Search Results (72)

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 fungi play a pivotal role in maintaining ecosystem functions and regulating plant health. Although plant root traits can significantly impact the abundance and diversity of different fungal groups, the mechanism by which plant root strategies drive the assembly of soil fungal guilds remains limited. Utilizing Root Economics Space theory, this study investigates how four green manures (hairy vetch, rye, radish, and rapeseed) with contrasting root functional strategies (along the ‘fast–slow’ and ‘outsourcing–DIY’ axes) regulate the composition and functional structure of soil fungal communities. Community characteristics of three functional guilds (plant pathogens, saprophytes, and arbuscular mycorrhizal fungi), as well as relationships between these communities and plant root traits, were evaluated using a combination of Illumina high-throughput sequencing, functional annotation, and multivariate statistical analysis. Overall, different root strategies were associated with distinct fungal community patterns, potentially related to differences in root-derived resource inputs and soil properties. The ‘slow’ and ‘DIY’ strategies were associated with lower relative abundance of plant pathogenic fungi and higher relative abundance of saprotrophic fungi, whereas the ‘fast’ and ‘outsourcing’ strategies were associated with higher relative abundance of plant pathogens and AMF. These findings suggest that root functional strategies may help explain variation in fungal guild composition under different green manure species. From a practical perspective, the results provide a basis for selecting green manure species to help manage soil-borne disease risk, regulate beneficial soil microbial communities, and support more sustainable soil management in agricultural production. Full article

Background and Objectives: Polyethylene (PE) mulching enhances crop productivity through microclimate optimization but introduces synthetic polymer-derived compounds into agricultural soils. Despite widespread use, biochemical and microbial impacts of PE mulch emissions remain poorly understood. This study investigated the impact of PE mulch emissions on soil metabolomes and microbial communities during field pea (Pisum sativum L.) cultivation. Methods: A 75-day field experiment compared PE-mulched and non-mulched soils across five temporal sampling points (T0–T4). Headspace solid-phase microextraction coupled with gas chromatography–mass spectrometry was used to identify PE-derived organic compounds in mulched soils. Microbial community structure was assessed through the phospholipids derived fatty acids (PLFA) approach, whereas mass spectrometric untargeted metabolomics was used to characterize the soil biochemical profiles. Results: Analysis identified 18 PE-derived organic compounds (n-alkanes, phthalates, and additives) in the mulched soils. PE mulching significantly increased bacterial abundance (anaerobic bacteria, actinomycetes, and aerobic bacteria) but suppressed all functional fungal guilds, particularly saprotrophic fungi (30% reduction) and arbuscular mycorrhizal symbionts. PE-derived organic compounds were associated primarily with the first RDA axis (RDA1), which alone explained 44.6% of the metabolome variance. These compounds presented strong positive correlations with organic nitrogen compounds and lipids and negative correlations with benzenoids and nucleotides. Pathway analysis revealed perturbations in energy metabolism, lipid metabolism, and xenobiotic degradation pathways. Conclusions: PE mulch emissions differentially shift soil microbial communities and metabolic networks, with bacterial proliferation contrasting with fungal suppression. These findings highlight the complex trade-offs between agronomic benefits and soil biological impacts, emphasizing the need for sustainable mulching alternatives. Full article

This study evaluates the ecological impact of Robinia pseudoacacia L. (black locust) invasion on native chestnut (Castanea sativa Mill.) groves on Mount Amiata (Central Italy), focusing on both plant and macrofungal community dynamics. Surveys were conducted over a three-year period (2022–2024) across 16 plots to assess shifts in taxonomic alpha diversity, species richness, and trophic guild structure. Our results demonstrate that while R. pseudoacacia stands exhibit a higher Shannon–Wiener index for plants, native chestnut groves host significantly greater species richness and higher taxonomic distinctiveness across both biological groups. A major shift in fungal functional structure was observed with chestnut-dominated plots characterized by a predominance of ectomycorrhizal species (58.3%), whereas invaded stands were heavily dominated by saprotrophic fungi (73.4%). Non-metric Multidimensional Scaling (NMDS) further confirmed a clear separation in community composition between the two forest types, indicating that R. pseudoacacia invasion leads to a homogenization of the forest biota and a potential decline in ecosystem health, as evidenced by the sharp reduction in mycorrhizal diversity. These findings highlight the importance of monitoring macrofungal communities as sensitive bioindicators of the ecological degradation caused by invasive woody species. Full article

Crop residues can harbor pathogens, making winter sanitation essential for sustainable viticulture. The grass–sheep–grape system could improve vineyard health through microbial optimization. To evaluate this, we assessed the effects of sheep feeding on fallen leaves on the occurrence of grape diseases through greenhouse experiments and used high-throughput-sequencing to compare microbial communities in grape fallen leaves and sheep feces, aiming to determine whether winter grazing reduces residue-borne pathogens. The results revealed that sheep grazing in vineyards significantly reduces the occurrence of grape leaf and cluster diseases, as well as a fundamental difference in microbial structures between leaves and feces, with no fungal taxa detected in the feces. The number of shared bacterial OTUs was minimal, while feces contained significantly more unique bacterial OTUs than fallen leaves. Additionally, bacterial diversity was significantly higher in feces than in fallen leaves. Sheep feces harbored a substantial number of highly efficient cellulose-degrading anaerobic bacteria, which may enhance organic matter conversion efficiency, and promote nutrient cycling in vineyards. Moreover, the grazing process directly reduced several pathogenic fungi associated with grape leaf, fruit, and root diseases. Functional analysis further indicated that fecal bacterial communities were primarily enriched in core metabolic and genetic processing functions, while leaf microbes were more involved in microbial interactions and secondary metabolism. More importantly, no function guilds of plant pathogenic fungi were present in feces. Overall, winter sheep grazing in vineyards can remove fallen leaves, not only reducing the risk of pathogen transmission but also potentially introducing beneficial bacterial communities. This study provides a feasible strategy for organic vineyard management in winter, and offers important insights for promoting sustainable vineyard production. Full article

Understanding the ecological drivers of plant-associated microbiota is essential for predicting grassland ecosystem resilience. This study aimed to characterize the community structure, functional potential, and soil environmental drivers of rhizosphere and root endophytic microbiota associated with Polygonum divaricatum across three Hulunbuir Grassland sites. A nested sampling design was applied with three replicated plots per site, from which paired rhizosphere soil and root samples were collected. Each sample represented a composite of 15 plants, yielding six samples per site (total n = 18) and allowing the separation of compartmental and environmental effects on community assembly. P. divaricatum plays a key role in nutrient cycling and soil stability; however, its rhizosphere and root microbiomes remain poorly characterized. Fungal diversity was consistently higher in the root endosphere, whereas bacterial diversity was greater in rhizosphere soils. Fungal assemblages were dominated by Ascomycota and Mortierellomycota, primarily represented by Mortierella and Trichoderma, while bacterial communities were dominated by Actinomycetota and Pseudomonadota, enriched in Bradyrhizobium and Pseudonocardia. Community differentiation reflected strong compartmental filtering and responses to soil pH, organic carbon, nitrogen, and enzyme activities. Functional prediction indicated clear compartmental partitioning: in the rhizosphere, bacterial communities were enriched in pathways related to carbon and nitrogen metabolism and secondary metabolite biosynthesis, whereas in the root endosphere, functional profiles were more associated with transport, uptake, and fermentation; fungal communities were dominated by saprotrophic and symbiotrophic guilds. These findings demonstrate that soil biochemical gradients and host-driven filtering jointly structure the P. divaricatum microbiome, providing ecological insights into plant–microbe–soil interactions and the maintenance of grassland ecosystem stability. Full article

Scutellaria baicalensis is an important medicinal plant, and the diversity of its rhizosphere microbiota may influence its growth, development, and yield. Numerous studies have reported that warming associated with global climate change significantly altered plant-associated soil microbial diversity. To reveal the effects of night-time warming on the rhizosphere microbial community of S. baicalensis, soil microbial diversity in the rhizosphere (RS) and bulk soil (BS) of S. baicalensis were analyzed by employing bacterial 16S rRNA and fungal ITS sequencing technology. Warming significantly altered both bacterial and fungal communities in the rhizosphere and bulk soils of S. baicalensis, with pronounced changes in OTU composition, relative abundances at both phylum and species levels. The analysis of alpha and beta diversity showed that warming significantly altered the fungal community structure in the rhizosphere soil (R² = 0.423, p < 0.05) and significantly reduced the species richness in the bulk soil of S. baicalensis (Shannon and Simpson index, p < 0.05). LEfSe and functional prediction analyses revealed that warming altered the taxonomic composition of both bacterial (35 taxa, LDA > 3) and fungal (24 taxa, LDA > 4) communities in rhizosphere and bulk soils of S. baicalensis, with multiple bacterial and fungal taxa serving as treatment-specific biomarkers. Functional predictions indicated that fungal functional groups, including saprotrophic and mycorrhizal guilds, were more strongly affected by warming than bacteria. Overall, warming has a significantly stronger impact on fungal communities in the rhizosphere and bulk soils of S. baicalensis than on bacteria, and has a significantly greater effect on the diversity of microbial communities in bulk soils than that in rhizosphere soils. This study provides important data for understanding the impact of global climate change on the rhizosphere microbial communities of cultivated plants. Full article

To elucidate the potential of integrated multi-omics approaches for studying systemic mechanisms of mycorrhizal fungi in mediating plant-microbe interactions, this study employed the Tuber-inoculated Corylus system as a model to demonstrate how high-throughput profiling can investigate how fungal inoculation reshapes the rhizosphere microbial community and correlates with host metabolism. A pot experiment was conducted comparing inoculated (CTG) and non-inoculated (CK) plants, followed by integrated multi-omics analysis involving high-throughput sequencing (16S/ITS), functional prediction (PICRUSt2/FUNGuild), and metabolomics (UPLC-MS/MS). The results demonstrated that inoculation significantly restructured the fungal community, establishing Tuber as a dominant symbiotic guild and effectively suppressing pathogenic fungi. Although bacterial alpha diversity remained stable, the functional profile shifted markedly toward symbiotic support, including antibiotic biosynthesis and environmental adaptation. Concurrently, root metabolic reprogramming occurred, characterized by upregulation of strigolactones and downregulation of gibberellin A5, suggesting a potential “symbiosis-priority” strategy wherein carbon allocation shifted from structural growth to energy storage, and plant defense transitioned from broad-spectrum resistance to targeted regulation. Multi-omics correlation analysis further revealed notable associations between microbial communities and root metabolites, proposing a model in which Tuber acts as a core regulator that collaborates with the host to assemble a complementary micro-ecosystem. In summary, the integrated approach successfully captured multi-level changes, suggesting that Tuber-Corylus symbiosis constitutes a fungus-driven process that transforms the rhizosphere from a competitive state into a mutualistic state, thereby illustrating the role of mycorrhizal fungi as “ecosystem engineers” and providing a methodological framework for green agriculture research. Full article

This study investigated the composition and temporal dynamics of wood-inhabiting fungal communities in four aging tree species in Lednice Castle Park (Czech Republic), located within the Lednice–Valtice Cultural Landscape, a UNESCO World Heritage Site. Forty wood cores were collected from 20 trees at two time points (2023 and 2024). The hosts included horse chestnut (Aesculus hippocastanum L.), copper beech (Fagus sylvatica ‘Atropunicea’ L.), oak (Quercus robur L.), and poplar (Populus alba L.), each exhibiting visual signs of decline. Fungal assemblages were profiled using ITS2 high-throughput amplicon sequencing. Ascomycota dominated across all hosts (72–89% of reads), while Basidiomycota contributed 8–24%, largely represented by Agaricomycetes in F. sylvatica. Alpha diversity varied significantly among hosts (Shannon: F_3,36 = 10.61, p = 0.001 in 2023; F_3,36 = 10.00, p = 0.001 in 2024). Temporal shifts were host-dependent: F. sylvatica exhibited the strongest year-to-year decline in richness (Chao1: −83%, p = 0.007) and increased beta dispersion, while A. hippocastanum and P. alba showed significant increases in diversity (+65% and +42%, respectively). Community composition was shaped by host species (PERMANOVA Bray–Curtis: p = 0.001) and shifted over time (Jaccard: p = 0.001), with F. sylvatica showing the highest temporal turnover. Functional guild analysis revealed consistent dominance of saprotrophs (29–41%) and mixed pathotroph–saprotroph guilds (23–36%) across hosts, indicating active degradation processes inside functional xylem. These results indicate that, within the studied system, the wood mycobiome of aging trees is host-dependent and temporally dynamic rather than static or functionally neutral. Short-term temporal turnover observed between sampling years may contribute to shifts in fungal community composition and succession within wood, with potential implications for tree decline processes in managed historical park landscapes. Full article

The aim of this study was to determine fungal diversity and composition in an area of high host diversity and identify the organisms involved in the appearance of symptoms in Pinus needles. Asymptomatic and symptomatic live needle samples were obtained from different Pinus spp. in an arboretum with confirmed presence of brown spot needle blight. The samples were analysed using high-throughput sequencing of fungal ITS2rDNA. Ascomycota dominated all samples, with Lophodermium as the most abundant genus, although it showed lower representation in symptomatic needles. Other genera with recognised pathogenic potential, including Lecanosticta, Pestalotiopsis, Cyclaneusma, Rhizosphaera, Neophysalospora, and Cenangium, were also detected, whereas the Dothistroma genus was absent despite its presence in the region. Alpha diversity was higher in asymptomatic needles, with a significant difference only for the Shannon index, while Bray–Curtis dissimilarity revealed significant shifts in community composition between needle types. Functional guilds were dominated by pathotroph–saprotroph trophic mode, and the functional guild ‘plant pathogen’ was the most abundant across samples. These findings identify fungal genera associated with symptomatic and asymptomatic needles and provide guidance for future targeted isolation and detailed morphological and molecular identification using more resolutive techniques, enabling a deeper understanding of pathogenic community presence and their potential synergistic interactions. Full article

Soil degradation from long-term chemical fertilization poses serious challenges to the sustainability of black soil agroecosystems in Northeast China, particularly for the cultivation of medicinal plants such as Aralia continentalis Kitag. To evaluate eco-friendly alternatives, we compared decomposed leaf mulching (LM), conventional fertilization (CF), and an untreated control (CK) in a five-year field experiment. LM significantly improved soil structure by reducing bulk density by 12.8% (p < 0.05) and increasing porosity by 15.6% while enhancing organic carbon and humus fractions by 23.4% and 31.7%, respectively. These changes promoted microbial biomass carbon by 28.2% (p < 0.01) and enriched beneficial fungi such as Mortierella, which correlated with nutrient mobilization and plant growth. Fungal richness and diversity were higher under LM (+18.4% and +12.6%, respectively), whereas CF reduced evenness and favored dominance of stress-tolerant taxa. Functional predictions indicated that LM sustained saprotrophic and symbiotic guilds, while CF weakened mycorrhizal associations. Structural equation modeling identified microbial community composition as a central mediator linking soil properties, microbial diversity, and biomass (R² = 0.78), with LM exerting the strongest cascading effects. At the plant level, LM achieved the highest above- and belowground biomass, outperforming CF and CK by 26.3% and 34.5%, respectively. Overall, decomposed leaf mulching represents a sustainable strategy to restore soil quality, enhance microbial diversity, and support medicinal plant cultivation in cold-region agroecosystems. Full article

The soil microbiome is an essential component of agroecosystems. However, managing it remains a challenge due to our limited knowledge of how various environmental factors interact and shape its spatial distribution. This study presents a hierarchical ecological model to explain the assembly of the microbiome in sloping agricultural landscapes. Through a comprehensive analysis of bacterial and fungal communities, as well as the examination of metabolic and phytopathogenic profiles across a topographic gradient, we have demonstrated that topography acts as the main filter, structuring bacterial communities. Land use, on the other hand, serves as a secondary filter, refining fungal functional guilds. Our results suggest that hydrological conditions in floodplains favor the growth of stress-tolerant bacterial communities with low diversity, dominated by Actinomycetota. Fungal communities, on the other hand, are directly influenced by land use. Long-term fallow periods lead to an enrichment of arbuscular mycorrhiza, while agroecosystems shift towards pathogenic and saprotrophic niches. Furthermore, we identify specific topographic positions that may be hotspots for phytopathogenic pressure. These hotspots are linked to certain taxa, such as Ustilaginaceae and Didymellaceae, which may pose a threat to plant health. The derived hierarchical model provides a scientific foundation for topography-aware precision agriculture. It promotes stratified management, prioritizing erosion control and soil restoration on slopes, customizing nutrient inputs in fertile floodplains, and implementing targeted phytosanitary monitoring in identified risk areas. Our research thus offers a practical framework for harnessing soil spatial variability to improve soil health and proactively manage disease risks in agricultural systems. Full article

Fungal communities inhabiting leaves are key players in ecosystem processes but remain largely unexplored in Southern Hemisphere temperate forests. We characterized the foliar mycobiota of Nothofagus pumilio, a dominant deciduous tree in Patagonian forests, using ITS1 metabarcoding across seasons and tree health conditions. We detected 426 fungal taxa, including a 40-Amplicon Sequence Variant (ASV) core mycobiome persisting year-round. Fungal richness and biomass increased significantly in autumn, coinciding with leaf senescence, and community composition shifted markedly between seasons. Spring leaves were enriched in pathogens and basidiomycetous yeasts, while autumn leaves hosted more saprotrophs, ascomycetous yeasts, and lichen-associated fungi. Tree health had limited influence on overall community structure, but symptomatic trees showed higher ASV richness and specific indicator taxa, including the pathogen Trichosporiella multisporum and members of the Taphrinaceae and Saccotheciaceae families. Despite taxonomic turnover, ecological guilds remained relatively stable, suggesting functional redundancy. These findings reveal a seasonal successional trajectory in the foliar mycobiota of N. pumilio, from early-colonizing endophytes in spring to diverse decomposer assemblages in autumn. This study provides the first high-throughput insight into the structure and dynamics of foliar fungal communities in Southern Hemisphere temperate forests, offering a baseline for understanding microbial roles in forest health and resilience. Full article

This study aims to evaluate the restoration effect of artificially mixed-sown grasslands by investigating the characteristics of plant communities and soil fungal communities in long-term (22-year-established) artificial grasslands under six Poaceae mixture combinations. The experiment took mixed-sown grasslands of grass species established in 2002 on the Qinghai–Tibet Plateau as the research object. It employed ITS gene high-throughput sequencing technology to construct a fungal community distribution map and combined it with FUNGuild (Functional Guilds of Fungi) functional predictions to analyze fungal species abundance, structural diversity, molecular co-occurrence networks, and functional characteristics. By integrating Mantel test and RDA (redundancy analysis), we identified key environmental factors driving soil microbial community structure in mixed-sown grasslands and revealed the plant–soil–microbe interaction mechanisms in a Poaceae mixture grassland. The results showed that the HC treatment (a mixture of three grass species) significantly enhanced plant biomass and soil nutrient accumulation. In 2023 and 2024, its aboveground biomass increased by 66.14% and 60.91%, respectively, compared to the HA treatment (monoculture). Soil organic matter increased by 52.32% and 48.35%, while electrical conductivity decreased by 48.99% and 51.72%, respectively. The fungal community structure improved under the HD treatment (a mixture of four grass species), with an increased abundance of the dominant phylum Ascomycota and a 14.44% rise in the Shannon index compared to the HA treatment. The network complexity under the HF treatment (a mixture of six grass species) increased (with edge numbers reaching 494), while the functional abundance of plant pathogen was significantly lower than that under the HA treatment. Mantel test and RDA revealed that SEC (soil electrical conductivity) was significantly positively correlated with pH, while both exhibited negative correlations with other plant and soil physicochemical indicators. Moreover, SEC emerged as the core factor driving fungal community assembly. Mixed sowing of three to four grass species effectively regulated soil electrical conductivity, simultaneously enhancing plant biomass, soil nutrients, and fungal community diversity, representing an optimal strategy for artificial restoration of degraded grasslands. Full article

Understanding the soil fungal community in vineyards sheds light on the interactions between plants and their associated microorganisms. For example, identifying arbuscular mycorrhizal fungi (AMF), which are beneficial to grapevine growth, is a good indicator of soil health. In contrast, other fungi, such as the pathogen group, can be detrimental to vine growth. The present study aimed to characterize the soil fungal community and the fungal diversity present at six Mediterranean vineyards located in Burgos (Spain), delving into fungal functional guilds and focusing on AMF and pathogenic fungal groups. The fungal structure was investigated using DNA metabarcoding in three soil samples taken from each vineyard, and differences in the abundance of functional guilds were assessed. Similar soil fungal community structures were observed among soil sample repetitions within vineyards. In contrast, adjacent vineyards presented differences in their microbial composition. Saprophytes followed by pathogens were the dominant fungal functional guilds across all vineyards. However, no differences in the relative abundance of the different fungal functional groups were observed among sites. The vineyard with the highest relative abundance of AMF (0.5%) also had the lowest pathogen relative abundance from all the sites (29.76%). Also, sites presenting a high relative abundance of pathogens in soil (>35%) had a low relative abundance of AMF (<0.05%). Our results suggest that the fungal community is affected by the intrinsic properties of the soil and the characteristics of each vineyard’s microsite over the effect of the geographical proximity. In addition, to improve our understanding of the soil microbial ecology, we highlight the necessity of prospecting soil fungal analyses into functional groups, interpreting diversity results within taxonomic groups alongside the total abundance of target groups/species. Full article