The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications

Habitat specialization and edge effects of soil microbial communities in a fragmented landscape

Soil microorganisms play outsized roles in nutrient cycling, plant health, and climate regulation. Despite their importance, we have a limited understanding of how soil microbes are affected by habitat fragmentation, including their responses to conditions at fragment edges, or "edge effects." To understand the responses of soil communities to edge effects, we analyzed the distributions of soil bacteria, archaea, and fungi in an experimentally fragmented system of open patches embedded within a forest matrix. In addition, we identified taxa that consistently differed among patch, edge, or matrix habitats ("specialists") and taxa that showed no habitat preference ("nonspecialists"). We hypothesized that microbial community turnover would be most pronounced at the edge between habitats. We also hypothesized that specialist fungi would be more likely to be mycorrhizal than nonspecialist fungi because mycorrhizae should be affected more by different plant hosts among habitats, whereas specialist prokaryotes would have smaller genomes (indicating reduced metabolic versatility) and be less likely to be able to sporulate than nonspecialist prokaryotes. Across all replicate sites, the matrix and patch soils harbored distinct microbial communities. However, sites where the contrasts in vegetation and pH between the patch and matrix were most pronounced exhibited larger differences between patch and matrix communities and tended to have edge communities that differed from those in the patch and forest. There were similar numbers of patch and matrix specialists, but very few edge specialist taxa. Acidobacteria and ectomycorrhizae were more likely to be forest specialists, while Chloroflexi, Ascomycota, and Glomeromycota (i.e., arbuscular mycorrhizae) were more likely to be patch specialists. Contrary to our hypotheses, nonspecialist bacteria were not more likely than specialist bacteria to have larger genomes or to be spore-formers. We found partial support for our mycorrhizal hypothesis: arbuscular mycorrhizae, but not ectomycorrhizae, were more likely to be specialists. Overall, our results indicate that soil microbial communities are sensitive to edges, but not all taxa are equally affected, with arbuscular mycorrhizae in particular showing a strong response to habitat edges. In the context of increasing habitat fragmentation worldwide, our results can help inform efforts to maintain the structure and functioning of the soil microbiome.

Differential contributions of microbial necromass to humic acid during composting of organic wastes

Microbial necromass is a crucial source of stable organic matter in composting, yet its role in the humification process remains poorly understood. This study aims to explore the contribution of microbial necromass carbon (MNC) to humic acid (HA) formation during the composting of sewage sludge (SS), kitchen waste (KW), and pig manure (PM), and to examine the involvement of fungal communities in microbial necromass humification. The results show that fungal necromass carbon (FNC) consistently contributes more to MNC than bacterial necromass carbon (BNC), with FNC accounting for over 60% of MNC across all treatments. KW exhibited the highest accumulation of FNC (4.09-98.92 g/kg), and its MNC contribution to total organic carbon was 23.63%, significantly higher than sewage sludge (5.57%) and pig manure (7.47%). The carbon-to-nitrogen (C/N) ratio was found to be a critical factor influencing microbial growth, necromass accumulation, and HA formation, with a lower C/N ratio promoting faster microbial turnover and enhancing MNC contribution to HA. The analysis also revealed that Ascomycota dominated the maturation phase, with a significant role in driving humification, especially in KW. Structural equation modeling confirmed that FNC and BNC are directly influenced by the C/N ratio, which in turn affects HA formation This study enhances our understanding of microbial necromass dynamics and its contribution to humic substance formation, providing valuable insights for improving compost quality and optimizing composting strategies for enhanced carbon sequestration.

Soil Microbial Co-Occurrence Networks Across Climate and Land Use Gradient in Southern Italy

Despite extensive research on microbiota across land use gradients, it remains unclear if microbial co-occurrence relationships exhibit consistent patterns. Here, we assessed microbial co-occurrence networks of seven natural ecosystems-Quercus ilex forest, Fagus sylvatica forest, Abies alba forest, Mediterranean and mountain grasslands, and subalpine and Mediterranean shrublands-and five agroecosystems, including vineyards, horticulture, greenhouse, a polluted agricultural system, and an arid greenhouse. Soil chemistry, such as pH, organic carbon and total nitrogen, was characterised, and soil microbiota were profiled using high-throughput sequencing from 242 soil samples. Our results revealed that mountain grasslands had the highest organic carbon (86.4 g/kg), while the arid greenhouse had the lowest (6.1 g/kg). Mediterranean grasslands had the lowest pH of 5.79, and vineyards had the highest electrical conductivity of 0.901 dS/m. Notably, natural ecosystem networks exhibited greater modularity, with protected horticulture showing exceptionally the highest (0.937), while intensive agriculture within agroecosystems had a significantly lower modularity of 0.282. Modularity and the number of modules were positively correlated with soil P2O5, while network diameter, path length and clustering coefficient were correlated with soil pH. Additionally, edges and nodes number, average degree and microbial diversity were positively associated with organic carbon and total nitrogen. These findings highlight that natural ecosystems foster more complex and resilient microbial networks, underscoring sustainable land management's importance to preserve soil health and microbial diversity.

Needle in a Haystack: Culturing Plant-Beneficial Helotiales Lineages From Plant Roots

Root-associated Helotiales fungi are increasingly recognised as beneficial fungal partners promoting plant growth under nutrient-limited conditions, particularly, in non-mycorrhizal hosts lacking the ancestral arbuscular mycorrhizal symbiosis. However, the ecology of these fungi is still cryptic as relatively few lineages have been successfully cultivated from roots for further study. Here, we attempted the mass isolation of root endophytic fungi to evaluate the recovery of known plant-beneficial Helotiales lineages using a tailored culture-based approach. We sampled six wild non-mycorrhizal species from the Brassicaceae, Caryophyllaceae, and Cyperaceae, growing in nutrient-limited alpine soils. We isolated 602 root endophytes and compared this culturable diversity with the one observed via fungal ITS2 metabarcoding. Metabarcoding revealed that Helotiales taxa dominated the fungal communities, with 43% of these detected taxa also represented in our collection. Accordingly, most root endophytes in our collection (53%) were Helotiales. These isolates, some with P solubilisation potential, belonged primarily to three Helotialean clades and were phylogenetically related to plant growth-promoting or mycorrhizal-like strains. This analysis highlights that the roots of alpine non-mycorrhizal plants harbour diverse plant-beneficial root-endophytic Helotiales, and the isolates obtained are a promising resource to explore the plant-beneficial mechanisms and ecological traits of these fungi.

Drivers of fungal and bacterial communities in ectomycorrhizospheres of birch, oak, and pine in a former uranium mining site, Ronneburg, Germany

The impact of soil and tree species on fungal and bacterial communities was investigated in a former uranium mining area with field and pot studies of the mycorrhizospheres of birch (Betula pendula), oak (Quercus robur), and pine (Pinus sylvestris). At the initial stages of succession re-created in the pot experiment, tree-species-specific microbial communities were detected. The pot microbiomes showed lower diversity and evenness of fungi and bacteria as compared to field-grown trees. In the natural field setting, the fungal community both in bulk and rhizosphere soil consisted of mainly Thelephoraceae, Inocybaceae and Russulaceae. They contributed with Leotiaceae and Herpotrichiellaceae to 52-85% of overall abundances, showing the soil hyphae impact of ectomycorrhiza in the tree stand. The fungal communities and their distribution patterns reflected host tree specificity and successional stage of the ectomycorrhizosphere. In the bacterial community, the most abundant bacterial classes were Alphaproteobacteria, Acidobacteria, Ktedonobacteria, Bacteroidia, Gammaproteobacteria, and Phycisphaerae representing about 59-80% of all bacterial sequences. The bacterial communities correlated with soil chemical parameters, particularly the content of toxic metals, total nitrogen and C/N ratio. This study allowed to identify drivers for microbial community composition, which might be helpful to develop afforestation strategies in post-mining landscapes.

Abiotic and biotic drivers of soil microbial diversity in an intensively grazed natural ecosystem

Many ecosystems worldwide are threatened by anthropogenic causes, with high-intensity grazing by large herbivores as a significant risk factor for biodiversity. Although the drivers of α-diversity are well-studied for animal and plant communities, they are often overlooked for soil microbes, particularly in natural systems. We therefore used a novel innovative information-theoretic approach to structural equation model selection and multimodel path coefficient averaging to identify these drivers. Our findings show that abiotic soil characteristics, primarily soil pH, significantly shape the α-diversity of both bacteria and fungi. Biotic factors like vegetation Shannon diversity and aboveground biomass also significantly drive microbial α-diversity, especially for fungi. Our statistical approach adds robustness to our results and conclusions, offering valuable insights into the complex interactions shaping soil microbial communities in intensively grazed natural systems. These insights are crucial for developing more effective and comprehensive future ecosystem management and restoration strategies.

Landscape-scale variation in the canopy mycobiome in temperate beech and spruce forest stands explained by leaf water content and elevation

Fungi represent a significant portion of Earth's biological diversity and are essential for ecosystem functions like organic matter decomposition and nutrient cycling. While fungi associated with plant roots have been extensively studied, our understanding of fungi in the forest canopies remains limited. To investigate the landscape-scale variation in the canopy mycobiome of temperate beech and spruce forest stands in the Bavarian Forest National Park (Germany), we examined the influence of geophysical conditions and host traits. We found that elevation significantly influenced fungal diversity and composition, with distinct effects observed in both beech and spruce stands. Moreover, canopy water content, a key indicator of tree vitality, was also strongly associated with changes in the canopy fungi community, suggesting a potential link between forest water stress and the forest canopy mycobiome. Our differential abundance analysis further identified a total of 41 fungal families as potential bioindicators: 17 families in beech stands and 9 in spruce stands were significantly associated with elevation, while 9 families in beech stands and 6 in spruce stands were linked to variations in leaf water content. These findings enhance our understanding of the spatial patterns of forest canopy microbial biodiversity and species distributions.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10342-025-01768-3.

Revealing microbial consortia that interfere with grapevine downy mildew through microbiome epidemiology

BACKGROUND

Plant and soil microbiomes can interfere with pathogen life cycles, but their influence on disease epidemiology remains understudied. Here, we analyzed the relationships between plant and soil microbiomes and long-term epidemiological records of grapevine downy mildew, a major disease caused by the oomycete Plasmopara viticola.

RESULTS

We found that certain microbial taxa were consistently more abundant in plots with lower disease incidence and severity and that the microbial community composition could predict disease incidence and severity. Microbial diversity was not strongly linked to epidemiological records, suggesting that disease incidence and severity is more related to the abundance of specific microbial taxa. These key taxa were identified in the topsoil, where the pathogen's oospores overwinter, and in the phyllosphere, where zoospores infect leaves. By contrast, the leaf endosphere, where the pathogen's mycelium develops, contained few taxa of interest. Surprisingly, the soil microbiota was a better predictor of disease incidence and severity than the leaf microbiota, suggesting that the soil microbiome could be a key indicator of the dynamics of this primarily aerial disease.

CONCLUSION

Our study integrates long-term epidemiological data with microbiome profiles of healthy plants to reveal fungi and bacteria relevant for the biocontrol of grapevine downy mildew. The resulting database provides a valuable resource for designing microbial consortia with potential biocontrol activity. The framework can be applied to other crop systems to guide the development of biocontrol strategies and reduce pesticide use in agriculture.

Opposite effects of N on warming-induced changes in bacterial and fungal diversity

The diversity of bacteria and fungi is linked to distinct ecosystem functions, and divergent responses to global changes in these two kingdoms affect the relative contributions of the kingdoms to the soil carbon and nutrient cycles. Climate warming and nitrogen (N) enrichment, which are projected to increase concurrently through modelling efforts, are considered the main drivers of biodiversity loss. However, it is unclear how bacterial and fungal diversity respond differently to the simultaneous occurrence of climate warming and nitrogen enrichment, and the underlying mechanisms involved remain unknown. Using a 9-yr warming and N enrichment experiment in an alpine permafrost area of the Tibetan Plateau, we demonstrated the contrasting response of bacterial and fungal diversity to combined warming and N enrichment, showing a reduction in bacterial richness (8.8%) and an increase in fungal diversity (33.6%). Furthermore, the negative effects of warming on fungal richness were reversed by N enrichment, and the negative effects of nitrogen enrichment on bacteria were amplified by warming. Our results also demonstrated that both biotic interactions, such as bacterial-fungal antagonism, and abiotic factors, primarily the soil C/N ratio and pH, play crucial roles in shaping microbial biodiversity. Our findings suggest that fungal diversity is expected to greatly increase in a warmer and more nitrogen-enriched world, potentially leading to the enhancement of ecosystem functions driven by fungi.

The relict plant Tetraena mongolica plantations increase the nutrition and microbial diversity in desert soil

Introduction

Tetraena mongolica was established in the West Ordos Region of northwest China approximately 140 million years ago. It plays an irreplaceable role in maintaining local ecosystem stability.

Methods

This study aimed to evaluate the effects of planting T. mongolica on soil nutrition and microbial communities by comparing the root zone soil (Rz_soil) and bare soil (B_soil) across three different plant communitie.

Results

The results showed that T. mongolica decreased soil pH and Na+ while increasing available potassium, soil organic matter, organic carbon, total nitrogen, and potassium. T. mongolica significantly improved the diversity indices (Sobs and Ace), as well as the richness index (Chao), of bacterial and fungal communities across three plant communities. Meanwhile, the relative abundances of Rubrobacter and norank_c_Actinobacteria in the bacterial communities declined significantly in the Rz_soil compared with the B_soil across all three plant communities. In contrast, the relative abundances of Fusarium and Penicillium were higher, whereas those of Monosporascus and Darksidea were lower in Rz_soil than in B_soil in the two plant communities. T. mongolica decreased the soil bacterial co-occurrence networks while increasing the soil fungal co-occurrence networks.

Discussion

These results provide a new perspective to understand the role of T. Mongolica in the desert ecosystems.

Mechanisms and impacts of Agaricus urinascens fairy rings on plant diversity and microbial communities in a montane Mediterranean grassland

Fungal fairy rings (FFRs) significantly influence plant communities and soil microbiota. This study investigated the development of Agaricus urinascens fairy rings in a species-rich montane Mediterranean grassland. By combining vegetation analysis, soil chemistry measurements, and next-generation sequencing, we assessed fairy rings' impact on soil properties, plants, fungi, and bacteria. Our findings reveal a fungal-driven transformation of biological communities, with significant variations across FFRs zones. At the fungal front (FF), plant biomass decreased slightly but increased more than threefold inside the ring (>1100 g m-2), favouring grasses like Brachypodium genuense over forbs. In addition, species richness dropped significantly in the FF (-40%) compared to surrounding grassland, particularly affecting perennials. Moreover, our findings reveal substantial alterations in soil properties at the FF, including a 534% increase in P₂O5, a 210% rise in electrical conductivity, and a 36% increase in soil hydrophobicity compared to the surrounding grassland. Clay content at the FF was nearly three times higher than outside the ring (162.8 versus 57.5 g kg-1), indicating potential structural modifications in the soil matrix. Organic carbon decreased by 10% in the FF, while the C/N ratio and cation exchange capacity dropped significantly. Distinct shifts in microbial composition were observed. Bacterial diversity declined at the FF, where Actinobacteria dominated (85%) and Proteobacteria dropped to 8%. Similarly, fungal diversity was lowest inside the ring but highest in the belt section, with Ascomycota reaching 97% at the FF. Certain taxa, such as Kribbella, Streptomyces, Trichoderma, Penicillium, and Dichotomopilus, coexisted with A. urinascens mycelium. Notably, hydrophobicity at the FF was linked to high calcium oxalate crystal coverage on fungal mycelium and plant roots. This may have accelerated root desiccation, ultimately leading to plant mortality. Overall, our findings provide strong evidence that fairy ring fungi act as ecosystem engineers, shaping the spatial patterns of biotic composition and diversity in Mediterranean grasslands.

Exploring Fungal Abundance and WHO Fungal Priority Pathogens in Agricultural Fields: A One Health Perspective in Northeast Thailand

Fungal pathogens prevalent in agricultural areas pose a significant risk to human health, with some exhibiting high fatality rates, as reported by the WHO Fungal Pathogen Priority List (WHO FPPL). This study investigates fungal communities in northeast Thailand's agricultural areas, focusing on potential reservoirs of the WHO FPPL. Samples were collected from rice, cassava, rubber trees, and sugarcane fields across 18 provinces with distinct geological features. Metabarcoding of the ITS1 region and taxonomic analysis were conducted, and potential pathogens were selected according to WHO FPPL criteria. The results showed that overall fungal community richness and diversity were influenced by plant fields but not significantly different by geological features. Soil organic matter and water content affected fungal dynamics only in rubber tree fields. Fungal pathogens from the WHO FPPL were found in all four plant fields, with higher abundance in Chaiyaphum province, especially in sugarcane fields, and the lowest in Nong Bua Lam Phu. Candida tropicalis, a high-priority pathogen, was predominantly associated with rock salt features. This study underscores the need for vigilance among farmers and emphasizes the importance of confirming fungal pathogenicity.

Phyllosphere mycobiome in two Lycopodiaceae plant species: unraveling potential HupA-producing fungi and fungal interactions

Huperzine A (HupA), a lycopodium alkaloid with therapeutic potential for neurodegenerative diseases such as Alzheimer's disease, is found exclusively in some species of the Huperzioideae subfamily of Lycopodiaceae. Fungi associated with Huperzioideae species are potential contributors to HupA biosynthesis, offering promising prospects for HupA production. Despite its medical significance, limited knowledge of fungal diversity in lycophytes and the variability of HupA production in fungal strains have impeded the discovery and applications of HupA-producing fungi. Here, we investigated HupA concentrations and the mycobiome across various tissues of two Lycopodiaceae species, Huperzia asiatica (a HupA producer) and Diphasiastrum complanatum (a non-HupA producer). We aim to unveil the distribution of potential HupA-producing fungi in different plant tissues and elucidate fungal interactions within the mycobiome, aiming to uncover the role of HupA-producing fungi and pinpoint their potential fungal facilitators. Among the tissues, H. asiatica exhibited the highest HupA concentration in apical shoots (360.27 μg/g fresh weight) whereas D. complanatum showed no HupA presence in any tissue. We obtained 441 amplicon sequence variants (ASVs) from H. asiatica and 497 ASVs from D. complanatum. The fungal communities in bulbils and apical shoots of H. asiatica were low in diversity and dominated by Sordariomycetes, a fungal class harboring the majority of reported HupA-producing fungi. Integrating bioinformatics with published experimental reports, we identified 27 potential HupA-producing fungal ASVs, primarily in H. asiatica, with 12 ASVs identified as hubs in the fungal interaction network, underscoring their pivotal roles in mycobiome stability. Members of certain fungal genera, such as Penicillium, Trichoderma, Dioszegia, Exobasidium, Lycoperdon, and Cladosporium, exhibited strong connections with the potential HupA producers in H. asiatica's network rather than in D. complanatum's. This study advances our knowledge of fungal diversity in Lycopodiaceae and provides insights into the search for potential HupA-producing fungi and fungal facilitators. It highlights the importance of exploring young tissues and emphasizes the ecological interactions that may promote the fungi-mediated production of complex bioactive compounds, offering new directions for research in fungal ecology and secondary metabolite production.

DNA in honey could describe the changes in flower visits and microbe encounters of honey bees over decades

Recent environmental changes due to land-use and climate change threaten biodiversity and the ecosystem services it provides. Understanding the true scope of these changes is complicated by the lack of historical baselines for many of the interactions underpinning ecosystem services, such as pollination, or disservices, such as disease spreading. To assess changes in such services, it is vital to find ways of comparing past and current interactions between species. Here, we focus on interactions between honey bees - one of the world's most important agricultural pollinators, the plants they visit, and the microbes they encounter in the environment. DNA in honey offers insights into the contemporary interactions of honey bees. Old honey samples could serve to describe honey bees' interactions in previous decades, providing a baseline against which to assess changes in interactions over time. By identifying the taxonomic origin of plant, bacterial and fungal DNA in fifty-year-old honey samples, we show that plant DNA can reveal which plants honey bees visited in the past. Likewise, microbe DNA records the microbes, including pollinator and plant pathogens, honey bees encountered and possibly spread. However, some differences in the DNA recovered between old and new honey suggest that differences in DNA degradation of different microbes could bias naive comparisons between samples. Like other types of ancient samples, old honey may be most useful for identifying interactions that historically occurred and should not be taken as proof that an interaction did not occur. Keeping these limits of the data in mind, time series of honey may offer unique information about how honey bees' associations with flowers and microbes have changed during decades of environmental change.

Effect of Wheat Varieties and Cultivation Environments on Grain Endophytes, Microbial Communities, and Quality of Medium-High Temperature Daqu in Chinese Baijiu

Wheat grain serves as the primary raw material for producing medium-high temperature (MT)-Daqu, a fermentation starter crucial for Chinese Baijiu production, characterized by spontaneous fermentation without the inoculation of exogenous substances. However, the interactions among wheat varieties, cultivation environments, and the resulting Daqu quality remain poorly understood. This study evaluates three wheat varieties harvested from three distinct cultivation environments, examining wheat grain quality, grain-associated endophytes, and physicochemical properties and microbial communities of MT-Daqu at 0, 9, and 90 days of fermentation. The results revealed the cultivation environment had the most pronounced impact on wheat fungal endophytes. The physicochemical properties of Daqu were primarily impacted by variety, namely, the enzyme activity impacted by environmental factors. Pantoea, Aspergillus, and Stephylium are key microbial genera shared between wheat grains and MT-Daqu. Redundancy analysis highlighted the critical roles of moisture content, starch content, and amino acid nitrogen levels in driving microbial succession in Daqu. Mantel analysis demonstrated significant correlations between the abundance of dominant fungal endophytes in wheat grains and Daqu quality parameters, including starch content (r = 0.45; p < 0.01), saccharifying activity (r = 0.41), liquefying activity (r = 0.31), and esterifying activity (r = 0.30) (p < 0.05). Spearman correlation analysis indicated that Nesterenkonia, Aspergillus, Cryptococcus, Dioszegia, Golubevia, Udeniomyces and Stemphylium are the dominant wheat-derived bacterial genera associated with the abundance of microorganisms in MT-Daqu. This study elucidated the "cultivation environment-grain endophyte-Daqu microorganism" microbial transmission pathway, providing a theoretical foundation for breeding wheat varieties optimized for Daqu production and identifying suitable production regions.

Microbial Metabolic Limitations and Their Relationships with Sediment Organic Carbon Across Lake Salinity Gradient in Tibetan Plateau

Inland lakes, contributing substantially to the global storage of sediment organic carbon (SOC), are subject to marked changes in salinity due to climate warming. The imbalance in the supply of resources, such as carbon, nitrogen, and phosphorus, in sediments leads to microbial metabolic limitations (MMLs). This, in turn, triggers the secretion of extracellular enzymes by microorganisms to mine for deficient resources by decomposing complex organic carbon. This process is a rate-limiting step in the degradation of organic carbon and, as a result, has the potential to regulate organic carbon stocks. However, the general understanding of MML patterns and their relationships with SOC content along lake salinity gradients remains elusive. This study examined 25 lakes on the Tibetan Plateau with salinity ranging from 0.13‱ to 31.06‱, analyzing MMLs through enzymatic stoichiometry. The results showed that sediment microbial metabolism was mainly limited by carbon and nitrogen, with stronger limitations at higher salinity. Water salinity and sediment pH were the main factors influencing microbial limitations, either directly or indirectly, through their effects on nutrients and microbial diversity. Additionally, the SOC content was negatively correlated with microbial carbon limitation, a relationship weakened when salinity and pH were controlled. These findings suggest that the decrease in SOC with increased salinity or pH could be driven by stronger microbial carbon limitations, offering insights into the impact of salinity changes on SOC stocks in inland lakes due to climate change.

Transcriptional reprogramming and microbiome dynamics in garden pea exposed to high pH stress during vegetative stage

MAIN CONCLUSION

High soil pH induces the upregulation of genes involved in oxidative stress and nutrient transport, while the enrichment of beneficial microbes (Variovorax, Chaetomium, and Pseudomonas) highlights their potential role in promoting stress adaptation. High soil pH severely impacts plant growth and productivity, yet the transcriptomic changes and microbial dynamics underlying stress adaptation in garden pea (Pisum sativum ssp. hortense) remain unclear. This study demonstrates that high soil pH leads to stunted growth, reduced biomass, impaired photosynthesis, and nutrient status in garden pea. Further, disruption in key nitrogen-fixing bacteria (Rhizobium indicum, R. leguminosarum, and R. redzepovicii), along with the downregulation of NifA and NifD genes and upregulation of NifH in nodules highlights the critical role of micronutrient balance in legume-microbe symbiosis and a compensatory response to maintain nitrogen status. RNA seq analysis revealed extensive transcriptional reprogramming in roots, characterized by the upregulation of oxidative stress response genes (e.g., oxidoreductase and glutathione transferase activities, metal ion transporters) and the downregulation of genes related to ammonia-lyase activity and ion binding, reflecting broader disruptions in nutrient homeostasis. KEGG pathway analysis identified enrichment of MAPK signaling pathway, likely interacting with other pathways associated with stress tolerance, metabolic adjustment, and structural reorganization as part of adaptive responses to high pH. Root microbiome analysis showed significant enrichment of Variovorax, Shinella, and Chaetomium, suggesting host-driven recruitment under high pH stress. Stable genera, such as Pseudomonas, Novosphingobium, Mycobacterium, Herbaspirillum, and Paecilomyces, displayed resilience to stress conditions, potentially forming core microbiome components for adaptation to high pH. In a targeted study, inoculation of plants with an enriched microbiome, particularly C. globosum, under high pH conditions improved growth parameters and increased the abundance of Stenotrophomonas and Pseudomonas in the roots. It suggests that these bacterial genera may act as helper microbes to C. globosum, collectively promoting stress resilience in pea plants suffering from high pH. These findings provide a foundation for microbiome-aided breeding programs and the development of microbial consortia to enhance the adaptation of pea plants to high pH conditions.

Native polymer degradation capacity of microorganisms in agricultural soils

With a growing global population increasing demand for food production, fertilisers are of paramount importance in the agricultural industry. New fertiliser coating candidates may reduce environmental harm but it is critical that they are evaluated for their native biodegradation potential within agricultural soils and their effects on microbial communities. Four of the seven compounds tested, poly(1,4-butylene adipate) (PBA), polyethylene adipate (PEA), polycaprolactone (PCL) and poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV), showed degradation by indigenous soil microorganisms with headspace CO2 concentrations increasing between 14 to 98 % compared to the soil only control. Surprisingly, two previously characterised biodegradable polymers, polyethylene succinate (PES) and poly(1,4-butylene succinate) (PBS), showed minimal biodegradation in our study. Polymer degradation was confirmed visually using scanning electron microscopy and occurred in conjunction with shifts in the bacterial and fungal community composition of the soils. Soils with PBA, PEA, PCL and PHBV were enriched with polymer degrading microorganisms, such as Streptomyces spp., Bacillus spp., Exophiala spp. and Talaromyces spp. Using whole soil microcosms under ambient conditions to investigate indigenous degradation potential of polymers for fertiliser coatings provides an initial holistic picture of their degradation potential compared with using axenic cultures alone, and provides crucial new insights into the future of eco-friendly controlled release fertilisers.

Evaluation the role of Luteibacter pinisoli DP2-30 in mitigating pine wilt disease caused by Bursaphelenchus xylophilus through modulation of host microbiome

Background and aim

Pine wilt disease (PWD), caused by the pine wood nematode (PWN) Bursaphelenchus xylophilus, poses a significant threat to pine forests worldwide. This study aimed to isolate bacterial strains from the rhizosphere of healthy Pinus massoniana and elucidate their biocontrol potential in mitigating PWD through direct nematicidal activity and manipulation of host microbiome.

Results

We successfully isolated the rhizobacterium strain DP2-30 from rhizosphere of healthy pine plants, which was identified as Luteibacter pinisoli on the basis of morphological, biochemical, and molecular analyses. The fermentation filtrates of strain DP2-30 displayed direct nematicidal activity of >95% (corrected mortality rate) on PWN after 48 hours of treatment. The fermentation broth and filtrates of strain DP2-30 significantly inhibited PWN egg hatching by 49.38% and 43.05%, respectively. Additionally, root drenching of strain DP2-30 fermentation broth significantly reduced PWD severity in pine seedlings (2 years old), with a control effect of 62.50%. Microbiome analyses revealed significant variations in the diversity, structure, and relative abundance of bacterial and fungal communities of pine plants combined treated with DP2-30 and PWN (T2), solely treated with PWN (T1), and control (treated with water). Bacterial phyla, Proteobacteria, Actinobacteriota, Chloroflexi, Acidobacteriota, and Armatimonadota and fungal phyla Ascomycota, Basidiomycota and Mortierellomycota were dominant in the all root and stem samples. The application of L. pinisoli DP2-30 significantly increased the relative abundance of the family Rhodanobacteraceae in the roots and stems of pine seedlings. Additionally, intra-kingdom co-occurrence network analysis revealed reduced complexity in the bacterial networks but increased complexity in the fungal networks of treated plants, suggesting enhanced functional redundancy and ecosystem stability.

Conclusions

Overall, this study highlights the potential of L. pinisoli DP2-30 as an effective biocontrol agent against PWD by directly killing PWN and manipulating the host microbiota.

Ubiquity and diversity of Basidiobolus across amphibian species inhabiting an urbanization gradient

The role of microfungal species in the environment is wide and well documented, especially in terms of symbiosis. Nonetheless, microfungal species are usually overseen and vastly understudied. One example of these understudied microfungal groups is the genus Basidiobolus, an ecologically diverse zoopagomycete genus found within vertebrate gastrointestinal systems, a saprobe across leaf litter, or as an opportunistic pathogen of immunocompromised humans. Studies of Basidiobolus diversity and distribution have been focused mostly on non-urbanized areas of subtropical regions, but there is a recent paucity of studies on this genus in temperate and densely human populated areas. Here, we present insights into the ubiquity and diversity of Basidiobolus species associated with amphibian species that live in the Worcester waterway system, a system of connecting streams and ponds that originate in pristine, protected wild management areas, and the highly urbanized downtown area of Worcester, Massachusetts. Our results show the ubiquitous presence of Basidiobolus across the gastrointestinal tract samples of amphibians spanning diverse species and habitats, including conservation areas, urban watersheds, and rural ecosystems. Our study reveals that multiple individuals and species of Basidiobolus coexist within a single host, suggesting complex interactions within amphibian gut microbiomes. Finally, we present possible novel diversity in the genus, indicating that further studies should be focused on understanding the species richness, genetic diversity, and ecological roles and associations of this interesting fungal group.

Life on the edge: mineral incrustations colonized by fungal communities in the sulfur fumarole on Sierra Negra volcano (Galápagos Archipelago)

Despite the extensive studies on plant and animal endemism in the Galápagos Islands, fungal diversity remains largely unexplored, particularly in fumarole environments. Here, we explore the fungal diversity in two gypsum incrustations within an active fumarole of Sierra Negra volcano (Isabela Island). We hypothesize that minor differences in the chemical and mineralogical characteristics of these substrates, despite similar environmental conditions, lead to distinct fungal communities with substrate-specialized taxa. Alpha diversity indices showed no significant differences, but beta diversity analysis revealed two distinct fungal communities (PERMANOVA p < 0.01), with only 3.31% of operational taxonomic units (OTUs) shared between incrustations and 37.75 and 14.57% uniquely associated with each incrustation. A strong correlation was found between beta diversity and most measured chemical parameters (Mg, S, Fe, Na, Al, Mn, Zn, K, P, Cu). Our findings indicate that even minor differences in the mineral and chemical composition of closely located incrustations significantly influence fungal communities, emphasizing these deterministic factors as key drivers in shaping fungal diversity.

Scheffersomyces tanahashii sp. nov., isolated from the cocoon wall of the stag beetle Prosopocoilus astacoides blanchardi

A previous investigation of symbiotic yeasts associated with the stag beetle Prosopocoilus astacoides blanchardi isolated strains of the genus Scheffersomyces from the cocoon walls, larval midgut, larval hindgut and larval tunnels. Phylogenetic analysis of the D1/D2 domains of the LSU rRNA gene sequences revealed identical sequences, indicating that they belonged to the same species, but suggested that the species was new. In this study, sequence analysis and physiological characterization identified a representative strain of these beetle-associated yeasts as a novel species in the genus Scheffersomyces. The sequence similarities of the concatenated LSU domains and internal transcribed spacer regions indicated that strain BCRC 23563T forms a well-supported and distinct species in the xylose-fermenting Scheffersomyces subclade, with the sequences for each gene differing in nt substitutions from those of previously described related species by at least 1.06% and 2.7% respectively. The physiological characteristics of the novel species were also distinct from those of the closely related described species, though it could still process xylose as is expected of stag beetle-associated Scheffersomyces symbionts. Based on the data, a novel yeast species, Scheffersomyces tanahashii sp. nov., is proposed to accommodate this strain. The holotype is BCRC 23563T (ex-type strains NBRC 116731 and NCYC 4470). The MycoBank accession number is 857608.

Microbial methods matter: Identifying discrepancies between microbiome denoising pipelines using a leaf biofilm taphonomic dataset

Premise

The occurrence of different microorganisms on aquatic macrophyte fossils suggests that biofilm microbes may facilitate leaf preservation. Understanding the impact of microorganisms on leaf preservation requires studies on living plants coupled with microbial amplicon sequencing. Choosing the most suitable bioinformatic pipeline is pivotal to accurate data interpretation, as it can lead to considerably different estimations of microbial community composition.

Methods

We analyze biofilms from floating and submerged leaves of Nymphaea alba and Nuphar lutea and mock communities using primers for the 16S ribosomal RNA (rRNA), 18S rRNA, and ITS amplicon regions and compare the microbial community compositions derived from three bioinformatic pipelines: DADA2, Deblur, and UNOISE.

Results

The choice of denoiser alters the total number of sequences identified and differs in the identified taxa. Results from all three denoising pipelines show that the leaf microbial communities differed between depths and that the effect of the environment varied depending on the amplicon region.

Discussion

Considering the performance of denoising algorithms and the identification of amplicon sequence variants (ASVs), we recommend DADA2 for analyzing 16S rRNA and 18S rRNA. For the ITS region, the choice is more nuanced, as Deblur identified the most ASVs and was compositionally similar to DADA2.

Application of Amplicon Metagenomics to Identify Fungal Pathogens in Formalin-Fixed Paraffin-Embedded Samples: Proof of Concept in Animals with Fungal Pathologies

The identification of fungal pathogens in formalin-fixed paraffin-embedded (FFPE) tissues is an unmet need in human and animal medicine, and sequence-agnostic approaches are needed to identify emerging pathogens. Eleven FFPE biopsy specimens with etiologic diagnoses of fungal disease based on standard testing of paired fresh tissue samples were utilized here to evaluate metabarcoding approaches. The cases included tissues from three dogs, three cats, one box turtle, one goat, one common loon, and one gray tree frog. The diagnoses from the fresh tissues in these cases were Microsporum canis, Penicillium sp., Exophiala sp. (likely E. jeanselmei), Verticillium sp., Rhizopus sp., atypical Cryptococcus neoformans, Conidiobolus spp., Aspergillus fumigatus, Cryptococcus neoformans var grubii, Batrachochytrium dendrobatidis, Fusarium solani, Blastomyces dermatitidis, Coccidiodes immitis, and Histoplasma capsulatum. We compared the ITS1 and 28S D1 rRNA gene genetic markers in combination with several bioinformatic strategies to identify fungal pathogens in the FFPE tissue samples, with a success rate of 9/11. These methods could allow diagnosticians who receive only FFPE tissues and see fungal pathogens to speciate the pathogens and could be of value in retrospective studies wherein FFPE tissue is the only archived tissue. Furthermore, these techniques could be of use to researchers investigating polymicrobial communities where DNA preservation is suboptimal.

Multi-omics analysis of the correlation between surface microbiome and metabolome in Saccharina latissima (Laminariales, Phaeophyceae)

The microbiome of Saccharina latissima, an important brown macroalgal species in Europe, significantly influences its health, fitness, and pathogen resistance. Yet, comprehensive studies on the diversity and function of microbial communities (bacteria, eukaryotes, and fungi) associated with this species are lacking. Using metabarcoding, we investigated the epimicrobiota of S. latissima and correlated microbial diversity with metabolomic patterns (liquid chromatography coupled to tandem mass spectrometry). Specific epibacterial and eukaryotic communities inhabit the S. latissima surface, alongside a core microbiota, while fungal communities show lower and more heterogeneous diversity. Metabolomic analysis revealed a large diversity of mass features, including putatively annotated fatty acids, amino derivatives, amino acids, and naphthofurans. Multiple-factor analysis linked microbial diversity with surface metabolome variations, driven mainly by fungi and bacteria. Two taxa groups were identified: one associated with bacterial consortia and the other with fungal consortia, each correlated with specific metabolites. This study demonstrated a core bacterial and eukaryotic microbiota associated with a core metabolome and highlighted interindividual variations. Annotating the surface metabolome using Natural Products databases suggested numerous metabolites potentially involved in interspecies chemical interactions. Our findings establish a link between microbial community structure and function, identifying two microbial consortia potentially involved in the chemical defense of S. latissima.

Discovering fungal communities in roots of Zoysiajaponica and characterising novel species and their antifungal activities

Turf-grasses are economically important horticultural crops, which have been utilised by humans to improve the environment for more than a thousand years. Turf-grasses are widely distributed in landscapes, slopes and sport fields, such as golf courses. Endophytic fungi are a resource of unexplored fungal diversity with potential bioactive compounds. In this study, culture-independent ITS amplicon sequencing and culture-dependent isolation methods were used to reveal fungal community in roots of the turf-grass Zoysiajaponica. A total of 317 OTUs were identified from root samples of Z.japonica by analysis of ITS amplicon reads. Fungal community was dominated by Sordariales (32.45%), followed by Chaetothyriales (18.16%), unknown taxa in Sordariomycetes (14.63%) and Pleosporales (12.48%). During isolation, 151 endophytic fungal strains were obtained from roots of Z.japonica and a variety of taxa were found by ITS amplification and sequencing. Moreover, 11 endophytic fungal species were further characterised in this study, based on morphological characterisation and multi-loci phylogenetic analysis, including Niessliadimorphospora, a newly-recorded species in Korea and 10 novel species (Dactylariahwasunensis sp. nov., Lophiostomajeollanense sp. nov., Magnaporthiopsiszoysiae sp. nov., Poaceascomaendophyticum sp. nov., P.koreanum sp. nov., P.magnum sp. nov., P.zoysiiradicicola sp. nov., Stagonosporaendophytica sp. nov., Setophomazoysiae sp. nov. and Pseudorhypophilapoae sp. nov.). Antifungal activities of these species were tested against the turf-grass brown patch pathogen Rhizoctoniasolani AG2-2(IIIB), with S.zoysiae being the best antagonist. In addition, butanol extract from mycelia of S.zoysiae strongly inhibited R.solani AG2-2(IIIB) in vitro and in planta. The results of this study expand the biodiversity of endophytic fungi and revealed potential biological resources for future turf-grass management and bioactive compound exploitation.

Influence of different diet categories on gut bacterial diversity in Frankliniella occidentalis

The microbial composition of insect guts is typically influenced by the type of food consumed, and conversely, these microbes influence the food habits of insects. Western flower thrips (WFT; Frankliniella occidentalis) is an invasive pest with a wide range of hosts, including vegetables and horticultural crops. To elucidate variations in gut bacteria among WFT feeding on rose (Rosa rugosa) flowers (FF), kidney bean (Phaseolus vulgaris) pods (PF), and kidney bean leaves (LF), we collected adult guts and extracted DNA for 16S ribosomal RNA gene sequencing of microbial communities. The results revealed that the FF population had the highest number of annotations. Alpha diversity analysis revealed that the Chao and Ace indexes were the greatest in the PF population, indicating a higher abundance of gut bacteria. Moreover, the Simpson index was the highest in the FF population, indicating that gut bacterial diversity was the highest in the FF population. Comparison of species composition demonstrated that Proteobacteria dominated all 3 populations at the phylum level, with Actinobacteria being the subdominant phylum. At the genus level, Stenotrophomonas was the dominant bacteria in the PF and LF populations, whereas Rosenbergiella was dominant in the FF population. KEGG pathway annotation predicted that the gut bacteria of adult WFT were mainly involved in carbohydrate and amino acid metabolism. Our results revealed that the diversity and composition of WFT gut microbiota are influenced by diet, offering evidence for future studies on the ecological adaptability of WFT and the mechanisms underlying the interaction between gut microbiota and host.

Just the tip of the iceberg: uncovering a hyperdiverse clade of African Russula (Basidiomycota, Russulales, Russulaceae) species with signs of evolutionary habitat adaptations

The diversity within the ectomycorrhizal genus Russula (Basidiomycota) in West Africa is largely unexplored. The study area was Benin, where only ten out of the 159 species endemic to tropical Africa have been previously reported. We focused on "Afrovirescentinae", which is a monophyletic lineage within Russulasubgen.Heterophyllidiaesister tosubsect.Virescentinae. The phylogenetic placement of this clade was analysed using sequence data from ITS, LSU, mtSSU, tef1, rpb1 and rpb2 regions. Ten "Afrovirescentinae" species are recognised, described and illustrated from Benin. Four of them, R.carmesina, R.hiemisilvae, R.inflata and R.sublaevis, were previously published. Five species, Russulaacrialbida sp. nov., R.beenkenii sp. nov., R.coronata sp. nov., R.florae sp. nov. and R.spectabilis sp. nov., are newly described. Species within this group are characterised by densely reticulated spore ornamentation, but they exhibit considerable variation in field appearance and pileipellis structure. In gallery forests, their basidiomata are ephemeral, small and their basidiospores have prominent ornamentation; while in savannah woodlands, the basidiomata are fleshy, large and basidiospores present low ornamentation. We suggest that these morphological traits may represent evolutionary adaptations to a specific environmental condition. We analysed the species richness, ecological range and distribution of the "Afrovirescentinae" clade globally based on data from the UNITE database, estimating a total diversity of 94 species primarily distributed in sub-Saharan Africa, but also in the Neotropics. Four additional previously described species not detected in Benin were assigned to this clade, based on holotype sequencing. Several species are widely distributed across tropical Africa and do not show specificity regarding their associated plant symbionts.

Effects of Monascus pilosus SWM 008-Fermented Red Mold Rice and Its Functional Components on Gut Microbiota and Metabolic Health in Rats

Red mold rice, fermented by Monascus spp., has been reported to modulate gut microbiota composition and improve metabolic health. Previous studies indicate that red mold rice can reduce cholesterol, inhibit hepatic lipid accumulation, and enhance bile acid excretion, while also altering gut microbiota under high-fat dietary conditions. However, it remains unclear whether these effects are directly due to Monascus-derived products modulating gut microbiota or are a consequence of improved metabolic health conditions, which indirectly influence gut microbiota. This study aimed to evaluate the effects of Monascus pilosus SWM 008 fermented red mold rice and its components-monascin, monascinol, ankaflavin, and polysaccharides-on gut microbiota and metabolic health in rats fed a normal diet. Over eight weeks, physiological, biochemical, and gut microbiota parameters were assessed. Results showed no significant changes in body weight or liver/kidney function, confirming safety. Gut microbiota analysis revealed that red mold rice, monascin, monascinol, and polysaccharides significantly altered gut microbiota composition by increasing the relative abundance of beneficial bacteria, such as Akkermansia muciniphila, Ligilactobacillus murinus, and Duncaniella dubosii. Functional predictions indicated enhanced vitamin K2 biosynthesis, nucleotide metabolism, and other metabolic pathways linked to improved gut health. In conclusion, Monascus pilosus SWM 008 fermented red mold rice demonstrated safety and beneficial effects, suggesting its potential as a functional food to maintain gut microbiota balance under normal dietary conditions.

A thallus-forming N-fixing fungus-cyanobacterium symbiosis from subtropical forests

Fungi engage in diverse symbiotic relationships with phototrophs. Lichens, symbiotic complexes involving fungi and either cyanobacteria, green algae, or both, have fungi forming the external layer and much of the interior. We found an erect thallus resembling a lichen yet with an unexpected thallus structure composed of interwoven cyanobacterial filaments with numerous fungal hyphae inserted within individual cyanobacterial sheaths, contrasting with typical lichen structure. Phylogenetics identified the fungus as a previously undescribed species, Serendipita cyanobacteriicola, closely related to endophytes, and the cyanobacterium belongs to the family Coleofasciculaceae, representing a genus and species not yet classified, Symbiothallus taiwanensis. These thalli exhibit nitrogen-fixing activity similar to mosses but lower than cyanolichens. Both symbiotic partners are distinct from known lichen-forming symbionts, uncovering a phylogenetically and morphologically unprecedented thallus-forming fungus-cyanobacterium symbiosis. We propose the name "phyllosymbia" for these thalli to underscore their unique symbiotic nature and leaf-like appearance. This finding marks a previously unknown instance of fungi solely residing within structures generated by cyanobacteria.

Comparison of microbial diversity and community structure in soils managed with organic and chemical fertilization strategies using amplicon sequencing of 16 s and ITS regions

Soil microbial species diversity and distribution of microbial communities are vital for soil and crop health, nutrient cycling, availability, and subsequent plant growth. These soil dynamics are highly influenced and altered by various soil management practices, inputs, and agricultural techniques. In the present study, the effects of chemical and organic management practices on soil microbial diversity and community structure were examined and compared using amplicon sequencing of the 16S and ITS regions. Two contrasting soil samples were selected from each crop fields at the International Rice Research Institute-South Asia Regional Centre (IRRI-SARC) in Varanasi: one field followed conventional chemical fertilizer inputs, while the other implemented natural farming practices, including tillage, on-farm crop residue management, and water management. Soil samples from each field were analyzed for bacterial and fungal diversity. Our findings showed that the two differently managed soils exhibited distinct microbial community compositions, with the organically managed soil exhibiting a higher diversity of decomposer bacteria and fungi, showing 40 unique elements in organic soil samples and 19 in chemically managed soil. Natural farming practices also demonstrated a higher relative abundance of bacterial and fungal phyla. Our results emphasize the significance of sustainable soil management techniques, suggesting that organic inputs can increase soil microbial diversity and richness. The functional roles of these microbial communities in soil ecosystems and their potential impact on crop yield and nutrient cycling warrant further study.

The tiny-leaved orchid Disperis neilgherrensis primarily obtains carbon from decaying litter via saprotrophic Ceratobasidium

While most green orchids establish associations with non-ectomycorrhizal rhizoctonias belonging to Ceratobasidiaceae, Tulasnellaceae, and Serendipitaceae, fully mycoheterotrophic orchids-excluding albino mutants-primarily depend on either ectomycorrhizal fungi or saprotrophic non-rhizoctonia fungi. This suggests that non-ectomycorrhizal rhizoctonias may be unable to meet the carbon demands of adult orchids that exhibit a high degree of mycoheterotrophy. To understand the physiological ecology of Disperis neilgherrensis, an orchid species with reduced leaves growing in decaying litter from non-ectomycorrhizal trees, we employed molecular and stable isotope analyses to identify its mycorrhizal partners and ultimate nutritional sources at two populations on Ishigaki Island, Japan. Molecular barcoding techniques revealed that D. neilgherrensis forms exclusive associations with non-ectomycorrhizal Ceratobasidiaceae fungi. The Disperis specimens exhibited δ13C and δ15N isotopic values similar to those found in fully mycoheterotrophic orchids that exploit litter-decaying fungi. Furthermore, the pelotons of D. neilgherrensis showed significantly elevated δ13C values similar to saprotrophic non-rhizoctonia fungi. Our findings indicate that D. neilgherrensis primarily obtains its carbon from decaying litter through a specialized relationship with non-ECM Ceratobasidiaceae. Given that saprotrophic Ceratobasidiaceae facilitate nearly fully mycoheterotrophic growth in D. neilgherrensis, at least under warm and humid conditions, it is plausible that other (nearly) fully mycoheterotrophic tropical orchids also meet their carbon requirements through associations with saprotrophic rhizoctonias.

Microbiome Analysis of Area in Proximity to White Spot Lesions Reveals More Harmful Plant Pathogens in Maize

Plant microbiomes play a major role in plant health, growth, and development, enhancing resistance to pathogen invasion. However, despite the extensive research on the phyllosphere microbiome, it remains unclear how the microbiome of leaves in proximity to diseased leaves responds to pathogen invasion. We investigate the response of the maize phyllosphere microbiome to maize white spot by assessing the microbiome dynamics associated with the white spot portion and the area in proximity using 16S and ITS high-throughput sequencing analysis. Our results showed that the bacterial diversities were higher in the diseased portion and area in proximity to the spot than those in healthy plants. At the same time, lower fungal diversity was recorded in the diseased portion compared to portions in proximity to it and healthy leaves. The spot portion had a significant influence on the microbial composition. The diseased portion, the area in proximity to it, and the healthy leaves were dominated by the bacterial genera Sphingomonas, Delftia, Chryseobacterium, Stenotrophomonas, Methylobacterium-methylorubrum, and Bacteroides. Still, the abundance of Sphingomonas decreased in the healthy leaves with a corresponding increase in Stenotrophomonas. Conversely, the fungal genus Setophoma dominated the diseased portion, while the fungal pathogens Cladosporium, Alternaria, and Exserohilum were highly abundant in the samples from the area in proximity to it. In addition, a co-occurrence network analysis revealed a complex fungal network in healthy leaves and those in proximity to leaves infected with white spot compared to the diseased portion. This study suggests that the area in proximity to the maize leaf infected with white spot disease is colonized by more harmful plant pathogenic fungi for disease progression.

Bacterial and Fungal Communities Respond Differently to Changing Soil Properties Along Afforestation Dynamic

Spontaneous afforestation following land abandonment has been increasingly recognized as a nature-based solution to mitigate climate change and provide measurable benefits to biodiversity. However, afforestation effects on biodiversity, particularly on soil microbial communities, are still poorly characterized, with most previous studies focusing on artificial plantations rather than forest rewilding dynamics. Here, we assessed changes in topsoil physical-chemical properties and related dynamics of bacterial and fungal community composition and structure following spontaneous afforestation of abandoned grasslands in Northeast Italy over the last 70 years. With a space-for-time approach, we selected four chronosequences representing different successional stages: grassland, early (2000-2020), intermediate (1978-2000), and late (1954-1978). Results showed that spontaneous afforestation progressively reduced topsoil pH and total phosphorus (P), while soil organic carbon (SOC), nitrogen (N), and C:N ratio increased. Correspondingly, the overall α-diversity of the fungal community, assessed by ITS DNA metabarcoding, progressively decreased after an initial increase from grassland conditions, following substrate acidification and trophic specialization. Bacterial diversity, assessed by 16S DNA metabarcoding, was highest at the initial stages, then progressively decreased at later stages, likely limited by lower organic matter quality. Shifts of fungal community composition included an increase of ectomycorrhizal Basidiomycota linked to topsoil's higher SOC, N, and C:N ratio. Differently, bacterial community composition responded substantially to pH, with topsoil acidity favoring Proteobacteria (Pseudomonadota) and Acidobacteria (Acidobacteriota) at the late afforestation stages. Our findings provide a first contribution to clarify how fungi and bacteria respond to spontaneous afforestation. This is particularly relevant in the context of climate change mitigation, considering the fundamental role of microorganisms in shaping soil carbon storage dynamics.

Reduction of microbial load in soil by gas generated using non-thermal atmospheric pressure plasma

Elevation of the microbial load in soil resulting from contamination with organic wastes of biological origin increases the chances of emerging soil-borne pathogens and disturbance of nutrient cycling. We analyzed the potential of gas generated using atmospheric-pressure non-thermal plasma as a tool for reducing the microbial load in soil and its impact on the soil microbial community and fertility. The gas generated by a cylinder-type single pair of dielectric barrier discharge (DBD) electrode plasma inactivated over 90 % of bacterial cells and fungal spores after 5 and 20 min of treatment, respectively, in both suspension and vermiculite. Gas generated using four pairs of DBD electrode plasma eradicated approximately 50 % of bacterial cells and 40 % of fungal spores in nursery soil. It also eliminated approximately 10-29 % of aerobic natural microbiota in field soil after 60 min of treatment. The diversity of microbial species in the plasma gas-treated field soil was slightly lower than that in the untreated soil, and the relative abundances of the phyla Proteobacteria and Basidiomycota were reduced in the plasma gas-treated soil. Spinach plant growth and nitrate levels increased significantly in the plasma gas-treated field soil. Our data suggest that plasma-generated gases can be used for soil sanitation with no drastic changes to the soil microbial community and soil fertility enhancement.

Desiccation as a suitable alternative to cold-storage of phyllosphere samples for DNA-based microbial community analyses

The study of microbial communities of the plant phyllosphere in remote locations using DNA-based approaches is limited by the challenges associated with their preservation in the field and during transportation. Freezing is a common DNA preservation strategy, but it may be unsuitable for leaf samples, or inaccessible in some locations. Other methods such as desiccation, ethanol or commercial preservatives are potential alternative DNA preservation methods for ambient temperature storage. In this study, we assessed the efficacy of desiccation (with silica gel packs), and of three preservation solutions (95% ethanol, RNAlater, LifeGuard) for the preservation of epiphytic phyllosphere communities of Populus tremuloides and Picea glauca at ambient indoor temperature (21 °C) for up to three weeks. We assessed effects on DNA concentration and quality and used metabarcoding to detect changes in bacterial and fungal communities between treatments over time. A secondary study was conducted on leaves of Populus grandidentata to further test the ability of the desiccation treatment to resolve differences between sampling sites. Silica gel packs were identified as effective ambient temperature preservative of phyllosphere bacterial and fungal communities. There were some changes in the communities compared to immediate extraction due to this treatment, but these changes did not affect the ability to distinguish tree species and sampling locations. Overall, our study supports the use of silica gel pack short term preservation at ambient temperature for phyllosphere samples intended for DNA-based microbial community analyses.

Implication of Gut Mycobiome and Virome in Type-2 Diabetes Mellitus: Uncovering the Hidden Players

Type-2 diabetes mellitus (T2DM) is a global epidemic with significant societal costs. The gut microbiota, including its metabolites, plays a pivotal role in maintaining health, while gut dysbiosis is implicated in several metabolic disorders, including T2DM. Although data exists on the relationship between the gut bacteriome and metabolic disorders, further attention is needed for the mycobiome and virome. Recent advancements have begun to shed light on these connections, offering potential avenues for preventive measures. However, more comprehensive investigations are required to untangle the interrelations between different microbial kingdoms and their role in T2DM development or mitigation. This review presents a simplified overview of the alterations in the gut bacteriome in T2DM and delves into the current understanding of the mycobiome and virome's role in T2DM, along with their interactions with the cohabiting bacteriome. Subsequently, it explores into the age-related dynamics of the gut microbiome and the changes observed in the microbiome composition with the onset of T2DM. Further, we explore the basic workflow utilized in gut microbiome studies. Lastly, we discuss potential therapeutic interventions in gut microbiome research, which could contribute to the amelioration of the condition, serve as preventive measures, or pave the way towards personalized medicine.

Plant interaction traits determine the biomass of arbuscular mycorrhizal fungi and bacteria in soil

Plant-arbuscular mycorrhizal fungal (AMF) mutualisms are crucial to ecosystem biodiversity and productivity. Yet, our understanding of the functional roles of plants as AMF generalists or specialists, and the consequences of these plant interaction traits for soil ecosystems are virtually unknown. We grew eight pasture plant species under two experimental conditions, sequencing their root AMF communities to assess interaction traits using a range of numeric and phylogenetic diversity metrics, thereby characterizing each plant species' interaction generalism with AMF. We used lipid analysis of rhizosphere soils and Bayesian modeling to explore how host interaction traits affected carbon allocation to AMF and bacteria. We found that plant interaction traits for AMF remained stable despite large variation in soil conditions and AMF pools. Host interaction generalism was linked to contrasting patterns in bacterial and AMF biomass: Phylogenetic diversity in plant interactions was positively associated with AMF biomass, while numeric diversity was negatively associated with bacterial biomass in rhizosphere soils. Explicit consideration of plant interaction niches may enhance understanding of how changes in biodiversity affect ecosystem carbon cycling.

Ecological divergence of sibling allopolyploid marsh orchids is associated with species specific plasticity and distinct fungal communities

Phenotypic plasticity, the dynamic adjustment of traits to environmental variations, is crucial for enabling species to exploit broader niches and withstand suboptimal conditions. This adaptability is particularly relevant for newly formed allopolyploids, which possess redundant gene copies and must become established in diverse environments distinct from their parents and other relatives. By evaluating gene expression and root mycobiome among two ecologically divergent sibling allopolyploid marsh orchids (Dactylorhiza majalis and D. traunsteineri) in reciprocal transplants at localities where both species are native, we aimed to understand the drivers of species persistence in the face of interspecific gene flow. Despite consistent abiotic differences characterising the alternative environments at each locality, the majority of gene expression differences between the allopolyploids appears to be plastic. Ecologically relevant processes, such as photosynthesis and transmembrane transport, include some genes that are differentially expressed between the two orchids regardless of the environment, while others change their activity plastically in one species or the other. This suggests that although plasticity helps define the specific ecological range of each sibling allopolyploid, it also mediates gene flow between them, thereby preventing differentiation. Extending our investigations to the root mycobiome, we uncover more diverse fungal communities for either species when grown in the environment with nutrient-poor soils, indicating that both abiotic and biotic factors drive the distribution of sibling marsh orchids. Altogether, our results indicate that plasticity can simultaneously promote diversification and homogenisation of lineages, influencing the establishment and persistence of recurrently formed allopolyploid species.

Invertebrate Decline Has Minimal Effects on Oak-Associated Microbiomes

Recently, biomass of invertebrates has declined substantially at many locations with the implications of this biodiversity loss for ecosystems yet unknown. Through multitrophic interactions, plant- and soil-associated microbiomes might be altered, causing a cascade of changes on diverse ecosystem processes. We simulated aboveground invertebrate decline in grassland ecosystems with two levels of invertebrate biomass (36% and 100% of current ambient conditions), plus a control with no invertebrates present. Each standardised grassland mesocosm additionally contained one clonal Quercus robur L. sapling to investigate the extent of invertebrate decline effects exceeding grasslands. We investigated oak biomass partitioning and mycorrhiza formation, oak leaf transcriptome and microbiome composition of leaves, roots and rhizosphere. While invertebrate decline did not significantly affect oak performance and herbivory-related gene expression, fungal communities presented an increase of saprotrophs and pathogens, especially in leaves. Among leaf-inhabiting bacteria, Proteobacteria and Actinobacteria increased under invertebrate decline. The belowground microbiome was only little affected. But, invertebrate decline came along with a reduced influence on predators leading to an elevated aphids infestation that proofed able to alter microbiota. Our findings establish a strong difference between above- and belowground, with the impacts of invertebrate decline being more pronounced in the leaf microbiome.

The responses of root exudates and microbiome in the rhizosphere of main plant and aromatic intercrops to soil Cr stress

Soil chromium (Cr) stress has a well-recognized negative impact on plant growth, and intercropping is a commonly used method to mitigate heavy metal toxicity to main plants. However, the responses of root exudates-microbial and their interactions among soil zones to soil Cr stress are always in need of clarification in intercropping system. In this study, three intercropping patterns (CT, Malus only; TM, Malus × Mentha and TA, Malus × Ageratum) with different soil Cr addition levels (NCR, LCR, HCR) were applied, and the rhizosphere ecological traits in the main plant (FRS) and intercrop (ARS) were investigated. The results indicate that intercropping with either Mentha or Ageratum has a positive effect on main plants response to soil Cr stress, and intercropping with Ageratum showing a more significant effect. Importantly, we found that the rhizosphere of main plant tends to alleviate stress by accumulating organic acids and amino acids, while aromatic plants exhibit a broader accumulation of metabolites. Additionally, we identified five core differential microbial genera. Our findings provide novel insights into intercrop Cr detoxification in the main plant.

Drastic mycorrhizal community shifts in Sceptridium ferns during the generation transition from fully mycoheterotrophic gametophytes to photosynthetic sporophytes

Many plant species experience a prolonged subterranean phase during which they rely entirely on mycorrhizal fungi for carbon. While this mycoheterotrophic strategy spans liverworts, lycophytes, and ferns, most empirical research has centered on angiosperms. This study explores the fungal associations of Sceptridium (Ophioglossaceae), an early-diverging fern with mycoheterotrophic gametophytes. We analyzed germination patterns and fungal associations in Sceptridium gametophytes, comparing them to the distribution and mycorrhizal partners of photosynthetic sporophytes. High-throughput sequencing data reveal that mycoheterotrophic gametophytes consistently associate with a single Entrophospora fungus in the order Entrophosporales (Glomeromycotina), while photosynthetic sporophytes primarily partner with fungi from Glomeraceae (Glomerales, Glomeromycotina). Consequently, gametophytes exhibit spatial clustering without association with adult plants. This is the first documentation of an association between Entrophosporaceae (and the order Entrophosporales) and mycoheterotrophic plants. The drastic shifts in Sceptridium mycorrhizal communities across life stages likely reflect changing physiological needs during development. Further research is essential to determine whether the association with Entrophosporaceae is widespread among mycoheterotrophic species and to elucidate the functional and physiological mechanisms underlying these mycorrhizal shifts.

Microbial Inoculants Drive Changes in Soil and Plant Microbiomes and Improve Plant Functions in Abandoned Mine Restoration

The application of microbial inoculants holds promise for the sustainable restoration of abandoned mine sites by affecting soil nutrients and microbial communities. However, the responses of plant microbial communities to microbial inoculants in mine restoration remain largely unknown. To bridge this knowledge gap, we conducted a 4-year field experiment at an abandoned carbonate mine site to assess the impacts of microbial inoculants on the soil-plant microbiome. Our findings revealed that microbial inoculants significantly changed roots, fine root bacterial and fungal communities. Further, no significant correlations were observed between the soil-plant nutrient content (Z-score) and microbial alpha diversity. However, a significantly positive correlation was found between the relative abundance of the keystone ecological cluster (Module #1) and soil-plant nutrient content. The application of microbial inoculants also increased complexity, albeit decreased stability of plant microbiome networks, alongside a reduction in stochastic assembly. Conversely, they decreased the complexity but increased the stability of soil microbiome networks, accompanied by an increase in stochastic assembly. Notably, the number of specifically enriched microbiome functional traits of roots and root nodules under the microbial inoculant treatments surpassed that of the control. In summary, our findings underscored the potential of microbial inoculants to enhance soil-plant functionality at abandoned mine restoration sites.

Climate Change Drives Changes in the Size and Composition of Fungal Communities Along the Soil-Seedling Continuum of Schima superba

Plant microbiomes have a major influence on forest structure and functions, as well as tree fitness and evolution. However, a comprehensive understanding of variations in fungi along the soil-plant continuum, particularly within tree seedlings, under global warming is lacking. Here, we investigated the dynamics of fungal communities across different compartments (including bulk soil and rhizosphere soil) and plant organs (including the endosphere of roots, stems and leaves) of Schima superba seedlings exposed to experimental warming and drought using AccuITS absolute quantitative sequencing. Our results revealed that warming and drought significantly reduced the number of specific fungal amplicon sequence variants (ASVs) in the bulk soil and rhizosphere soil, respectively. Variations in fungal communities were mainly explained by compartments and plant organs, with the composition of endophytic fungal communities within leaves (primarily attributed to species gain or loss) being most influenced by climate change. Moreover, warming significantly reduced the migration of Ascomycota, soil saprotrophs, wood saprotrophs and yeasts from the bulk soil to the rhizosphere soil but increased that of plant pathogens from the roots to the stems. Drought significantly decreased the absolute abundances of Chytridiomycota, Glomeromycota and Rozellomycota, as well as the migration of ectomycorrhizal fungi from the bulk soil to the rhizosphere soil but increased that of plant pathogens. Warming could indirectly reduce leaf area by increasing the diversity of leaf pathogens. These findings have potential implications for enhancing the resilience and functioning of natural forest ecosystems under climate change through the manipulation of plant microbiomes, as demonstrated in agroecosystems.

Subterranean morphology underpins the degree of mycoheterotrophy, mycorrhizal associations, and plant vigor in a green orchid Oreorchis patens

The evolution of full heterotrophy is a fascinating topic in plant evolution, with recent studies suggesting that partial mycoheterotrophy (mixotrophy) serves as a transitional stage toward full mycoheterotrophy in orchids. However, the adaptive significance of fungal-derived carbon in mixotrophic plants remains largely unexplored. In this study, we investigated the photosynthetic orchid Oreorchis patens, a species related to the leafless genus Corallorhiza within the subtribe Calypsoinae. Using high-throughput DNA sequencing, 13C and 15N isotopic analyses, and phenotypic evaluations, we explored the role of coralloid rhizomes - a feature common in fully mycoheterotrophic orchids - in fungal partnerships, the degree of mycoheterotrophy, and plant vigor. Our findings reveal that O. patens plants with coralloid rhizomes predominantly associate with saprotrophic Psathyrellaceae fungi, whereas those without coralloid rhizomes also partner with rhizoctonias and other potentially orchid mycorrhizal fungi. Notably, plants with coralloid rhizomes exhibited enriched 13C signatures, indicating a greater reliance on fungal-derived carbon. These plants also demonstrated more vigorous flowering scapes and produced a higher number of flowers, suggesting that mycoheterotrophy significantly enhances plant vigor. This study provides rare insights into the adaptive significance of mycoheterotrophy. Recent research suggests that some partially mycoheterotrophic orchids can adjust their heterotrophic status to optimize carbon resource use under specific conditions, such as low-light environments. However, an increased proportion of fungal-derived carbon may sometimes merely reflect reduced photosynthesis in such conditions, thereby amplifying the apparent contribution of fungal-derived carbon. Our findings offer more direct evidence that carbon acquisition via mycoheterotrophy is beneficial for partially mycoheterotrophic orchids.

Fungal and bacterial diversity present on the rind and core of Natural Bloomy Rind Artisanal Minas Cheese from the Canastra region, Brazil

Globally recognized for its unique sensory attributes, Natural Bloomy Rind Artisanal Minas Cheese (NBRAMC) from the Canastra microregion is made from raw cow's milk using a natural starter culture derived from the local environment. During ripening process, microorganisms, predominantly Geotrichum candidum, develop on the surface, with the microbial community playing a crucial role in shaping the cheese's distinctive characteristics. This study aimed to characterize the microbial community, including filamentous fungi, yeasts, and bacteria, present in the rind and core of NBRAMC. Amplicon sequencing of the ITS and 16S rRNA gene regions was performed on rind and core samples from cheeses produced at six distinct producers. Results indicated that G. candidum and Diutina catenulata were the most prevalent fungal species, and Candida intermedia being more abundant exclusively in the interior of the cheeses. The bacterial community displayed greater diversity in the rind, with genera such as Lactococcus, Brevibacterium, and Corynebacterium variabile, while Lactococcus and Streptococcus dominated the core. An inverse relationship between D. catenulata and G. candidum abundance was noted. Significant variations in microbial community profiles were found among producers, despite their geographical proximity. While low levels of undesirable fungi were detected, some samples showed a notable presence of undesirable bacteria, indicating potential hygiene issues during cheese handling. These findings provide valuable insights into the microbial dynamics of NBRAMC, supporting the implementation of strategies that can enhance the quality and safety of the product.

Microbial Communities in Agave Fermentations Vary by Local Biogeographic Regions

The production of traditional agave spirits in Mexico, such as mezcal, involves a process that uses environmental microorganisms to ferment the cooked must from agave plants. By analysing these microorganisms, researchers can understand the dynamics of microbial communities at the interface of natural and human-associated environments. This study involved 16S and ITS amplicon sequencing of 99 fermentation tanks from 42 distilleries across Mexico. The Agave species used, production methods, climatic conditions and biogeographic characteristics varied significantly among sites. However, certain taxa were found in most fermentations, indicating a core group of microorganisms common to these communities. The primary variable consistently associated with the composition of both bacterial and fungal communities was the distillery, suggesting that local production practices and site-specific attributes influence the microbiomes. The fermentation stage, climate and producing region also affected community composition but only for prokaryotes. Analysis of multiple tanks within three distilleries showed taxa enriched in specific fermentation stages or agave species. This research provides a detailed analysis of the microbiome of agave fermentations, offering important knowledge for its management and conservation.

Insights into lignin bioconversion: lignin-derived compounds treatment of a novel marine fungus K-2

BACKGROUND

The potential for the efficient conversion of lignocellulosic biomass has been extensively explored to produce a wide range of bioproducts. Many approaches have been sought for the deep conversion of lignin to generate products that are toxin-free and beneficial for processing into high-value-added components.

RESULTS

This study reported a fungus isolated from the deep sea with strong synthesis of multiple lignocellulases, conversion of lignin and guaiacol (0.1%) by 71.6% and 86.1% within 9 days at 30 °C respectively, and outstanding environmental adaptability (20-50 °C and pH 3-8). Metabolic pathway profiling showed that this fungus utilized lignin to rapidly activate multiple ring-opening reactions including the 2,3- and 3,4-cleavage pathways, with the 2,3-cleavage pathway predominating after 5 days. Conversion of metabolic intermediates confirmed the superb potential of this strain for lignin treatment. Meanwhile, its shikimic acid pathway was metabolically active under lignin.

CONCLUSION

This further expands the potential to produce valuable bioproducts during lignin treatment, especially under ambient conditions, which can significantly enhance high-value precursor compound production. © 2024 Society of Chemical Industry.

Untrimmed ITS2 metabarcode sequences cause artificially reduced abundances of specific fungal taxa

Advances in DNA metabarcoding have greatly expanded our knowledge of microbial communities in recent years. Pipelines and parameters have been tested extensively for bacterial metabarcoding using the 16S rRNA gene and best practices are largely established. For fungal metabarcoding using the internal transcribed spacer (ITS) gene, however, only a few studies have considered how such pipelines and parameters can affect community prediction. Here, we report a novel bias uncovered during ITS region 2 (ITS2) sequencing of Trichoderma-infected ant fungus gardens and confirmed this bias using mock communities. Abnormally low forward read quality caused Trichoderma ITS2 reads to be computationally filtered before and during read pair merging, thus almost entirely eliminating Trichoderma amplicon sequence variants from the resulting fungal community profiles. Sliding window quality trimming before filtering allowed most of these reads to pass filtering and merge successfully, producing community profiles that now correlated with visual signs of Trichoderma infection and matched the composition of the mock communities. Applying such sliding window trimming to a previously generated environmental ITS2 data set increased the detected fungal diversity and again overcame read quality biases against Trichoderma to detect it in nearly every sample instead and often at high relative abundances. This analysis additionally identified a similar, but distinct, bias against a second fungal genus Meyerozyma. The prevalence of such quality biases against other fungal ITS sequences is unknown but may be widespread. We, therefore, advocate for the routine use of sliding window quality trimming as a best practice in ITS2 metabarcoding analysis.

IMPORTANCE

Metabarcode sequencing produces DNA abundance profiles that are presumed to reflect the actual microbial composition of their corresponding input samples. However, this assumption is not always tested, and taxon-specific biases are often not apparent, especially for low-abundance taxa in complex communities. Here, we identified internal transcribed spacer region 2 (ITS2) read quality aberrations that caused dramatic reductions in the relative abundances of specific taxa in multiple data sets characterizing ant fungus gardens. Such taxon-specific biases in read quality may be widespread in other environments and for other fungal taxa, thereby causing incorrect descriptions of these mycobiomes.

Deciphering the Distinct Associations of Rhizospheric and Endospheric Microbiomes with Capsicum Plant Pathological Status

Exploring endospheric and rhizospheric microbiomes and their associations can help us to understand the pathological status of capsicum (Capsicum annuum L.) for implementing appropriate management strategies. To elucidate the differences among plants with distinct pathological status in the communities and functions of the endospheric and rhizospheric microbiomes, the samples of healthy and diseased capsicum plants, along with their rhizosphere soils, were collected from a long-term cultivation field. The results indicated a higher bacterial richness in the healthy rhizosphere than in the diseased rhizosphere (P < 0.05), with rhizospheric bacterial diversity surpassing endospheric bacterial diversity. The community assemblies of both the endospheric and rhizospheric microbiomes were driven by a combination of stochastic and deterministic processes, with the stochastic processes playing a primary role. The majority of co-enriched taxa in the healthy endophyte and rhizosphere mainly belonged to bacterial Proteobacteria, Actinobacteria, and Firmicutes, as well as fungal Ascomycota. Most of the bacterial indicators, primarily Alphaproteobacteria and Actinobacteria, were enriched in the healthy rhizosphere, but not in the diseased rhizosphere. In addition, most of the fungal indicators were enriched in both the healthy and diseased endosphere. The diseased endophyte constituted a less complex and stable microbial community than the healthy endophyte, and meanwhile, the diseased rhizosphere exhibited a higher complexity but lower stability than the healthy rhizosphere. Notably, only a microbial function, namely biosynthesis of other secondary metabolites, was higher in the healthy endophytes than in the diseased endophyte. These findings indicated the distinct responses of rhizospheric and endospheric microbiomes to capsicum pathological status, and in particular, provided a new insight into leveraging soil and plant microbial resources to enhance agriculture production.