Global patterns in endemicity and vulnerability of soil fungi

Fungi are highly diverse organisms, which provide multiple ecosystem services. However, compared with charismatic animals and plants, the distribution patterns and conservation needs of fungi have been little explored. Here, we examined endemicity patterns, global change vulnerability and conservation priority areas for functional groups of soil fungi based on six global surveys using a high-resolution, long-read metabarcoding approach. We found that the endemicity of all fungi and most functional groups peaks in tropical habitats, including Amazonia, Yucatan, West-Central Africa, Sri Lanka, and New Caledonia, with a negligible island effect compared with plants and animals. We also found that fungi are predominantly vulnerable to drought, heat and land-cover change, particularly in dry tropical regions with high human population density. Fungal conservation areas of highest priority include herbaceous wetlands, tropical forests, and woodlands. We stress that more attention should be focused on the conservation of fungi, especially root symbiotic arbuscular mycorrhizal and ectomycorrhizal fungi in tropical regions as well as unicellular early-diverging groups and macrofungi in general. Given the low overlap between the endemicity of fungi and macroorganisms, but high conservation needs in both groups, detailed analyses on distribution and conservation requirements are warranted for other microorganisms and soil organisms

Sequence alignments and phylogenetic trees for Lophiostoma carabassense - Fungal Planet description sheets: 1436-1477 - December 2022

Sequence alignments and phylogenetic trees for Lophiostoma carabassense - Fungal Planet description sheets: 1436–1477 - December 2022</p

Data and code for Maciá-Vicente et al. (2016) Low diversity and abundance of root endophytes prevail throughout the life cycle of an annual halophyte. Mycological Progress 15(12): 1303-1311

Data and code for analyses published in Maciá-Vicente et al. (2016) Low diversity and abundance of root endophytes prevail throughout the life cycle of an annual halophyte. Mycological Progress 15(12): 1303-1311.<div><br></div><div>Contains:</div><div>- Methods S1. Shell script and data files with the steps for clustering and annotation of DNA sequences.</div><div><br></div><div>- Methods S2. Script and data files with the steps for data analyses in R.</div><div><br></div

Data and code from 'Facultative root-colonizing fungi dominate endophytic assemblages in roots of non-mycorrhizal Microthlaspi species'

Data and code for analyses in Glynou et al., Facultative root-colonizing fungi dominate endophytic assemblages in roots of non-mycorrhizal Microthlaspi species.<div><br></div><div>Contains:</div><div>- README.pdf: Description of contents.</div><div><br></div><div>- MiSeq_process.sh : Bash script with the bioinformatic pipeline used for process and annotation of Illumina MiSeq reads (R1 reads only). Demultiplexed sequence data is deposited in the NCBI Sequence Read Archive under accession SRP106137.</div><div><br></div><div>- Phylogenetic_analyses : Bash script and data for phylogenetic analyses of all OTUs obtained after the MiSeq reads processing.<br></div><div><br></div><div>- All_OTU_phylogenies.zip : Maximum-likelihood phylogenetic trees (Newick format) and associated sequence annotations used for OTU classifications.</div><div><br></div><div>- R_code.zip : R commands and data sets for statistical analyses.</div

Data and code from 'Host species identity in annual Brassicaceae has a limited effect on the assembly of root-endophytic fungal communities'

Data and code for analysis in Glynou, Thines, and Maciá-Vicente (2018) Host species identity in annual Brassicaceae has a limited effect on the assembly of root-endophytic fungal communities. Plant Ecology & Diversity, https://doi.org/10.1080/17550874.2018.1504332.<div><br></div><div>Contains: </div><div>- README.pdf: Description of contents.</div><div>- R_code.zip: R commands and data sets for statistical analysis.</div

Data from: Genotypic diversity in root-endophytic fungi reflects efficient dispersal and environmental adaptation

Studying community structure and dynamics of plant-associated fungi is the basis for unravelling their interactions with hosts and ecosystem functions. A recent sampling revealed that only a few fungal groups, as defined by internal transcribed spacer region (ITS) sequence similarity, dominate culturable root endophytic communities of nonmycorrhizal Microthlaspi spp. plants across Europe. Strains of these fungi display a broad phenotypic and functional diversity, which suggests a genetic variability masked by ITS clustering into operational taxonomic units (OTUs). The aims of this study were to identify how genetic similarity patterns of these fungi change across environments and to evaluate their ability to disperse and adapt to ecological conditions. A first ITS-based haplotype analysis of ten widespread OTUs mostly showed a low to moderate genotypic differentiation, with the exception of a group identified as Cadophora sp. that was highly diverse. A multilocus phylogeny based on additional genetic loci (partial translation elongation factor 1α, beta-tubulin and actin) and amplified fragment length polymorphism profiling of 185 strains representative of the five dominant OTUs revealed a weak association of genetic differences with geography and environmental conditions, including bioclimatic and soil factors. Our findings suggest that dominant culturable root endophytic fungi have efficient dispersal capabilities, and that their distribution is little affected by environmental filtering. Other processes, such as inter- and intraspecific biotic interactions, may be more important for the local assembly of their communities

DNA alignments and phylogenetic trees

DNA alignments and phylogenetic tree

Details of all fungal isolates in this study, including GenBank sequence accessions, classification into ITS-based haplotypes, and data on their location of origin.

Details of all fungal isolates in this study, including GenBank sequence accessions, classification into ITS-based haplotypes, and data on their location of origin

Supplementary Material for: The effects of fungal root endophytes on plant growth are stable along gradients of abiotic habitat conditions

Supplementary files for paper 'The effects of fungal root endophytes on plant growth are stable along gradients of abiotic habitat conditions.'<div><br></div><div>Includes data files and script with R commands to reproduce the statistical analyses.</div><div><br></div

Matrices with binary AFLP data generated in this study

Matrices with binary AFLP data generated in this stud