Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
114
datasets available to search
ShareScore release 0.9.0
Dataset results
114 results for “fungal diversity”
Dead wood diversity promotes fungal diversity
Open the record for dataset details and reuse information.
Data from: Ion Torrent PGM as tool for fungal community analysis: a case study of endophytes in Eucalyptus grandis reveals high taxonomic diversity
Open the record for dataset details and reuse information.
Genetic composition and diversity of Arabica coffee in the crop’s center of origin and its impact on four major fungal diseases
Open the record for dataset details and reuse information.
Data from: The chestnut blight fungus world tour: successive introduction events from diverse origins in an invasive plant fungal pathogen.
Open the record for dataset details and reuse information.
Data from: Shifts in diversification rates and host jump frequencies shaped the diversity of host range among Sclerotiniaceae fungal plant pathogens
Open the record for dataset details and reuse information.
Dryness weakens the positive effects of plant and fungal β diversities on above- and belowground biomass
Open the record for dataset details and reuse information.
Data from: Species delimitation in fungal endophyte diversity studies and its implications in ecological and biogeographic inferences
Open the record for dataset details and reuse information.
Integrative biodiversity inventories: characterizing lichen-forming fungal diversity in Glen Canyon National Recreation Area using DNA barcoding and vouchered specimens
Open the record for dataset details and reuse information.
Data from: Long-lasting modification of soil fungal diversity associated with the introduction of rabbits to a remote sub-Antarctic archipelago
Open the record for dataset details and reuse information.
Data from: The rise and fall of arbuscular mycorrhizal fungal diversity during ecosystem retrogression
Open the record for dataset details and reuse information.
Species diversity of fungal endophytes across a stress gradient for plants
Open the record for dataset details and reuse information.
Data from: Reduced aboveground tree growth associated with higher arbuscular mycorrhizal fungal diversity in tropical forest restoration
Open the record for dataset details and reuse information.
Ectomycorrhizal fungal diversity predicted to substantially decline due to climate changes in North American Pinaceae forests.
<p>AIM: Ectomycorrhizal fungi (ECMF) are partners in a globally distributed tree symbiosis implicated in most major ecosystem functions. However, resilience of ECMF to future climates is uncertain. We forecast these changes over the extent of North American Pinaceae forests.</p> <p>LOCATION: 68 sites from North American Pinaceae forests ranging from Florida to Ontario in the east and southern California to Alaska in the west.</p> <p>TAXON: Ectomycorrhizal fungi (Asco- and Basidiomycetes).</p> <p>METHODS: We characterized ECMF communities at each site using molecular methods and modeled climatic drivers of diversity and community composition with general additive, generalized dissimilarity models, and Taxonomic Indicator Threshold Analysis (TITAN). Next, we projected our models across the extent of North American Pinaceae forests and forecast ECMF responses to climate changes in these forests over the next 50 years.</p> <p>RESULTS: We predict median declines in ECMF species richness as high as 26% in Pinaceae forests throughout a climate zone comprising more than 3.5 million square kilometers of North America (an area twice that of Alaska state). Mitigation of greenhouse gas emissions can reduce these declines, but not prevent them. The existence of multiple diversity optima along climate gradients suggest regionally divergent trajectories for North American ECMF, which is corroborated by corresponding ECMF community thresholds identified in TITAN models. Warming of forests along the boreal-temperate ecotone results in projected ECMF species loss and declines in the relative abundance of long-distance foraging ECMF species, whereas warming of eastern temperate forests has the opposite effect.</p> <p>MAIN CONCLUSIONS: Our results reveal potentially unavoidable ECMF species-losses over the next 50 years, which is likely to have profound (if yet unclear) effects of ECMF associated biogeochemical cycles.</p>
Data from: A new promising phylogenetic marker to study the diversity of fungal communities: the Glycoside Hydrolase 63 gene
In molecular ecology, the development of efficient molecular markers for fungi remains an important research domain. Nuclear ribosomal internal transcribed spacer (ITS) region was proposed as universal DNA barcode marker for fungi, but this marker was criticized for Indel-induced alignment problems and its potential lack of phylogenetic resolution. Our main aim was to develop a new phylogenetic gene and a putative functional marker, from single-copy gene, to describe fungal diversity. Thus, we developed a series of primers to amplify a polymorphic region of the Glycoside Hydrolase GH63 gene, encoding exo-acting α-glucosidases, in basidiomycetes. These primers were validated on 125 different fungal genomic DNAs, and GH63 amplification yield was compared with that of already published functional markers targeting genes coding for laccases, N-acetylhexosaminidases, cellobiohydrolases and class II peroxidases. Specific amplicons were recovered for 95% of the fungal species tested, and GH63 amplification success was strikingly higher than rates obtained with other functional genes. We downloaded the GH63 sequences from 483 fungal genomes publicly available at the JGI mycocosm database. GH63 was present in 461 fungal genomes belonging to all phyla, except Microsporidia and Neocallimastigomycota divisions. Moreover, the phylogenetic trees built with both GH63 and Rpb1 protein sequences revealed that GH63 is also a promising phylogenetic marker. Finally, a very high proportion of GH63 proteins was predicted to be secreted. This molecular tool could be a new phylogenetic marker of fungal species as well as potential indicator of functional diversity of basidiomycetes fungal communities in term of secretory capacities.
Data from: Root biomass and exudates link plant diversity with soil bacterial and fungal biomass
Plant diversity has been shown to determine the composition and functioning of soil biota. Although root-derived organic inputs are discussed as the main drivers of soil communities, experimental evidence is scarce. While there is some evidence that higher root biomass at high plant diversity increases substrate availability for soil biota, several studies have speculated that the quantity and diversity of root inputs into the soil, i.e. though root exudates, drive plant diversity effects on soil biota. Here we used a microcosm experiment to study the role of plant species richness on the biomass of soil bacteria and fungi as well as fungal-to-bacterial ratio via root biomass and root exudates. Plant diversity significantly increased shoot biomass, root biomass, the amount of root exudates, bacterial biomass, and fungal biomass. Fungal biomass increased most with increasing plant diversity resulting in a significant shift in the fungal-to-bacterial biomass ratio at high plant diversity. Fungal biomass increased significantly with plant diversity-induced increases in root biomass and the amount of root exudates. These results suggest that plant diversity enhances soil microbial biomass, particularly soil fungi, by increasing root-derived organic inputs.
Data from: Fungal specificity and selectivity for algae play a major role in determining lichen partnerships across diverse ecogeographic regions in the lichen-forming family Parmeliaceae
Microbial symbionts are instrumental to the ecological and long-term evolutionary success of their hosts, and the central role of symbiotic interactions is increasingly recognized across the vast majority of life. Lichens provide an iconic group for investigating patterns in species interactions; however, relationships among lichen symbionts are often masked by uncertain species boundaries or an inability to reliably identify symbionts. The species-rich lichen-forming fungal family Parmeliaceae provides a diverse group for assessing patterns of interactions of algal symbionts, and our study addresses patterns of lichen symbiont interactions at the largest geographic and taxonomic scales attempted to date. We analysed a total of 2356 algal internal transcribed spacer (ITS) region sequences collected from lichens representing ten mycobiont genera in Parmeliaceae, two genera in Lecanoraceae and 26 cultured Trebouxia strains. Algal ITS sequences were grouped into operational taxonomic units (OTUs); we attempted to validate the evolutionary independence of a subset of the inferred OTUs using chloroplast and mitochondrial loci. We explored the patterns of symbiont interactions in these lichens based on ecogeographic distributions and mycobiont taxonomy. We found high levels of undescribed diversity in Trebouxia, broad distributions across distinct ecoregions for many photobiont OTUs and varying levels of mycobiont selectivity and specificity towards the photobiont. Based on these results, we conclude that fungal specificity and selectivity for algal partners play a major role in determining lichen partnerships, potentially superseding ecology, at least at the ecogeographic scale investigated here. To facilitate effective communication and consistency across future studies, we propose a provisional naming system for Trebouxia photobionts and provide representative sequences for each OTU circumscribed in this study.
Data from: Genetic diversity, virulence and fitness evolution in an obligate fungal parasite of bees
Within-host competition is predicted to drive the evolution of virulence in parasites, but the precise outcomes of such interactions are often unpredictable due to many factors including the biology of the host and the parasite, stochastic events and co-evolutionary interactions. Here, we use a serial passage experiment (SPE) with three strains of a heterothallic fungal parasite (Ascosphaera apis) of the Honey bee (Apis mellifera) to assess how evolving under increasing competitive pressure affects parasite virulence and fitness evolution. The results show an increase in virulence after successive generations of selection and consequently faster production of spores. This faster sporulation, however, did not translate into more spores being produced during this longer window of sporulation; rather, it appeared to induce a loss of fitness in terms of total spore production. There was no evidence to suggest that a greater diversity of competing strains was a driver of this increased virulence and subsequent fitness cost, but rather that strain-specific competitive interactions influenced the evolutionary outcomes of mixed infections. It is possible that the parasite may have evolved to avoid competition with multiple strains because of its heterothallic mode of reproduction, which highlights the importance of understanding parasite biology when predicting disease dynamics.
Data from: Host plant phylogeny and abundance predict root-associated fungal community composition and diversity of mutualists and pathogens
• Interactions between plants and their root-associated fungi (RAF) may influence the relative abundance of tree species and determine forest community diversity. Such plant-soil feedbacks in turn depend on the degree to which spatial distance and phylogenetic relatedness of host trees structure pathogen and mutualist communities, but research detailing these aspects of RAF communities is lacking. Here, we characterize plant-RAF associations across a diverse plant community, focusing on the degree to which RAF communities are structured by spatial distance, host phylogenetic relatedness, and host abundance. We compare results for different functional groups, including both putative mutualists and pathogens, an aspect poorly examined hitherto. • We collected roots at regular intervals along ten 50 m by 2 m transects, then used DNA barcoding to identify host plants, and characterize the associated fungal community. Variance partitioning was used to measure the relative contributions of host phylogenetic relatedness and spatial distance to explaining RAF community composition. A weighted linear regression was used to measure the correlation between host abundance and RAF diversity. • Phylogenetic distance among hosts was a better predictor of RAF community composition than spatial distance, but this relationship was stronger for putative pathogens than for mutualists, suggesting that pathogens show stronger host preference than mutualists. Across all functional groups, RAF showed similar levels of spatial structure. Additionally, RAF communities of locally abundant plants were less diverse than RAF communities of rare plants. • Synthesis: We found that RAF communities are structured by the phylogenetic relatedness of hosts and, to a lesser extent, by spatial distance, with pathogens showing stronger host preference than mutualists. Abundant hosts had less diverse RAF communities than rare hosts, which is notable because abundant plants tend to experience weaker negative plant-soil feedback. Going forward, mechanisms underlying the host abundance-RAF diversity relationship warrant further investigation. Additionally, the survey approach presented here could be paired with experiments linking RAF community composition to plant recruitment.
Data from: Interactions between functionally diverse fungal mutualists inconsistently affect plant performance and competition
Plants form mutualistic relationship with a variety of belowground fungal species. Such a mutualistic relationship can enhance plant growth and resistance to pathogens. Yet, we know little about how interactions between functionally diverse groups of fungal mutualists affect plant performance and competition. We experimentally determined the effects of interaction between two functional groups of belowground fungi that form mutualistic relationship with plants, arbuscular mycorrhizal (AM) fungi and Trichoderma, on interspecific competition between pairs of closely related plant species from four different genera. We hypothesized that the combination of two functionally diverse belowground fungal species would allow plants and fungi to partition their symbiotic relationships and relax plant‐plant competition. Our results show that: 1) the AM fungal species consistently outcompeted the Trichoderma species independent of plant combinations; 2) the fungal species generally had limited effects on competitive interactions between plants; 3) however, the combination of fungal species relaxed interspecific competition in one of the four instances of plant–plant competition, despite the general competitive superiority of AM fungi over Trichoderma. We highlight that the competitive outcome between functionally diverse fungal species may show high consistency across a broad range of host plants and their combinations. However, despite this consistent competitive hierarchy, the consequences of their interaction for plant performance and competition can strongly vary among plant communities.
Data from: Coalescent-based species delimitation approach uncovers high cryptic diversity in the cosmopolitan lichen-forming fungal genus Protoparmelia (Lecanorales, Ascomycota)
Species recognition in lichen-forming fungi has been a challenge because of unsettled species concepts, few taxonomically relevant traits, and limitations of traditionally used morphological and chemical characters for identifying closely related species. Here we analyze species diversity in the cosmopolitan genus Protoparmelia s.l. The ~25 described species in this group occur across diverse habitats from the boreal -arctic/alpine to the tropics, but their relationship to each other remains unexplored. In this study, we inferred the phylogeny of 18 species currently assigned to this genus based on 160 specimens and six markers: mtSSU, nuLSU, ITS, RPB1, MCM7, and TSR1. We assessed the circumscription of species-level lineages in Protoparmelia s. str. using two coalescent-based species delimitation methods – BP&P and spedeSTEM. Our results suggest the presence of a tropical and an extra-tropical lineage, and eleven previously unrecognized distinct species-level lineages in Protoparmelia s. str. Several cryptic lineages were discovered as compared to phenotype-based species delimitation. Many of the putative species are supported by geographic evidence.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.