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114 results for “fungal diversity”
Fungal Diversity in Sarracenia Purpurea Pitchers at Harvard Forest 2009-2010
The carnivorous pitcher plant Sarracenia purpurea is widely distributed in the United States and Canada, and is host to a variety of symbiotic organisms, including symbiotic fungi. Culturing of S. purpurea pitcher contents in its native range uncovers diverse single-celled (yeast) communities; these yeast communities are dominated by the ascomycete yeast Candida pseudoglaebosa. We set out to understand how fungal diversity in S. purpurea pitchers changes over space and time, and how C. pseudoglaebosa might influence this diversity. In the summer of 2009, we assayed S. purpurea pitcher water fungal succession in Tom Swamp in Harvard Forest. We sequenced fungal DNA barcodes from 43 pitchers at different times throughout the growing season, and found that C. pseudoglaebosa has a strong impact on fungal diversity. It generally appears in pitchers early in succession, and once it arrives, it often becomes dominant quickly and decreases community evenness. We also identified two other culturable yeasts, Rhodotorula babjevae and Moesziomyces aphidis, which are common but not dominant in pitchers. In laboratory experiments, C. pseudoglaebosa outcompetes these two yeasts, but only if it is inoculated in large numbers, suggesting that C. pseudoglaebosa’s dominance is a consequence of early arrival during pitcher succession. The following summer (2010), we collected water from pitchers at five distant sites in the United States and Canada, and assayed fungal community diversity and C. pseudoglaebosa genetic diversity. We sampled pitcher plants from Tom Swamp in Harvard Forest, plus four other sites in British Columbia, Newfoundland, Georgia, and Florida (Floridian plants were Sarracenia rosea, a close relative of S. purpurea). Fungal communities tended to be structured geographically, with close communities resembling each other more than distant communities. In contrast, C. pseudoglaebosa exhibited three populations: one well-mixed population including isolates from Harvard F
Effects of factorial nitrogen, phosphorus, and potassium with micronutrient addition and Host Community on Fungal Endophyte Diversity at Cedar Creek Ecosystem Reserve, 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 a factorial nitrogen, phosphorus, and potassium addition experiment in Minnesota, USA. We found limited evidence of direct effects of nutrients on endophyte diversity. Instead, the effects of nutrients on endophyte diversity appeared to be mediated by accumulation of plant litter and plant diversity loss. Specifically, nitrogen addition is associated with a 40% decrease in plant diversity and an 11% decrease in endophyte richness. Although nitrogen, phosphorus, and potassium addition increased aboveground live biomass and decreased relative Andropogon cover, endophyte diversity did not covary with live plant biomass or Andropogon cover. Our results suggest that fungal endophyte diversity within this focal host is determined in part by the diversity of the surrounding plant community and its potential impact on immigrant propagules and dispersal dynamics. Our results suggest that elemental nutrients reduce endophyte diversity indirectly via impacts on the local plant community, not direct response to nutrient addition.
Supplementary data files for exploring a diverse world of effector domains and amyloid signaling motifs in fungal NLR proteins
<p>This dataset includes 20 supplementary data files for manuscript <em>Exploring a diverse world of effector domains and amyloid signaling motifs in fungal NLR proteins </em>by Jakub W. Wojciechowski, Emirhan Tekoglu, Marlena Gąsior-Głogowska, Virginie Coustou, Natalia Szulc, Monika Szefczyk, Marta Kopaczyńska, Sven J. Saupe, and Witold Dyrka (under revision). </p> <ul> <li>SF2. Profile HMMs of NLR effector domains. The file includes previously unpublished models.</li> <li>SF3. Multiple sequence alignments of N-termini clusters. </li> <li>SF4. Tabularized results of N-termini annotation.</li> <li>SF5. Structure prediction of HeLo-/Goodbye-/MLKL-like domains. Full AlphaFold2/ColabFold outputs.</li> <li>SF6. Structure prediction of previously unannotated domains. Full AlphaFold2/ColabFold outputs.</li> <li>SF7. PCFGs for BASS. The file includes previously unpublished grammars and a sample scanning configuration.</li> <li>SF8. Candidate short NLR N-termini with ASMs. The FASTA file includes sequences from clusters with high content of ASM-like sequences, according to the BASS PCFGs (SF7).</li> <li>SF9. Profile HMMs of ASMs found in short NLR N-termini.</li> <li>SF10. Profile HMM of HeLo-related HRAMs.</li> <li>SF11. Genomic neighbors of candidate short N-termini NLRs with ASMs The list includes accessions of proteins encoded by genes within the neighborhood of 20kbp of genes encoding the query proteins (SF8).</li> <li>SF12. Short C-termini of 200–400 aa long proteins genomically neighboring candidate short NLR N-termini with ASMs. The FASTA file concerns target proteins listed in SF11.</li> <li>SF13. Pairwise hits of the same ASMs in N-termini of NLRs and C-termini of genomically neighboring proteins. The table is based on SF8–9 and SF11–12. </li> <li>SF14. Lists of HMMER domain hits of effector domain profiles. The lists were obtained through iterative searches in NCBI “nr” starting from Pfam profiles of known NLR effector domains.</li> <li>SF15. Short C-termini of effector proteins. The FASTA file concerns target proteins listed in SF14.</li> <li>SF16. Short N-termini of Pfam NACHT and NB-ARC proteins. The FASTA file concerns proteins from NCBI “nr” associated with the two families in the Pfam database.</li> <li>SF17. Profile HMMs of ASMs found both in effector C-termini and NLR N-termini of genomically neighboring proteins.</li> <li>SF18. Genomic neighbors of candidate short N-termini Pfam NACHT and NB-ARC proteins. The list includes accessions of proteins encoded by genes within the neighborhood of 20kbp of genes encoding the query proteins (SF16).</li> <li>SF19. Pairwise hits of the same ASMs in N-termini of NACHT/NB-ARC NLRs and C-termini of genomically neighboring effector proteins. The table is based on SF15–18. </li> <li>SF20. Pairwise hits of the same ASMs in N-termini of NLRs and C-termini of genomically co-occurring effector proteins. The table is based on SF8–9 and SF15. </li> <li>SF21. BaMLKL homologs identified with hmmsearch in Basidiomycota. A FASTA file.</li> </ul>
Raw Data for Publication: Fungal colonisation on wood surfaces weathered at diverse climatic conditions
<p>Colour_Changes_Izola.csv</p> <p>This file contains CIE Lab* color coordinates measured on the surface of Scots pine during the natural weathering test in Izola, Slovenia.</p> <p>Colour_Changes_Skelleftea.csv</p> <p>This file contains CIE Lab* color coordinates measured on the surface of Scots pine during the natural weathering test in Skelleftea, Sweden.</p> <p>Contact_Angles_Izola.csv</p> <p>This file contains dynamic contact angle with distilled water measured on the surface of Scots pine during the natural weathering test in Izola, Slovenia.</p> <p>Contact_Angles_Skelleftea.csv</p> <p>This file contains dynamic contact angle with distilled water measured on the surface of Scots pine during the natural weathering test in Skelleftea, Sweden.</p> <p>Gloss.csv</p> <p>This file contains the gloss value measured on the surface of Scots pine during the natural weathering test in Izola, Slovenia and Skelleftea, Sweden.</p> <p><strong>Note:</strong> The sample IDs are structured as follows: The first letter represents the treatment condition, with "R" indicating untreated wood. The second letter (A, B, C) represents the board's ID. The third letter represents the location, with "S" indicating Skelleftea and "I" representing Izola, Slovenia. The number indicates the exposure time in weeks.</p> <p>FUNGAL STRAIS_DNA sequence analysis.xlsx</p> <p>This file contains the Genomic DNA of the fungal strains detected on the surface of Scots pine during the natural weathering test in Izola, Slovenia and Skelleftea, Sweden.</p> <p>Weather_Data_Izola.csv</p> <p>This file contains hourly local weather conditions in Izola, Slovenia</p> <p>Weather_Data_Skelleftea.csv</p> <p>This file contains hourly local weather conditions in Skelleftea, Sweden</p> <p><strong>Note:</strong> The weather conditions including the following parameters:1. Air temperature (°C), 2. Dew point (°C), 3. Relative humidity (%), 4. One-hour precipitation total (mm), 5. Snow depth (mm), 6. Wind direction (°), 7. Average wind speed (km/h), 8.Sea-level air pressure (hPa)</p>
Connecting the multiple dimensions of global soil fungal diversity
<p>How the multiple facets of soil fungal diversity vary worldwide remains virtually unknown, hindering the management of this essential species-rich group. By sequencing high-resolution DNA markers in over 4000 topsoil samples from natural and human-altered ecosystems across all continents, we illustrate the distributions and drivers of different levels of taxonomic and phylogenetic diversity of fungi and their ecological groups. We show the impact of precipitation and temperature interactions on fungal local species richness (alpha diversity) across different climates. Our findings reveal how temperature drives fungal compositional turnover (beta diversity) and phylogenetic diversity, linking them with regional species richness (gamma diversity). Our work integrates fungi into the principles of global biodiversity distribution and presents detailed maps for biodiversity conservation and modeling of global ecological processes.</p> <p><strong>### Data overview</strong></p> <p>These datasets contain comprehensive estimates of alpha, beta, and gamma diversity. The data are provided in two formats: TIFF (Tagged Image File Format) and GeoPackage formats, which are commonly used to store geospatially-referenced data.</p> <p><strong>Alpha Diversity</strong>:</p> <ul> <li>`<em>Alpha_S_</em>*` files: These files contain estimates of alpha diversity (local species diversity) for each grid cell of a raster file.</li> <li>`<em>Alpha_AOA_</em>*` files: These files outline the 'Area of Applicability' for the alpha diversity estimates.</li> <li>`<em>Alpha_Uncertainty_</em>*` files: These files contain data related to the uncertainty of the alpha diversity predictions. Uncertainty here represents the range or degree of error associated with the diversity estimates.</li> <li> `<em>Alpha_Hotspots_and_ProtectedAreas</em>` contains information on fungal diversity hotspots and their area under protection (based on IUCN classification). 'Hotspots' are areas with exceptionally high alpha diversity.</li> </ul> <p><strong>Beta Diversity</strong>:</p> <ul> <li>`<em>Beta_</em>*` files: These files include results of beta diversity analyses: maps of global compositional dissimilarity among soil fungal communities and maps of compositional turnover rate.</li> </ul> <p><strong>Other files</strong>:</p> <ul> <li>`<em>EcM_and_AM_GlobalDistribution</em>`: the global distribution of areas with high richness of ectomycorrhizal and arbuscular mycorrhizal fungi.</li> <li>`<em>Ecoregions_Alpha,Beta,Gamma_Diversities</em>`: estimates of alpha, beta, and gamma diversity at the level of ecoregion cf. Tedersoo et al., 2022 (DOI:10.1111/gcb.16398).</li> </ul> <p> </p> <p><strong>### Data description</strong></p> <p>Alpha diversity, which is a measure of local species richness (number of Operational Taxonomic Unit (OTU) representing distinct taxa, roughly corresponding to species level). Alpha diversity is represented by the residuals from a model adjusting for sequencing depth, with zero equating to the average OTU richness in the training data set.</p> <p><br> `<strong>Alpha_S_AllFungi_Consensus.tif</strong>`: This file provides consensus estimates for total fungal alpha diversity.<br> Within the file, there are two types of consensus estimates:</p> <ul> <li> <em>AvgW</em> - weighted consensus estimates for alpha diversity. The weighting takes into account both the area of applicability and the goodness-of-fit for the model used to generate the estimates.</li> <li> <em>Avg</em> - non-weighted consensus estimates for alpha diversity. Unlike <em>AvgW</em>, these estimates give equal weight to all models regardless of their goodness-of-fit or area of applicability.</li> </ul> <p><br> `<strong>Alpha_AOA_*</strong>`: Files containing Area of Applicability information:</p> <ul> <li> A raster value of '1' represents areas that are outside the Area of Applicability</li> <li> A raster value of '2' denotes areas that are inside the Area of Applicability</li> </ul> <p><br> In the files containing prediction uncertainties (`<strong>Alpha_Uncertainty_*</strong>`), two types of data are presented to quantify the amount of uncertainty in model predictions, each represented by a different band:</p> <ul> <li>The SD band represents the standard deviation of predictions based on different folds of cross-validation. A larger standard deviation indicates greater variability in the predictions.</li> <li>The IQR band represents the interquartile range (the difference between the upper and lower quartiles) of predictions. The wider the IQR, the greater variability in the predictions.</li> </ul> <p><br> `<strong>Alpha_Hotspots_and_ProtectedAreas.tif</strong>`: This file provides information on regions of exceptionally high species richness, referred to as 'hotspots', along with information about protected areas. Hotspots are identified as the top 2.5% quantiles of the richest grid cells on the map in terms of OTU richness.</p> <ul> <li><em>IUCN_1_4</em> - terrestrial protected areas that fall into categories I-IV, as classified by the International Union for Conservation of Nature (IUCN). These categories typically represent areas with high levels of protection, often prohibiting extractive and destructive activities to preserve biodiversity.</li> <li><em>IUCN_all</em> - all terrestrial protected areas as recorded in the World Database on Protected Areas (WDPA) database v.1.6. It includes a wider range of protected areas beyond the categories I-IV.</li> <li><em>All_Avg</em> - Hotspots of total fungal alpha diversity, based on the consensus map</li> <li><em>GSM_All</em> - Hotspots of total fungal alpha diversity, based on the GSMc dataset</li> <li><em>GSM_EcM</em> - Hotspots of ectomycorrhizal alpha diversity</li> <li><em>GSM_AM</em> - Hotspots of arbuscular mycorrhizal alpha diversity</li> <li><em>GSM_AgarNM</em> - Hotspots of non-EcM Agaricomycetes alpha diversity</li> <li><em>GSM_Mold</em> - Hotspots of mold alpha diversity</li> <li><em>GSM_Pathog</em> - Hotspots of opportunistic human parasitic fungal alpha diversity</li> <li><em>GSM_OHP</em> - Hotspots of putative pathogenic fungal alpha diversity</li> <li><em>GSM_Unicel</em> - Hotspots of unicellular, non-yeast fungal alpha diversity</li> <li><em>GSM_Yeast</em> - Hotspots of yeast alpha diversity</li> <li><em>GSMc_PD</em> - Hotspots of phylogenetic alpha diversity</li> <li><em>GSM_PDst</em> - Hotspots of phylogenetic dispersion</li> </ul> <p><br> `<strong>EcM_and_AM_GlobalDistribution.tif</strong>`: To illustrate the worldwide distribution of ectomycorrhizal (EcM) and arbuscular mycorrhizal (AM) fungi, we have categorized their richness into three distinct groups with low (1), medium (2), and high (3) alpha diversity. These categories have been encoded in the raster file using a bitcode system. Specifically, a value of '9' indicates that both EcM and AM fungal communities have low alpha diversity, while a value of '27' signifies that both groups of fungi are OTU-rich To assist with interpretation, a color legend has been provided in a separate QML style file (`<strong>EcM_and_AM_GlobalDistribution.qml</strong>`). This should be automatically recognized by geographic information system software, such as QGIS, to aid in visual analysis.</p> <p><br> `<strong>Beta_Taxonomic_AllFungi.tif</strong>` and `<strong>Beta_Phylogenetic_AllFungi.tif</strong>`: These files quantify the degree of difference in OTU composition of fungal communities. The measurements are based on the Generalized Dissimilarity Modelling (GDM) framework, as described by Mokany et al., 2022 (DOI:10.1111/geb.13459). Each file provides a different perspective on beta diversity: taxonomic (which is the change in species composition between different locations), and phylogenetic (the change in phylogenetic lineage composition between different locations). Each of these raster files contains three bands, with each band representing a scaled axis from a Principal Component Analysis (PCA) of the GDM-transformed environmental predictors.</p> <p><br> `<strong>Beta_LocalTurnover.tif</strong>`: This file contains estimates of local turnover in fungal communities composition estimated as the median expected compositional dissimilarity (taxonomic or phylogenetic) between each location and its closest neighbors within a 150 km radius. In addition, interquartile range (IQR) of dissimilarities is also provided.</p> <p> </p> <p>`<strong>Ecoregions_Alpha,Beta,Gamma_Diversities.gpkg</strong>`: Median alpha, beta, and gamma diversity estimates within ecoregions.</p> <ul> <li><em>Ecoregion</em> - Ecoregion name (cf. Tedersoo et al., 2022, DOI:10.1111/gcb.16398)</li> <li><em>area</em> - Ecoregion area, m<sup>2</sup></li> <li><em>Alpha_S_AllFungi_Consensus</em> - Richness of all fungi (S'<sub>tot</sub>), consensus map</li> <li><em>Alpha_S_AllFungi_GSMc</em> - Richness of all fungi (S'<sub>GSMc</sub>), based on GSMc dataset</li> <li><em>Alpha_S_EcM_GSMc</em> - Richness of ectomycorrhizal fungi (S'<sub>ecm</sub>)</li> <li><em>Alpha_S_AM_GSMc</em> - Richness of arbuscular mycorrhizal fungi (S'<sub>am</sub>)</li> <li><em>Alpha_S_NMA_GSMc</em> - Richness of non-EcM Agaricomycetes (S'<sub>nma</sub>)</li> <li><em>Alpha_S_Mold_GSMc</em> - Richness of molds (S'<sub>mold</sub>)</li> <li><em>Alpha_S_OHP_GSMc</em> - Richness of opportunistic human parasitic fungi (S'<sub>ohp</sub>)</li> <li><em>Alpha_S_Path_GSMc</em> - Richness of putative pathogenic fungi (S'<sub>path</sub>)</li> <li><em>Alpha_S_Ucel_GSMc</em> - Richness of unicellular, non-yeast fungi (S'<sub>ucel</sub>)</li> <li><em>Alpha_S_Yeast_GSMc</em> - Richness of yeasts (S'<sub>yeast</sub>)</li> <li><em>Alpha_SESPD_GSMc</em> - Phylogenetic dispersion of fungal communities (SES<sub>PD</sub>)</li> <li><em>Beta_Taxonomic_Median</em> - Median taxonomic dissimilarity of fungal communities (Simpson's index)</li> <li><em>Beta_Taxonomic_IQR</em> - Interquartile range of taxonomic dissimilarities of fungal communities</li> <li><em>Beta_Phylogenetic_Median</em> - Median phylogenetic dissimilarity of fungal communities</li> <li><em>Beta_Phylogenetic_IQR</em> - Interquartile range of phylogenetic dissimilarities of fungal communities</li> <li><em>Gamma_AllFungi</em> - Gamma diversity (regional species richness) for all fungi (G<sub>tot</sub>)</li> <li><em>Gamma_EcM</em> - Gamma diversity of ectomycorrhizal fungi (G<sub>ecm</sub>)</li> <li><em>Gamma_AM</em> - Gamma diversity of arbuscular mycorrhizal fungi (G<sub>am</sub>)</li> <li><em>Gamma_NMA</em> - Gamma diversity of non-EcM Agaricomycetes (G<sub>nma</sub>)</li> <li><em>Gamma_Mold</em> - Gamma diversity of molds (G<sub>mold</sub>)</li> <li><em>Gamma_Path</em> - Gamma diversity of opportunistic human parasitic fungi (G<sub>ohp</sub>)</li> <li><em>Gamma_OHP</em> - Gamma diversity of putative pathogenic fungi (G<sub>path</sub>)</li> <li><em>Gamma_Ucel</em> - Gamma diversity of unicellular, non-yeast fungi (G<sub>ucel</sub>)</li> <li><em>Gamma_Yeast</em> - Gamma diversity of yeasts (G<sub>yeast</sub>)</li> </ul> <p> </p> <p><strong>### Source code</strong></p> <p>The code used for data analysis and visualization of the main results of the study are available at GitHub:</p> <p><a href="https://github.com/Mycology-Microbiology-Center/Global_fungal_diversity">https://github.com/Mycology-Microbiology-Center/Global_fungal_diversity</a></p> <p> </p>
Figure 2 in Contributions to the fungal diversity of the Cerrado: new records of lignocellulolytic Agaricomycetes
Figure 2. Some lignocellulolytic Agaricomycetes collected in the Cerrado region. A. Inonotus portoricensis (Overh.) Baltazar & Gibertoni; B. Stiptophyllum erubescens (Berk.) Ryvarden; C. Donkia pulcherrima (Berk. & M. A. Curtis) Pilát; D. Perenniporiella tepeitensis (Murril) Decock & R. Valenz.; E. Pleurotus djamor (Ruph. ex. Fr.) Boedijn; F. Pleurotus pulmonarius (Fr.) Quél. Bar = 2 cm. Photos: Melissa Palacio.
Figure 1 in Contributions to the fungal diversity of the Cerrado: new records of lignocellulolytic Agaricomycetes
Figure 1. Some lignocellulolytic Agaricomycetes collected in the Cerrado region. A. Gloeophyllum striatum (Fr.) Murril; B. Auricularia nigricans (Sw.) Birkebak, Looney & Sánchez-García; C. Trametes elegans (Spreng) Fr.; D. Auricularia delicata (Mont. ex Fr.) Henn; E. Daedalea quercina (L.) Pers.; F. Auricularia mesenterica (Dicks.) Pers. Bar = 2 cm. Photos: Melissa Palacio.
Figure 3 in Contributions to the fungal diversity of the Cerrado: new records of lignocellulolytic Agaricomycetes
Figure 3. Some lignocellulolytic Agaricomycetes collected in the Cerrado region. A. Coriolopsis aspera (Jungh.) Teng; B. Microporellus dealbatus (Berk. & M. A. Curtis) Murril; C. Perenniporia alboincarnata (Pat. & Gaillard) Decock & Ryvarden; D. Perenniporia tephropora (Mont.) Ryvarden; E. Trichaptum sector (Ehrenb.) Kreisel; F. Phellinus extensus (Lév.) Pat. Bar = 2 cm. Photos: Melissa Palacio.
Fungal species diversity in French bread sourdoughs made of organic wheat flour
<p>Datasets describing the fungal species diversity, microbial density and acidity of French sourdoughs as well as the diversity of bread-making practices.The species diversity of 14 sourdoughs collected from bakeries located all over France was analyzed. Bakeries were chosen to represent diverse bakery practices and included bakers and farmer-bakers. Both non-culture-based (pyrosequencing of Internal Transcribed Spacer 1 amplicons) and culture-based methods were used.</p> <p>The data were collected, analyzed, and reported within the following publication :</p> <p>Charlotte Urien, Judith Legrand, Pierre Montalent, Serge Casaregola and Delphine Sicard. Fungal species diversity in French bread sourdoughs made of organic wheat flour. Frontier in Microbiology. Submitted</p>
Data from: Fungal symbionts generate water-saver and water-spender plant drought strategies via diverse effects on host gene expression
<p><em>Panicum</em> <em>hallii</em> var <em>hallii</em> HAL2 plants were inoculated individually with six foliar fungal endophytes or fungus-free controls and subjected to 5% or 20% soil moisture treatments. The fungi were selected for their previously observed effects on plant drought physiology, inducing either a "water saver" or a "water spender" strategy in the host. Plants were grown in enclosed microcosms to prevent cross-contamination and each treatment and control included 6 replicates. All fungi were Ascomycetes isolated from plants in central Texas. Plants were monitored for height, wilt, water loss, and survival. At the harvest, we also measured biomass and leaf colonization by the fungi and flash-froze leaf tissue for transcriptomic analyses. Both plant response and gene expression data are provided.</p>
Data from: Fungal symbionts generate water-saver and water-spender plant drought strategies via diverse effects on host gene expression
Open the record for dataset details and reuse information.
Arbuscular mycorrhizal fungal diversity and functioning in urban desert preserves and surrounding deserts in the central Arizona
The creation of urban preserves has been proposed to as a method of reducing the impact of urbanization on biodiversity of native ecosystems. This research compared root colonization by two important fungal root symbionts, arbuscular mycorrhizal (AM) fungi and dark septate endophytes (DSE), at two urban desert preserve sites located in Phoenix, Arizona and at two surrounding Sonoran desert sites. Diversity of AM fungi was also compared between sites. AM root colonization was greater in surrounding deserts in comparison to urban preserves, but root colonization by DSE was not significantly different. A greater number of AM fungal species was detected in surrounding deserts in comparison to urban preserves, although the number of species/sample was not significantly different. About 70% of the AM fungal species were detected at both urban preserve and surrounding desert sites, but species in the family Acaulosporaceae were only detected at the surrounding deserts. Decreases in AM functioning and diversity observed at urban preserves may reduce the ability of preserves to sustain biodiversity.
Fungal sporocarps house diverse and host-specific communities of fungicolous fungi
<p class="Corps"><span><span><span><span><span><span><span><span><span><span>Sporocarps (fruit bodies) are the sexual reproductive stage in the life cycle of many fungi. They are highly nutritious and consequently vulnerable to grazing by birds and small mammals, and invertebrates, and can be infected by microbial and fungal parasites and pathogens. The complexity of communities thriving inside sporocarps is largely unknown. In this study, we revealed the diversity, taxonomic composition and host-preference of fungicolous fungi (i.e fungi that feed on other fungi) in sporocarps. We carried out DNA metabarcoding of the ITS2 region from 176 sporocarps of 11 wood-decay fungal host species, all collected within a forest in northeast Finland. We assessed the influence of sporocarp traits, such as lifespan, morphology and size, on the fungicolous fungal community. The level of colonisation by fungicolous fungi, measured as the proportion of non-host ITS2 reads, varied between 2.8-39.8% across the 11 host species and was largely dominated by Ascomycota. Host species was the major determinant of the community composition and diversity of fungicolous fungi, suggesting that host adaptation is important for many fungicolous fungi. Furthermore, the alpha-diversity was consistently higher in short-lived and resupinate sporocarps compared to long-lived and pileate ones, perhaps due to a more hostile environment for fungal growth in the latter too. The fungicolous fungi represented numerous lineages in the fungal tree of life, among which a significant portion was poorly represented with reference sequences in databases. </span></span></span></span></span></span></span></span></span></span></p>
Data from: Contrasting patterns of functional diversity in coffee root fungal communities associated with organic and conventionally-managed fields
<p>The structure and function of fungal communities in the coffee rhizosphere is shaped by crop environment. Because coffee can be grown along a management continuum from conventional application of pesticides and fertilizers in full sun to organic management in a shaded understory, we used coffee fields to hold host constant while comparing rhizosphere fungal communities in markedly different environmental conditions with regard to shade and inputs. We characterized the shade and soil environment in 25 fields under conventional, organic or transitional management in two regions of Costa Rica. We amplified the ITS2 region of fungal DNA from coffee roots in these fields and characterized the rhizosphere fungal community via high-throughput sequencing. Sequences were assigned to guilds to determine differences in functional diversity and trophic structure among coffee field environments. Organic fields had more shade, a greater richness of shade tree species, more leaf litter, and were less acidic, with lower soil nitrate availability and higher soil copper, calcium, and magnesium than conventionally-managed fields, although differences between organic and conventionally-managed fields in shade, calcium and magnesium depended on region. Differences in richness and community composition of rhizosphere fungi between organic and conventionally-managed fields were also correlated with shade, soil acidity, nitrate, and copper. Trophic structure differed with coffee field management. Saprotrophs, plant pathogens, and mycoparasites were more diverse and plant pathogens were more abundant in organic than in conventionally-managed fields, while saprotroph-plant pathogens were more abundant in conventionally-managed fields. These differences reflected environmental differences and depended on region.</p> <p><b>IMPORTANCE</b></p> <p>Rhizosphere fungi play key roles in ecosystems, as nutrient cyclers, pathogens, and mutualists, yet little is currently known about which environmental factors and how agricultural management shape rhizosphere fungal communities and their functional diversity. This field study of the coffee agroecosystem suggests that organic management not only fosters a greater overall diversity of fungi, but also maintains a greater richness of saprotrophic, plant pathogenic and mycoparasitic fungi that has implications for efficiency of nutrient cycling and regulation of plant pathogen populations in agricultural systems. As well as influencing community composition and richness of rhizosphere fungi, shade management and use of fungicides and synthetic fertilizers altered the trophic structure of the coffee agroecosystem.</p>
Fungal symbiont diversity drives growth of Holcus lanatus depending on soil nutrient availability
<ol> <li>Arbuscular mycorrhizal (AM) fungi frequently colonise plant roots and can affect plant morphology and physiology through their contribution to plant nutrition. However, the functional role of AM fungi in the presence of other microbial symbionts, including widespread Mucoromycotina 'fine root endophytes' (MFRE) fungi, remains largely unknown.</li> <li>While both AM fungi and MFRE transfer nutrients, including nitrogen, from inorganic and organic sources to host plants, their combined effects on co-colonised plants have only been investigated in liverworts. Here, we compare the morphology and physiology of the grass <em>Holcus lanatus</em> grown with an AM fungal community versus a more diverse symbiotic fungal community containing both AM fungi and MFRE. </li> <li> <em>Holcus lanatus</em> plants were grown in the presence of either a diverse MFRE+AM fungi soil inoculum or a multi-species AM fungal inoculum. Plant traits associated with growth were quantified, along with fungal transfer of <sup>15</sup>N tracer to plants from a variety of sources (ammonium chloride, alanine, glycine, algal necromass). </li> <li> <em>Holcus lanatus</em> grown with the AM fungal community had greater root and shoot growth during early development and prior to the addition of <sup>15</sup>N-labelled sources, compared to plants grown with the more diverse symbiotic fungal community. When nitrogen sources were made available to the fungal symbionts in the pot microcosms, plants growing with the MFRE+AM fungi soil inoculum had a faster growth rate than plants growing with the AM fungal community. At harvest, <em>H. lanatus</em> grown with the AM fungal community had a larger biomass and there were no differences in <sup>15</sup>N tracer assimilation in plants across the two fungal community treatments.</li> <li>Our results demonstrate that the diversity of fungal inocula in conjunction with soil nutrient availability determines the benefits derived by plants from diverse fungal symbionts. Our research contributes to understanding host plant outcomes in diverse multi-symbiont scenarios.</li> </ol>
Large-scale fungal strain sequencing unravels the molecular diversity in mating loci maintained by long-term balancing selection
<p><span>Balancing selection, an evolutionary force that retains genetic diversity, has been detected in multiple genes and organisms, such as the sexual mating loci in fungi. However, to quantify the strength of balancing selection and define the mating-related genes require a large number of strains. In tetrapolar basidiomycete fungi, sexual type is determined by two unlinked loci, <em>MATA </em>and <em>MATB</em>. Genes in both loci define mating type identity, control successful mating and completion of the life cycle. These loci are usually highly diverse. Previous studies have speculated, based on culture crosses, that species of the non-model genus <em>Trichaptum </em>(Hymenochaetales, Basidiomycota) possess a tetrapolar mating system, with multiple alleles. Here, we sequenced a hundred and eighty strains of three <em>Trichaptum </em>species. We characterized the chromosomal location of <em>MATA </em>and <em>MATB</em>, the molecular structure of <em>MAT </em>regions and their allelic richness. The sequencing effort was sufficient to molecularly characterize multiple <em>MAT </em>alleles segregating before the speciation event of <em>Trichaptum </em>species. Analyses suggested that long-term balancing selection has generated trans-species polymorphisms. Mating sequences were classified in different allelic classes based on an amino acid identity (AAI) threshold supported by phylogenetics. 17,550 mating types were predicted based on the allelic classes. <em>In vitro </em>crosses allowed us to support the degree of allelic divergence needed for successful mating. Even with the high amount of divergence, key amino acids in functional domains are conserved. We conclude that the genetic diversity of mating loci in <em>Trichaptum </em>is due to long-term balancing selection, with limited recombination and duplication activity. The large number of sequenced strains highlighted the importance of sequencing multiple individuals from different species to detect the mating-related genes, the mechanisms generating diversity and the evolutionary forces maintaining them.</span></p>
Data from: Mast seeding in European beech (Fagus sylvatica L.) is associated with reduced fungal sporocarp production and community diversity
<p>A time series of seed production data from European beech (<em>Fagus sylvatica</em>) was combined with a fungal census (1977 to 2006) from La Chanéaz Fungus Reserve to evaluate the relationship between mast seeding and fungal resource availability. Annual fungal species' counts, traits, contemporaneous weather and seed production data are available here, alongside the code used to complete the analyses.</p>
The role of chemical properties of the material deposited in nests of white stork in shaping enzymatic activity and fungal diversity - dataset
<p>Dataset to paper: Błońska E., Jankowiak R., Lasota J., Krzemińska N., Zbyryt A., Ciach M. 2024. The role of chemical properties of the material deposited in nests of white stork in shaping enzymatic activity and fungal diversity. Environmental Science and Pollution Research 31, 2: 2583-2594. https://doi.org/10.1007/s11356-023-31383-x</p> <p>This study was financially supported by the National Science Centre, Poland (grant no. 2021/41/B/NZ8/03456).</p>
Saprotrophic fungal diversity predicts ectomycorrhizal fungal diversity along the timberline in the framework of island biogeography theory
<p></p><p>In the context of a timberline tree species (Betula ermanii) as "virtual island", we surveyed ectomycorrhizal (EcM) fungal diversity along a 430-m vertical gradient on the top of Changbai Mountain, China, sampling fine roots and neighboring soils of B. ermanii. Besides elevation, soil properties and plant functional traits, endophytic and saprotrophic fungal diversity were assessed as candidate predictors to construct integrative models. EcM fungal diversity decreased with increasing elevation, and exhibited positive diversity to diameter at breast height and negative diversity to distance from forest edge relationships in both roots and soils. Integrative models further showed that saprotrophic fungal diversity was the strongest predictor of EcM fungal diversity, directly enhancing EcM fungal diversity in roots and soils. All the metadata were stored here for use.</p><p></p>
eDNA metabarcoding reveals high soil fungal diversity and variation in community composition among Spanish cliffs
<p><span>Environments characterized by physical extremes harbor unique species diversity with particular adaptations. Cliffs are harsh environments for organisms but host a great diversity of specialized plants with many endemics, rare and even endangered species. It is, however, less known which fungal diversity the cliff habitats contain and whether it differs among different cliff locations. We thus sampled soil from three separate cliff locations in the North, Centre and South of Spain and used eDNA metabarcoding to determine fungal diversity. To better understand whether cliff specialist plants may promote particular fungal communities, we have sampled soil from crevices with cliff specialist plants and no apparent plants as controls. Major lifestyles found in cliff soils were saprotrophs, and major fungal orders were Dothideomycetes, Sordariomycetes, and Eurotiomycetes, while the amount of symbiotrophic fungi was relatively low. We found no significant differences in fungal amplicon sequence variant (ASV) richness among the three sampled locations, but the sites were significantly different in their community composition and their main indicator species. Overall, there were no significant differences in fungal ASV richness or composition between soils from cliff specialist plants and soils without plants, suggesting a unique fungal diversity in cliff soils independent from specialized plants. However, preliminary findings on soils of the specialist cliff plant Sedum dasyphyllum against control soils suggest that the presence of a specialist plant may be a relevant factor affecting the specificity of the fungal community in cliff soils. Our results indicate the existence of particular cliff fungal communities in each location, and that, despite limited and poorly developed soils and harsh conditions, cliffs can harbor a great diversity of fungal species, comparable to other ecosystems of Spain. This study points out that some fungi may be cliff-specific, shaping particular communities that mediate plant adaptations to cliffs' extreme conditions.</span></p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.