNA (nrDNA ITS and LSU) phylogenetic analyses, 20 Xylaria specimens were examined. As a result, ten species were recognized: Xylaria adscendens, X. cf. anisopleura, X. apiculata, X. curta, X. enterogena, X. fissilis, X. globosa, X. aff. telfairii, X. tuberoides, and X. aenea, the latter representing a new record for Ecuador. The phylogenetic analysis presented here serves as a preliminary systematic positioning of these specimens within the genus rather than a comprehensive global reconstruction. While these ribosomal markers provided preliminary insights into species relationships, partial incongruence with morphospecies highlights the evolutionary complexity of certain lineages and underscores the need for future multilocus studies. Furthermore, four additional phylotypes found in their anamorphic state are documented, suggesting that local diversity exceeds current records. By providing detailed morphological documentation supported by preliminary barcode data from a poorly sampled region, this study contributes vital information to the global understanding of Xylaria and underscores the importance of Southern Ecuador as a reservoir of fungal diversity. Full article

Soil fungi are pivotal drivers of biogeochemical cycling, mediating nutrient transformation, plant–soil feedbacks, and ecosystem stability. Understanding their responses to vegetation succession is essential for predicting ecosystem recovery in fragile volcanic landscapes. We investigated soil fungal communities across five successional stages on the Jingpo Lake lava plateau—grassland (GL), shrubland (SL), deciduous broad-leaved forest (DB), coniferous and broad-leaved mixed forest (CB), and coniferous forest (CF)—using high-throughput ITS sequencing and soil physicochemical analysis. Basidiomycota and Ascomycota dominated at the phylum level, with Sebacina, Cortinarius, and Mortierella as core genera. Alpha diversity (Shannon, Simpson, Chao1) was significantly higher in early-successional GL and SL than in DB (p < 0.05), while CB exhibited the lowest community evenness (Pielou-e). Co-occurrence networks revealed greater connectivity in GL, whereas forest types showed simplified topologies. LEfSe identified distinct fungal biomarkers for each vegetation type. PICRUSt2-based functional prediction indicated biosynthesis as the dominant pathway (>40%), with significant variation among vegetation types. Redundancy analysis (RDA) identified soil organic matter (SOM) as the primary predictor of fungal community composition. Our findings indicate that vegetation succession is associated with changes in fungal diversity and function primarily linked to variations in SOM, with moisture regimes as a secondary contextual factor. Notably, advanced forest stages exhibited reduced fungal diversity and simplified community structure—highlighting a trade-off between nutrient enrichment and microbial complexity in volcanic ecosystems. These insights advance our understanding of plant–soil–microbe coupling during ecosystem restoration on lava plateaus. Full article

Arid salt marsh ecosystems endure chronic water scarcity and high salinity stress, with the stability of their functions inextricably linked to the pivotal role of the rhizosphere microenvironment of halophytes. This study focused on three typical halophytes (Kalidium cuspidatum, Nitraria tangutorum, Reaumuria soongarica) in the Jiantan wetland, and deeply explore how these halophytes differently regulate the soil microenvironment through the rhizosphere effect. The results showed that the rhizosphere soil of Kalidium cuspidatum had higher pH, Na⁺, and K⁺ contents, while the rhizosphere soil of R. soongarica had higher total carbon, soil organic carbon, alkali-hydrolyzable nitrogen, and microbial biomass. Microbial community analysis revealed that rhizosphere soil of fungal diversity was significantly higher in K. cuspidatum than in R. soongarica, with distinct differences in bacterial and fungal community structures. These differences were closely associated with factors such as Na⁺, Olsen phosphorus, microbial biomass carbon and alkali-hydrolyzable nitrogen. Among the dominant phyla, Proteobacteria and Ascomycota predominate, with Desulfobacterota and Mortierellomycota exhibiting the highest explanatory power (>48%) for physicochemical property variations. The microbial network of rhizosphere soil of R. soongarica has the highest complexity (with 633 nodes and 3300 edges), but the proportion of positive correlation edges was the lowest (21.58%). Structural equation modeling indicates that soil physical properties indirectly influence network complexity by negatively regulating chemical properties and microbial biomass, while microbial diversity had a direct positive effect on dominant phylum composition and network complexity. This study elucidated the differentiated adaptive strategies of rhizosphere microenvironment-microbe interactions in halophytes, providing a theoretical basis for wetland ecological restoration. Full article

Cattle manure composting is an effective strategy for recycling agricultural waste. However, the presence of lignocellulosic materials in cattle manure–maize straw mixtures can limit the degradation efficiency during composting. This study investigated the effects of microbial inoculation on composting performance using three treatments: a lignocellulose-degrading microbial consortium (MC1), a commercial microbial inoculant (BS1), and a non-inoculated control (CK). The results showed that the MC1-treated pile entered the thermophilic phase (>50 °C) earlier than the BS1-treated pile. After 49 days of composting, the lignocellulose degradation rates in the MC1, BS1, and CK treatments were 46.25%, 37.5%, and 29.8%, respectively. Based on compost maturity indicators, including temperature, C/N ratio, pH, and electrical conductivity (EC), the composting period required to reach maturity was shortened by 8 days in the MC1 treatment compared with the BS1 treatment (37 vs. 45 days). Microbial community analysis indicated that MC1 inoculation increased the relative abundance of key microbial groups, particularly Ascomycota and Firmicutes, thereby enhancing lignocellulose degradation and accelerating composting. These findings provide insights into the application of lignocellulose-degrading microbial inoculants for improving cattle manure composting efficiency. Full article

Soil degradation remains a major challenge in sub-Saharan Africa, particularly within smallholder farming systems characterized by low-input agriculture and unsustainable land use practices. Sustainable agriculture production requires a good understanding of soil characteristics across diverse farming contexts. This study assessed soil health and microbial diversity across three contrasting systems: long-term fallow (aggregated farm A), high-input (aggregated farm B), and conventional smallholder (non-aggregated farm C) farms experiencing declining productivity. Soil samples collected from the three contrasting systems were analyzed for physicochemical properties and microbial communities using high-throughput DNA sequencing. Microbial communities were characterized by using amplicon sequencing targeting bacterial 16S rRNA and fungal ITS gene regions, allowing taxonomic profiling and inference of microbial diversity patterns. The two aggregated farms predominantly had clay soils, with pH values ranging from 6.78 to 7.39 and organic carbon content from 1.17% to 1.64%. In contrast, conventional farms had loamy to clayey soils with a pH value of 5.88 and an organic carbon content of 1.25%. Both types of aggregated farms showed moderate to high concentrations of total nitrogen (0.12–0.13%), phosphorus (38.79–151.36 mg/kg), and potassium (548.84–943.52 mg/kg), along with elevated levels of calcium and magnesium, though fertilizer application was inconsistent across the sites. Microbial diversity analysis revealed significant differences among the systems. The dominant bacterial phyla were Pseudomonadota (48.5%), Acidobacteriota (34.2%) and Actinomycetota (19.6%), while the primary fungi included Ascomycota, Basidiomycota and Mortierellomycota. Functional profiling using COG and KEGG databases showed distinct variations in microbial potentials, with a high diversity of Actinobacteria, Acidobacteria and Proteobacteria. Functional profiles inferred from amplicon-based predictions represent potential metabolic capabilities and should be interpreted cautiously as indicative rather than direct functional gene quantification. Correlation analyses between soil and microbial communities provided essential baseline data to support the development of sustainable farming practices and land restoration strategies aimed at improving soil fertility and agricultural productivity in these degraded landscapes. Full article