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114 results for “fungal diversity”
Effects of Nutrient Supply, Herbivory, and Host Community on Fungal Endophyte Diversity, Kentucky, Iowa, Kansas, Minnesota, USA, 2014
The microbes contained within free-living organisms can alter host growth, reproduction, and interactions with the environment. In turn, processes occurring at larger scales determine the local biotic and abiotic environment of each host that may affect the diversity and composition of the microbiome community. Here, we examine variation in the diversity and composition of the foliar fungal microbiome in the grass host, Andropogon gerardii, across four mesic prairies in the central USA. Composition of fungal endophyte communities differed among sites and among individuals within a site, but was not consistently affected by experimental manipulation of nutrient supply to hosts (A. gerardii) or herbivore reduction via fencing. In contrast, mean fungal diversity was similar among sites but was limited by total plant biomass at the plot scale. Our work also demonstrates distributed experiments motivated by ecological theory are a powerful tool to unravel the multi-scale processes governing microbial community composition and diversity.
Species diversity of fungal endophytes across a stress gradient for plants
<ul> <li>Foliar fungal endophytes are one of the most diverse guilds of symbiotic fungi found in the photosynthetic tissues of every plant lineage, but it is unclear how plant environments and leaf resource availability shape their diversity.</li> <li>We explored correlations between leaf nutrient availability and endophyte diversity among <i>Pinus muricata </i>and <i>Vaccinium ovatum </i>plants growing across a soil nutrient gradient spanning a series of coastal terraces in Mendocino, California.</li> <li>Endophyte richness decreased in plants with higher leaf nitrogen‐to‐phosphorus ratios for both host species, but increased with sodium, which may be toxic to fungi at high concentrations. Isolation frequency, a proxy of fungal biomass, was not significantly predicted by any of the same leaf constituents in the two plant species.</li> <li>We propose that stressed plants can exhibit both low foliar nutrients or high levels of toxic compounds, and that both of these stress responses predict endophyte species richness. Stressful conditions that limit growth of fungi may increase their diversity due to the suppression of otherwise dominating species. Differences between the host species in their endophyte communities may be explained by host specificity, leaf phenology, or microclimates.</li> </ul>
Data from: Shifts in diversification rates and host jump frequencies shaped the diversity of host range among Sclerotiniaceae fungal plant pathogens
The range of hosts that a parasite can infect in nature is a trait determined by its own evolutionary history and that of its potential hosts. However, knowledge on host range diversity and evolution at the family level is often lacking. Here, we investigate host range variation and diversification trends within the Sclerotiniaceae, a family of Ascomycete fungi. Using a phylogenetic framework, we associate diversification rates, the frequency of host jump events, and host range variation during the evolution of this family. Variations in diversification rate during the evolution of the Sclerotiniaceae define three major macro-evolutionary regimes with contrasted proportions of species infecting a broad range of hosts. Host-parasite co-phylogenetic analyses pointed towards parasite radiation on distant hosts long after host speciation (host jump or duplication events) as the dominant mode of association with plants in the Sclerotiniaceae. The intermediate macro-evolutionary regime showed a low diversification rate, high frequency of duplication events, and the highest proportion of broad host range species. Our findings suggest that the emergence of broad host range fungal pathogens results largely from host jumps, as previously reported for oomycete parasites, probably combined with low speciation rates. These results have important implications for our understanding of fungal parasites evolution and are of particular relevance for the durable management of disease epidemics.
Data from: An exotic invader drives the evolution of plant traits that determine mycorrhizal fungal diversity in a native competitor.
The symbiosis between land plants and arbuscular mycorrhizal fungi (AMF) is one of the most widespread and ancient mutualisms on the planet. However, relatively little is known about the evolution of these symbiotic plant-fungal interactions in natural communities. In this study, we investigated the symbiotic AMF communities of populations of the native plant species Pilea pumila (Urticaceae) with varying histories of coexistence with an non-mycorrhizal invasive species, Alliaria petiolata (Brassicaceae), known to affect mycorrhizal communities. We found that native populations of P. pumila with a long history of coexistence with the invasive species developed more diverse symbiotic AMF communities. This effect was strongest when A. petiolata plants were actively growing with the natives, and in soils with the longest history of A. petiolata growth. These results suggest that despite the ancient and widespread nature of the plant-AMF symbiosis, the plant traits responsible for symbiotic preferences can nevertheless evolve rapidly in response to environmental changes.
Data from: Ion Torrent PGM as tool for fungal community analysis: a case study of endophytes in Eucalyptus grandis reveals high taxonomic diversity
The Kingdom Fungi adds substantially to the diversity of life, but due to their cryptic morphology and lifestyle, tremendous diversity, paucity of formally described specimens, and the difficulty in isolating environmental strains into culture, fungal communities are difficult to characterize. This is especially true for endophytic communities of fungi living in healthy plant tissue. The developments in next generation sequencing technologies are, however, starting to reveal the true extent of fungal diversity. One of the promising new technologies, namely semiconductor sequencing, has thus far not been used in fungal diversity assessments. In this study we sequenced the internal transcribed spacer 1 (ITS1) nuclear encoded ribosomal RNA of the endophytic community of the economically important tree, Eucalyptus grandis, from South Africa using the Ion Torrent Personal Genome Machine (PGM). We determined the impact of various analysis parameters on the interpretation of the results, namely different sequence quality parameter settings, different sequence similarity cutoffs for clustering and filtering of databases for removal of sequences with insufficient taxonomy. Sequence similarity cutoff values only had a marginal effect on the identified family numbers, whereas different sequence quality filters had a large effect (89 vs. 48 families between least and most stringent filters). Database filtering had a small, but statistically significant, effect on the assignment of sequences to reference sequences. The community was dominated by Ascomycota, and particularly by families in the Dothidiomycetes that harbor well-known plant pathogens. The study demonstrates that semiconductor sequencing is an ideal strategy for environmental sequencing of fungal communities. It also highlights some potential pitfalls in subsequent data analyses when using a technology with relatively short read lengths.
Integrative biodiversity inventories: characterizing lichen-forming fungal diversity in Glen Canyon National Recreation Area using DNA barcoding and vouchered specimens
<p>The Colorado River and its tributaries on the Colorado Plateau are home to unique desert river ecosystems and changing environmental conditions. Within this region, the Glen Canyon National Recreation Area (GCNRA) is comprised of rugged, high desert terrain and is managed by the United States National Parks Service as both a recreational and conservation area. Despite the ecological and economic importance of GCNRA, significant components of the ecological communities therein remain poorly characterized, including lichens. Accurately characterizing lichen-forming fungal diversity is challenging due to poorly known taxonomic groups, underexplored regions/habitats, and varying interpretations of morphological differences, including the recognition of environmentally modified forms. To better understand lichen diversity in GCNRA, we used an integrative taxonomic approach, incorporating both traditional morphology-based identification and information from the standard fungal DNA barcoding marker, the ITS, to compile a thorough inventory of lichen-forming fungi in Fifty-Mile Canyon. Vouchered lichen specimens were collected in 2019, and from these the ITS marker was sequenced. Candidate species-level lineages were delimited from family-level multiple sequence alignments using the Assemble Species by Automatic Partitioning web server. Specimens comprising DNA-based candidate species were then evaluated using traditional taxonomically diagnostic characters to link these, where possible, to currently described species. For Fifty-Mile Canyon, we document 100 putative species in 15 families, each represented by vouchered specimens, ITS sequence data, and photographic documentation. For comparison, a survey of historic records from GCNRA revealed a total of 124 documented lichen-forming fungal species throughout the NRA and adjacent land. Approximately 50% of the species documented in Fifty-Mile Canyon had not previously been found in GCNRA, and similar proportions of species diversity have been documented in GCNRA but not observed in our survey. We report three species new to North America – <em>Calogaya ferrugineoides</em> (H. Magn.) Arup, Froden & Sochting, <em>Endocarpon deserticola</em> T. Zhang, X. L. Wei & J. C. Wei and <em>Xanthocarpia ferrari</em> (Bagl.) Frödén, Arup & Søchting – verified using ITS sequencing data. In addition, <em>Circinaria squamulosa</em> sp. nov. is formally described here, currently known only from sandstone slabs in Fifty-Mile Canyon. However, the taxonomic identity of many of the candidate species from Fifty-Mile Canyon remained ambiguous at the species level, and some collections likely represent undescribed species-level lineages. Our results revealed unexpected, high species-level diversity of lichen-forming fungi at local scales and that overall lichen diversity across the entire GCNRA is likely vastly undercounted. These data – including DNA barcodes for the vast majority of lichen-forming fungi occurring in this canyon – provide an important resource that can be integrated into subsequent lichen biodiversity research in the southwestern United States and other semi-arid climates.</p>
Genetic composition and diversity of Arabica coffee in the crop's center of origin and its impact on four major fungal diseases
<p><span>Conventional wisdom states that </span><span>genetic variation reduces disease levels in plant populations. Nevertheless, crop species have been subject to a gradual loss of genetic variation through selection for specific traits during breeding, thereby increasing their vulnerability to biotic stresses such as pathogens. We explored how genetic variation in Arabica coffee sites in southwestern Ethiopia was related to the incidence of four major fungal diseases. Sixty sites were selected along a gradient of management intensity, ranging from nearly wild to intensively managed coffee stands. We used genotyping-by-sequencing of pooled leaf samples (pool-GBS) derived from 16 individual coffee shrubs in each of the sixty sites to assess the variation in genetic composition (multivariate: reference allele frequency) and genetic diversity (univariate: mean expected heterozygosity) between sites. </span><span>We found that genetic composition had a clear spatial pattern and that genetic diversity was higher in less managed sites</span><span>. The incidence of the four fungal diseases was related to the genetic composition of the coffee stands, but in a specific way for each disease. In contrast, genetic diversity was only related to the within-site variation of coffee berry disease, but not to the mean incidence of any of the four diseases across sites. Given that fungal diseases are major challenges of Arabica coffee in its native range, our findings that genetic composition of coffee sites impacted the major fungal diseases may serve as baseline information to study the molecular basis of disease resistance in coffee. </span><span>Overall, our study illustrates the need to consider both host genetic composition and genetic diversity when investigating the genetic basis for variation in disease levels</span><span>. </span></p>
Dryness weakens the positive effects of plant and fungal β diversities on above- and belowground biomass
<p><span>Plant and microbial diversity are key to determine ecosystem functioning. Despite the well-known role of local-scale α diversity in affecting vegetation productivity, it still remains unclear about the effects of community heterogeneity (β diversity) of plants and soil microbes on above- and belowground productivity (AGB and BGB) across contrasting environments. Here, we conducted a dryness-gradient transect survey over 3000 km across grasslands on the Tibetan Plateau. We found that plant β diversity was more dominant than α diversity in stimulating AGB, while soil fungal β diversity was the key driver in enhancing BGB. However, these positive effects of plant and microbial β diversity on AGB and BGB were strongly weakened by increasing climatic dryness, mainly because higher soil available phosphorus caused by increasing dryness reduced both plant and soil fungal </span><span>β diversities. </span><span>Overall, these new findings highlight the </span><span>critical role of</span><span> above- and belowground </span><span>β diversity in sustaining grassland productivity, raising our awareness to the ecological risks of large-scale biotic homogenization under future climate change.</span></p>
FIGURE 3 in The wood-decaying fungal diversity unveiled by morphology and phylogeny in Ailaoshan Mountain, Yunnan, China
FIGURE 3. Fruiting bodies in situ of (A) Abundisporus quercicola (CLZhao 4895) (B) Alloexidiopsis yunnanensis (CLZhao 9200) (C) Coltricia weii (CLZhao 4773) (D) Daedaleopsis confragosa (CLZhao 4813) (E) Fuscoporia pulviniformis (CLZhao 8327) (F) Hymenochaete rheicolor (CLZhao 4829) (G) Hymenochaete xerantica (CLZhao 8397) (H) Laetiporus ailaoshanensis (CLZhao 3913) (I) Lenzites betulinus (CLZhao 3825) (J) Lyomyces macrosporus (CLZhao 8605) (K) Megasporoporiella pseudocavernulosa (CLZhao 2803) (L) Microporus vernicipes (CLZhao 5510) in the Ailaoshan Mountains. Bars: (A), (B), (E) = 2 cm; (C), (F), (G), (H), (I), (J), (K), (L) = 1 cm; (D) = 3 cm.
FIGURE 2 in The wood-decaying fungal diversity unveiled by morphology and phylogeny in Ailaoshan Mountain, Yunnan, China
FIGURE 2. Taxonomic composition of 103 corticioid fungal species at the order level in the Ailaoshan Mountains.
FIGURE 1 in The wood-decaying fungal diversity unveiled by morphology and phylogeny in Ailaoshan Mountain, Yunnan, China
FIGURE 1. Maximum parsimony strict consensus tree illustrating the phylogeny of 103 species in Agaricomycetes based on ITS sequences. Branches are labelled with a maximum likelihood boot-strap>70%, a parsimony bootstrap>50%, and Bayesian posterior probabilities>0.97, respectively. The sequences of collections labelled in black are downloaded from GenBank, while those in purple are generated in this study.
Data for "Unexpected suppressive fungal diversity and stimulative soil carbon loss under soil acidification in an alkaline grassland"
<p>This dataset was used to make tables and figures for the study entitled "Unexpected suppressive fungal diversity and stimulative soil carbon loss under soil acidification in an alkaline grassland", which was submitted to Functional Ecology in May 2024. It contains data of soil properties, plant and microbial communities under soil acidification in an alkaline grassland on the Loess Plateau. </p>
Data from: Fungal disease incidence along tree diversity gradients depends on latitude in European forests
European forests host a diversity of tree species that are increasingly threatened by fungal pathogens, which may have cascading consequences for forest ecosystems and their functioning. Previous experimental studies suggest that foliar and root pathogen abundance and disease severity decrease with increasing tree species diversity, but evidences from natural forests are rare. Here, we tested whether foliar fungal disease incidence was negatively affected by tree species diversity in different forest types across Europe. We measured the foliar fungal disease incidence on 16 different tree species in 209 plots in six European countries, representing a forest-type gradient from the Mediterranean to boreal forests. Forest plots of single species (monoculture plots) and those with different combinations of two to five tree species (mixed species plots) were compared. Specifically, we analyzed the influence of tree species richness, functional type (conifer vs. broadleaved) and phylogenetic diversity on overall fungal disease incidence. The effect of tree species richness on disease incidence varied with latitude and functional type. Disease incidence tended to increase with tree diversity, in particular in northern latitudes. Disease incidence decreased with tree species richness in conifers, but not in broadleaved trees. However, for specific damage symptoms, no tree species richness effects were observed. Although the patterns were weak, susceptibility of forests to disease appears to depend on the forest site and tree type.
Dead wood diversity promotes fungal diversity
<p>Dead wood is a source of life as it provides habitat and substrate for a wide range of fungal species. A growing number of studies show an important role of wood quality for fungal diversity, but in most cases for a limited number of wood traits or tree species. In this study, we evaluate how abiotic and biotic factors affect the fungal diversity and composition during dead wood decomposition. For 10 common European tree species, fresh similar-sized logs were incubated simultaneously in two Dutch forests. Annual surveys of fungal fruiting bodies were made for an 8-year period. For each tree species, 20 fresh stem traits were measured that are important for chemical and physical defence and for nutritional quality. Throughout 8 years, 4,644 fruiting bodies belonging to 255 species and 90 genera were recorded on the logs of 10 tree species. Fungal frequency and richness were higher for Angiosperms than for Gymnosperms, both for individual tree species and as a group, and higher for tree species with more acquisitive stem trait strategies (i.e., high nutritional value and low physical defence). Differences in fungal communities were strongly driven by phylogenetic group (Gymnosperms vs. Angiosperms), stem traits, decay time and forest sites, together explaining 23% of the variation. Fungal communities in sandy site diverged early in the decay process but converged later because of substrate homogenization. Of the 128 fungal species included in the analyses, 41% showed a preference for specific tree species and 34% for a specific successional year. In conclusion, dead wood quality, determined by tree species and decay stage, is an important driver of fungal diversity. For forest management, promoting a wide array of dead tree species (especially angiosperm species), a range of stem trait values and decay stages will increase fungal and, thereby, forest biodiversity.</p>
Soil acidification reduces soil fungal diversity, alters microbial carbon metabolism and enhances soil C persistence in an alkaline grassland
<p>This dataset was used to make tables and figures for the study entitled "Soil acidification reduces soil fungal diversity, alters microbial carbon metabolism and enhances soil C persistence in an alkaline grassland", which will be recently submitted to Global Change Biology in October 2023. It contains data of soil properties, plant and microbial communities under soil acidification in an alkaline grassland on the Loess Plateau. </p>
The Diversity of the Fungal and Bacterial in Colon Mucosa of Patients With Different Degree of Inflammation of Ulcerative Colitis
ClinicalTrials.gov study NCT03151850. IPD Sharing: NO. Countries: 1. Publications: 3.
Data from: Fungal symbiont effects on dune plant diversity depend on precipitation
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Data from: Fungal disease incidence along tree diversity gradients depends on latitude in European forests
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Data from: The spatial scaling of saprotrophic fungal beta diversity in decomposing leaves
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Data from: An exotic invader drives the evolution of plant traits that determine mycorrhizal fungal diversity in a native competitor.
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