Fungal Operational Taxonomic Units Research Articles

Species composition of root-associated mycobiome of ruderal invasive Anthemis cotula L. varies with elevation in Kashmir Himalaya.

Investigating the microbial communities associated with invasive plant species can provide insights into how these species establish and thrive in new environments. Here, we explored the fungal species associated with the roots of the invasive species Anthemis cotula L. at 12 sites with varying elevations in the Kashmir Himalaya. Illumina MiSeq platform was used to identify the species composition, diversity, and guild structure of these root-associated fungi. The study found a total of 706 fungal operational taxonomic units (OTUs) belonging to 8 phyla, 20 classes, 53 orders, 109 families, and 160 genera associated with roots of A. cotula, with the most common genus being Funneliformis. Arbuscular mycorrhizal fungi (AMF) constituted the largest guild at higher elevations. The study also revealed that out of the 12 OTUs comprising the core mycobiome, 4 OTUs constituted the stable component while the remaining 8 OTUs comprised the dynamic component. While α-diversity did not vary across sites, significant variation was noted in β-diversity. The study confirmed the facilitative role of the microbiome through a greenhouse trial inwhich a significant effect of soil microbiome on height, shoot biomass, root biomass, number of flower heads, and internal CO2 concentration of the host plantwas observed. The study indicates that diverse fungal mutualists get associated with this invasive alien species even in nutrient-rich ruderal habitats and may be contributing to its spread intohigher elevations. This study highlights the importance of understanding the role of root-associated fungi in invasion dynamics and the potential use of mycobiome management strategies to control invasive species.

Diversity and assembly of root-associated microbiomes of rubber trees.

Understanding the diversity and assembly of the microbiomes of plant roots is crucial to manipulate them for sustainable ecosystem functioning. However, there are few reports about microbial communities at a continuous fine-scale of roots for rubber trees. We investigate the structure, diversity, and assembly of bacterial and fungal communities for the soil (non-rhizosphere), rhizosphere, and rhizoplane as well as root endosphere of rubber trees using the amplicon sequencing of 16S ribosomal ribonucleic acid (rRNA) and Internally Transcribed Spacer (ITS) genes. We show that 18.69% of bacterial and 20.20% of fungal operational taxonomic units (OTUs) in the rhizoplane derived from the endosphere and 20.64% of bacterial and 20.60% of fungal OTUs from the soil. This suggests that the rhizoplane microbial community was a mixed community of soil and endosphere microbial communities and that microorganisms can disperse bidirectionally across different compartments of the plant root. On the other hand, in the absence of an enrichment or depletion of core bacterial and fungal OTUs in the rhizosphere, little differences in microbial composition as well as a more shared microbial network structure between the soil and the rhizosphere support the theory that the rhizosphere microbial community is a subset of the soil community. A large number of functional genes (such as nitrogen fixation and nitrite reduction) and more enriched core OTUs as well as a less stable but more complex network structure were observed in the rhizoplane of rubber tree roots. This demonstrated that the rhizoplane is the most active root compartment and a hotspot for plant-soil-environment interactions. In addition, bacterial and fungal communities in the rhizoplane were more stochastic compared to the rhizosphere and soil. Our study expands our understanding of root-associated microbial community structure and function, which may provide the scientific basis for sustainable agriculture through biological process management.

Community assembly and network structure of epiphytic and endophytic phyllosphere fungi in a subtropical mangrove ecosystem.

Microorganisms can influence plant growth and health, ecosystem functioning, and stability. Community and network structures of mangrove phyllosphere fungi have rarely been studied although mangroves have very important ecological and economical values. Here, we used high throughput sequencing of the internal transcribed spacer 2 (ITS2) to assess epiphytic and endophytic phyllosphere fungal communities of six true mangrove species and five mangrove associates. Totally, we obtained 1,391 fungal operational taxonomic units (OTUs), including 596 specific epiphytic fungi, 600 specific endophytic fungi, and 195 shared fungi. The richness and community composition differed significantly for epiphytes and endophytes. Phylogeny of the host plant had a significant constraint on epiphytes but not endophytes. Network analyses showed that plant-epiphyte and plant-endophyte networks exhibited strong specialization and modularity but low connectance and anti-nestedness. Compared to plant-endophyte network, plant-epiphyte network showed stronger specialization, modularity, and robustness but lower connectance and anti-nestedness. These differences in community and network structures of epiphytes and endophytes may be caused by spatial niche partitioning, indicating their underlying ecological and environmental drivers are inconsistent. We highlight the important role of plant phylogeny in the assembly of epiphytic but not endophytic fungal communities in mangrove ecosystems.

Fallopia japonica and Impatiens glandulifera are colonized by species-poor root-associated fungal communities but have minor impacts on soil properties in riparian habitats

Fallopia japonica and Impatiens glandulifera are major plant invaders on a global scale that often become dominant in riparian areas. However, little is known about how these species affect interactions in soil–plant systems. The aim of this study was to investigate the impact of both species on abiotic and biotic soil properties, with a special focus on fungi. We investigated eight sites along small streams invaded by F. japonica and I. glandulifera, respectively, and compared each with nearby sites dominated by the native species Urtica dioica. Three different types of samples were collected: bulk soil, rhizosphere soil and roots from invasive and native stands at each site. Bulk soil samples were analysed for soil physicochemical, microbial properties (soil microbial respiration and ergosterol) and soil arthropod abundance (Acari and Collembola). Soil respiration was also evaluated in rhizosphere samples. The fungal community composition of both bulk soil and roots were analysed using a metabarcoding approach. Soil physicochemical properties as well as soil microbial activity, fungal biomass and soil fungal operational unit taxonomic unit (OTU) richness did not differ between invaded and native riparian habitats, indicating only minor belowground impacts of the two invasive plant species. Soil microbial activity, fungal biomass and soil fungal OTU richness were rather related to the soil physicochemical properties. In contrast, Acari abundance decreased by 68% in the presence of F. japonica, while Collembola abundance increased by 11% in I. glandulifera sites. Moreover, root-associated fungal communities differed between the invasive and native plants. In F. japonica roots, fungal OTU richness of all investigated ecological groups (mycorrhiza, endophytes, parasites, saprobes) were lower compared to U. dioica. However, in I. glandulifera roots only the OTU richness of mycorrhiza and saprobic fungi was lower. Overall, our findings show that F. japonica and I. glandulifera can influence the abundance of soil arthropods and are characterized by lower OTU richness of root-associated fungi.

Stand age alters fungal community composition and functional guilds in subalpine Picea asperata plantations

Soil fungi participate in a variety of forest ecological processes and drive the succession of degraded forests. However, how the soil fungal community and functional taxa change with stand age remains unclear in subalpine plantations. We established five vegetation survey plots in four planted Picea asperata forests aged 25, 40, 50 and 75 years and one natural P. asperata forest aged approximately 200 years in a subalpine region and randomly collected rhizosphere and bulk soils of two representative P. asperata individuals in each plot for high-throughput sequencing of fungal communities and determination of soil properties. The fungal community composition in both rhizosphere and bulk soils varied significantly among different stand ages. Fungal operational taxonomic unit (OTU) richness and Shannon diversity in bulk but not rhizosphere soil changed significantly with stand age. Except for the 75-year-old plantation, there was no difference in the fungal community composition between rhizosphere soil and bulk soil. Soil properties, plant production (P. asperata growth indicators) and plant richness jointly determined the fungal community composition, and soil total phosphorous (TP) accounted for the most variation in the fungal community. P. asperata regulated the community composition of fungal functional guilds (i.e., plant pathogens, saprophytes, ectomycorrhizal fungi and endophytes) mainly by changing soil properties rather than plant richness. Interestingly, the community composition of fungi and functional guilds in plantations became increasingly similar to that in the natural forest over time, and the fungal restoration rate (represented by the Bray–Curtis distance between plantations and natural forest) in bulk soil was faster than that in rhizosphere soil. In addition, with increasing stand age, the relative abundance of ectomycorrhizal fungi increased, and the diversity of plant pathogens decreased, both of which were significantly associated with the reduction in soil total phosphorus. These results suggest that stand age is a major factor affecting soil fungal community variation in subalpine P. asperata plantations, which is largely dependent on soil property changes. In particular, soil TP may play a key role in the regulation of different ecological functional fungi.

DOP52 The faecal bacterial and fungal microbiome of newly-diagnosed, treatment naïve children with Crohn’s disease and the modifying effects of exclusive enteral nutrition and re-introduction of habitual diet

Abstract Background The fungal community (mycobiome) and immunological responses to specific fungi have been implicated in Crohn’s disease (CD) pathogenesis and its phenotype. There is limited data on profiling the mycobiome in paediatric CD and how it changes during treatment Methods Fungal (ITS2) and bacterial (16S rRNA) microbiome analysis in faecal samples (n=124) from n=34 CD children before, during (30 and 60 days) and after exclusive enteral nutrition (EEN) at food reintroduction (within 60 days of EEN completion), and from 31 healthy controls were profiled. IgA and IgG anti-Saccharomyces cerevisiae antibodies (ASCA) analysis by enzyme-linked immunosorbent assay, in blood, was also carried out for CD patients prior to EEN initiation. Results The global mycobiome composition (β diversity) was different between CD and healthy children (R2=0.050; p=0.007) and presented lower Chao1 richness (mean 24.3 vs 33.0; p=0.005) for the CD cases; 13 fungal operational taxonomic units (OTUs) differed between the two groups. Similar signals were observed for the bacterial microbiome but the difference in global community structure (β diversity) was more profound than the fungal community (R2=0.094; p<0.001). Treatment with EEN induced drastic changes in mycobiome composition (β diversity), which were more profound and more variable than the effects observed for the bacterial community. Of the OTUs with abundance significantly lower in CD than healthy controls prior to EEN, one, belonging to S. cerevisiae, significantly decreased during EEN (compared with baseline; p<0.001 and p=0.086 at 30 and 60 days on EEN). Patients whose faecal calprotectin was low (<250 mg/kg) during food reintroduction had a lower mycobiome richness than those whose FC was raised (>250 mg/kg). 29 fungal OTUs were significantly different between these two groups in samples taken during food reintroduction, following EEN. Patients who were ASCA positive had a higher abundance of three OTUs of S. cerevisiae. In co-occurrence network analysis, Simplicillium chinense, presented significant more interactions with members of the bacterial community, particularly OTUs which changed during EEN. After participants had returned to their regular diets these microbial effects reversed and community structure moved towards that observed prior to EEN. Conclusion The mycobiome of children with CD present features of dysbiosis similar to the bacterial microbiome and improvement in disease condition during EEN is strongly associated with changes in its composition.

Fungal Diversity and Its Relationship with Environmental Factors in Coastal Sediments from Guangdong, China.

As one core of the Guangdong-Hong Kong-Macao Greater Bay Area (GBA), Guangdong is facing some serious coastal environmental problems. Fungi are more vulnerable to changes in coastal environments than bacteria and archaea. This study investigated the fungal diversity and composition by high-throughput sequencing and detected basic parameters of seven environmental factors (temperature, dissolved oxygen, pH, salinity, total organic carbon, total nitrogen, and total phosphorus) at 11 sites. A total of 2056 fungal operational taxonomic units (OTUs) belonging to 147 genera in 6 phyla were recovered; Archaeorhizomyces (17.5%) and Aspergillus (14.19%) were the most dominant genera. Interestingly, a total of 14 genera represented the first reports of coastal fungi in this study. Furthermore, there were nine genera of fungi that were significantly correlated with environmental factors. FUNGuild analysis indicated that saprotrophs and pathogens were the two trophic types with the highest proportions. Saprotrophs were significantly correlated with total organic carbon (TOC), total nitrogen (TN), and total phosphorus (TP), while pathogens were significantly correlated with pH. This study provides new scientific data for the study of the diversity and composition of fungal communities in coastal ecosystems.

The impact of Beauveria species bioinocula on the soil microbial community structure in organic strawberry plantations.

The multifunctionality of microorganisms, including entomopathogenic fungi, represents a feature that could be exploited to support the development, marketing, and application of microbial-based products for plant protection. However, it is likely that this feature could affect the composition and dynamics of the resident soil microorganisms, possibly over a longer period. Therefore, the methodology utilized to evaluate such impact is critical for a reliable assessment. The present study was performed to evaluate the impact of strains of Beauveria brongniartii and Beauveria bassiana on soil bacterial and fungal communities using an approach based on the terminal restriction fragment polymorphism (T-RFLP) analysis. Soil samples in the vicinity of the root system were collected during a 3-year period, before and after the bioinocula application, in two organic strawberry plantations. Specific primers were used for the amplification of the bacterial 16S rRNA gene and the fungal ITS region of the ribosome. Data of the profile analysis from T-RFLP analysis were used to compare the operational taxonomic unit (OTU) occurrence and intensity in the inoculated soil with the uninoculated control. With regard to the impact on the bacterial community, both Beauveria species were not fully consistently affecting their composition across the seasons and fields tested. Nevertheless, some common patterns were pointed out in each field and, sometimes, also among them when considering the time elapsed from the bioinoculum application. The impact was even more inconsistent when analyzing the fungal community. It is thus concluded that the application of the bioinocula induced only a transient and limited effect on the soil microbial community, even though some changes in the structure dynamic and frequency of soil bacterial and fungal OTUs emerged.

Fungal diversity and community composition responses to the reintroduction of fire in a non-managed Mediterranean shrubland ecosystem

BackgroundMore than a decade of fire suppression has changed the structure of fire-adapted shrubland ecosystems in Spain's National Parks, which are now at extreme risk of uncontrolled wildfires. Prescribed burning can mitigate the risk of wildfires by reducing the fuel load but prescribed burning may also alter the soil properties and reduce microbial and fungal activity, causing changes in the availability of nutrients deep in the soil layer. Although fungal communities are a vital part of post-fire restoration, some fire effects remain unclear. To examine the short-term effects of prescribed burning on soil fungal communities in Doñana Biological Reserve (SW Spain), we collected soil samples pre-burn and 1 day, 6 and 12 months post-burn from burned plots to perform physicochemical and metabarcode DNA analyses. ResultsPrescribed burning had no significant effect on the total fungal operational taxonomic unit richness and abundance. However, changes in soil pH, nitrogen and potassium content post-burn affected fungal community composition. Small non-significant changes in pH and phosphorous affected the composition of ectomycorrhizal fungi. ConclusionsThe ectomycorrhizal fungal community appears to be resilient to the effects of low-to moderate-intensity fires and saprotrophic taxa may benefit from this kind of fire. This finding revealed that prescribed burning is a potentially valuable management tool for reducing fire hazards in shrublands that has little effect on the total richness and abundance of fungal communities.

Biocontrol and plant growth promotion by combined Bacillus spp. inoculation affecting pathogen and AMF communities in the wheat rhizosphere at low salt stress conditions.

Applying plant growth-promoting rhizobacteria (PGPR) improves the efficiency of soil-borne disease control and is considered a sustainable practice. However, the effect of PGPR on the fungal community, especially pathogenic fungi and arbuscular mycorrhizal fungi (AMF), remains unclear. In this study, we examined the effects of a compound microbial agent (consisting of Bacillus subtilis HG-15 and Bacillus velezensis JC-K3) on the incidence and yield of wheat under low salt stress, as well as compared the diversity and community composition of the rhizosphere fungal and AMF communities of wheat in the CK (not inoculated bacterial agent) and BIO (inoculated with a bacterial agent) groups. Chlorophyll relative content (SPAD), net photosynthesis rate (Pn), transpiration rate (Tr), leaf water use efficiency (WUE L), grains per spike and wheat yield in the BIO group increased more than in the CK group. The number of diseased plants and disease incidence was observed to be reduced. The relative efficacy reached 79.80%. We classified 1007 fungal operational taxonomic units (OTU) based on Miseq sequencing data: 11 phyla, 173 families, 319 genera, and 521 species. Fifty-four OTUs were classified from the AMF effective sequences, including 1 phylum, 3 families, 3 genera, and 17 species. The inoculation of bacterial agents reduced the relative abundance of pathogen genera such as Gibberella, Fusarium, Cladosporium, and Alternaria in wheat rhizosphere. It increased the relative abundance of AMF species such as Glomus-group-B-Glomus-lamellosu-VTX00193, Glomus-viscosum-VTX00063, and Glomus-Glo2-VTX00280. In addition, pH, EC, exchangeable K, available N, total N, organic matter, and olsen P were the main driving forces for shaping wheat rhizosphere fungi. The pH value was positively correlated with the relative abundance of fungal communities in soil, especially Gibberella, Cladosporium, Fusarium, and Alternaria. In summary, inoculation with Bacillus subtilis HG-15 and Bacillus velezensis JC-K3 affected wheat yield, incidence, rhizosphere soil chemical properties, rhizosphere fungi, and AMF fungal diversity and community. The findings may provide a theoretical foundation and strain support for constructing efficient PGPR-community and clarifying its mechanism of pathogenic bacteria inhibition.

Changes in soil fungal community composition and functional groups during the succession of Alpine grassland

Background and aimsThis study explores trends in soil fungal patterns, potential functions and their responses to carbon and nitrogen applications over alpine grassland succession in the Qilian Mountain area of China.MethodsThe soil fungal community was characterized via Illumina sequencing of ITS genes. The FUNGuild database was used to predict functional groups in alpine grassland succession from swamp meadow to alpine meadow and steppe meadow. The levels of soil carbon and nitrogen, vegetation carbon and nitrogen, and soil enzyme activity were also assessed.ResultsSoil fungal operational taxonomic units increased from swamp meadow to alpine meadow stage and then reached a relatively stable state in steppe meadow successional stage. This result is consistent with the changing trend of sobs and Chao1 index. Moreover, the soil fungal community differed significantly between different succession stages. During succession, while most phyla of soil fungi followed linear decreasing trends, Ascomycota was the dominant fungal phylum. Its abundance increased significantly, from 60.00% in swamp meadow to 72.26% in steppe meadow. The relative abundances of Pathotroph and Saprotroph fungal functions increased with successional stages, while Symbiotroph did not change significantly. Soil ammonium nitrogen and organic carbon levels dominated the effect on the soil fungal microbial community and functional groups.ConclusionThese findings indicate that the fungal community shifted dramatically in the first stage(swamp to alpine meadow) of succession but then reached a relatively stable state in the second(alpine to steppe meadow) successional stage. The soil fungal function group did not follow the same successional trajectory. Soil ammonium nitrogen and soil organic carbon levels imposed the strongest influence on the fungal community and its function, respectively.

Honeybees affect floral microbiome composition in a central food source for wild pollinators in boreal ecosystems

Basic knowledge on dispersal of microbes in pollinator networks is essential for plant, insect, and microbial ecology. Thorough understanding of the ecological consequences of honeybee farming on these complex plant–pollinator–microbe interactions is a prerequisite for sustainable honeybee keeping. Most research on plant–pollinator–microbe interactions have focused on temperate agricultural systems. Therefore, information on a wild plant that is a seasonal bottleneck for pollinators in cold climate such as Salix phylicifolia is of specific importance. We investigated how floral visitation by insects influences the community structure of bacteria and fungi in Salix phylicifolia inflorescences under natural conditions. Insect visitors were experimentally excluded with net bags. We analyzed the microbiome and measured pollen removal in open and bagged inflorescences in sites where honeybees were foraging and in sites without honeybees. Site and plant individual explained most of the variation in floral microbial communities. Insect visitation and honeybees had a smaller but significant effect on the community composition of microbes. Honeybees had a specific effect on the inflorescence microbiome and, e.g., increased the relative abundance of operational taxonomic units (OTUs) from the bacterial order Lactobacillales. Site had a significant effect on the amount of pollen removed from inflorescences but this was not due to honeybees. Insect visitors increased bacterial and especially fungal OTU richness in the inflorescences. Pollinator visits explained 38% variation in fungal richness, but only 10% in bacterial richness. Our work shows that honeybee farming affects the floral microbiome in a wild plant in rural boreal ecosystems.

Spatio-temporal succession of microbial communities in plastisphere and their potentials for plastic degradation in freshwater ecosystems

Plastics in the environment provide a new and unique habitat for microorganisms - known as the plastisphere. The microbial succession within the plastisphere and their potentials for plastic degradation in freshwater ecosystems is still not clear. Here, we investigated variation of microbial communities in plastisphere and their capacity to biodegrade non-biodegradable plastics (non-BPs), i.e., polypropylene (PP) and polyethylene (PE), and biodegradable plastics (BPs), i.e., polylactic acid+polybutylene adipate-co-terephthalate (PLA+PBAT) for four-time periods (15, 30, 45, and 80 days) in three freshwaters. Results showed that the aging degree of plastics increased with succession of plastisphere, with higher degradation rates of BP blends than those of non-BPs. High-throughput sequencing from 112 biofilm samples revealed that bacterial and fungal community structure of the plastisphere were potentially affected by plastic types and gradually converge during biofilm succession. The plastisphere of BPs reached the mature phase more quickly than those of non-BPs and increased co-exclusion to complete for resources. Furthermore, ecological networks involving plastic aging indices, environmental factors and bacterial and fungal operational taxonomic units were established. Ecological networks revealed that BPs may pose the ability to attract and retain key microorganisms (of the orders Bacillales, Myxococcales and Xanthomonadales) that significantly influence community composition such that biodegradative functions were increased in freshwaters.

Variation in Community Structure of the Root-Associated Fungi of Cinnamomum camphora Forest.

Plant-associated microbial communities play essential roles in the vegetative cycle, growth, and development of plants. Cinnamomum camphora is an evergreen tree species of the Lauraceae family with high ornamental, medicinal, and economic values. The present study analyzed the composition, diversity, and functions of the fungal communities in the bulk soil, rhizosphere, and root endosphere of C. camphora at different slope positions by high-throughput sequencing. The results showed that the alpha diversity of the fungal communities in the bulk soil and rhizosphere of the downhill plots was relatively higher than those uphill. A further analysis revealed that Mucoromycota, the dominant fungus at the phylum level, was positively correlated with soil bulk density, total soil porosity, mass water content, alkaline-hydrolyzable nitrogen, maximum field capacity, and least field capacity. Meanwhile, the prevalent fungus at the class level, Mortierellomycetes, was positively correlated with total phosphorus and available and total potassium, but negatively with alkaline-hydrolyzable nitrogen. Finally, the assignment of the functional guilds to the fungal operational taxonomic units (OTUs) revealed that the OTUs highly enriched in the downhill samples compared with the uphill samples, which were saprotrophs. Thus, this study is the first to report differences in the fungal community among the different soil/root samples and between C. camphora forests grown at different slope positions. We also identified the factors favoring the root-associated beneficial fungi in these forests, providing theoretical guidance for managing C. camphora forests.

Changes in Chemical Properties and Fungal Communities of Mineral Soil after Clear-Cutting and Reforestation of Scots Pine (Pinus sylvestris L.) Sites

This study aimed to assess the changes in chemical properties and fungal communities in the upper mineral soil layer in managed Scots pine (Pinus sylvestris L.) ecosystems. Study sites were located in the three largest P. sylvestris massifs in Lithuania, and six sampling sites, representing different development stages of the P. sylvestris forest ecosystem, were selected in each of them: mature P. sylvestris forest stands; clear-cuts of former P. sylvestris mature stand; and the P. sylvestris plantations aging from the 1st to 4th year. High-throughput sequencing was performed to evaluate the soil fungus community at clear-cuts, early-stage reforested sites, and mature forests in Lithuania. This study has shown that, among other chemical soil parameters, the mean concentrations of mineral nitrogen (N), total phosphorus (P), and P2O5 were slightly higher in the clear-cut sites, and significantly higher in the 1st year plantations compared to the mature forests. The quality filtering after PacBio sequencing showed the presence of 60,898 high-quality fungal sequences, and 1143 fungal operational taxonomic units (OTUs). The most abundant fungal OTU in our study was Archaeorhizomyces sp. 5425_1. In total, 70 mycorrhizal fungal OTUs were found in the soil samples at the studied sites. The most abundant ectomycorrhizal fungus identified was Amanita fulva (Schaeff.) Fr. The highest amount of ectomycorrhizal fungal OTUs was found in the clear-cut sites and in the mature forests. The concentrations of mineral N and P2O5 in the upper mineral soil layer did not significantly affect fungal OTUs diversity. Conversely, a relatively strong correlation was obtained between the number of mycorrhizal fungal OTUs and the concentrations of total N and soil organic carbon (SOC), as well as between the numbers of saprotrophic fungal OTUs and the concentration of magnesium ions (Mg2+).

Community composition and trophic mode diversity of fungi associated with fruiting body of medicinal Sanghuangporus vaninii

Background:The microbial symbionts of macrofungal fruiting body have been shown to play momentous roles in host growth, development, and secondary metabolism. Nevertheless, there is no report on the fungal diversity of Sanghuangporus, a medicinal and edible homologous macrofungus as “forest gold”, which has good effects on antioxidation, boosting immunity and curing stomachache. Here, the diversity and functional group of fungi associated with the fruiting body of the most widely applied S. vaninii were characterized by high-throughput sequencing and FUNGuild tool for the first time.Results:Total 11 phyla, 34 classes, 84 orders, 186 families, and 328 genera were identified in the fruiting body, and our results revealed that the fungal community was dominated by the host fungal taxonomy with absolute superiority (more than 70%), namely, Basidiomycota, Agaricomycetes, Hymenochaetales, Hymenochaetaceae, and genus of Phellinus corrected to Sanghuangporus. Simultaneously, the reads allocated into non-host fungal operational taxonomic units were largely dominated by Ascomycota, Sordariomycetes, Sordariales, Mortierellaceae, and Mortierella. Furthermore, the endophytic fungi were assigned into three trophic modes of “saprotroph” (53.2%), “symbiotroph” (32.2%), and “pathotroph” (14.1%), in which the category of “plant pathogen” was highest enriched with relative abundance of 91.8%, indicating that the endophytic fungi may have the potential to adjust the growth and metabolism of host S. vaninii.Conclusion:Altogether, this report firstly provided new findings that can be inspiring for further in-depth studies to exploit bioactive microbial resources for increased production of Sanghuangporus via coculture, as well as to explore the relationship between macrofungi and their associated endophytes.

Causes and consequences of differences in soil and seed microbiomes for two alpine plants.

Seed and soil microbiomes strongly affect plant performance, and these effects can scale-up to influence plant community structure. However, seed and soil microbial community composition are variable across landscapes, and different microbial communities can differentially influence multiple plant metrics (biomass, germination rate), and community stabilizing mechanisms. We determined how microbiomes inside seeds and in soils varied among alpine plant species and communities that differed in plant species richness and density. Across 10 common alpine plant species, we found a total of 318 bacterial and 128 fungal operational taxonomic units (OTUs) associated with seeds, with fungal richness affected by plant species identity more than sampling location. However, seed microbes had only marginally significant effects on plant germination success and timing. In contrast, soil microbes associated with two different plant species had significant effects on plant biomass, and their effect depended both on the plant species and the location the soils were sampled from. This led to significant changes in plant-soil feedback at different locations that varied in plant density and richness, such that plant-soil feedback favored plant species coexistence in some locations and opposed coexistence at other locations. Importantly, we found that coexistence-facilitating feedback was associated with low plant species richness, suggesting that soil microbes may promote the diversity of colonizing plants during the course of climate change and glacial recession.

Long-term fungus–plant covariation from multi-site sedimentary ancient DNA metabarcoding

Climate change has a major impact on arctic and boreal terrestrial ecosystems as warming leads to northward treeline shifts, inducing consequences for heterotrophic organisms associated with the plant taxa. To unravel ecological dependencies, we address how long-term climatic changes have shaped the co-occurrence of plants and fungi across selected sites in Siberia.We investigated sedimentary ancient DNA from five lakes spanning the last 47,000 years, using the ITS1 marker for fungi and the chloroplast P6 loop marker for vegetation metabarcoding. We obtained 706 unique fungal operational taxonomic units (OTUs) and 243 taxa for the plants. We show higher OTU numbers in dry forest tundra as well as boreal forests compared to wet southern tundra. The most abundant fungal taxa in our dataset are Pseudeurotiaceae, Mortierella, Sordariomyceta, Exophiala, Oidiodendron, Protoventuria, Candida vartiovaarae, Pseudeurotium, Gryganskiella fimbricystis, and Trichosporiella cerebriformis. The overall fungal composition is explained by the plant composition as revealed by redundancy analysis. The fungal functional groups show antagonistic relationships in their climate susceptibility. The advance of woody taxa in response to past warming led to an increase in the abundance of mycorrhizae, lichens, and parasites, while yeast and saprotroph distribution declined. We also show co-occurrences between Salicaceae, Larix, and Alnus and their associated pathogens and detect higher mycorrhizal fungus diversity with the presence of Pinaceae. Under future warming, we can expect feedbacks between fungus composition and plant diversity changes which will affect forest advance, species diversity, and ecosystem stability in arctic regions.

Community Structures and Dynamic Changes of Rhizosphere Microorganisms of Rhododendron agastum at Different Ages

This research aimed at studying the community structural characteristics and changes of rhizospheric microorganisms of Rhododendron agastum at different ages to provide useful information for introduction, domestication, and growth management of R. agastum. The rhizosphere bacterial and fungal communities of R. agastum were sequenced. Meanwhile, the richness and diversity indexes in the V3–V4 regions of bacterial 16S rRNA genes and internal transcribed spacer (ITS) region of fungi were investigated. Results showed that, R. agastum at different ages differs in the rhizospheria microbial community structure. The Shannon, ACE index, and Chao1 index of rhizospheria bacterial and fungal communities of 6-year-old R. agastum are all higher than those of 1- and 3-year-old ones. A total of 7,493 bacterial operational taxonomic units (OTUs) were obtained in root samples of R. agastum at different ages, covering 402 genera, which belong to 169 families, 98 order, 64 classes, and 23 phyla. The dominant rhizospheria bacterial communities of R. agastum included Proteobacteria, Actinobacteria, and Acidobacteria. Meanwhile, 1,583 fungal OTUs were obtained, belonging to 226 genera, 126 families, 89 orders, 38 classes, and 12 phyla, and the dominant fungal communities included Ascomycota, Basidiomycota, and Glomeromycota. The root system of R. agastum has abundant rhizospheria microorganisms, ample microbial OTUs and specific OTUs. With increased planting years of R. agastum, Proteobacteria and Actinobacteria displayed decreased and then increased trend. Bacteroidete was reduced year by year, and Acidobacteria showed increased and then decreased trend in bacterial communities. As for fungi, Ascomycota and Glomeromycota both exhibited decreased trend. Changes in rhizospheric microorganisms are probably an important factor that influences the growth of R. agastum, and rhizospheric microorganisms play a significant ecological role in maintaining growth of the plant.

Patterns of community composition and diversity in latent fungi of living Quercus serrata trunks across a range of oak wilt prevalence and climate variables in Japan

Given that forest dieback due to emerging pests is increasing under global warming, understanding the relationships between pests, climate, and forest biodiversity is an urgent priority. In Japan, mass attacks of an ambrosia beetle, vectoring a pathogenic fungus, cause oak wilt outbreaks in recent decades. Here, the associations of oak wilt and climate with wood-inhabiting fungal communities in apparently healthy Quercus serrata trunks were investigated using DNA metabarcoding in seven sites along a climatic gradient in Japan. Amplicon sequencing of the fungal internal transcribed spacer 1 region generated 1,339,958 sequence reads containing 879 fungal operational taxonomic units (OTUs) in 234 wood samples. OTU compositions were significantly different between sites with and without oak wilt. OTU richness increased with temperature and precipitation at sites where oak wilt was present, but this relationship was not observed at sites without oak wilt, possibly due to interaction between oak wilt and climate. • Oak wilt disease is correlated with fungal communities in living oak trees. • OTU richness increased with temperature and precipitation at sites with oak wilt. • OTU richness was not correlated with macroclimate at sites without oak wilt. • Oak wilt was correlated with absence of some white-rot decomposer fungi. • Precipitation had a negative correlation with the species richness of brown-rot fungi.