Microbial communities play essential roles in mediating plant defenses against insect pests. However, how host-associated microbiota and metabolites jointly respond to bark beetle infestation remains largely unexplored. Here, we integrated microbiome and metabolome profiling to elucidate how Pinus tabuliformis regulates its phloem and rhizosphere responses under varying levels of Dendroctonus valens infestation. Both bacterial and fungal diversity, as well as the relative abundance of dominant taxa such as Erwinia and Pseudoxanthomonas , shifted significantly with infestation intensity. Concurrently, key plant defense metabolites—including terpenoids, jasmonates, and polyphenols—were markedly elevated. Pathway enrichment analysis indicated that the phloem was characterized by enhanced phenylpropanoid and flavonoid biosynthesis, whereas the rhizosphere soil accumulated terpenoids and polyketides, implicating both compartments in resistance modulation. In the phloem, differential bacterial and fungal taxa displayed distinct positive and negative correlations with phenylpropanoid intermediates and downstream derivatives, while in the rhizosphere, bacteria from Bacillota and fungi such as Candida and Ogataea were strongly linked to diterpenoids, sesquiterpenoids, flavonoids, and indole derivatives. These findings demonstrate that P. tabuliformis mounts a compartment-specific, microbiome-associated metabolic response to D. valens infestation, providing new insights into the ecological roles of symbiotic microbiota in plant defense and offering a mechanistic foundation for microbe-based pest management strategies.

Old-growth oak (Quercus robur) forests in Europe are biodiversity hotspots, yet their airborne fungal diversity remains poorly studied. We investigated aeromycobiota in three Lithuanian oak stands (Punia, Dūkštos and Šilinė) using passive spore traps combined with DNA metabarcoding. Weekly sampling between August and September 2022 yielded 75 spore samples, producing 262,755 high-quality fungal sequences clustered into 1,881 operational taxonomic units (OTUs) representing six phyla and 36 classes. Ascomycota (53.1% of OTUs) and Basidiomycota (44.3%) dominated in richness, while Basidiomycota prevailed in relative sequence abundance (62.8%). Major taxa included Exobasidiaceae sp., Cladosporium sp., Melampsora sp., and Thelephora terrestris. Airborne fungal communities exhibited a substantial core assemblage shared among stands, accompanied by stand-associated differences in species richness and relative sequence abundance. The Punia stand showed the highest richness and the greatest proportion of stand-specific OTUs. Temporal variation was detectable but moderate relative to spatial differences among stands. Functional guild analysis revealed dominance of saprotrophs (46.5% of assigned OTUs), followed by pathotrophs (14.5%) and symbiotrophs (13.2%). Overall, our results demonstrate that passive spore traps-based airborne metabarcoding captures high fungal diversity and resolves both widespread and stand-associated community patterns in old-growth oak forests. This study provides the first characterization of aeromycobiota in old-growth Q. robur forests of Northern Europe and highlights the value of airborne metabarcoding for fungal biodiversity assessment and long-term forest monitoring.

Despite the widely recognized importance of grassland restoration for soil multifunctionality (SMF), its temporal dynamics along the restoration chronosequence and the relative contributions of bacterial and fungal diversity to SMF remain poorly understood, particularly in alpine grasslands. Here, we examined SMF along an alpine grassland restoration chronosequence (1, 5, 7, 13, and 20 years) on the Qinghai–Tibet Plateau. We found that SMF exhibited a pronounced non-linear trajectory, increasing by 39.13% from year 1 to year 7, subsequently declining by 50% and 46.88% at years 13 and 20, respectively, relative to the peak at year 7. Fungal richness varied markedly across the restoration chronosequence, peaking in year 5 with a 16.03% increase relative to year 1, and was positively associated with SMF, whereas bacterial richness showed no significant relationship. Structural equation modeling further confirmed that, along with soil moisture, fungal richness was significantly associated with SMF. Together, our findings highlight fungal diversity as a key driver of SMF during alpine grassland restoration and improve process-based predictions of alpine grassland functioning under ongoing climate change.

Soil microbiome drives soil multifunctionality across slope positions in a mountain tea plantation ecosystem.

Phoenix Nirvana and rebirth-pyrophilous microbes reconstruct soil microbial communities in a short term post-fire forest.

Ecosystems worldwide are undergoing unprecedented changes, and as a result amphibians are experiencing devastating population declines driven by subsequent habitat loss and emerging pathogens. The skin microbiota is an important first line of defence for amphibians against pathogens. Here, for the first time, we characterised the bacteria and fungi comprising the skin microbiota of 56 individual golden Alpine salamanders (Salamandra atra aurorae, Trevisan, 1982), a highly endemic and endangered amphibian subspecies. In addition, we investigated the impact of the 2018 Vaia windstorm on skin microbiota of salamanders in plots classified as impacted or non-impacted based on windthrows. Salamander sex, weather during sampling, and dominant tree species in plots were also investigated as influencers of microbiota. Beta diversity estimates revealed greater variation in bacterial microbiota composition among individuals from non-impacted plots compared to plots impacted by Vaia. Notably, we found differential abundances of five genera of bacteria and eight genera of fungi in the skin microbiota of salamanders from impacted compared with non-impacted plots. Further analyses revealed that median relative abundances of Aeromonas hydrophila, the causative agent of the potentially fatal red-leg syndrome, were significantly higher in microbiota of salamanders from impacted plots. Weather conditions during sampling significantly influenced both alpha and beta diversity of the skin microbiota, and explained up to 9% of bacterial and 6% of fungal variation. Bacterial richness and phylogenetic diversity were lower during rainfall, whereas fungal beta diversity increased, suggesting contrasting moisture preferences. These findings suggest that extreme weather events, as well as moderate daily weather fluctuations, may be associated with the microbial communities of amphibian skin, potentially affecting their resilience to pathogens. This study underscores the importance of considering both natural and human-mediated disturbances in conservation strategies for vulnerable species like the golden Alpine salamander.

Characterization and analysis of the skin mycobiome in keloid: A case-control study.

Karst desertification (KD) severely constrains regional ecological security and sustainable development. As an important ecological restoration measure, soil and water conservation agroforestry (SWCAF) systems have unclear mechanisms for soil microbial responses. This study investigated the effects of potential–light (PL), light–moderate (LM), and moderate–high (MH) KD on soil physicochemical properties and microbial communities in Karst SWCAF (KSWCAF) systems. It explored the drivers of microbial community changes. The results showed that (1) Soil physicochemical properties exhibited nonlinear changes along the KD gradient. Key soil-fertility indicators including silt, clay, total porosity (TP), total phosphorus (Total_P), total nitrogen (Total_N), soil organic carbon (SOC), and carbon nitrogen ratio (C_N) showed significant unimodal patterns, peaking at the LM stage with optimal overall soil quality; (2) The dominant bacterial phyla were Pseudomonadota, Acidobacteriota, Actinomycetota, and Planctomycetota, while the dominant fungal phyla were Ascomycota, Basidiomycota, and Mortierellomycota. The overall abundance of these dominant phyla increased with intensifying KD, except that the relative abundance of Pseudomonadota was lowest in the QZ study area, while Acidobacteriota was highest in the QZ area. The dominant fungal phylum Ascomycota increased with KD intensification; (3) KD significantly influenced microbial community structure and beta diversity. Fungi showed stronger responses to the KD gradient than bacteria. Bacterial alpha diversity was significantly higher in the LM stage compared to the PL and MH stages (p < 0.05), while fungal alpha diversity was significantly lowest in the MH stage (p < 0.05); (4) Bacterial networks exhibited highest complexity but reduced stability at the LM stage, whereas fungal networks enhanced stability at the MH stage by increasing modularization and positive correlation proportions; (5) RDA revealed that soil physicochemical factors explained 66.89% and 98.82% of bacterial and fungal community variation, respectively, with pH, moisture, and C_N as key drivers. Overall, KD regulates microbial community structure and functional allocation by reshaping the soil environmental gradient, with the LM stage potentially representing a “transitional optimization window” for KSWCAF ecosystem structure and function. This study provides a theoretical basis for microbial regulation strategies in KD control and soil and water conservation (SWC) processes.

Both fungi and bacteria contribute to the efficiency of activated sludge processes. However, fungal degradability has historically been overlooked in the anaerobic fermentation of waste-activated sludge (WAS). This study investigated the role of an enriched microbial consortium of degrading fungi (MCDF) in WAS fermentation. MCDF was initially enriched using a mixture of WAS and two mesophilic anaerobic sludges with chitin as the substrate. Fungal diversity and key cell wall polysaccharides, including chitin, mannan, and glucans, were identified in WAS. The addition of enriched MCDF to WAS significantly increased methane production by 35% and disrupted the floc structure through degradation of native fungi. The enriched MCDF also utilized fungal polysaccharides from four fungal species (Candida albicans, Trichosporon asahii, Geotrichum sp., and Magnusiomyces capitatus) and facilitated the release of intracellular organics. Proteinophilum and Petrimonas were identified as the main producers of chitinase (EC 3.2.1.14). Additional microbial producers were identified for mannanase (EC 3.2.1.78), β-1,4-glucanase (EC 3.2.1.4), and β-1,3-glucanase (EC 3.2.1.6). The relative activities of these four hydrolases in WAS were only 0.01%-12.3% of those in enriched MCDF. These results highlight the multifunctional potential of MCDF enrichment in WAS digestion, including degradation of fungal cell wall polysaccharides, release of intracellular fungal organics, and hydrolysis of bacterial extracellular organics. Overall, this study demonstrates that the destruction of native fungi in WAS provides a promising approach to enhance methane production and anaerobic digestion efficiency in wastewater treatment plants.IMPORTANCEBoth fungi and bacteria contribute to maintaining the floc structure of waste-activated sludge (WAS). This study highlights that MCDF enrichment significantly enhances methane production and disrupts the floc structure through the degradation of native fungi in WAS. Fungal diversity and key fungal cell wall polysaccharides-chitin, mannan, and glycans-were identified in WAS. The MCDF consortium was shown to utilize extracellular organics from four fungal species (Candida albicans, Trichosporon asahii, Geotrichum sp., and Magnusiomyces capitatus) and promote the release of intracellular organics. Multi-omics analysis revealed Proteinophilum and Petrimonas as the main chitinase producers in MCDF. Additional hydrolytic activities were observed: Fermentimonas and Petrimonas for mannanase, Mesotoga and Proteinophilum for β-1,4-glucanase, and Syntrophorhabdus for β-1,3-glucanase. Notably, the activities of these four hydrolases were significantly higher in MCDF than in WAS, indicating that MCDF is the main source of key functional enzymes. These findings highlight the multifunctional potential of MCDF enrichment in enhancing methane production during WAS digestion.

The Inner Mongolia Autonomous Region, located in northern China, represents a temperate semi-arid ecosystem dominated by steppe vegetation and characterized by rich, yet understudied, fungal diversity. During an investigation of microfungi associated with decaying plant materials in the desert regions of Inner Mongolia, two novel species of Comoclathris were collected and isolated. Detailed morphological examinations and multi-locus phylogenetic analyses based on ITS, LSU, SSU, and rpb 2 sequence data support the establishment of these taxa as novel species: Comoclathris desertica and C. xiangshawanensis . These two species are described and illustrated herein, with particular attention to their differences from similar species with respect to ascomatal structures and ascospore morphology. The discovery of these new taxa expands the known diversity and distribution of Comoclathris in China and provides new insights into the saprobic fungal communities of semi-arid regions. This study also highlights the ecological and taxonomic significance of continued surveys on saprobic fungi in grassland and desert ecosystems of northern China.

ABSTRACT Mexican dry ecosystems, mainly tropical dry forests, harbor a vast and largely undiscovered fungal diversity. The stalked puffballs of Tulostoma (Basidiomycota: Agaricales) are highly cryptic, necessitating detailed and expert examination to accurately distinguish the species. A revision of the MEXU national fungarium and recent sampled specimens revealed fruiting bodies that did not match any known species. This led us to propose T. parvirufula and T. chamelensis as new species. Six collections were morphologically characterized using two microscopy techniques: light and scanning electron microscopy. DNA was extracted, the nuc rDNA internal transcribed spacer region ITS15.8S-ITS2 (ITS barcode) and D1–D2 domains of the nuc 28S rDNA were amplified and sequenced. Phylogenetic analyses were conducted using maximum likelihood and Bayesian inference methods, incorporating sequences from previous studies. Tulostoma chamelensis is distinguished by its medium-sized spore sac, a hyphal exoperidium that persists at the base, a tubular ostiole, and verrucose to subreticulate basidiospores. Tulostoma parvirufula is characterized by minute spore sacs, a tubular ostiole, a hyphal exoperidium, a reddish-brown endoperidium, and spiny basidiospores. Phylogenetic analyses place both species in a sister clade to clade 11, alongside other taxa with tubular ostioles and coarsely ornamented basidiospores, further expanding our understanding of the Tulostoma genus and its diversity in dry ecosystems.

This study aims to enhance our understanding of Ascomycota biodiversity in Bingöl Province by presenting data obtained through systematic macrofungal field surveys conducted between 2018 and 2025. As a result of this research, a total of 16 species belonging to the classes Pezizomycetes, Leotiomycetes, and Sordariomycetes were identified. Among these species, Ascobolus lignatilis Alb. & Schwein. (1805), Ascocoryne albida (Berk.) Seifert (2014), and Olla scrupulosa (P. Karst.) Svrček (1986) are newly recorded for Türkiye, while the remaining 13 species represent new records for Bingöl Province. Notably, the genus Olla is reported from Türkiye for the first time, representing a novel contribution to the national mycobiota. Species identification was based on macro- and micromorphological features, supported by detailed descriptions, calibrated microscopic measurements, digital illustrations, and habitat photographs, all of which clarify the diagnostic characteristics. These findings reveal that Bingöl Province hosts a previously underestimated diversity of Ascomycota and underscore its significance as a regional reservoir of fungal diversity.

Soil microorganisms mediate critical ecosystem processes, including nutrient cycling and climate regulation. However, the extent to which their functional resilience and microbial food web dynamics respond uniformly to organic amendment across two land-use types remain poorly understood. In this study, we conducted a 30-day microcosm experiment to investigate how exogenous resources addition restructures the assembly of primary microbial functional groups (bacteria, fungi, and protists) in urine-amended soils under contrasting land-use regimes: intensively managed maize fields and natural woodlands. Results showed that straw addition consistently reduced both OTU richness and Shannon diversity of bacteria (by 8% and15%, respectively), fungi (26% and 21%), and protists (21% and 29%) in both soil types, yet enhanced cross-domain microbial interactions. Co-occurrence network analysis revealed variation in trophic interaction based on network parameters: maize soils fostered bacteria-dominated networks, whereas fungal hubs dominated in woodland systems. Deterministic processes predominantly govern bacterial community assembly, contrasting with the stochastic dominance observed in fungal and protist communities. Notably, both land use regimes showed consistent decreases in α-diversity, increased network complexity, and shifts toward similar assembly processes despite initial differences in community structure. Our findings demonstrate that organic amendments can override land-use legacies in shaping microbial community dynamics, highlighting the integrated impact of availability and biotic interactions in driving soil microbial food web dynamics.

Wild populations possess higher endophytic fungal diversity and structural complexity than ex-situ plants in coralloid roots of a cycad in Southwest China

Cinnamomum cassia is a renowned medicinal and aromatic plant with significant economic importance and broad pharmacological applications. This study investigates the taxonomy and diversity of endophytic fungi belonging to the order Diaporthales, isolated from this plant in Guangdong Province, China. A total of six isolates were obtained from healthy leaves. These isolates were examined using morphological characteristics and multilocus phylogenetic analyses based on the internal transcribed spacer (ITS), large subunit ribosomal RNA gene (LSU), and translation elongation factor 1-alpha (tef1). Phylogenetic reconstructions inferred from maximum likelihood and Bayesian inference, together with morphological evidence, revealed that the isolates represent three distinct and previously undescribed species, which are herein described as Gnomoniopsis luodingensis sp. nov. (Gnomoniaceae), Ternstroemiomyces cinnamomi sp. nov., and Ternstroemiomyces zhaoqingensis sp. nov. (Ternstroemiomycetaceae). These findings expand the known host range of endophytic fungi and provide essential taxonomic data for the fungal community associated with this economically important medicinal plant.

Organic soybean seeds are susceptible to colonization by numerous fungal pathogens, which can reduce their germination capacity and nutritional quality. This study evaluated fungi transmitted by seeds and their effects on selected seed quality parameters, as well as the influence of variety, location and growing season. In total, 471 fungal isolates belonging to 24 genera and 37 species were obtained from three soybean varieties (Erica, Es Commandor and Cerez PZO) cultivated at two locations during the 2022-2023 seasons. All obtained isolates were identified based on ITS sequencing, and Fusarium isolates were further characterized to the species level using TEF and RPB2 markers. Fusarium spp. was the most frequently isolated genus, accounting for 35.7% of all isolates, followed by Alternaria spp. (15.9%) and Aspergillus spp. (11.9%). Fungal frequency and species diversity differed significantly between years. Seed germination capacity was significantly lower in 2023 than in 2022 and coincided with higher fungal colonization, lower spring temperatures, and increased rainfall. A significant negative Pearson's correlation (r = -0.58, p < 0.05) was found between fungi abundance and seed oil content, indicating a direct impact of fungal colonization on nutritional quality. These results highlight the role of environmental conditions in seed-borne pathogen communities and the need for monitoring and seed health management to ensure soybean seed quality.

The Arabian Sea is ecologically and environmentally significant due to its high biotic diversity and its potential role as a reservoir of emerging resistance determinants. However, molecular-level insights into the taxonomic composition, functional potential, and resistome of sediment associated communities from deep-sea seamount sediments remain limited. A metagenomic approach was employed to investigate the biotic composition, metabolic potential, resistome profiles, and physicochemical characteristics of two seamount sediment samples (SM1 and SM7) collected from the Arabian Sea. Distinct environmental conditions were observed, with SM1 enriched in inorganic nitrogen, whereas SM7 exhibited higher organic carbon content and pigment concentrations, indicating differences in substrate availability. These variations were consistent with differences in the community structure, with SM1 harbouring a less diverse assemblage dominated by Actinomycetota and fungi, while SM7 supported a broader community comprising Actinomycetota, diverse fungi, protists, metazoans, and a richer viral component. Functional annotation revealed enrichment of nitrogen metabolism pathways in SM1, whereas SM7 showed increased representation of carbohydrate metabolism and a higher proportion of novel gene content. Both sediment samples encoded antibiotic and heavy metal resistance genes; however, SM7 exhibited greater abundance and diversity of putative resistance-associated genes, including resistance to mupirocin, triclosan, and sulfonamides, along with broader metal resistance and stress response genes. The results based on two samples demonstrate pronounced sample specific variation in community structure, metabolic potential, and resistome profiles across Arabian Sea seamount sediments. These findings highlight Arabian Sea deep-sea sediments as important molecular reservoirs of microbial diversity and adaptive potential shaped by local environmental conditions.

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.

Fungal community structure and network connectivity as indicators of soil health under long-term land use.

Aflatoxin B1 contamination and fungal diversity in oilseed cakes and formulated feeds from livestock feed markets in Addis Ababa and surrounding areas.