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Soil desertification poses a critical ecological challenge in arid and semiarid climates worldwide, leading to decreased soil productivity due to the disruption of essential microbial community processes. Fungi, as one of the most important soil microbial communities, play a crucial role in enhancing nutrient and water uptake by plants through mycorrhizal associations. However, the impact of overgrazing-induced desertification on fungal community structure, particularly in the Caatinga biome of semiarid regions, remains unclear. In this study, we assessed the changes in both the total fungal community and the arbuscular mycorrhizal fungal community (AMF) across 1. Natural vegetation (native), 2. Grazing exclusion (20 years) (restored), and 3. affected by overgrazing-induced degradation (degraded) scenarios. Our assessment, conducted during both the dry and rainy seasons in Irauçuba, Ceará, utilized Internal Transcribed Spacer (ITS) gene sequencing via Illumina® platform. Our findings highlighted the significant roles of the AMF families Glomeraceae (∼71% of the total sequences) and Acaulosporaceae (∼14% of the total sequences) as potential key taxa in mitigating climate change within dryland areas. Moreover, we identified the orders Pleosporales (∼35% of the total sequences) and Capnodiales (∼21% of the total sequences) as the most abundant soil fungal communities in the Caatinga biome. The structure of the total fungal community differed when comparing native and restored areas to degraded areas. Total fungal communities from native and restored areas clustered together, suggesting that grazing exclusion has the potential to improve soil properties and recover fungal community structure amid global climate change challenges.

[Display omitted] • Larvae of Hermetia illucens regularly develop on PVC-MPs-supplemented diet. • PVC-MPs are ingested by the larvae and reduced in their size. • Midgut morphology is not affected by PVC-MPs in the larval diet. • PVC-MPs in the larval diet do not affect microbial alpha- and beta-diversity. • PVC-MPs selectively affect the abundances of gut bacterial and fungal taxa. In a world with a population exceeding 8 billion people and continuing to grow, pollution from food and plastic waste is causing long-term issues in ecosystems. Potential solutions may be found by exploiting insect-based bioconversion. In this context, we investigated the impact of polyvinyl chloride microparticles (PVC-MPs) on the development of Hermetia illucens (black soldier fly; BSF) and its midgut bacterial and fungal microbiota. The impact of PVC-MPs was evaluated feeding BSF larvae with a PVC-MPs-supplemented diet. The larvae exposed to different PVC-MPs concentrations (2.5%, 5%, 10% and 20% w/w) developed into adults with no significant increase in pupal mortality. Faster development and smaller pupae were observed when 20% PVC-MPs was provided. The BSF larvae ingest PVC-MPs, resulting in a reduction in MPs size. Larvae exposed to PVC-MPs did not exhibit differences in gut morphology. Regarding the impact of PVC-MPs on the structure of both bacterial and fungal communities, the overall alpha- and beta-diversity did not exhibit significant changes. However, the presence of PVC-MPs significantly affected the relative abundances of Enterobacteriaceae and Paenibacillaceae among the bacteria and of Dipodascaceae and Plectospharellaceae among the fungi (including yeast and filamentous life forms), suggesting that PVC-MP contamination has a taxa-dependent impact. These results indicate that BSF larvae can tolerate PVC-MPs in their diet, supporting the potential use of these insects in organic waste management, even in the presence of high levels of PVC-MP contamination. [ABSTRACT FROM AUTHOR]

Summary: Plants naturally harbor diverse microbiomes that can dramatically impact their health and productivity. However, it remains unclear how fungal microbiome diversity, especially in the phyllosphere, impacts intermicrobial interactions and consequent nonadditive effects on plant productivity.Combining manipulative experiments, field collections, culturing, microbiome sequencing, and synthetic consortia, we experimentally tested for the first time how foliar fungal community diversity impacts plant productivity. We inoculated morning glories (Ipomoea hederifolia L.) with 32 phyllosphere consortia of either low or high diversity or with single fungal taxa, and measured effects on plant productivity and allocation.We found the following: (1) nonadditive effects were pervasive with 56% of fungal consortia interacting synergistically or antagonistically to impact plant productivity, including some consortia capable of generating acute synergism (e.g. > 1000% increase in productivity above the additive expectation), (2) interactions among 'commensal' fungi were responsible for this nonadditivity in diverse consortia, (3) synergistic interactions were approximately four times stronger than antagonistic effects, (4) fungal diversity affected the magnitude but not frequency or direction of nonadditivity, and (5) diversity affected plant performance nonlinearly with the highest performance in low‐diversity treatments.These findings highlight the importance of interpreting plant–microbiome interactions under a framework that incorporates intermicrobial interactions and nonadditive outcomes to understand natural complexity. See also the Commentary on this article by Whitaker, 243: 2050–2051. [ABSTRACT FROM AUTHOR]

The underlying processes of plant‐microbe associations particularly their interactions with their mycorrhizal fungal partners have been extensively studied. However, considerably less is known about the consequences of tree‐tree interactions on rooting zone soil microbiota when tree species of different mycorrhizal type (myco‐type) grow together as mono and mixed myco‐type mixtures along a tree diversity gradient. Using the MyDiv tree diversity experiment, where arbuscular mycorrhizal (AM) and ectomycorrhizal (EcM) trees and their mixtures were planted in monocultures, two‐species and four‐species mixture plots, we investigated the interplay of target tree myco‐type, myco‐type mixture, tree diversity and rooting zone compartment (target tree dominated and its interaction zones with neighbour trees) on the rooting zone soil mycobiota employing meta‐barcoding of the ITS2 rDNA fragment of the fungal internal transcribed spacer (ITS). Our results revealed significant individual and interaction effects of tree myco‐type, myco‐type mixture and tree diversity but not rooting zone compartment on the fungal taxonomic and functional alpha and beta diversity. This implies intermingling of roots of target and neighbouring tree species there by reducing the target tree species effect in its rooting zone. As tree diversity increases, we found convergence of the fungal community in general, where the fungal community dissimilarity varies depending on the co‐existing tree species myco‐type and tree species diversity. Furthermore, the fungal community composition in the two and four species mixtures were consistently influenced by soil pH, whereas in the mixed multi‐species stands basal respiration, N, PO4−, NO3− were found to be equally important unlike in AM and EcM multi‐species stands. Comparative analysis of the fungal taxa specialisation between mono and mixed myco‐type multi‐species stands revealed that the mixed myco‐type plots shared 23.5% (AM) and 19.7% (EcM) of the generalist fungal communities However, the percentage of specialised fungal community in mixed myco‐type plots (13.2%) was significantly higher as compared to EcM (9.5%), and significantly lower (9%) as compared to AM (11.7%) plots, resulting in myco‐type and myco‐type mixture specific fungal communities and functional guild patterns Our results provide novel insights on the significance of tree species and its co‐existing trees preferred mycorrhizal association in shaping the target tree rooting zone soil mycobiome along a tree diversity gradient. Furthermore, it highlights the significance of generalist and specialist fungal communities in mono and mixed myco‐type stands in modulating tree‐tree interaction, tree species co‐existence and regulating soil properties and ecosystem functions. Read the free Plain Language Summary for this article on the Journal blog. [ABSTRACT FROM AUTHOR]

Introduction: The relationships among microelements and soil microbial communities are essential for understanding the maintenance of soil's ecological functions and their effects on fruit quality in orchards. However, these relationships have not been adequately studied, despite the importance of microelements for the growth of microorganisms and plants. Methods: To address this research gap, we investigated the relationships among microelements (K, Ca, Na, Mg, Fe, Mn, Zn, and Cu), the diversity and composition of soil microbiomes, and fruit quality in loquat orchards. Results: We found that microelements explained more variations in microbial community structures than geographic position, basic soil properties, and macroelements, with 19.6-42.6% of bacterial, 4.3-27.7% of fungal, and 5.9- 18.8% of protistan genera significantly correlated with microelements. Among the microelements, AMg and ACu were the most influential in determining the soil microbiome. The soil microbes exhibited varied threshold values for environmental breadth among the microelements, with the broadest range for AMg and the narrowest for AZn. Additionally, the microbes showed significant phylogenetic signals for all microelements, with an increasing divergence of soil microelements. The dominant community assembly shifted from homogeneous selection to stochastic, and then to heterogeneous selection. Moreover, microelements and the microbiome were the top two factors individually explaining 11.0 and 11.4% of fruit quality variation, respectively. Discussion: These results highlight the importance of microelement fertilization in orchard management and provide scientific guidance for improving fruit quality. [ABSTRACT FROM AUTHOR]

The process of formation of aromatic components for agarwood in Aquilaria sinensis is closely related to endophytic fungi and the result of complex multiple long-term joint interactions with them. However, the interactions between the aromatic components and endophytic fungi remain unclear during the formation of agarwood. In this study, precise mixed solution of hormones, inorganic salts, and fungi was used to induce its formation in A. sinensis, and sample blocks of wood were collected at different times after inoculation. This study showed that the aromatic compounds found in the three treatments of A. sinensis were primarily chromones (31.70-33.65%), terpenes (16.68-27.10%), alkanes (15.99-23.83%), and aromatics (3.13-5.07%). Chromones and terpenes were the primary components that characterized the aroma. The different sampling times had a more pronounced impact on the richness and diversity of endophytic fungal communities in the A. sinensis xylem than the induction treatments. The species annotation of the operational taxonomic units (OTUs) demonstrated that the endophytic fungi were primarily composed of 18 dominant families and 20 dominant genera. A linear regression analysis of the network topology properties with induction time showed that the interactions among the fungal species continued to strengthen, and the network structure tended to become more complex. The terpenes significantly negatively correlated with the Pielou evenness index (p < 0.05), while the chromones significantly positively correlated with the OTUs and Shannon indices. [ABSTRACT FROM AUTHOR]

The surge in global energy demand mandates a significant expansion of electric power substations. Nevertheless, the ecological consequences of electric power substation operation, particularly concerning the electromagnetic field, on soil microbial communities and nitrogen enrichment remain unexplored. In this study, we collected soil samples from six distinct sites at varying distances from an electric power substation in Xintang village, southeastern China, and investigated the impacts of electromagnetic field on the microbial diversity and community structures employing metagenomic sequencing technique. Our results showed discernible dissimilarities in the fungal community across the six distinct sites, each characterized by unique magnetic and electric intensities, whereas comparable variations were not evident within bacterial communities. Correlation analysis revealed a diminished nitrogen fixation capacity at the site nearest to the substation, characterized by low moisture content, elevated pH, and robust magnetic induction intensity and electric field intensity. Conversely, heightened nitrification processes were observed at this location compared to others. These findings were substantiated by the relative abundance of key genes associated with ammonium nitrogen and nitrate nitrogen production. This study provides insights into the relationships between soil microbial communities and the enduring operation of electric power substations, thereby contributing fundamental information essential for the rigorous environmental impact assessments of these facilities. [ABSTRACT FROM AUTHOR]

Type 2 diabetes mellitus (T2DM) is globally recognized as a significant health concern, with diabetic foot (DF) identified as a severe long-term complication that can lead to tissue death or amputation. The discovery of the impact of mycobiota, a diverse group of multicellular eukaryotes in the gut microbiome, on the onset of endocrine disorders holds great significance. Therefore, this research aimed to examine variations in fungal mycobiome and identify potential biomarkers for T2DM and T2DM-DF. Fecal and blood samples were collected from 33 individuals with T2DM, 32 individuals with T2DM-DF, and 32 healthy individuals without any health conditions (HC). Blood samples were used for laboratory parameters analysis, while total DNA was extracted from fecal samples and sequenced using Illumina 18s rRNA. Bioinformatics tools were employed to analyze fungal abundance and diversity, revealing differentially expressed fungal species and signature fungi that distinguished between T2DM, T2DM-DF, and HC groups. Firstly, significant alterations in some laboratory parameters were observed among the three groups, which also differed between T2DM and T2DM-DF. The diversity of gut fungi in T2DM and T2DM-DF significantly differed from that of the HC group; however, more pronounced changes were observed in T2DM-DF. Additionally, two significantly altered phyla, Ascomycota and Basidiomycota, were identified with higher Ascomycota abundance but lower Basidiomycota abundance in both the T2DM and T2DM-DF compared to the HC group. Furthermore, the top 15 fungi showing significant changes at the species level included a notable decrease in Rhodotorula_mucilaginosa abundance in patients with T2DM compared to HC and a substantial increase in unclassified_g_Candida abundance specifically seen only among patients with T2DM-DF, but not among those diagnosed with T2DM or HC. Thirdly, KEGG was employed to analyze enzyme expression across the three groups, revealing a more pronounced alteration in gut fungal function within T2DM-DF compared to T2DM. Subsequently, to accurately identify signature fungi in each group, a random forest was utilized to rank the top 15 significant fungi. Notably, 11 fungi were identified as potential biomarkers for distinguishing T2DM or T2DM-DF from HC, while eight fungi could discriminate between T2DM and T2DM-DF. Furthermore, receiver operating characteristic curve (ROC) analysis demonstrated enhanced accuracy of predicted outcomes. These findings suggest that changes in fungal mycobiome are closely associated with the progression and complications of T2DM and DF, offering promising prospects for diagnosis and treatment. [ABSTRACT FROM AUTHOR]

Greipsson, S.; Stover, K.; Whitney, S., and McElroy, T., 2024. Arbuscular mycorrhizal fungi and soil fungi associated with Uniola paniculata L. (sea oats) on restored and natural sand dunes on the Georgia Coast, U.S.A. Journal of Coastal Research, 40(5), 875–886. Charlotte (North Carolina), ISSN 0749-0208. Coastal sand dunes are fragile ecosystems that serve as natural defenses to protect barrier islands and the adjacent mainland during severe storms. A high frequency of disturbances may result in dune erosion. Several strategies have been used for coastal restoration; however, previous practices often lack the connection between plants and below-ground microbial communities. Symbiotic arbuscular mycorrhizal fungi (AMF) are beneficial in supplying a range of limiting nutrients to the host plant while improving dune stability. This study assessed the diversity of the indigenous AMF and soil fungal communities associated with Uniola paniculata L. (sea oats) on natural dunes and restored dunes at Jekyll and Tybee Islands on U.S. Georgia's coast. The phosphorus (P) concentrations of dune sand were also analyzed. At each site, samples were collected from 10 dune ridges that were randomly selected along a 100-m transect where sea oats were growing. The genomic DNA was extracted from 60 sand and sea oats root samples. A total of 13 amplicon sequence variants of AMF were identified; seven were classifiable to the species level. The most abundant genera of AMF were Glomus; the most abundant species were unclassified Glomus spp., followed by Glomus custos and G. deserticola. Using the Sorensen-Dice coefficient, the study showed that AMF assemblages of the natural dunes of both sites shared a high similarity (0.73). However, AMF assemblages of the Jekyll Island natural site had no (0) similarity to Jekyll Island restored site 1. The greatest number of classes of soil fungi were found at Jekyll Island's restored site 1 (18 classes); conversely, the lowest number was found at Jekyll Island's natural site (nine classes). Natural dunes contained significantly greater levels of P in the sand compared with restored dunes. These findings demonstrate the need to manage sand material and AMF assemblages during coastal dune restoration. [ABSTRACT FROM AUTHOR]

Forest dynamics are driven by micro‐disturbances leading to gap formation. Root rot pathogens can cause mortality to adult trees, which die forming gaps. However, little is known about the biotic and abiotic factors that govern gap creation and expansion such as tree infection or drought resilience, and what are the consequences for nutrient cycling and soil microbiota.We studied the dynamics of gaps created by Heterobasidion abietinum in mountain silver fir (Abies alba) forests from the Spanish Central Pyrenees. Tree‐ring width information was used to evaluate growth patterns of trees located within and at the edge of gaps and under closed canopy conditions. We analysed soil nutrient content and microbial structure at different positions with respect to the gap. Soil fungal community was also characterized by sequencing the ITS2 region.Gaps created by H. abietinum ranged 582–1072 m2 and gathered large amounts of standing and laying dead wood biomass amounting to up to 500 m3 ha−1 of coarse woody debris. This indicates that tree mortality had been occurring over decades, and it was preceded by a long‐term growth decline and impaired drought resilience. Root rot affected trees beyond the current limit of the gaps leading to growth decline, preventing canopy closure and allowing the release of suppressed trees within the gap. Gap formation did neither affect soil fertility nor fungal and bacterial biomass and diversity, but long‐distance ectomycorrhizal fungi were more abundant within gaps.Synthesis. Root rot pathogens play key ecological roles in forest dynamics at fine spatial scale. Heterobasidion abietinum infection, and its interaction with drought, creates and expands gaps by killing large trees and preventing surrounding trees from closing the gap. The survival of mycorrhizal networks to gap formation suggests little disruption of soil fungal communities. [ABSTRACT FROM AUTHOR]

BACKGROUND: The development of agricultural practices requires an understanding of the improvement of salt tolerance and crop growth in agricultural systems through magnetized‐ionized water irrigation. METHOD: This study examined the impacts of fresh water (F), brackish water (B), magnetized‐ionized fresh water (MIF), and magnetized‐ionized brackish water (MIB) on soil properties and the growth of cotton seedlings through microbial analysis during the cotton seedling period. RESULTS: The results revealed that magnetized‐ionized water irrigation improved soil water retention and promoted salt leaching. In comparison with F irrigation, plant height, leaf area index (LAI), dry matter accumulation (DM), and chlorophyll content (SPAD) levels increased by 3.61%, 4.07%, 5.76%, and 1.33%, respectively, under MIF irrigation. Similarly, when compared with B irrigation, LAI, DM, and SPAD increased by 5.13%, 6.12%, and 3.12% under MIB irrigation. Magnetized‐ionized water irrigation also led to a notable rise in the relative abundance of beneficial soil bacterial communities, particularly Pseudomonas and Azoarcus, as well as fungal communities like Trichoderma, while reducing the prevalence of pathogenic fungi, such as Lasionectria, Gibberella, and Alternaria. Notably, this irrigation approach induced alterations in soil properties, and partial least squares path modeling revealed significant links between soil properties and both cotton growth and fungal community structure (with path coefficients of −0.884 and 0.693, respectively). CONCLUSION: This study elucidated the distinct effects of soil properties and growth indices on cotton yield during the seedling period, providing a crucial scientific foundation for enhancing future agricultural production through the use of magnetized‐ionized water irrigation. © 2024 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

BACKGROUND: Rice vinegar is a popular cereal vinegar worldwide and is typically produced in an open environment, and the ecosystem of solid‐state fermentation is complicated and robust. The present study aimed to reveal the shaping force of the establishment of the ecosystem of Beijing rice vinegar, the core function microbiota and their correlation with critical environmental factors. [Correction added after first online publication on 29 May 2024; the word "worldwide" has been removed from the first sentence under the section Background.] RESULTS: The experimental findings revealed the changes in environmental factors, major metabolites and microbial patterns during Beijing rice vinegar fermentation were obtained. The major metabolites accumulated at the middle and late acetic acid fermentation (AAF) periods. Principal coordinates and t‐test analyses revealed the specific bacterial and fungal species at corresponding stages. Kosakonia, Methlobacterium, Sphingomonas, unidentified Rhizobiaceae, Pseudozyma and Saccharomycopsis dorminated during saccharification and alcohol fermentation and early AAF, whereas Lactococcus, Acetobacter, Rhodotorula and Kazachstania dominated the later AAF stages. Canonical correspondence analysis of environmental factors with core microbiota. Temperature and total acid were the most significant factors correlated with the SAF bacterial profile (Pediococcus, Weissella, Enterococcus and Kosakonia). Ethanol was the most significant factor between AAF1 and AAF3, and mainly affected Acetobacter and Lactobacillus. Conversely, ethanol was the most significant factor in the SAF, AAF1 and AAF3 fungi communities; typical microorganisms were Saccharomyces and Malassezia. Furthermore, the predicted phenotypes of bacteria and their response to environmental factors were evaluated. CONCLUSION: In conclusion, the present study has provided insights into the process regulation of spontaneous fermentation and distinguished the key driving forces in the microbiota of Beijing rice vinegar fermentation. © 2024 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

Aim: Revealing the role of regional species pool size in community assembly rules is essential for extending the species‐pool framework to large‐scale community ecology, and thus for more comprehensive understanding of biodiversity formation. However, little has been done to couple the regional species‐pool effect into local ecological processes in soil fungal communities, which play essential roles in ecosystems worldwide. Here, we performed large‐scale soil surveys of fungal communities to examine the linkage between regional species pool size and Dispersal–Selection Relationships (DSRs), and their relations to community structure. Location: China. Time period: July–August 2019. Major taxa studied: Fungal communities. Methods: By conducting the nationwide soil survey of ~1200 samples from various ecosystems across China, including agricultural, forest, grassland, and wetland soils, we examined the linkage between regional species pool size and DSRs, and their relationship to fungal community structure. Results: We found that selection was negatively related to dispersal, which was consistent with the general view that the strength of selection is weakened by dispersal homogenization, and that this relationship was stronger in regions with larger species pools. Moreover, an increase in community dispersion was correlated with stronger effect size of DSRs, implying greater heterogeneity among fungal communities under larger species pools. Main conclusions: Our study clearly illustrates the association of regional species pool size with local assembly rules and community formation of soil fungi across terrestrial ecosystems. [ABSTRACT FROM AUTHOR]

BACKGROUND: The microbial community plays a crucial role in Chinese strong‐flavor baijiu (SFB) fermentation. However, the seasonal dynamics of the microbial community in the SFB fermentation system and its contribution to the unique flavor of SFB have not been fully elucidated. In this study, we investigated the seasonal dynamics of the microbial community through 16S rRNA and ITS gene sequencing. RESULTS: The results revealed significant temporal dynamics of microbial communities and environmental variables throughout the four seasons. The influence of seasons on fungal communities was found to be more significant than on bacterial communities. The diversity of bacteria was higher during the winter and summer, whereas fungal diversity was more prominent in summer and autumn. Stochastic processes maintained their dominance in microbial assembly throughout all four seasons but the significance of heterogeneous selection increased during summer for both bacteria and fungi, whereas homogeneous selection became more pronounced during winter for fungi. The pH and environmental temperature were important drivers of microbial community assembly across different seasons, primarily impacting the core genera responsible for the production of major volatile flavor compounds (VFCs), especially ethyl caproate. CONCLUSION: These findings provide new insights into the impact of seasons on microbial communities and hold promise for improving the quality‐control measures for SFB brewed in different seasons. © 2024 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

Despite that climate change is currently one of the most pervasive challenges, its effects on the plant-associated microbiome is still poorly studied. The aim of this study was to evaluate the impact of the independent and combinatory effect of climate warming and drought on the microbiome assembly of oak from seed to seedling. In a multifactorial experimental set up, acorns were subjected to different temperatures (15 °C, 20 °C, and 25 °C) and soil moisture levels (drought (15%) and control (60%)) from germination until the seedling stage, after which the bacterial and fungal communities associated to the rhizosphere and phyllosphere were characterized by amplicon sequencing and qPCR. The results showed a stronger effect of temperature on fungal than on bacterial diversity and the effect was more pronounced in the phyllosphere. Under drought condition, temperature had a significantly negative effect on phyllosphere fungal diversity. In the rhizosphere, temperature had a significant effect on the fungal community composition which was primarily caused by species turnover. Regardless of temperature, Actinobacteriota was significantly enriched in drought, a group of bacteria known to increase plant drought tolerance. This study provides new insights into the effect of climate change on the plant microbiome in natural ecosystems. [ABSTRACT FROM AUTHOR]

Plant–soil feedback (PSF) plays a central role in determining plant community dynamics, yet our understanding of how different combinations of plants and microbes influence PSF remains limited. Plants of different mycorrhizal types often exhibit contrasting PSF outcomes, influencing plant recruitment and spatial structure. Generalizing across plant species based on mycorrhizal type creates the potential to examine broader effects on ecological communities. We review mechanisms contributing to different PSF outcomes between arbuscular mycorrhizal and ectomycorrhizal trees. We focus on how plant and fungal traits that differ between mycorrhizal types interact with pathogenic and saprotrophic microorganisms and nutrient and carbon cycling. Synthesis. Building on this framework, we propose several new research directions. First, mycorrhizal‐induced changes in soils can operate beyond the conspecific level, spilling over from abundant plant species onto less abundant ones. This community‐level ‘mycorrhizal spillover’ is hypothesized to affect PSF in ways that are additive and interactive with conspecific density dependence. Second, we describe how mycorrhizal effects on PSF could structure the way plant communities respond to global change. Third, we discuss how they may influence plant evolution by altering the balance of selection pressures on traits and genes related to pathogen defence and mutualism formation. [ABSTRACT FROM AUTHOR]

The structure of the leaf microbiome can alter host fitness and change in response to abiotic and biotic factors, like seasonality, climate, and leaf age. However, relatively few studies consider the influence of host age on microbial communities at a time scale of a few days, a short time scale relevant to microbes. To understand how host age modulates changes in the fungal and bacterial leaf microbiome on a short time scale, we ran independent field and greenhouse-based studies and characterized phyllosphere communities using next-generation sequencing approaches. Our field study characterized changes in the fungal and bacterial phyllosphere by examining leaves of different relative ages across individuals, whereas the greenhouse study examined changes in the fungal microbiome by absolute leaf age across individuals. Together, these results indicate that fungal communities are susceptible to change as a leaf ages as evidenced by shifts in the diversity of fungal taxa both in the field and the greenhouse. Similarly, there were increases in the diversity of fungal taxa by leaf age in the greenhouse. In bacterial communities in the field, we observed changes in the diversity, composition, and relative abundance of common taxa. These findings build upon previous literature characterizing host-associated communities at longer time scales and provide a foundation for targeted work examining how specific microbial taxa might interact with each other, such as fine-scale interactions between pathogenic and non-pathogenic species. [ABSTRACT FROM AUTHOR]

Although overlooked in post‐mining rehabilitation, soil mycobiota constitute an important fraction of biodiversity, playing pivotal functions in soil that contribute to the revegetation process and soil stability in post‐mining environments. Evaluating the rehabilitation progress requires comparing it, when possible, with a reference site, preferably identical or similar to pre‐mining characteristics. Here, we investigated the mycobiota from a reference site, comparable to pre‐mining characteristics, and a post‐mining revegetated site 10 years after decommissioning and revegetation, during rainy and dry seasons. We combined the metabarcoding approach with functional traits from fungal operational taxonomic units and complemented our results with traditional techniques for arbuscular mycorrhizal fungi (AMF) surveys using spore morphology and mycorrhizal colonization. Our findings demonstrated that the composition of the fungal community exhibited more differences between the two sites studied than the intra‐annual periods assessed, even though the sites were under the same climatic conditions, spatially nearby, and without barriers between them. The mycobiota composition displayed differences between sites from phylum to genus levels. However, the predictive trophic modes (pathotrophs, saprotrophs, and symbionts) were equivalent in the two sites. All roots of plants assessed had AMF colonization, and AMF spore densities were similar. While many fungal taxa were present at both sites, the spatial connectivity between both sites was insufficient for equivalence of fungal community structure and composition. Differences in chemical and physical soil characteristics may have shaped the fungal communities. This study highlights the need to comprehend the fungal community from mining environments, considering concepts of landscape connectivity. [ABSTRACT FROM AUTHOR]

Bean paste is a traditional Chinese fermented condiment, which is loved by consumers for its pleasant flavor and nutritional properties. However, the microbial communities and related flavor compounds in bean paste remain unclear. We studied the correlation between the core functional microorganisms and flavor compounds in bean paste samples at different fermentation stages. Bacterial and fungal communities changed significantly during fermentation. The results indicated that the dominant bacterial genera were Staphylococcus, Lactococcus, and Bacillus. The dominant fungi were Aspergillus and Lichtheimia. During the early and late stages of bean paste fermentation, alcohols, hydrocarbons, esters, and phenols were the main flavor compounds detected. The types and proportions of alcohols and esters in the bean pastes fermented for different durations were similar, whereas the relative contents of phenols and hydrocarbons were higher in the later stages of fermentation. Correlation analysis revealed that core functional microorganisms played a key role in the fermentation process, and the potential correlation between bacterial genera and flavors was stronger than that of fungal genera. Staphylococcus abundance was significantly correlated with the flavor levels of ethyl oleate, ç‐pinene, diallyl disulfide, á‐myrcene, D‐limonene, and tetradecanoic acid, ethyl ester. The abundance of Aspergillus and Lichtheimia was significantly correlated with the flavor levels of á‐myrcene, ç‐pinene, and DL‐3‐phenyllactic acid. This study explored the relationship between microorganisms and flavor compounds in bean paste to deepen our understanding of the mechanism of flavor formation for bean paste. [ABSTRACT FROM AUTHOR]

Introduction: Soil fungal communities play a crucial role in maintaining the ecological functions of alpine forest soil ecosystems. However, it is currently unclear how the distribution patterns of fungal communities in different soil layers of alpine forests will change along the elevational gradients. Material and methods: Therefore, Illumina MiSeq sequencing technology was employed to investigate fungal communities in three soil layers (0-10, 10-20, and 20-30 cm) along an elevational gradient (3500 m to 4300 m) at Sygera Mountains, located in Bayi District, Nyingchi City, Tibet. Results and discussion: The results indicated that: 1) Soil depth had a greater impact on fungal diversity than elevation, demonstrating a significant reduction in fungal diversity with increased soil depth but showing no significant difference with elevation changes in all soil layers. Within the 0-10 cm soil layer, both Basidiomycota and Ascomycota co-dominate the microbial community. However, as the soil depth increases to 10-20 and 20-30 cm soil layers, the Basidiomycota predominantly dominates. 2) Deterministic processes were dominant in the assembly mechanism of the 0-10 cm fungal community and remained unchanged with increasing elevation. By contrast, the assembly mechanisms of the 10-20 and 20-30 cm fungal communities shifted from deterministic to stochastic processes as elevation increased. 3) The network complexity of the 0-10 cm fungal community gradually increased with elevation, while that of the 10-20 and 20-30 cm fungal communities exhibited a decreasing trend. Compared to the 0-10 cm soil layer, more changes in the relative abundance of fungal biomarkers occurred in the 10-20 and 20-30 cm soil layers, indicating that the fungal communities at these depths are more sensitive to climate changes. Among the key factors driving these alterations, soil temperature and moisture soil water content stood out as pivotal in shaping the assembly mechanisms and network complexity of fungal communities. This study contributes to the understanding of soil fungal community patterns and drivers along elevational gradients in alpine ecosystems and provides important scientific evidence for predicting the functional responses of soil microbial ecosystems in alpine forests. [ABSTRACT FROM AUTHOR]

Pyrazines are important flavor components and healthy active components in Baijiu, which including tetramethylpyrazine (TTMP). During the brewing process, the traceability of microbial communities and the content distribution characteristics of TTMP are important for improving the quality and style characteristics of compound-flavored Baijiu (CFB). However, the traceability analysis of microorganisms in fermented grains (FG)--used in the production of CFB--lacks quantitative and systematic evaluation. In this study, the microbial communities and TTMP content of Jiuqu (JQ), Liangpei (LP), FG, and pitmud (CP) used in CFB production were characterized; further, coordinate and discriminant analyses were employed to determine differences in microbial communities. Additionally, traceability and correlation analyses were performed to reveal the origin of microbial communities in FG. The source, content, and distribution characteristics of TTMP based on the brewing process have also been discussed. The results showed thatmost of the bacterial and fungal communities at different levels of FG came fromother sources, and themicroorganisms of Cladosporium, Acetobacter, Aspergillus, Methanosarcina, and Bacillus were considered have a osculating correlations with TTMP content of FG. Taken together, this study provides insights into the origin of microbial communities in FG and the distribution characteristics of TTMP based on the CFB brewing process. The current findings are conducive for optimizing the fermentation process and improving the quality and style characteristics of CFB. [ABSTRACT FROM AUTHOR]

The closed nutrient solution management method allows for the recycling and utilization of nutrient solutions, improving the efficiency of water and fertilizer utilization. This study was conducted to investigate the effects of changing the frequency of nutrient solution renewal and method of nutrient supply on the microbial communities composition, yield, and quality in closed soilless systems by using high-throughput sequencing technology and combining the physicochemical properties of root exudate solution. The results showed that different nutrient solution management modes had a significant impact on the structure and diversity of root exudate solution microbial communities. The abundance and diversity of microorganisms in inorganic perlites were correlative with EC. The abundance and diversity of bacterial communities in the root exudate solution of open liquid supply (CK) were higher than that of closed liquid supply, while the abundance and diversity of fungal communities in the root exudate solution of closed liquid supply (T1, T2, T3) were higher than that of open liquid supply. As the frequency of nutrient solution interval decreased, the accumulation of salt in root exudate solution and the richness and diversity of the fungal community also decreased, especially increasing the K+, Ca2+, and Mg2+ contents, which were positively correlated with potential beneficial Candidatus_Xiphinematobacter, Arachidicoccus, Cellvibrio, Mucilaginibacter, Taibaiella communities and decreasing the content of soluble protein, Vitamin C content, but not significantly increased cucumber yield. [ABSTRACT FROM AUTHOR]

Sugarcane smut, caused by the fungus Sporisorium scitamineum (Sydow), significantly affects sugarcane crops worldwide. Infected plants develop whip-like structures known as sori. Significant variations in these whip lengths are commonly observed, but the physiological and molecular differences causing these morphological differences remain poorly documented. To address this, we employed conventional microbe isolation, metagenomic, and metabolomic techniques to investigate smut-infected sugarcane stems and whips of varying lengths. Metagenomics analysis revealed a diverse fungal community in the sugarcane whips, with Sporisorium and Fusarium genera notably present (>1%) in long whips. Isolation techniques confirmed these findings. Ultra-performance liquid chromatography analysis (UHPLC-MS/MS) showed high levels of gibberellin hormones (GA3, GA1, GA4, GA8, and GA7) in long whips, with GA4 and GA7 found exclusively in long whips and stems. Among the prominent genera present within long whips, Fusarium was solely positively correlated with these gibberellin (GA) hormones, with the exception of GA8, which was positively correlated with Sporisorium. KEGG enrichment analysis linked these hormones to pathways like diterpenoid biosynthesis and plant hormone signal transduction. These findings suggest that Fusarium may influence GA production leading to whip elongation. Our study reveals fungal dynamics and gibberellin responses in sugarcane smut whips. Future research will explore the related molecular gibberellin synthesis mechanisms. [ABSTRACT FROM AUTHOR]

Soil microorganisms play a crucial role in the plant invasion process, acting as both drivers of and responders to plant invasion. However, the effects of plant invasion on the complexity and stability of co-occurrence networks of soil microbial communities remain unclear. Here, we investigated how the invasion of Spartina alterniflora affected the diversity, composition, and co-occurrence networks of soil bacterial and fungal communities in the Yellow River Delta, China. Compared to the native plant (Suaeda salsa), S. alterniflora invasion decreased the α-diversity of soil bacterial communities but did not affect that of fungal communities. The β-diversity of soil bacterial and fungal communities under S. salsa and S. alterniflora habitats also differed dramatically. S. alterniflora invasion increased the relative abundance of the copiotrophic phylum Bacteroidota, whereas decreased the relative abundances of the oligotrophic phyla Acidobacteriota and Gemmatimonadota. Additionally, the relative abundance of Chytridiomycota, known for its role in degrading recalcitrant organic matter, increased substantially within the soil fungal community. Functional predictions revealed that S. alterniflora invasion increased the relative abundance of certain soil bacteria involved in carbon and nitrogen cycling, including aerobic chemoheterotrophy, nitrate reduction, and nitrate respiration. More importantly, S. alterniflora invasion reduced the complexity and stability of both soil bacterial and fungal community networks. The shifts in soil microbial community structure and diversity were mainly induced by soil available nutrients and soil salinity. Overall, our study highlights the profound impacts of S. alterniflora invasion on soil microbial communities, which could further indicate the modification of ecosystem functioning by invasive species. [ABSTRACT FROM AUTHOR]

Hot springs contain many microorganisms, and a great deal of research has been conducted on the bacteria in hot springs but less on the fungi. Microbial diversity research in hot springs will help to further develop and utilize the microbial resources from hot springs. This is the first study to analyze the fungal diversity and ecological functions in Tangchi hot spring (China). In this paper, the fungal ITS sequences in the water samples of Tangchi hot spring were sequenced by Illumina MiSeq high-throughput sequencing technology and bioinformatically analyzed to explore the fungal diversity and ecological functions in the hot spring. The results revealed that the dominant fungal phylum was Ascomycota, followed by Basidiomycota, Chytridiomycota, and Olpidiomycota, and the dominant fungal genera were Rhizophydium, Aureobasidium, Rhodotorula, and Sclerotinia in Tangchi hot spring. The FUNGuild functional analysis results revealed that the dominant guilds in Tangchi hot spring were plant pathogens followed by the undefined saprotroph and the animal endosymbiont–animal pathogen–endophyte–plant pathogen–undefined saprotroph. This study can fill the gap in people's understanding of fungal resources and offer theoretical support for understanding the fungal diversity and fungal resource development and utilization in Tangchi hot spring. [ABSTRACT FROM AUTHOR]

Chronic liver disease and its complications are a significant global health burden. Changes in fungal communities (mycobiome), an integral component of the gut microbiome, are associated with and contribute to the development of liver disease. Fungal dysbiosis can induce intestinal barrier dysfunction and allow fungal products to translocate to the liver causing progression of disease. This review explores recent progress in understanding the compositional and functional diversity of gut mycobiome signatures across different liver diseases. It delves into causative connections between gut fungi and liver diseases. We emphasize the significance of fungal translocation, with a particular focus on fungal-derived metabolites and immune cells induced by fungi, as key contributors to liver disease. Furthermore, we review the potential impact of the intrahepatic mycobiome on the progression of liver diseases. [ABSTRACT FROM AUTHOR]

Background: Subsurface microorganisms contribute to important ecosystem services, yet little is known about how the composition of these communities is affected by small scale heterogeneity such as in preferential flow paths including biopores and fractures. This study aimed to provide a more complete characterization of microbial communities from preferential flow paths and matrix sediments of a clayey till to a depth of 400 cm by using 16S rRNA gene and fungal ITS2 amplicon sequencing of environmental DNA. Moreover, shotgun metagenomics was applied to samples from fractures located 150 cm below ground surface (bgs) to investigate the bacterial genomic adaptations resulting from fluctuating exposure to nutrients, oxygen and water. Results: The microbial communities changed significantly with depth. In addition, the bacterial/archaeal communities in preferential flow paths were significantly different from those in the adjacent matrix sediments, which was not the case for fungal communities. Preferential flow paths contained higher abundances of 16S rRNA and ITS gene copies than the corresponding matrix sediments and more aerobic bacterial taxa than adjacent matrix sediments at 75 and 150 cm bgs. These findings were linked to higher organic carbon and the connectivity of the flow paths to the topsoil as demonstrated by previous dye tracer experiments. Moreover, bacteria, which were differentially more abundant in the fractures than in the matrix sediment at 150 cm bgs, had higher abundances of carbohydrate active enzymes, and a greater potential for mixotrophic growth. Conclusions: Our results demonstrate that the preferential flow paths in the subsurface are unique niches that are closely connected to water flow and the fluctuating ground water table. Although no difference in fungal communities were observed between these two niches, hydraulically active flow paths contained a significantly higher abundance in fungal, archaeal and bacterial taxa. Metagenomic analysis suggests that bacteria in tectonic fractures have the genetic potential to respond to fluctuating oxygen levels and can degrade organic carbon, which should result in their increased participation in subsurface carbon cycling. This increased microbial abundance and activity needs to be considered in future research and modelling efforts of the soil subsurface. [ABSTRACT FROM AUTHOR]

While afforestation mitigates climate concerns, the impact of afforestation on ecological assembly processes and multiple soil functions (multifunctionality) in afforested areas remains unclear. The Xiong'an New Area plantation forests (Pinus and Sophora forests) in North China were selected to examine the effects of plantation types across four distinct seasons on soil microbiomes. Three functional categories (nutrient stocks, organic matter decomposition, and microbial functional genes) of multifunctionality and the average (net) multifunctionality were quantified. All these categories are directly related to soil functions. The results showed that net soil multifunctionality as a broad function did not change seasonally, unlike other narrow functional categories. Bacterial communities were deterministically (variable selection and homogenous selection) structured, whereas the stochastic process of dispersal limitation was mainly responsible for the assembly and turnover of fungal and protist communities. In Pinus forests, winter initiates a sudden shift from deterministic to stochastic processes in bacterial community assembly, accompanied by decreased Shannon diversity and heightened nutrient cycling (nutrient stocks and organic matter decomposition). This indicates the potential vulnerability of deterministic assembly to seasonal fluctuations, particularly in environments rich in nutrients. The results predicted that protist community composition was uniquely structured with C-related functional activities relative to bacterial and fungal β-diversity variations, which were mostly explained by seasonal variations. Our study highlighted the importance of the protist phagocytosis process on soil microbial interactions through the predicted impact of protist α-diversity on microbial cooccurrence network parameters. This association might be driven by the high abundance of protist consumers as the main predators of bacterial and fungal lineages in our sampling plots. Our findings reveal that the complexity of microbial co-occurrence interactions was considerably higher in spring, perhaps attributing thermal variability and increased resource availability within spring that foster microbial diversity and network complexity. This study contributes to local ecosystem prospects to model the behavior of soil biota seasonally and their implied effects on soil functioning and microbial assembly processes, which will benefit global-scale afforestation programs by promoting novel, precise, and rational plantation forests for future environmental sustainability and self-sufficiency. [ABSTRACT FROM AUTHOR]

Introduction: Citrus is one of the most important fruit crops worldwide, and the root-associated microbiota can have a profound impact on tree health and growth. Methods: In a collaborative effort, the International Citrus Microbiome Consortium investigated the global citrus root microbiota with samples collected from nine citrus-producing countries across six continents. We analyzed 16S rDNA and ITS2 amplicon sequencing data to identify predominant prokaryotic and fungal taxa in citrus root samples. Comparative analyses were conducted between root-associated microbial communities and those from the corresponding rhizosphere and bulk soil samples. Additionally, genotype-based group-wise comparisons were performed to assess the impact of citrus genotype on root microbiota composition. Results: Ten predominant prokaryotic phyla, containing nine bacterial phyla including Proteobacteria, Actinobacteria, Acidobacteria, and Bacteroidetes and one archaeal phylum (Thaumarchaeota), and multiple fungal phyla including Ascomycota and Basidiomycota were identified in the citrus root samples. Compared with the microbial communities from the corresponding rhizosphere and bulk soil samples from the same trees, the prokaryotic and fungal communities in the roots exhibited lower diversity and complexity but greater modularity compared to those in the rhizosphere. In total, 30 root-enriched and 150 root-depleted genera in bacterial community were identified, whereas 21 fungal genera were enriched, and 147 fungal genera were depleted in the root niche compared with the rhizosphere. The citrus genotype significantly affected the root prokaryotic and fungal communities. In addition, we have identified the core root prokaryotic genera comprising Acidibacter, Allorhizobium, Bradyrhizobium, Chitinophaga, Cupriavidus, Devosia, Dongia, Niastella, Pseudomonas, Sphingobium, Steroidobacter and Streptomyces, and the core fungal genera including Acrocalymma, Cladosporium, Fusarium, Gibberella, Mortierella, Neocosmospora and Volutella. The potential functions of these core genera of root microbiota were predicted. Conclusion: Overall, this study provides new insights into the assembly of microbial communities and identifies core members of citrus root microbiota across a wide geographic range. The findings offer valuable information for manipulating root microbiota to enhance plant growth and health. [ABSTRACT FROM AUTHOR]

The intricate relationship between regeneration and microbiota has recently gained attention, spanning diverse model organisms. Axolotl (Ambystoma mexicanum) is a critically endangered salamander species and a model organism for regenerative and developmental biology. Despite its significance, a noticeable gap exists in understanding the interplay between axolotl regeneration and its microbiome. Here, we analyse in depth bacterial 16S rRNA amplicon dataset that we reported before as data resource and profile fungal community by sequencing ITS amplicons at the critical stages of limb regeneration (0–1–4–7–30–60 days post amputation, ‘dpa’). Results reveal a decline in richness and evenness in the course of limb regeneration, with bacterial community richness recovering beyond 30 dpa unlike fungi community. Beta diversity analysis reveals precise restructuring of the bacterial community along the three phases of limb regeneration, contrasting with less congruent changes in the fungal community. Temporal dynamics of the bacterial community highlight prevalent anaerobic bacteria in initiation phase and Flavobacterium bloom in the early phase correlating with limb blastema proliferation. Predicted functional analysis mirrors these shifts, emphasising a transition from amino acid metabolism to lipid metabolism control. Fungal communities shift from Blastomycota to Ascomycota dominance in the late regeneration stage. Our findings provide ecologically relevant insights into stage specific role of microbiome contributions to axolotl limb regeneration. [ABSTRACT FROM AUTHOR]

The colonization of alien plants in new habitats is typically facilitated by microorganisms present in the soil environment. However, the diversity and structure of the archaeal, bacterial, and fungal communities in the latitudinal spread of alien plants remain unclear. In this study, the rhizosphere and bulk soil of Chromolaena odorata were collected from five latitudes in Pu' er city, Yunnan Province, followed by amplicon sequencing of the soil archaeal, bacterial, and fungal communities. Alpha and beta diversity results revealed that the richness indices and the structures of the archaeal, bacterial, and fungal communities significantly differed along the latitudinal gradient. Additionally, significant differences were observed in the bacterial Shannon index, as well as in the structures of the bacterial and fungal communities between the rhizosphere and bulk soils. Due to the small spatial scale, trends of latitudinal variation in the archaeal, bacterial, and fungal communities were not pronounced. Total potassium, total phosphorus, available nitrogen, available potassium and total nitrogen were the important driving factors affecting the soil microbial community structure. Compared with those in bulk soil, co-occurrence networks in rhizosphere microbial networks presented lower complexity but greater modularity and positive connections. Among the main functional fungi, arbuscular mycorrhizae and soil saprotrophs were more abundant in the bulk soil. The significant differences in the soil microbes between rhizosphere and bulk soils further underscore the impact of C. odorata invasion on soil environments. The significant differences in the soil microbiota along latitudinal gradients, along with specific driving factors, demonstrate distinct nutrient preferences among archaea, bacteria, and fungi and indicate complex microbial responses to soil nutrient elements following the invasion of C. odorata. [ABSTRACT FROM AUTHOR]

Fungi have been used for medicinal purposes for many centuries. This study, based on 35 historical written sources and 581 in-depth semi-structured interviews from eight countries in the western borderlands of the former Soviet Union, investigates the medicinal use of fungi by local communities. We compared the taxa and uses obtained from fieldwork and historical sources with works that advocated fungi use within Soviet herbals, representing the centralised medical system. During fieldwork, we identified eight locally used fungi and one lichen. The highest numbers of medicinal uses were documented in Russia, Estonia and Ukraine. Studies published before the Soviet era listed 21 fungal taxa and one lichen species used in the study region. However, only six of these taxa were mentioned as used by people in our field studies (Amanitamuscaria, Boletusedulis, Lycoperdon, Morchella, Phallusimpudicus and Cetrariaislandica). Notably, these same six taxa were consistently endorsed in Soviet herbals. Of the remaining three taxa recorded in the fieldwork, none were mentioned in historical written sources. However, they were promoted either in Soviet herbals (Inonotusobliquus, Kombucha) or later popular publications (Cantharelluscibarius). This highlights the significant influence of written sources on the use of fungi for medicinal purposes within the studied local communities. [ABSTRACT FROM AUTHOR]

Background: Taxol, derived from Taxus trees, is a valuable natural resource for the development of anticancer drugs. Endophytic fungi from Taxus trees are a promising alternative source of Taxol. However, the impact of plant-endophytic microbial interaction on the host's Taxol biosynthesis is largely unknown. Results: In the current study, the diversity of endophytic fungi in three different Taxus species was analyzed using Internal Transcribed Spacer sequencing. A total of 271 Operational Taxonomic Units (OTUs) were identified, grouping into 2 phyla, 8 classes, 16 orders, 19 families, and 19 genera. Alpha and beta diversity analysis indicated significant differences in endophytic fungal communities among the various Taxus trees. At the genus level, Alternaria and Davidiella were predominantly found in T. mairei and T. media, respectively. By utilizing a previously published dataset, a Pearson correlation analysis was conducted to predict the taxol biosynthesis-related fungal genera. Following screening, two isolates of Alternaria (L7 and M14) were obtained. Effect of inoculation with Alternaria isolates on the gene expression and metabolite accumulation of T. mairei was determined by transcriptomic and untargeted metabolomic studies. The co-inoculation assay suggests that the two Alternaria isolates may have a negative regulatory effect on taxol biosynthesis by influencing hormone signaling pathways. Conclusion: Our findings will serve as a foundation for advancing the production and utilization of Taxus and will also aid in screening endophytic fungi related to taxol production. [ABSTRACT FROM AUTHOR]

Sustainable waste management through composting has gain renewed attention since it could upcycle organic waste into valuable bio-organic fertiliser. This study explored the composition of fungal communities in leaf litter and organic waste composts ecosystems by employing advanced internal transcribed spacer (ITS) metagenomic profiling. This approach provides insights into the diversity, composition, and potential functions of these fungi, offering practical implications for optimising composting processes and enhancing sustainable waste management practices. Various organic composts were collected, including leaf litter composts, from different sources in Delhi-National Capital Region, India, and fungal microbiome composition were characterised through ITS profiling. Results revealed that leaf litter composts and cow dung manure had the highest fungal read counts, while kitchen waste compost had the lowest. Alpha diversity indices, including Chao1 and Shannon, exhibited differences in species richness and diversity among composts, though statistical significance was limited. The leaf composts had relatively higher alpha diversity than the other organic waste composts analysed. The study also identified dominant fungal genera specifically, Wallemia, Geotrichum, Pichia, Mycothermus, Mortierella, Aspergillus, Fusarium, and Basidiobolus, across the compost samples. The presence of beneficial fungal genera like Pichia, Geotrichum, Trichoderma, Mortierella, Basidiobolus, Aspergillus, and others were detected in leaf waste compost and the other organic waste composts. There was also presence of some pathogenic genera viz. Alternaria, Fusarium, and Acremonium, in these composts which underscored the need for proper composting practices and source selection to optimise soil fertility and minimise disease risks in agriculture. Remarkably, leaf compost has highest proportion of beneficial genera with least observed abundance of pathogens. On the other hand, the municipal organic waste compost has least proportion of beneficial genera with higher abundance of pathogens. Overall, these findings contributed to characterisation of composting processes, advancing waste management practices, and enhancing the use of leaf compost as a bio-organic fertiliser. [ABSTRACT FROM AUTHOR]

Microbiome assembly critically impacts the ability of hosts to access beneficial symbiont functions. Fungus-farming termites have co-evolved with a fungal cultivar as a primary food source and complex gut microbiomes, which collectively perform complementary degradation of plant biomass. A large subset of the bacterial community residing within termite guts are inherited (vertically transmitted) from parental colonies, while the fungal symbiont is, in most termite species, acquired from the environment (horizontally transmitted). It has remained unknown how the gut microbiota sustains incipient colonies prior to the acquisition of the fungal cultivar, and how, if at all, bacterial contributions are modulated by fungus garden establishment. Here, we test the latter by determining the composition and predicted functions of the gut microbiome using metabarcoding and shotgun metagenomics, respectively. We focus our functional predictions on bacterial carbohydrate-active enzyme and nitrogen cycling genes and verify compositional patterns of the former through enzyme activity assays. Our findings reveal that the vast majority of microbial functions are encoded in the inherited microbiome, and that the establishment of fungal gardens incurs only minor modulations of predicted bacterial capacities for carbohydrate and nitrogen metabolism. While we cannot rule out that other symbiont functions are gained post-fungus garden establishment, our findings suggest that fungus-farming termite hosts are equipped with a near-complete set of gut microbiome functions at the earliest stages of colony life. This inherited, incipient bacterial microbiome likely contributes to the high extent of functional specificity and coevolution observed between termite hosts, gut microbiomes, and the fungal cultivar. [ABSTRACT FROM AUTHOR]

The variation in the soil microbial community along the altitude gradient has been widely documented. However, the structure and function of the microbial communities distributed along the altitude gradient in the crater still need to be determined. We gathered soil specimens from different elevations within the Nushan volcano crater to bridge this knowledge gap. We investigated the microbial communities of bacteria and fungi in the soil. It is noteworthy that the microbial alpha diversity peaks in the middle of the crater. However, network analysis shows that bacterial (nodes 760 vs 613 vs 601) and fungal (nodes 328 vs 224 vs 400) communities are most stable at the bottom and top of the crater, respectively. Furthermore, the soil microbial network exhibited a decline, followed by an increase across varying altitudes. The core microorganisms displayed the highest correlation with pH and alkaline phosphatase (AP, as determined through redundancy analysis (RDA) and Mantel tests for correlation analysis. The fungal community has a higher number of core microorganisms, while the bacterial core microorganisms demonstrate greater susceptibility to environmental factors. In conclusion, we utilized Illumina sequencing techniques to assess the disparities in the structure and function of bacteria and fungi in the soil. [ABSTRACT FROM AUTHOR]

Soil fungi participate in various ecosystem processes and are important factors driving the restoration of degraded forests. However, little is known about the changes in fungal diversity and potential functions under the development of different vegetation types during natural (secondary forest succession) and anthropogenic (reforestation) forest restoration. In this study, we selected typical forest succession sequences (including Pinus densiflora Siebold & Zucc., pine‐broadleaf mixed forest of P. densiflora and Quercus acutissima Carruth., and Q. acutissima), as well as natural secondary deciduous broadleaved mixed forests and planted forests of Robinia pseudoacacia on Kunyu Mountain for analysis. We used ITS rRNA gene sequencing to characterize fungal communities and used the FUNGuild database to predict fungal functional groups. The results showed that forest succession affected fungal β‐diversity, but not the α‐diversity. There was a significant increase in Basidiomycota and a decrease in Ascomycota in the later successional stage, accompanied by an increase in the functional groups of ectomycorrhizal fungi (ECM). Conversely, planted forests exhibited decreased fungal α‐diversity and altered community compositions, characterized by fewer Basidiomycota and more Ascomycota and Mucoromycota. Planted forests led to a decrease in the relative abundances of ECM and an increase in animal pathogens. The TK content was the major factor explaining the distinction in fungal communities among the three successional stages, whereas pH, AP, and NH4+ were the major factors explaining community variations between natural and planted forests. Changes in vegetation types significantly affected the diversity and functional groups of soil fungal communities during forest succession and reforestation, providing key insights for forest ecosystem management in temperate forests. [ABSTRACT FROM AUTHOR]

In Europe, Pinus sylvestris and Picea abies are the most common coniferous tree species used in commercial forestry, which rely on high‐quality reproductive material for successful reforestation. Clear‐cut harvested forest sites are often replanted using tree seedlings, which are produced in forest nurseries using seeds from seed orchards. However, incidences of fungal diseases in seedling production show that a better knowledge of seedborne fungi, including fungal pathogens, is needed to manage diseases in forest nurseries. This study aimed to assess seedborne fungal communities associated with commercial seeds of P. abies, P. sylvestris and Larix sp. seeds originated from geographically separated regions in Sweden, Belarus, Finland and Poland. Fungal communities were obtained first from the seed surface and then from the seed tissue. These were analysed using high‐throughput sequencing of the ITS2 rDNA region. The results showed that fungal diversity and community composition differed between the seed surface and the seed tissue. Picea abies accommodated a higher fungal diversity than P. sylvestris. In addition, a strong host affinity of the fungal community composition on the seed surface and a weaker association in the seed tissue was found. Fungal communities on P. abies and P. sylvestris seed surface differed significantly between geographical regions, whereas no regional differences were found in the seed tissue. The seedborne fungal communities included a high proportion of plant pathogens, among which the most abundant were Sydowia polyspora (13.3%), Phoma herbarum (11.2%) and Sirococcus conigenus (3.8%). In conclusion, the results showed (a) characteristic fungal diversity and community composition between the seed surface and the seed tissue; (b) a host‐specific fungal community composition on the seed surface and in the seed tissue; (c) regional difference in fungal communities on P. abies and P. sylvestris seed surface, thus the movement of seeds between different regions can contribute to the spread of fungal diseases; and (d) the presence of a high incidence of seedborne fungal pathogens which suggest a potential need of preventative or control measures to reduce the occurrence of these fungi on the seed surface. [ABSTRACT FROM AUTHOR]

Summary: Climate warming is severely affecting high‐latitude regions. In the Arctic tundra, it may lead to enhanced soil nutrient availability and interact with simultaneous changes in grazing pressure. It is presently unknown how these concurrently occurring global change drivers affect the root‐associated fungal communities, particularly mycorrhizal fungi, and whether changes coincide with shifts in plant mycorrhizal types.We investigated changes in root‐associated fungal communities and mycorrhizal types of the plant community in a 10‐yr factorial experiment with warming, fertilisation and grazing exclusion in a Finnish tundra grassland.The strongest determinant of the root‐associated fungal community was fertilisation, which consistently increased potential plant pathogen abundance and had contrasting effects on the different mycorrhizal fungal types, contingent on other treatments. Plant mycorrhizal types went through pronounced shifts, with warming favouring ecto‐ and ericoid mycorrhiza but not under fertilisation and grazing exclusion. Combination of all treatments resulted in dominance by arbuscular mycorrhizal plants. However, shifts in plant mycorrhizal types vs fungi were mostly but not always aligned in their magnitude and direction.Our results show that our ability to predict shifts in symbiotic and antagonistic fungal communities depend on simultaneous consideration of multiple global change factors that jointly alter plant and fungal communities. [ABSTRACT FROM AUTHOR]

Plant–microbe interactions are key to nutrient-use efficiency. Root microbes are influenced by rhizosphere soil and plant cultivars. The impact of cultivar-by-nitrogen (N) interactions on the maize-root microbiome remains unclear, yet it is crucial for understanding N use efficiency in maize. This study evaluated the effects of maize cultivars and N forms, along with their interactions, on the diversity and composition of root bacteria and fungi. Additionally, we examined correlations between soil microbes and root metabolites. The maize cultivar Zhengdan 958 (ZD958) showed a positive response to the mixture of nitrate and ammonium N, resulting in increased in biomass, grain yield, shoot N content, grain N content, and root area. In contrast, the cultivar Denghai605 (DH605) did not exhibit a similar response. The diversity and composition of root bacteria and fungi differed between ZD958 and DH605. The N form primarily affected the community structure of rhizospheric fungi in ZD958 and rhizospheric bacteria in DH605, rather than endophytic microbes. A mixed N supply increased the relative abundance of Basidiomycota, which was positively correlated with ZD958 yield. For DH605, a mixed N treatment enhanced nitrification functions involving Bacteroidetes and Proteobacteria, while it reduced the effects of ammonium N supply. The dominant rhizospheric microbes in DH605 showed a stronger response to changes in root metabolites compared to those in ZD958. A mixed N supply increased the content of palmitoleic acid in ZD958 root exudates, facilitating the recruitment of beneficial rhizospheric microbes, which promotes maize growth. In DH605, a mixed N supply decreased the concentration of sphinganine, which is significantly correlated with Acidobacteria (negatively), Proteobacteria (negatively), Bacteroidetes (positively), and TM7 (positively). Our findings suggest that different maize cultivars respond differently to N forms, causing distinct rhizospheric microbial effects, and that root metabolites send metabolic signals to regulate and recruit key bacterial and fungal communities. [ABSTRACT FROM AUTHOR]

Fungal contamination in rice and mycotoxins present significant challenges to both rice quality and food safety. However, there is a dearth of comprehensive research on the compositional and structural changes within fungal colonies in rice, particularly in typical rice-producing regions, as well as their underlying influencing factors. In this study, a comprehensive analysis of fungal taxa in rice grains was conducted using amplicon sequencing and bioinformatics methods on 99 rice samples collected in three major rice-producing regions in China: Northeast Plain (NP), Yangtze River Basin (YR), and Southeast Coastal Area (SC). A total of 6,019,722 fungal ITS sequences were obtained with an average sequence length of 235 base pairs, and effective ASVs (2014) accounted for approximately 97.58% of the total ASVs (2064). The fungal community diversity in rice grains exhibited significant variations across the three regions, with deterministic processes playing a predominant role in shaping the ecological dynamics of fungal taxa. Among the core microbiota (92 shared ASVs), the first five species (Alternaria, Fusarium, Curvularia, Epicoccum, and Ustilaginoidea) accounting for a proportion greater than 5% had been reported as potential pathogens for plants. Geographical variations in fungal community composition were evident, with a significantly higher number of shared populations observed between YR and CS regions compared to those in the NP region. Nutrient elements and climatic conditions were the internal and external driving factors of rice fungal community composition. Additionally, notable regional variations in fungal functionality were observed. The findings have significant implications for gaining a comprehensive understanding of the distribution patterns of fungal communities in the major rice-producing regions in China. Additionally, it provides valuable insights into controlling key influencing factors to effectively reduce the occurrence of toxin-producing fungi and mitigate the associated risks related to mycotoxin contamination, thereby contributing to improved risk management and assessment. [ABSTRACT FROM AUTHOR]

Plants thrive in diverse environments, where root-microbe interactions play a pivotal role. Date palm (Phoenix dactylifera L.), with its genetic diversity and resilience, is an ideal model for studying microbial adaptation to different genotypes and stresses. This study aimed to analyze the bacterial and fungal communities associated with traditional date palm cultivars and the widely cultivated "Deglet Nour" were explored using metabarcoding approaches. The microbial diversity analysis identified a rich community with 13,189 bacterial and 6442 fungal Amplicon Sequence Variants (ASVs). Actinobacteriota, Proteobacteria, and Bacteroidota dominated bacterial communities, while Ascomycota dominated fungal communities. Analysis of the microbial community revealed the emergence of two distinct clusters correlating with specific date palm cultivars, but fungal communities showed higher sensitivity to date palm genotype variations compared to bacterial communities. The commercial cultivar "Deglet Nour" exhibited a unique microbial composition enriched in pathogenic fungal taxa, which was correlated with its genetic distance. Overall, our study contributes to understanding the complex interactions between date palm genotypes and soil microbiota, highlighting the genotype role in microbial community structure, particularly among fungi. These findings suggest correlations between date palm genotype, stress tolerance, and microbial assembly, with implications for plant health and resilience. Further research is needed to elucidate genotype-specific microbial interactions and their role in enhancing plant resilience to environmental stresses. [ABSTRACT FROM AUTHOR]

Vermicompost (VC) produced by African nightcrawler earthworms (Eudrilus eugeniae) is a natural fertilizer with a rich microbial community. Trichoderma asperelloides PSU-P1 is an effective antagonistic microorganism with multifaceted activity mechanisms. This research aimed to develop Trichoderma-bioenriched vermicompost (TBVC) to promote plant growth and induce the defense response in the Thai rice variety "Chor Khing". T. asperelloides PSU-P1 was tested against Rhizoctonia solani, the pathogen of sheath blight disease, using a dual-culture assay. The results showed that T. asperelloides PSU-P1 effectively inhibited R. solani in vitro growth by 70.48%. The TBVC was prepared by adding a conidial suspension (108 conidia/mL) to vermicompost. The viability of Trichoderma persisted in the vermicompost for 6 months and ranged from 1.2 to 2.8 × 107 CFU/mL. Vermicompost water extracts significantly enhanced seed germination, root length, and shoot length compared to a control group (p < 0.05). Plants that received the TBVC displayed significantly longer shoot and root lengths and higher total chlorophyll content than control plants (p < 0.05). The TBVC induced defense response by increasing the enzyme activity of peroxidase (POD) and polyphenol oxidase (PPO) in comparison with control plants. Rice grown in the TBVC had a significantly reduced incidence of sheath blight caused by R. solani in comparison with control rice (p < 0.05). Furthermore, the fungal community of rice plants was analyzed via the high-throughput next-generation sequencing of the internal transcribed spacer (ITS). The fungal community in the TBVC had greater alpha diversity than the community in the VC. Phylum Ascomycota was dominant in both samples, and a heat map showed that Trichoderma was more prevalent in the TBVC than in the VC. Our results indicate that the enrichment of VC with Trichoderma increases growth, enhances the defense response, and reduces the incidence of sheath blight disease in the Thai rice variety "Chor Khing". [ABSTRACT FROM AUTHOR]

Xylem-associated fungus can secrete many secondary metabolites to help Aquilaria trees resist various stresses and play a crucial role in facilitating agarwood formation. However, the dynamics of endophytic fungi in Aquilaria sinensis xylem after artificial induction have not been fully elaborated. Endophytic fungi communities and xylem physio-biochemical properties were examined before and after induction with an inorganic salt solution, including four different times (pre-induction (0M), the third (3M), sixth (6M) and ninth (9M) month after induction treatment). The relationships between fungal diversity and physio-biochemical indices were evaluated. The results showed that superoxide dismutase (SOD) and peroxidase (POD) activities, malondialdehyde (MDA) and soluble sugar content first increased and then decreased with induction time, while starch was heavily consumed after induction treatment. Endophytic fungal diversity was significantly lower after induction treatment than before, but the species richness was promoted. Fungal β-diversity was also clustered into four groups according to different times. Core species shifted from rare to dominant taxa with induction time, and growing species interactions in the network indicate a gradual complication of fungal community structure. Endophytic fungi diversity and potential functions were closely related to physicochemical indices that had less effect on the relative abundance of the dominant species. These findings help assess the regulatory mechanisms of microorganisms that expedite agarwood formation after artificial induction. [ABSTRACT FROM AUTHOR]

Populus euphratica, Tamarix ramosissima, and Sophora alopecuroides are, respectively, typical arboreal, shrubby, and herbaceous species in oases of arid regions. It is important to study the difference in metabolic characteristics of the rhizosphere fungal community of these plant species and their relationships with soil factors for the preservation of delicate arid oasis ecosystems with future environmental changes. In this study, we, respectively, collected 18 rhizosphere soil samples of P. euphratica, T. ramosissima, and S. alopecuroides to explore the difference in rhizosphere fungal metabolic characteristics of different plant life forms and their underlying driving factors. The results showed that (1) soil physicochemical properties (including soil water content, pH, etc.) were significantly different among different plant species (p < 0.05). (2) Rhizosphere fungal metabolic characteristics were significantly different between S. alopecuroides and T. ramosissima (ANOSIM, p < 0.05), which was mainly caused by the different utilization of carboxylic carbon. (3) The RDA showed that the main driving factors of the variations in rhizosphere fungal metabolic characteristics were different among different plant species. The main explanatory variables of the variations in the metabolic characteristics of the rhizosphere fungal community were carbon to nitrogen ratio (23%) and available potassium (17.4%) for P. euphratica, while soil organic carbon (23.1%), pH (8.6%), and total nitrogen (8.2%) for T. ramosissima, and soil clay content (36.6%) and soil organic carbon (12.6%) for S. alopecuroides. In conclusion, the variations in rhizosphere fungal metabolic characteristics in arid oases are dominantly affected by soil factors rather than plant life forms. [ABSTRACT FROM AUTHOR]

Exploring species diversity along elevational gradients is important for understanding the underlying mechanisms. Our study focused on analyzing the species diversity of fungal communities and their subcommunities at different trophic and taxonomic levels across three high mountains of the Korean Peninsula, each situated in a different climatic zone. Using high-throughput sequencing, we aimed to assess fungal diversity patterns and investigate the primary environmental factors influencing fungal diversity. Our results indicate that soil fungal diversity exhibits different elevational distribution patterns on different mountains, highlighting the combined effects of climate, soil properties, and geographic topology. Notably, the total and available phosphorus contents in the soil emerged as key determinants in explaining the differences in diversity attributed to soil properties. Despite the varied responses of fungal diversity to elevational gradients among different trophic guilds and taxonomic levels, their primary environmental determinants remained remarkably consistent. In particular, total and available phosphorus contents showed significant correlations with the diversity of the majority of the trophic guilds and taxonomic levels. Our study reveals the absence of a uniform diversity pattern along elevational gradients, underscoring the general sensitivity of fungi to soil conditions. By enriching our understanding of fungal diversity dynamics, this research enhances our comprehension of the formation and maintenance of elevational fungal diversity and the response of microbial communities in mountain ecosystems to climate change. This study provides valuable insights for future ecological studies of similar biotic communities. [ABSTRACT FROM AUTHOR]

Rocky habitats, globally distributed ecosystems, harbour diverse biota, including numerous endemic and endangered species. Vascular plants thriving in these environments face challenging abiotic conditions, requiring diverse morphological and physiological adaptations. Their engagement with the surrounding microbiomes is, however, equally vital for their adaptation, fitness, and long‐term survival. Nevertheless, there remains a lack of understanding surrounding this complex interplay within this fascinating biotic ecosystem. Using microscopic observations and metabarcoding analyses, we examined the fungal abundance and diversity in the root system of the rock‐dwelling West Carpathian endemic shrub, Daphne arbuscula (Thymelaeaceae). We explored the diversification of root‐associated fungal communities in relation to microclimatic variations across the studied sites. We revealed extensive colonization of the Daphne roots by diverse taxonomic fungal groups attributed to different ecological guilds, predominantly plant pathogens, dark septate endophytes (DSE), and arbuscular mycorrhizal fungi (AMF). Notably, differences in taxonomic composition and ecological guilds emerged between colder and warmer microenvironments. Apart from omnipresent AMF, warmer sites exhibited a prevalence of plant pathogens, while colder sites were characterized by a dominance of DSE. This mycobiome diversification, most likely triggered by the environment, suggests that D. arbuscula populations in warmer areas may be more vulnerable to fungal diseases, particularly in the context of global climate change. [ABSTRACT FROM AUTHOR]

Background and aims: Wild fruit forests are vital reservoirs of germplasm genetic and biodiversity. Unfortunately, wild fruit forests of Central Asia are in the decline due to fungal disease and insect pest outbreaks. A health soil microbial community may help ameliorate the degradation of wild trees by increasing their systematic resistance, stabilizing soil carbon pool, and maintaining the quality of the habitat environment. We evaluated soil bacterial and fungal community beneath the dominant tree species, Malus sieversii (Ledeb.) M. Roem, to identify potential interactions between wild fruit forest degradation events and soil microorganisms in the Tianshan Mountain, China. Methods: Based on targeted metagenomics of the 16S rRNA and ITS (Internal Transcribed Spacer), we explored the bacterial and fungal microbial communities in soils beneath healthy and degraded M. sieversii trees (i.e., microbial biomass, species interactions, potential and niche breadth), and soil physicochemical properties. Results: We found that the degradation of M. sieversii reduced the beta diversity of topsoil bacterial communities and fungal symbiotic groups. The decline in M. sieversii abundance loosened connections within bacterial and fungal co-occurrence networks. Community assembly identified higher migration rates in the topsoil around degraded M. sieversii for bacteria and for fungi, suggesting that dispersal restricted in degraded wild fruit forest soils. Ultimately, the demise of M. sieversii homogenized the soil bacteria resulting in a narrow niche-breadth, enhanced pathogenetic fungal species, and reduced beneficial symbiotic and saprotrophic fungal diversity. Conclusions: Our results demonstrated that the degradation of M. sieversii leads to alterations in diversity, self-assembling and resource competitiveness of forest soil-dwelling microorganisms. [ABSTRACT FROM AUTHOR]

Aims: Endophytes could assist the host plant in the acquisition of nutrients and tolerance of stresses during their long symbiotic life cycle with the host plant. Blueberry (Vaccinium spp.) is adapted to acidic soils and can inhabit harsh soil conditions. However, the dynamic variation of its endosphere microbial community under long-term cultivation remains unclear. Methods: We collected blueberry root samples of four age groups (4a, 8a, 17a, and 33a). The diversity and composition of bacterial and fungal communities in the root endosphere were analyzed, and their co-occurrence networks were constructed to explore interkingdom interactions and keystone taxa. Results: As the major phylum of the endosphere, the relative abundance of Actinobacteria decreased with the age of the blueberry, whereas Proteobacteria increased. The fungal communities were dominated by Sordariomycetes, Eurotiomycetes, and Agaricomycetes, and these were not regularly altered with the increased blueberry age. The co-occurrence network revealed that positive interactions were observed in the bacterial and fungal communities and were consistently dominant within both intrakingdom and interkingdom networks. Among the interkingdom network, keystone taxa were identified for bacteria mainly belonging to Proteobacteria and Actinobacteria of bacteria, as well as for fungi of Ascomycota, which have potentially beneficial effects on host plants. Conclusions: Our study reveals although the diversity and composition varied with blueberry age in the root endosphere, their positive interactions of intrakingdom or interkingdom consistently dominate the network, and it may be such positive beneficial interactions that maintain the health of host plant during long-term symbiosis. [ABSTRACT FROM AUTHOR]