FungalTraits vs. FUNGuild: Comparison of Ecological Functional Assignments of Leaf- and Needle-Associated Fungi Across 12 Temperate Tree Species

Functional adaptation of PM2.5 microbiomes to varying environmental conditions in Northeast Asia: Ulaanbaatar, Seoul, and Noto

This study examined the bacterial and fungal communities associated with PM2.5 collected from three geographically distinct locations in Northeast Asia-Ulaanbaatar (high pollution), Seoul (moderate pollution), and Noto (low pollution)-which collectively represent a gradient of urbanization and environmental conditions during the spring sampling period from March 15 to April 7, 2022. Ulaanbaatar exhibited the highest abundance of both bacteria and fungi, yet exhibited the lowest fungal diversity. In contrast, Noto exhibited the lowest microbial abundance but the highest fungal diversity, while Seoul displayed intermediate values. Dominant bacterial genera, including Caldalkalibacillus, Halomonas, and Nesterenkonia, demonstrated notable resilience across all three locations, highlighting their adaptability to diverse environmental conditions. The dominant fungal genera were Cladosporium and Candida. Analyses revealed significant correlations between microbial community structures and environmental factors. In Ulaanbaatar, microbial communities were strongly associated with meteorological parameters such as temperature, humidity, and wind speed. In Seoul, stronger correlations were observed with polycyclic aromatic hydrocarbons (PAHs). Noto exhibited weaker correlations with both meteorological factors and organic compounds. Across all sites, bacteria consistently showed broader niche breadths compared to fungi, reflecting their greater metabolic versatility and resource utilization capacity. Both bacterial and fungal niche breadths generally increased at intermediate concentrations of alkanes and DCAs but declined at extreme concentrations, suggesting optimal survival ranges. These findings highlight the complex interplay of environmental factors and pollutants in shaping microbial community structures and functional diversity across diverse geographical settings during the spring season.

Esophageal cancer and precancerous lesions: focus on resident bacteria and fungi

Accumulating evidence highlights the pivotal role of microbiomes in cancer development. To elucidate the esophageal microbiome's characteristics during esophageal squamous cell carcinoma (ESCC) progression, normal tissues from 13 healthy controls (HC), paired esophageal squamous intraepithelial neoplasia (ESIN) lesional and adjacent (ESINA) tissues from 10 ESIN individuals, and ESCC lesional and adjacent (ESCCA) tissues from 12 ESCC individuals were collected. Following 16S rRNA and ITS sequencing, analyses encompassed α/β-diversity assessments, shared species identification, Type-I Taylor's Power Law Extensions (TPLE), linear discriminant analysis effect size (LEfSe), co-occurrence networks, receiver operating characteristic (ROC) curve analysis, and functional predictions. Distinct microbial signatures characterized HC, precancerous, and cancerous groups. The ESIN group exhibited unique microbial features, including diminished bacterial and fungal species sharing relative to the ESINA group and maximal b values in TPLE for both taxa. Despite the absence of significant bacterial composition differences between HC and ESIN in β-diversity analysis, notable alterations in the oral microbiome were observed. ESIN was marked by Lactobacillus and Aspergillus enrichment, while ESCC was predominantly associated with Fusobacterium, Streptococcus, and Alternaria. Disease progression led to shifts and reductions in species co-occurrence network interactions. Aspergillus demonstrated potential diagnostic value for ESIN, and its ratio to pathogenic functional clusters within network analysis significantly enhanced ESCC detection accuracy. Functional predictions revealed stage-specific pathway enrichments. These findings delineate microbiome alterations across ESCC stages, emphasizing ESIN-specific microbial shifts that may inform microbiome-based strategies for early detection and intervention.

IMPORTANCE

This study collected esophageal tissues through gastroscopic biopsy and conducted sequencing and analyses to explore the diversity, heterogeneity, key microbial composition, interaction networks, and functional predictions of resident bacteria and fungi in esophageal squamous cell carcinoma (ESCC) progression. The esophageal squamous intraepithelial neoplasia group showed the highest heterogeneity in oral microbiome and fungi, with certain species potentially contributing to ESCC progression. Targeting the oral microbiome in high-risk populations may thus provide a valuable approach for improving early diagnosis and potentially intervening in disease progression.

Metabarcoding with Illumina and Oxford Nanopore Technologies provides complementary insights into tree seed mycobiota

BACKGROUND

Culturing of fungi is labor-intensive and reveals limited diversity, while high-throughput sequencing of barcodes (i.e., metabarcoding) enables a simultaneous detection of fungi from multiple environmental samples. Metabarcoding using short-read sequencers, such as Illumina platforms, provides high sequencing depths but results in many unidentified taxa. Long-read sequencing can improve species and genus assignments but might encompass lower sequencing depth and limit diversity coverage. In this study, fungi in seeds of eleven angiosperm and gymnosperm tree species were assessed using traditional culturing, Illumina short-read metabarcoding, and Oxford Nanopore Technologies long-read metabarcoding. We focused on seed-borne fungi as understanding their diversity and potential impacts on seedlings is crucial for securing plant health. We compared (1) the number and identity of fungal genera and species between metabarcoding approaches and traditional culturing and (2) fungal alpha- and beta-diversity between metabarcoding methods, considering different hosts and fungal lifestyles.

RESULTS

In both short- and long-read metabarcoding datasets, similar numbers of fungal reads and operational taxonomic units were assigned to comparable numbers of fungal genera and species. About one-third of the identified genera were plant pathogens, followed by saprotrophs and endophytes. Culturing overall revealed fewer fungal genera, while most of the fungal reads in short-read metabarcoding datasets stemmed from cultured taxa. Long-read metabarcoding revealed lower per-sample diversity than short-read metabarcoding and distinct fungal communities compared to those from the short-read datasets. Host-dependent patterns in alpha- and beta-diversity were observed across methods, with angiosperms harboring more fungal taxa than gymnosperms, and distinct community structuring across host tree groups and species, although the differences were stronger in short-read than long-read metabarcoding datasets.

CONCLUSIONS

Illumina and Oxford Nanopore Technologies metabarcoding captured similar host-dependent diversity patterns despite observed differences in numbers and composition of fungi. Short-read metabarcoding might be optimal for fungal biodiversity studies due to higher sequencing depths and resultant breadth of diversity. As error rates are continuing to decrease, reference databases expand, and throughput improves, long-read metabarcoding is becoming a strong candidate for future diagnostic studies of fungi. Traditional culturing captures most of the fungi from short-read metabarcoding and remains valuable for obtaining isolates for further research.

Diversity, Composition, and Ecological Function of Endophytic Fungal Communities Associated with Erigeron breviscapus in China

Endophytic fungi (EF) play crucial roles in accelerating the accumulation of medicinal components and regulating the survival and reproduction of medicinal plants. Erigeron breviscapus is a well-known traditional Chinese medicinal plant with effective therapeutic effects and a wide application, but little is known about the diversity, community structure, and ecological roles of EF in this plant. Here, the EF communities associated with different tissues of E. breviscapus at two seasons were studied by high-throughput sequencing methods. Furthermore, FUNGuild was performed to predict the ecological functions of the fungi. Didymella was found to be the most dominant genus across all four tissues, followed by Plectosphaerella, Filobasidium, Cystofilobasidium, and Cladosporium. Notably, the dominant and unique genera and biomarkers of four tissues were different. Interestingly, it was found that the roots had the highest fungal richness and diversity in summer. Moreover, both PCoA plots and PERMANOVA analyses indicated that the tissue and season were main factors contributing to the differences in the fungal communities of E. breviscapus. FUNGuild prediction revealed that pathotroph-saprotroph fungi and undefined taxa accounted for a high proportion in the EF of E. breviscapus. We also found some valuable endophytes that encouraged deeper investigation. These findings provide a theoretical reference for the further development and utilization of EF resources in E. breviscapus.

Microbial community formation during dietary exposure to Fe3O4-urease nanoconjugates in silkworm (Bombyx mori): Principal fungi groups facilitate functional flux

The gut microbiota of the silkworm (Bombyx mori) is essential for metabolic processes, including digestion and immunity. Nonetheless, the role of specific gut fungi in optimizing nutrient recycling influenced by infiltrated biomaterials remains inadequately elucidated. This study investigates the potential mechanisms through which gut fungi affect the dynamics of nutrient absorption in silkworms. For this purpose, 5th instar silkworms were exposed to Fe3O4-urease nanoconjugates for 168 h following the utilization of high-throughput microbiome sequencing to identify shifts in principal fungal groups. The conditional fungi groups Mucoromycota and Basidiomycota significantly increased from 10.28 % to 47.16 % and 0.53 % to 2.63 % respectively (p < 0.05), while Ascomycota decreased from 86.57 % to 52.29 %, having no negative impact on the growth and sustainability of the host insect. Functional analysis using FunGuild showed enriched trophic nodes including pathotrophs, saprotrophs and symbiotrophs while functions of DEGs demonstrated an increased metabolic capacity associated with iron and heme binding, and lipase activity. This reveals significant restructuring of the gut fungi microbiota with specific fungal taxa exhibiting enhanced abundance and diversity correlated with the presence of Fe3O4-urease nanoconjugates, serving as a potential for engineered nanomaterials to promote the sustainability and development of sericulture.

Historical Lead Contamination Linked to Atmospheric Deposition is Associated With Declines in Ectomycorrhizal Diversity and Shifts in Fungal Community Composition

Ectomycorrhizal and saprotrophic fungi respond differently to changing edaphic conditions caused by atmospheric deposition. Within each guild, responses can vary significantly, reflecting the diversity of species and their specific adaptations to environmental changes. Metal contaminants are often deposited onto earth's surface through atmospheric deposition, yet few studies have assessed the relationship between soil metal contamination and fungal communities. The goal of this study was to understand how soil metal contamination and other edaphic factors vary across the spruce-fir ecosystem in the Southern Appalachians and influence fungal diversity and function. Here, we characterize soil fungal communities using high-throughput sequencing of the ITS2 gene region and found that higher soil lead (Pb) concentrations were associated with lower fungal diversity. Ectomycorrhizal fungi were less diverse (specifically hydrophilic ectomycorrhizal functional types) at plots with elevated soil Pb concentrations, while saprotrophic fungi were less diverse at plots with elevated soil carbon:nitrogen ratios. Fungal community composition was significantly influenced by pH, Pb, and spatial factors. This study identifies important relationships between fungal diversity and soil Pb concentrations and indicates variable responses of genera within well-defined ecological guilds. Our work highlights the need to characterize poorly understood taxonomic groups of fungi and their function prior to further environmental degradation.

Native mixed microbe inoculants (M1H) optimize soil health to promote Cajanus cajan growth: the soil fungi are more sensitive than bacteria

Microbial inoculant is widely used in plant growth and crop production. However, the effect of native mixed microbial inoculants on soil microbiota and plant growth remain to be elucidated. Here, we used pot experiment for 5 months to determine the microbial inoculants treatments with growth-promoting effect on Cajanus cajan, such as M1P (Serratia marcescens) treatment and M1H treatment: the mixture of M1P and M45N (Paenibacillus polymyxa), and investigate the effect of these inoculants on the capacity of soil nutrients and rhizosphere microbiomes in promoting C. cajan growth. Further, the adaptability of these strains to environmental stress (temperature and pH) was determined by using stress-resistant growth experiment. The results showed that M1H treatment resulted in soil nutrients consumption and led to substantial alterations in the microbial community that were more effective in promoting C. cajan growth. The enhanced plant growth observed with M1H inoculation may be due to its impact on the soil micro-environment, particularly through increasing beneficial genera (e.g., Cunninghamella, Mortierella, Chryseolinea, and Bacillus) and decreasing potential genera (e.g., Zopfiella and Podospora). In addition, at the genus level (top 10), the effect of M1H inoculation on soil fungal community was higher than that of bacteria, which shows that the change of soil fungal community after M1H inoculation was more sensitive than that of bacteria. Spearman correlation analysis further revealed that the abundance of Cunninghamella, Mortierella, Chryseolinea, Zopfiella and Podospora were the key factors affecting C. cajan growth. Moreover, FUNGuild function prediction clearly indicated distinct differences in the fungal functions of CK, MIP and M1H treatment, in which a lower relative abundance of saprotroph fungi in M1H treatment compared to CK, these results may confirmed the possibility of decreasing the abundance of Zopfiella and Podospora under M1H treatment. Taken together, our findings highlight the role of M1H inoculant in promoting C. cajan growth and ameliorating soil health, and providing valuable insight of using native mixed microbial inoculants to cultivate C. cajan and optimize soil micro-environment.

Study of the Correlation Between Endophyte Abundances and Metabolite Levels in Different Parts of the Tissue of Cultivated and Wild Arnebia euchroma (Royle) Johnst. Based on Microbiome Analysis and Metabolomics

Arnebia euchroma (Royle) Johnst. has high medicinal and economic value, but in recent years, wild resources of this species have been depleted and the quality of artificially cultivated A. euchroma has been poor. The endophyte community of medicinal plants is rich, serving as an internal resource that promotes the growth of medicinal plants and the accumulation of secondary metabolites, and has important potential application value in improving the quality of medicinal materials. A. euchroma cultivars and wild varieties contain abundant endophyte communities and metabolites in different tissues. However, the relationships between A. euchroma endophytes and metabolites with different growth patterns and different tissue sites remain unclear. In this study, microbiome analysis and metabolomics were used to analyze the diversity of endophytes in the root and leaf tissues of cultivated and wild A. euchroma and their correlations with metabolites. The results revealed that the diversity of endophytes in A. euchroma was different from that in wild A. euchroma and that there was tissue specificity among different tissues. A species composition analysis revealed that the dominant endophytic fungi belonged to Ascomycota and Basidiomycota, and the dominant endophytic bacteria belonged to Proteobacteria and Cyanobacteria. A total of 248 metabolites, including quinones, flavonoids, alkaloids, organic acids, sugars, amino acids, coumarins, sterols, terpenoids, polyphenols, fatty ketones, and their derivatives, were identified in positive ion mode via LC-MS/MS. According to their different growth patterns and associated tissue parts, 9 differentially abundant metabolites were screened between AEZ-L (cultivated leaf tissue of A. euchroma) and AEY-L (wild leaf tissue of A. euchroma), 6 differentially abundant metabolites were screened between AEZ-R (cultivated root tissue of A. euchroma) and AEY-R (wild root tissue of A. euchroma), and 104 differentially abundant metabolites were screened between AEZ-R and AEZ-L. Eighty-two differentially abundant metabolites were screened between AEY-R and AEY-L. The contents of eight naphthoquinones in AEZ-R and AEY-R were determined via HPLC. The contents of β,β'-dimethylacrylylakanin in wild A. euchroma were greater than those in cultivated A. euchroma. A correlation analysis revealed that the dominant endophytes in the four groups were significantly correlated with a variety of metabolites, and the eight naphthoquinones in the root tissue were also significantly correlated with the dominant endophytes. The diversity of the A. euchroma endophyte community differed across different growth patterns and different tissue parts. There were significant differences in the relative contents of A. euchroma metabolites in different tissues. A correlation analysis verified the correlation between A. euchroma endophytes and metabolites.

Feels Like Home: A Biobased and Biodegradable Plastic Offers a Novel Habitat for Diverse Plant Pathogenic Fungi in Temperate Forest Ecosystems

Poly(butylene succinate-co-adipate) (PBSA), a biodegradable plastic, is significantly colonized and degraded by soil microbes under natural field conditions, especially by fungal plant pathogens, raising concerns about potential economic losses. This study hypothesizes that the degradation of biodegradable plastics may increase the presence and abundance of plant pathogens by serving as an additional carbon source, ultimately posing a risk to forest ecosystems. We investigated (i) fungal plant pathogens during the exposure of PBSA in European broadleaved and coniferous forests (two forest types), with a specific focus on potential risk to tree health, and (ii) the response of such fungi to environmental factors, including tree species, soil pH, nutrient availability, moisture content, and the physicochemical properties of leaf litter layer. Next-generation sequencing (NGS) revealed that PBSA harbored a total of 318 fungal plant pathogenic amplicon sequence variants (ASVs) belonging to 108 genera. Among the identified genera (Alternaria, Nectria, Phoma, Lophodermium, and Phacidium), some species have been reported as causative agents of tree diseases. Plenodomus was present in high relative abundances on PBSA, which have not previously been associated with disease in broadleaved and coniferous forests. Furthermore, the highest number of fungal plant pathogens were detected at 200 days of PBSA exposure (112 and 99 fungal plant pathogenic ASV on PBSA degraded under Q. robur and F. sylvatic-dominated forest, respectively), which was double compared mature leaves and needles from the same forest sites. These findings suggest that PBSA attracts fungal plant pathogens in forests as an additional carbon source, potentially leading to increased disease outbreaks and disrupting the stability of forest ecosystems. The fungal plant pathogenic community compositions were mainly shaped by forest type, PBSA exposure time, site locations, leaf litter layer water content, and N:P ratio from leaf litter layer in both forest types. This study provides valuable insights into the potential risks posed by biodegradable plastic degradation in forests after 200 and 400 days of exposure, respectively. Further comprehensive evaluations of their effects on tree health and ecosystems, ideally on a long-term basis, are needed. These evaluations should include integrating microbial investigation, soil health monitoring, and ecosystem interaction assessments. Nevertheless, it should be noted that our interpretation of plant pathogens is solely based on high-throughput sequencing, bioinformatics, and annotation tools.

Microbial and mineral interactions decouple litter quality from soil organic matter formation

Current understanding of soil carbon dynamics suggests that plant litter quality and soil mineralogy control the formation of mineral-associated soil organic carbon (SOC). Due to more efficient microbial anabolism, high-quality litter may produce more microbial residues for stabilisation on mineral surfaces. To test these fundamental concepts, we manipulate soil mineralogy using pristine minerals, characterise microbial communities and use stable isotopes to measure decomposition of low- and high-quality litter and mineral stabilisation of litter-C. We find that high-quality litter leads to less (not more) efficient formation of mineral-associated SOC due to soil microbial community shifts which lower carbon use efficiency. Low-quality litter enhances loss of pre-existing SOC resulting in no effect of litter quality on total mineral-associated SOC. However, mineral-associated SOC formation is primarily controlled by soil mineralogy. These findings refute the hypothesis that high-quality plant litters form mineral-associated SOC most efficiently and advance our understanding of how mineralogy and litter-microbial interactions regulate SOC formation.

The Fungal Side of the Story: Saprotrophic- vs. Symbiotrophic-Predicted Ecological Roles of Fungal Communities in Two Meromictic Hypersaline Lakes from Romania

Over three-quarters of Earth's surface exhibits extreme environments where life thrives under harsh physicochemical conditions. While prokaryotes have often been investigated in these environments, only recent studies have revealed the remarkable adaptability of eukaryotes, in particular fungi. This study explored the mycobiota of two meromictic hypersaline lakes, Ursu and Fără Fund, in Transylvania (Romania). The intrinsic and extrinsic fungal diversity was assessed using amplicon sequencing of environmental DNA samples from sediments, water columns, surrounding soils, and an associated rivulet. The fungal communities, illustrated by the 18S rRNA gene and ITS2 region, exhibited contrasting patterns between the lakes. The ITS2 region assessed better than the 18S rRNA gene the fungal diversity. The ITS2 data showed that Ascomycota was the most abundant fungal group identified in both lakes, followed by Aphelidiomycota, Chytridiomycota, and Basidiomycota. Despite similar α-diversity levels, significant differences in fungal community structure were observed between the lakes, correlated with salinity, total organic carbon, total nitrogen, and ammonium. Taxonomic profiling revealed depth-specific variations, with Saccharomycetes prevalent in Ursu Lake's deeper layers and Lecanoromycetes prevalent in the Fără Fund Lake. The functional annotation using FungalTraits revealed diverse ecological roles within the fungal communities. Lichenized fungi were dominant in Fără Fund Lake, while saprotrophs were abundant in Ursu Lake. Additionally, wood and soil saprotrophs, along with plant pathogens, were more prevalent in the surrounding soils, rivulet, and surface water layers. A global overview of the trophic relations in each studied niche was impossible to establish due to the unconnected graphs corresponding to the trophic interactions of the analyzed fungi. Plotting the unweighted connected subgraphs at the genus level suggests that salinity made the studied niches similar for the identified taxa. This study shed light on the understudied fungal diversity, distribution, and ecological functions in hypersaline environments.

Community Assembly Processes of Deadwood Mycobiome in a Tropical Forest Revealed by Long-Read Third-Generation Sequencing

Despite the importance of wood-inhabiting fungi on nutrient cycling and ecosystem functions, their ecology, especially related to their community assembly, is still highly unexplored. In this study, we analyzed the wood-inhabiting fungal richness, community composition, and phylogenetics using PacBio sequencing. Opposite to what has been expected that deterministic processes especially environmental filtering through wood-physicochemical properties controls the community assembly of wood-inhabiting fungal communities, here we showed that both deterministic and stochastic processes can highly contribute to the community assembly processes of wood-inhabiting fungi in this tropical forest. We demonstrated that the dynamics of stochastic and deterministic processes varied with wood decomposition stages. The initial stage was mainly governed by a deterministic process (homogenous selection), whereas the early and later decomposition stages were governed by the stochastic processes (ecological drift). Deterministic processes were highly contributed by wood physicochemical properties (especially macronutrients and hemicellulose) rather than soil physicochemical factors. We elucidated that fine-scale fungal-fungal interactions, especially the network topology, modularity, and keystone taxa of wood-inhabiting fungal communities, strongly differed in an initial and decomposing deadwood. This current study contributes to a better understanding of the ecological processes of wood-inhabiting fungi in tropical regions where the knowledge of wood-inhabiting fungi is highly limited.

Age-Related Conservation in Plant-Soil Feedback Accompanied by Ectomycorrhizal Domination in Temperate Forests in Northeast China

This study investigates the effects of forest aging on ectomycorrhizal (EcM) fungal community and foraging behavior and their interactions with plant-soil attributes. We explored EcM fungal communities and hyphal exploration types via rDNA sequencing and investigated their associations with plant-soil traits by comparing younger (~120 years) and older (~250 years) temperate forest stands in Northeast China. The results revealed increases in the EcM fungal richness and abundance with forest aging, paralleled by plant-soil feedback shifting from explorative to conservative nutrient use strategies. In the younger stands, Tomentella species were prevalent and showed positive correlations with nutrient availability in both the soil and leaves, alongside rapid increases in woody productivity. However, the older stands were marked by the dominance of the genera Inocybe, Hymenogaster, and Otidea which were significantly and positively correlated with soil nutrient contents and plant structural attributes such as the community-weighted mean height and standing biomass. Notably, the ratios of longer-to-shorter distance EcM fungal exploration types tended to decrease along with forest aging. Our findings underscore the integral role of EcM fungi in the aging processes of temperate forests, highlighting the EcM symbiont-mediated mechanisms adapting to nutrient scarcity and promoting sustainability in plant-soil consortia.

The interaction of climate, plant, and soil factors drives putative soil fungal pathogen diversity and community structure in dry grasslands

Soil pathogens play important roles in shaping soil microbial diversity and controlling ecosystem functions. Though climate and local environmental factors and their influences on fungal pathogen communities have been examined separately, few studies explore the relative contributions of these factors. This is particularly crucial in eco-fragile regions, which are more sensitive to environmental changes. Herein we investigated the diversity and community structure of putative soil fungal pathogens in cold and dry grasslands on the Tibetan Plateau, using high-throughput sequencing. The results showed that steppe soils had the highest diversity of all pathogens and plant pathogens; contrastingly, meadow soils had the highest animal pathogen diversity. Structural equation modelling revealed that climate, plant, and soil had similar levels of influence on putative soil fungal pathogen diversity, with total effects ranging from 52% to 59% (all p < 0.001), with precipitation exhibiting a stronger direct effect than plant and soil factors. Putative soil fungal pathogen community structure gradually changed with desert, steppe, and meadow, and was primarily controlled by the interactions of climate, plant, and soil factors rather than by distinct factors individually. This finding contrasts with most studies of soil bacterial and fungal community structure, which generally report dominant roles of individual environmental factors.

Oral Bacteriome and Mycobiome across Stages of Oral Carcinogenesis

Oral microbial dysbiosis contributes to the development of oral squamous cell carcinoma (OSCC). Numerous studies have focused on variations in the oral bacterial microbiota of patients with OSCC. However, similar studies on fungal microbiota, another integral component of the oral microbiota, are scarce. Moreover, there is an evidence gap regarding the role that microecosystems play in different niches of the oral cavity at different stages of oral carcinogenesis. Here, we catalogued the microbial communities in the human oral cavity by profiling saliva, gingival plaque, and mucosal samples at different stages of oral carcinogenesis. We analyzed the oral bacteriome and mycobiome along the health-premalignancy-carcinoma sequence. Some species, including Prevotella intermedia, Porphyromonas endodontalis, Acremonium exuviarum, and Aspergillus fumigatus, were enriched, whereas others, such as Streptococcus salivarius subsp. salivarius, Scapharca broughtonii, Mortierella echinula, and Morchella septimelata, were depleted in OSCC. These findings suggest that an array of signature species, including bacteria and fungi, are closely associated with oral carcinogenesis. OSCC-associated diversity differences, species distinction, and functional alterations were most remarkable in mucosal samples, not in gingival plaque or saliva samples, suggesting an urgent need to define oral carcinogenesis-associated microbial dysbiosis based on the spatial microbiome. IMPORTANCE Abundant oral microorganisms constitute a complex microecosystem within the oral environment of the host, which plays a critical role in the adjustment of various physiological and pathological states of the oral cavity. In this study, we demonstrated that variations in the "core microbiome" may be used to predict carcinogenesis. In addition, sample data collected from multiple oral sites along the health-premalignancy-carcinoma sequence increase our understanding of the microecosystems of different oral niches and their specific changes during oral carcinogenesis. This work provides insight into the roles of bacteria and fungi in OSCC and may contribute to the development of early diagnostic assays and novel treatments.

A poisoned apple: First insights into community assembly and networks of the fungal pathobiome of healthy-looking senescing leaves of temperate trees in mixed forest ecosystem

Despite the abundance of observations of foliar pathogens, our knowledge is severely lacking regarding how the potential fungal pathobiome is structured and which processes determine community assembly. In this study, we addressed these questions by analysing the potential fungal pathobiome associated with the senescing leaves and needles of 12 temperate tree species. We compared fungal plant pathogen load in the senescing leaves/needles and demonstrated that healthy-looking leaves/needles are inhabited by diverse and distinct fungal plant pathogens. We detected 400 fungal plant pathogenic ASVs belonging to 130 genera. The fungal plant pathogenic generalist, Mycosphaerella, was found to be the potential most significant contributor to foliar disease in seedlings. The analyses of assembly process and co-occurrence network showed that the fungal plant pathogenic communities in different tree types are mainly determined by stochastic processes. However, the homogenising dispersal highly contributes in broadleaf trees, whereas ecological drift plays an important role in coniferious trees. The deterministic assembly processes (dominated by variable selection) contributed more in broadleaf trees as compared to coniferous trees. We found that pH and P level significantly corresponded with fungal plant pathogenic community compositions in both tree types. Our study provides the first insight and mechanistic understanding into the community assembly, networks, and complete taxonomy of the foliar fungal pathobiome in senescing leaves and needles.

Elevated O3 Exerts Stronger Effects than Elevated CO2 on the Functional Guilds of Fungi, but Collectively Increase the Structural Complexity of Fungi in a Paddy Soil

Global climate change is characterized by altered global atmospheric composition, including elevated CO₂ and O₃, with important consequences on soil fungal communities. However, the function and community composition of soil fungi in response to elevated CO₂ together with elevated O₃ in paddy soils remain largely unknown. Here we used twelve open-top chamber facilities (OTCs) to evaluate the interactive effect of CO₂ (+ 200 ppm) and O₃ (+ 40 ppb) on the diversity, gene abundance, community structure, and functional composition of soil fungi during the growing seasons of two rice cultivars (Japonica, Wuyujing 3 vs. Nangeng 5055) in a Chinese paddy soil. Elevated CO₂ and O₃ showed no individual or combined effect on the gene abundance or relative abundance of soil fungi, but increased structural complexity of soil fungal communities, indicating that elevated CO₂ and/or O₃ promoted the competition of species-species interactions. When averaged both cultivars, elevated CO₂ showed no individual effect on the diversity or abundance of functional guilds of soil fungi. By contrast, elevated O₃ significantly reduced the relative abundance and diversity of symbiotrophic fungi by an average of 47.2% and 39.1%, respectively. Notably, elevated O₃ exerts stronger effects on the functional processes of fungal communities than elevated CO₂. The structural equation model revealed that elevated CO₂ and/or O₃ indirectly affected the functional composition of soil fungi through community structure and diversity of soil fungi. Root C/N and soil environmental parameters were identified as the top direct predictors for the community structure of soil fungi. Furthermore, significant correlations were identified between saprotrophic fungi and root biomass, symbiotrophic fungi and root carbon, the pathotroph-symbiotroph and soil pH, as well as pathotroph-saprotroph-symbiotroph and soil microbial biomass carbon. These results suggest that climatic factors substantially affected the functional processes of soil fungal, and threatened soil function and food production, highlighting the detrimental impacts of high O₃ on the function composition of soil biota.

View from the Top: Insights into the Diversity and Community Assembly of Ectomycorrhizal and Saprotrophic Fungi along an Altitudinal Gradient in Chinese Boreal Larix gmelinii-Dominated Forests

The altitudinal patterns of soil fungi have attracted considerable attention; however, few studies have investigated the diversity and community assembly of fungal functional guilds along an altitudinal gradient. Here, we explored ectomycorrhizal (EcM) and saprotrophic (SAP) fungal diversity and community assembly along a 470 m vertical gradient (ranging from 830 to 1300 m) on Oakley Mountain, sampling bulk soils in the 0-10 cm and 10-20 cm soil layers of Larix gmelinii-dominated forests. Illumina MiSeq sequencing of the ITS genes was employed to explore the fungal community composition and diversity. The relative abundance of EcM and SAP fungi showed a divergent pattern along an altitudinal gradient, while we observed a consistent altitudinal tendency for EcM and SAP fungal diversity and community assembly. The diversity of both fungal guilds increased with increasing altitude. Altitude and soil moisture were the key factors affecting the community composition of both fungal guilds. In addition, the plant community composition significantly affected the EcM fungal community composition, whereas the dissolved organic nitrogen and ammonium nitrogen contents were the driving factors of SAP fungal community. Despite the effects of vegetation and soil factors, EcM and SAP fungal communities were mainly governed by stochastic processes (especially drift) at different altitudes and soil depths. These results shed new light on the ecology of different fungal functional guilds along an altitudinal gradient, which will provide a deeper understanding of the biogeography of soil fungi.

More than you can see: Unraveling the ecology and biodiversity of lichenized fungi associated with leaves and needles of 12 temperate tree species using high-throughput sequencing

Currently, lichen surveys are generally based on the examination of fruiting bodies. Lichens in the mycelial stage, in spores, or awaiting conditions for fruiting body formation are usually overlooked, even though they are important for maintaining biodiversity and ecosystem functions. This study aimed to explore the lichenized fungal community composition and richness associated with leaves and needles of 12 temperate tree species using Illumina MiSeq-based amplicon sequencing of the internal transcribed spacer (ITS) 2 region. Picea abies harbored the highest richness and number of lichenized fungal species. We found that the lichenized fungus Physcia adscendens dominated the leaves and needles of the most temperate tree species. Eleven lichenized fungal species detected in this study were recorded for the first time on leaves and needles. In addition, we identified Athallia cerinella, Fellhanera bouteillei, and Melanohalea exasperata that are on the German national red lists. Lichenized fungal richness was higher in conifer compared to broadleaf trees. Overall, tree species (within coniferous trees) and tree types (broadleaved vs. coniferous trees) harbored significantly different lichenized fungal community compositions pointing out the importance of host species. Diversity and community composition patterns of lichenized fungi were correlated mainly with tree species. Our study demonstrates that the diversity of foliicolous lichens associated with leaves and needles of 12 temperate tree species can be appropriately analyzed and functionally assigned using the ITS-based high-throughput sequencing. We highlighted the importance of conifers for maintaining the biodiversity of foliicolous lichens. Based on the discovery of many red list lichens, our methodological approach and results are important contributions to subsequent actions in the bio-conversation approaches.

Applying EDTA in Chelating Excess Metal Ions to Improve Downstream DNA Recovery from Mine Tailings for Long-Read Amplicon Sequencing of Acidophilic Fungi Communities

The hostile environment of mine tailings contains unique microbial life capable of bioleaching. The metagenomic analysis of such an environment provides an in-depth understanding of the microbial life and its potential, especially in biomining operations. However, DNA recovery from samples collected in those environments is challenging due to the presence of metal ions that interfere with the DNA analysis. A varied concentration of EDTA (4–13 µg/µL) to chelate the metal ions of enriched tailing samples prior to DNA extraction was performed. The results show that 9 µg/µL of EDTA was effective in most samples. However, the increasing concentration of EDTA negatively affected the DNA recovery. The sequencing of the successfully extracted DNA revealed a diverse range of fungal genera, some of which have not been previously reported in tailing or bioleaching applications. The dominant genera include Fodinomyces, Penicillium, Recurvomuces, Trichoderma, and Xenoacremonium; their traits were determined using the FungalTraits database. This study demonstrates the need to include a preliminary metal-chelating step using EDTA before DNA extractions for samples collected from metal-rich environments. It further showed the need for optimization but provided a benchmark range, particularly for tailings. However, we caution that a further EDTA removal step from the extracted DNA should be included to avoid its interferences in downstream applications.