Forest Age and Plant Species Composition Determine the Soil Fungal Community Composition in a Chinese Subtropical Forest

Fungal diversity and community composition are mainly related to soil and vegetation factors. However, the relative contribution of the different drivers remains largely unexplored, especially in subtropical forest ecosystems. We studied the fungal diversity and community composition of soils sampled from 12 comparative study plots representing three forest age classes (Young: 10–40 yrs; Medium: 40–80 yrs; Old: ≥80 yrs) in Gutianshan National Nature Reserve in South-eastern China. Soil fungal communities were assessed employing ITS rDNA pyrotag sequencing. Members of Basidiomycota and Ascomycota dominated the fungal community, with 22 putative ectomycorrhizal fungal families, where Russulaceae and Thelephoraceae were the most abundant taxa. Analysis of similarity showed that the fungal community composition significantly differed among the three forest age classes. Forest age class, elevation of the study plots, and soil organic carbon (SOC) were the most important factors shaping the fungal community composition. We found a significant correlation between plant and fungal communities at different taxonomic and functional group levels, including a strong relationship between ectomycorrhizal fungal and non-ectomycorrhizal plant communities. Our results suggest that in subtropical forests, plant species community composition is the main driver of the soil fungal diversity and community composition.     

Particle-size distributions and seasonal diversity of allergenic and pathogenic fungi in outdoor air

Fungi are ubiquitous in outdoor air, and their concentration, aerodynamic diameters and taxonomic composition have potentially important implications for human health. Although exposure to fungal allergens is considered a strong risk factor for asthma prevalence and severity, limitations in tracking fungal diversity in air have thus far prevented a clear understanding of their human pathogenic properties. This study used a cascade impactor for sampling, and quantitative real-time PCR plus 454 pyrosequencing for analysis to investigate seasonal, size-resolved fungal communities in outdoor air in an urban setting in the northeastern United States. From the 20 libraries produced with an average of ∼800 internal transcribed spacer (ITS) sequences (total 15 326 reads), 12 864 and 11 280 sequences were determined to the genus and species levels, respectively, and 558 different genera and 1172 different species were identified, including allergens and infectious pathogens. These analyses revealed strong relationships between fungal aerodynamic diameters and features of taxonomic compositions. The relative abundance of airborne allergenic fungi ranged from 2.8% to 10.7% of total airborne fungal taxa, peaked in the fall, and increased with increasing aerodynamic diameter. Fungi that can cause invasive fungal infections peaked in the spring, comprised 0.1–1.6% of fungal taxa and typically increased in relative abundance with decreasing aerodynamic diameter. Atmospheric fungal ecology is a strong function of aerodynamic diameter, whereby through physical processes, the size influences the diversity of airborne fungi that deposit in human airways and the efficiencies with which specific groups of fungi partition from outdoor air to indoor environments.     

Global distribution and diversity of marine Verrucomicrobia

Verrucomicrobia is a bacterial phylum that is commonly detected in soil, but little is known about the distribution and diversity of this phylum in the marine environment. To address this, we analyzed the marine microbial community composition in 506 samples from the International Census of Marine Microbes as well as 11 coastal samples taken from the California Current. These samples from both the water column and sediments covered a wide range of environmental conditions. Verrucomicrobia were present in 98% of the analyzed samples, and thus appeared nearly ubiquitous in the ocean. Based on the occurrence of amplified 16S ribosomal RNA sequences, Verrucomicrobia constituted on average 2% of the water column and 1.4% of the sediment bacterial communities. The diversity of Verrucomicrobia displayed a biogeography at multiple taxonomic levels and thus, specific lineages appeared to have clear habitat preference. We found that subdivision 1 and 4 generally dominated marine bacterial communities, whereas subdivision 2 was more frequent in low salinity waters. Within the subdivisions, Verrucomicrobia community composition were significantly different in the water column compared with sediment as well as within the water column along gradients of salinity, temperature, nitrate, depth and overall water column depth. Although we still know little about the ecophysiology of Verrucomicrobia lineages, the ubiquity of this phylum suggests that it may be important for the biogeochemical cycle of carbon in the ocean.     

Wildfire severity reduces richness and alters composition of soil fungal communities in boreal forests of western Canada

Wildfire is the dominant disturbance in boreal forests and fire activity is increasing in these regions. Soil fungal communities are important for plant growth and nutrient cycling postfire but there is little understanding of how fires impact fungal communities across landscapes, fire severity gradients, and stand types in boreal forests. Understanding relationships between fungal community composition, particularly mycorrhizas, and understory plant composition is therefore important in predicting how future fire regimes may affect vegetation. We used an extreme wildfire event in boreal forests of Canada's Northwest Territories to test drivers of fungal communities and assess relationships with plant communities. We sampled soils from 39 plots 1 year after fire and 8 unburned plots. High‐throughput sequencing (MiSeq, ITS) revealed 2,034 fungal operational taxonomic units. We found soil pH and fire severity (proportion soil organic layer combusted), and interactions between these drivers were important for fungal community structure (composition, richness, diversity, functional groups). Where fire severity was low, samples with low pH had higher total fungal, mycorrhizal, and saprotroph richness compared to where severity was high. Increased fire severity caused declines in richness of total fungi, mycorrhizas, and saprotrophs, and declines in diversity of total fungi and mycorrhizas. The importance of stand age (a surrogate for fire return interval) for fungal composition suggests we could detect long‐term successional patterns even after fire. Mycorrhizal and plant community composition, richness, and diversity were weakly but significantly correlated. These weak relationships and the distribution of fungi across plots suggest that the underlying driver of fungal community structure is pH, which is modified by fire severity. This study shows the importance of edaphic factors in determining fungal community structure at large scales, but suggests these patterns are mediated by interactions between fire and forest stand composition.     

Do foliar fungal communities of Norway spruce shift along a tree species diversity gradient in mature European forests?

Foliar fungal species are diverse and colonize all plants, though whether forest tree species composition influences the distribution of these fungal communities remains unclear. Fungal communities include quiescent taxa and the functionally important and metabolically active taxa that respond to changes in the environment. To determine fungal community shifts along a tree species diversity gradient, needles of Norway spruce were sampled from trees from four mature European forests. We hypothesized that the fungal communities and specific fungal taxa would correlate with tree species diversity. Furthermore, the active fungal community, and not the total community, would shift along the tree diversity gradient. High-throughput sequencing showed significant differences in the fungal communities in the different forests, and in one forest, tree diversity effects were observed, though this was not a general phenomenon. Our study also suggests that studying the metabolically active community may not provide additional information about community composition or diversity.     

High diversity and low specificity of fungi associated with seedless epiphytic plants

Epiphytes, which grow on other plants for support, make up a large portion of Earth's plant diversity. Like other plants, their surfaces and interiors are colonized by diverse assemblages of fungi that can benefit their hosts by increasing tolerance for abiotic stressors and resistance to disease or harm them as pathogens. Fungal communities associated with epiphytic plants and the processes that structure these communities are poorly known. To address this, we sampled seven epiphytic seedless plant taxa in a Costa Rican rainforest and examined the effects of host identity and microhabitat on external and endophytic fungal communities. We found low host specificity for both external and endophytic fungi and weak differentiation between epiphytic and neighboring epilithic plant hosts. High turnover in fungi within and between hosts and habitats reveals that epiphytic plant-associated fungal communities are highly diverse and suggests that they are structured by stochastic processes.     

Host effects in high ectomycorrhizal diversity tropical rainforests on ultramafic soils in New Caledonia

Tropical rainforests have been thought to have low prevalence and diversity of ectomycorrhizal symbioses. However, to date, tropical regions have been poorly sampled for ectomycorrhizal fungi. Here, we investigated ectomycorrhizal fungal community diversity and the role of host plants in shaping this diversity in three main ultramafic rainforests in New Caledonia, an archipelago renowned for its exceptional plant diversity and recognized as a biodiversity hotspot. Sampling of ectomycorrhizal root tips and fruit bodies in Nothofagus aequilateralis-dominated, Arillastrum gummiferum-dominated and mixed rainforests showed high fungal diversity with, in total, 28 lineages and 311 operational taxonomic units (OTUs), of which 95% might be endemic. We also found that host preference and host density influenced ectomycorrhizal community composition and contributed to the high fungal diversity of New Caledonian rainforests. Finally, the /cortinarius lineage dominated the below- and above-ground communities, which suggests that this lineage plays a central role in ultramafic ecosystems functioning.     

Effects of an introduced mustard,Thlaspi arvense,on soil fungal communities in subalpine meadows

The subalpine meadows of the Rocky Mountains, USA, are at the advancing front of global change; however, little is known about the sensitivities of high-elevation soil fungal communities to ongoing ecological changes. Soil fungi are sensitive to abiotic and biotic environmental stressors, including climate change, soil disturbance, and the presence of introduced, non-native plants. Invasive plants in the Brassicaceae (mustard family) are known to alter fungal community structure, suppress arbuscular mycorrhizal fungi, and change their relationship with native plant hosts in forest ecosystems, but these phenomena have not been studied in the subalpine zone where non-native mustard plants are becoming established. Here, we investigated whether the presence of the introduced mustard plant, Thlaspi arvense, is associated with distinct properties of the whole fungal and arbuscular mycorrhizal fungal communities in subalpine meadow ecosystems. We observed clear differences in the composition, relative abundance of core taxa, and mean taxon relatedness of soil fungal communities in plots with T. arvense relative to those with only native vegetation. A suite of novel fungi were associated with T. arvense, and overall patterns of AMF phylogenetic diversity were drastically reduced in association with its presence. Our results suggest that T. arvense introduction impacts the soil fungal community, with potential implications for native plant communities and soil nutrient cycling in high elevation meadows of the Rocky Mountains.     

Coastal marine habitats harbor novel early-diverging fungal diversity

Despite nearly a century of study, the diversity of marine fungi remains poorly understood. Historical surveys utilizing microscopy or culture-dependent methods suggest that marine fungi are relatively species-poor, predominantly Dikarya, and localized to coastal habitats. However, the use of high-throughput sequencing technologies to characterize microbial communities has challenged traditional concepts of fungal diversity by revealing novel phylotypes from both terrestrial and aquatic habitats. Here, I used ion semiconductor sequencing (Ion Torrent) of the ribosomal large subunit (LSU/28S) to explore fungal diversity from water and sediment samples collected from four habitats in coastal North Carolina. The dominant taxa observed were Ascomycota and Chytridiomycota, though all fungal phyla were represented. Diversity was highest in sand flats and wetland sediments, though benthic sediments harbored the highest proportion of novel sequences. Most sequences assigned to early-diverging fungal groups could not be assigned beyond phylum with statistical support, suggesting they belong to unknown lineages.     

Macrofungi associated with vegetation and soils at Ha Ha Tonka State Park, Missouri

Fungi and vascular plant interactions are necessary components of natural community establishment, productivity and degradation. While many fungal species serve as decomposers of organic matter, others have evolved mutualistic or parasitic relationships with vascular plants. This research focused on characterizing associations among macrofungi, vascular plant communities and soils. Ha Ha Tonka State Park is in central Missouri and has a varying landscape with numerous natural community types that provide diverse habitats and microhabitats that are ideally suited to the investigation of fungal, floral and soil associations. Five communities sampled within the park included glades, open woodlands, flatwoods, closed-canopy forests and karst sinks. Permanent 0.01 ha. plots were surveyed in the 2006 and 2007 growing seasons. Surveys of plots and entire communities yielded 249 fungal taxa and approximately 265 floral taxa. Soils were analyzed to help define specific edaphic components of each community and used to associate soil attributes with plant and fungal communities. Forest communities contained the most ectomycorrhizal (ECM) fungi species. Karst sinks and glades had higher soil pH and phosphorus and fewer ectomycorrhizal fungi. Statistical analyses included non-metric multidimensional scaling, multiresponse permutation procedure and indicator species analysis. Indicator species were identified for flatwood, forest and karst communities, but results were inconclusive for glades and open woodlands.     

Comparative analysis of fungal communities in colonies of two leaf-cutting ant species with different substratum preferences

Fungus gardens of leaf-cutting ants harbor diverse alien fungi in addition to their fungal cultivar. Previous work suggested that alien microorganisms are likely derived from the substrata foraged by ant workers and incorporated into the fungus gardens. To test this hypothesis, we sampled 1014 garden fragments from 16 field colonies of Atta sexdens rubropilosa (a dicot-cutting ant) and Atta capiguara (a grass-cutting ant) in Brazil. From a total of 615 fungal isolates recovered, we observed similar diversity of fungi between colonies of both ant species. However, fungal communities differed in composition of taxa between ant colonies. Trichoderma spirale, Trichosporon chiarellii and Penicillium citrinum were prevalent accounting for 18.5%, 12.2% and 11.7% of the total isolates, respectively. As expected, fungal communities clustered in two major groups supporting the hypothesis that plant substratum has an impact on the composition of the alien fungi found in leaf-cutting ant gardens.     

Environmental metabarcoding reveals heterogeneous drivers of microbial eukaryote diversity in contrasting estuarine ecosystems

Assessing how natural environmental drivers affect biodiversity underpins our understanding of the relationships between complex biotic and ecological factors in natural ecosystems. Of all ecosystems, anthropogenically important estuaries represent a ‘melting pot'' of environmental stressors, typified by extreme salinity variations and associated biological complexity. Although existing models attempt to predict macroorganismal diversity over estuarine salinity gradients, attempts to model microbial biodiversity are limited for eukaryotes. Although diatoms commonly feature as bioindicator species, additional microbial eukaryotes represent a huge resource for assessing ecosystem health. Of these, meiofaunal communities may represent the optimal compromise between functional diversity that can be assessed using morphology and phenotype–environment interactions as compared with smaller life fractions. Here, using 454 Roche sequencing of the 18S nSSU barcode we investigate which of the local natural drivers are most strongly associated with microbial metazoan and sampled protist diversity across the full salinity gradient of the estuarine ecosystem. In order to investigate potential variation at the ecosystem scale, we compare two geographically proximate estuaries (Thames and Mersey, UK) with contrasting histories of anthropogenic stress. The data show that although community turnover is likely to be predictable, taxa are likely to respond to different environmental drivers and, in particular, hydrodynamics, salinity range and granulometry, according to varied life-history characteristics. At the ecosystem level, communities exhibited patterns of estuary-specific similarity within different salinity range habitats, highlighting the environmental sequencing biomonitoring potential of meiofauna, dispersal effects or both.     

Diversity and bioprospecting of fungal communities associated with endemic and cold-adapted macroalgae in Antarctica

We surveyed the distribution and diversity of fungi associated with eight macroalgae from Antarctica and their capability to produce bioactive compounds. The collections yielded 148 fungal isolates, which were identified using molecular methods as belonging to 21 genera and 50 taxa. The most frequent taxa were Geomyces species (sp.), Penicillium sp. and Metschnikowia australis. Seven fungal isolates associated with the endemic Antarctic macroalgae Monostroma hariotii (Chlorophyte) displayed high internal transcribed spacer sequences similarities with the psychrophilic pathogenic fungus Geomyces destructans. Thirty-three fungal singletons (66%) were identified, representing rare components of the fungal communities. The fungal communities displayed high diversity, richness and dominance indices; however, rarefaction curves indicated that not all of the fungal diversity present was recovered. Penicillium sp. UFMGCB 6034 and Penicillium sp. UFMGCB 6120, recovered from the endemic species Palmaria decipiens (Rhodophyte) and M. hariotii, respectively, yielded extracts with high and selective antifungal and/or trypanocidal activities, in which a preliminary spectral analysis using proton nuclear magnetic resonance spectroscopy indicated the presence of highly functionalised aromatic compounds. These results suggest that the endemic and cold-adapted macroalgae of Antarctica shelter a rich, diversity and complex fungal communities consisting of a few dominant indigenous or mesophilic cold-adapted species, and a large number of rare and/or endemic taxa, which may provide an interesting model of algal–fungal interactions under extreme conditions as well as a potential source of bioactive compounds.     

Alien plants associate with widespread generalist arbuscular mycorrhizal fungal taxa: evidence from a continental‐scale study using massively parallel 454 sequencing

Aim The biogeography of arbuscular mycorrhizal (AM) fungi is poorly understood, and consequently the potential of AM fungi to determine plant distribution has been largely overlooked. We aimed to describe AM fungal communities associating with a single host‐plant species across a wide geographical area, including the plant’s native, invasive and experimentally introduced ranges. We hypothesized that an alien AM plant associates primarily with the geographically widespread generalist AM fungal taxa present in a novel range. Location Europe, China. Methods We transplanted the palm Trachycarpus fortunei into nine European sites where it does not occur as a native species, into one site where it is naturalized (Switzerland), and into one glasshouse site. We harvested plant roots after two seasons. In addition, we sampled palms at three sites in the plant’s native range (China). Roots were subjected to DNA extraction, polymerase chain reaction (PCR) and 454 sequencing of AM fungal sequences. We analysed fungal communities with non‐metric multidimensional scaling (NMDS) ordination and cluster analysis and studied the frequency of geographically widespread fungal taxa with log‐linear analysis. We compared fungal communities in the roots of the palm with those in resident plants at one site in the introduced range (Estonia) where natural AM fungal communities had previously been studied. Results We recorded a total of 73 AM fungal taxa. AM fungal communities in the native and introduced ranges differed from one another, while those in the invasive range contained taxa present in both other ranges. Geographically widespread AM fungal taxa were over‐represented in palm roots in all regions, but especially in the introduced range. At the Estonian site, the palm was colonized by the same community of widespread AM fungal taxa as associate with resident habitat‐generalist plants; by contrast, resident forest‐specialist plants were colonized by a diverse community of widespread and other AM fungal taxa. Main conclusions AM fungal communities in the native, invasive and experimentally introduced ranges varied in taxonomic composition and richness, but they shared a pool of geographically widespread, non‐host‐specific taxa that might support the invasion of a generalist alien plant. Our dataset provides the first geographical overview of AM taxon distributions obtained using a single host‐plant species.     

Co-existing grass species have distinctive arbuscular mycorrhizal communities

Arbuscular mycorrhizal (AM) fungi are biotrophic symbionts colonizing the majority of land plants, and are of major importance in plant nutrient supply. Their diversity is suggested to be an important determinant of plant community structure, but the influence of host-plant and environmental factors on AM fungal community in plant roots is poorly documented. Using the terminal restriction fragment length polymorphism (T-RFLP) strategy, the diversity of AM fungi was assessed in 89 roots of three grass species (Agrostis capillaris, Festuca rubra, Poa pratensis) that co-occurred in the same plots of a field experiment. The impact of different soil amendments (nitrogen, lime, nitrogen and lime) and insecticide application on AM fungal community was also studied. The level of diversity found in AM fungal communities using the T-RFLP strategy was consistent with previous studies based on clone libraries. Our results clearly confirm that an AM fungal host-plant preference exists, even between different grass species. AM communities colonizing A. capillaris were statistically different from the others (P < 0.05). Although grass species evenness changed in amended soils, AM fungal community composition in roots of a given grass species remained stable. Conversely, in plots where insecticide was applied, we found higher AM fungal diversity and, in F. rubra roots, a statistically different AM fungal community.     

Strong coupling of plant and fungal community structure across western Amazonian rainforests

The Amazon basin harbors a diverse ecological community that has a critical role in the maintenance of the biosphere. Although plant and animal communities have received much attention, basic information is lacking for fungal or prokaryotic communities. This is despite the fact that recent ecological studies have suggested a prominent role for interactions with soil fungi in structuring the diversity and abundance of tropical rainforest trees. In this study, we characterize soil fungal communities across three major tropical forest types in the western Amazon basin (terra firme, seasonally flooded and white sand) using 454 pyrosequencing. Using these data, we examine the relationship between fungal diversity and tree species richness, and between fungal community composition and tree species composition, soil environment and spatial proximity. We find that the fungal community in these ecosystems is diverse, with high degrees of spatial variability related to forest type. We also find strong correlations between α- and β-diversity of soil fungi and trees. Both fungal and plant community β-diversity were also correlated with differences in environmental conditions. The correlation between plant and fungal richness was stronger in fungal lineages known for biotrophic strategies (for example, pathogens, mycorrhizas) compared with a lineage known primarily for saprotrophy (yeasts), suggesting that this coupling is, at least in part, due to direct plant–fungal interactions. These data provide a much-needed look at an understudied dimension of the biota in an important ecosystem and supports the hypothesis that fungal communities are involved in the regulation of tropical tree diversity.