Ectomycorrhizal (ECM) fungi play a vital role in temperate and boreal forests where they are the dominant type of mycorrhizal fungi. Characterising the environmental niche (EN) of ECM fungi can help understand their distribution and predict their response to environmental change. Typically, occurrence records of fruitbodies from field observations or reproductive structures archived in collections are used to model species distributions. However, our understanding of ECM fungal distributions is hindered by species with cryptic life cycles or fruiting patterns and can be greatly improved using observations based on DNA sequences obtained from ECM roots or from soil. We assessed how well a single data source could predict the niche of ECM fungi for species with conspicuous and inconspicuous fruitbodies. We used fruitbody and root data from 66 common ECM fungal species in same geographic extent in dominant forests of Europe, classified into conspicuous and inconspicuous species. The fruitbody data were extracted from public databases, and the root data from soil sampling of 136 European forest monitoring plots. We estimated the niches for combined data sources (fruitbody and root data) and for each individual data source using six key environmental variables for ECM fungal composition. We then examined how estimated niche overlap and area (number of grid cells within niche) varied for the two data sources between conspicuous and inconspicuous species. We found that although the niches estimated using combined data from the two data sources had high overlap with the niches estimated from fruitbody data for conspicuous fungi, the niches estimated from fruitbody data had low or medium overlap with the niches estimated using root data for most species. The overlap between the two data sources for conspicuous species was significantly larger than that for inconspicuous species. Root data were important for estimating the niche of inconspicuous species, which had a high ratio of root data to fruitbody data. These results can guide future sampling and conservation of fungi.

We used fungal records obtained from fruitbody and root data to estimate the environmental niche of 66 common ECM fungal species in European forests, classified into conspicuous and inconspicuous species based on the visibility of their fruitbodies, which may significantly affect both niche and distribution inferences for these fungi. The fruitbody data were extracted from public databases (GBIF, UNITE) while the root data (from individual ectomycorrhizas) were obtained from a dataset of 136 ICP Forests long-term monitoring plots. We estimated the niches for fruitbody data, root data, and their combined data separately using six key environmental variables known to affect ECM fungal community composition: mean annual air temperature, isothermality, annual precipitation amount, soil total nitrogen, soil pH, and soil organic carbon stock. We then examined how estimated niche overlap and area (number of grid cells within niche) varied for the two data sources between conspicuous and inconspicuous species. 

All analyses are finished in R Studio.

1. The 'CoordinateCleaner'  R package** was used for GBIF data cleaning.
2. The 'usdm' R package was used to test the multicollinearity of selected environmental variables.
3. The 'ecospat' R package was used to calculate species environmental niche, including niche area, niche density, and niche overlap.