# GlobalFungi, a global database of fungal occurrences from high-throughput-sequencing metabarcoding studies

Tomáš Větrovský, Daniel Morais, Petr Kohout, Clémentine Lepinay, Camelia Algora, Sandra Awokunle Hollá, Barbara Doreen Bahnmann, Květa Bílohnědá, Vendula Brabcová, Federica D'alò, et al.

<figure><img src="image_1.png" /></figure>

## To cite this version:

Tomáš Větrovský, Daniel Morais, Petr Kohout, Clémentine Lepinay, Camelia Algora, et al. GlobalFungi, a global database of fungal occurrences from high-throughput-sequencing metabarcoding studies. Scientific Data, 2020, 7 (1), pp.228. 10.1038/s41597-020-0567-7. hal-04617534

HAL Id: hal-04617534

https://hal.inrae.fr/hal-04617534

Submitted on 19 Jun 2024

HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers.

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<figure><img src="image_2.png" /></figure>

Distributed under a Creative Commons Attribution 4.0 International License
# GlobalFungi, a global database of fungal occurrences from high-throughput-sequencing metabarcoding studies

Tomáš Větrovský, Daniel Morais, Petr Kohout, Clémentine Lepinay, Camelia Algora, Sandra Awokunle Hollá, Barbara Doreen Bahnmann, Květa Bílohnědá, Vendula Brabcová, Federica D'alò, et al.

► To cite this version:

Tomáš Větrovský, Daniel Morais, Petr Kohout, Clémentine Lepinay, Camelia Algora, et al. GlobalFungi, a global database of fungal occurrences from high-throughput-sequencing metabarcoding studies. Scientific Data, 2020, 7 (1), pp.228. 10.1038/s41597-020-0567-7. hal-04617534

HAL Id: hal-04617534

https://hal.inrae.fr/hal-04617534v1

Submitted on 19 Jun 2024

HAL is a multi-disciplinary open access
archive for the deposit and dissemination of sci-
entific research documents, whether they are pub-
lished or not. The documents may come from
teaching and research institutions in France or
abroad, or from public or private research centers.

L'archive ouverte pluridisciplinaire HAL, est
destinée au dépôt et à la diffusion de documents
scientifiques de niveau recherche, publiés ou non,
émanant des établissements d'enseignement et de
recherche français ou étrangers, des laboratoires
publics ou privés.

<figure><img src="image_1.png" /></figure>

Distributed under a Creative Commons Attribution 4.0 International License
SCIENTIFIC DATA

110110
0111101
11011110
011101101

<figure><img src="image_3.png" /></figure>

Check for updates

OPEN

DATA DESCRIPTOR

GlobalFungi, a global database
of fungal occurrences from
high-throughput-sequencing
metabarcoding studies

Tomáš Větrovský<fnref n="1" />,<fnref n="6" />, Daniel Morais<fnref n="1" />,<fnref n="6" />, Petr Kohout<fnref n="1" />,<fnref n="6" />, Clémentine Lepinay<fnref n="1" />,<fnref n="6" />, Camelia Algora<fnref n="1" />, Sandra Awokunle Hollá<fnref n="1" />, Barbara Doreen Bahnmann<fnref n="1" />, Květa Bílohnědá<fnref n="1" />, Vendula Brabcová<fnref n="1" />, Federica D'Alò<fnref n="2" />, Zander Rainier Human<fnref n="1" />, Mayuko Jomura ID ³, Miroslav Kolařík<fnref n="1" />, Jana Kvasničková<fnref n="1" />, Salvador Lladó<fnref n="1" />, Rubén López-Mondéjar<fnref n="1" />, Tijana Martinović<fnref n="1" />, Tereza Mašínová<fnref n="1" />, Lenka Meszárošová<fnref n="1" />, Lenka Michalčíková<fnref n="1" />, Tereza Michalová<fnref n="1" />, Sunil Mundra⁴,⁵, Diana Navrátilová<fnref n="1" />, Iňaki Odriozola ID <fnref n="1" />, Sarah Piché-Choquette ID <fnref n="1" />, Martina Štursová<fnref n="1" />, Karel Švec<fnref n="1" />, Vojtěch Kláškal ID <fnref n="1" />, Michaela Urbanová<fnref n="1" />, Lukáš Vlk<fnref n="1" />, Jana Voříšková<fnref n="1" />, Lucia Žifčáková<fnref n="1" /> & Petr Baldrian ID <fnref n="1" />✉

Fungi are key players in vital ecosystem services, spanning carbon cycling, decomposition, symbiotic associations with cultivated and wild plants and pathogenicity. The high importance of fungi in ecosystem processes contrasts with the incompleteness of our understanding of the patterns of fungal biogeography and the environmental factors that drive those patterns. To reduce this gap of knowledge, we collected and validated data published on the composition of soil fungal communities in terrestrial environments including soil and plant-associated habitats and made them publicly accessible through a user interface at https://globalfungi.com. The GlobalFungi database contains over 600 million observations of fungal sequences across > 17 000 samples with geographical locations and additional metadata contained in 178 original studies with millions of unique nucleotide sequences (sequence variants) of the fungal internal transcribed spacers (ITS) 1 and 2 representing fungal species and genera. The study represents the most comprehensive atlas of global fungal distribution, and it is framed in such a way that third-party data addition is possible.

Background & Summary

Fungi play fundamental roles in the ecosystem processes across all terrestrial biomes. As plant symbionts, pathogens or major decomposers of organic matter they substantially influence plant primary production, carbon mineralization and sequestration, and act as crucial regulators of the soil carbon balance<fnref n="1" />,<fnref n="2" />. The activities of fungal communities contribute to the production of clean water, food, and air and the suppression of disease-causing soil organisms. Soil fungal biodiversity is thus increasingly recognized to provide services critical to food safety and human health³.

It is of high importance to determine how environmental factors affect the diversity and distribution of fun-
gal communities. So far, only a few studies have focused on fungal distribution and diversity on global scale⁴⁻<fnref n="6" />.
Importantly, these single survey studies focused either on a limited number of biomes⁴,⁵, fairly narrow groups
within the fungal kingdom<fnref n="6" />, or were restricted only to fungi inhabiting soil. Although individual studies have

<footnote n="1">¹Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic.</footnote>

<footnote n="2">²Laboratory of Systematic Botany and Mycology, University of Tuscia, Largo dell'Università snc, Viterbo, 01100, Italy.
³Department of Forest Science and Resources, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, Japan.
⁴Department of Biology, United Arab Emirates University, Al Ain, Abu Dhabi, United Arab Emirates.
⁵Section for Genetics and Evolutionary Biology, University of Oslo, Blindernveien 31, 0316, Oslo, Norway.</footnote>

<footnote n="6">⁶These authors contributed equally: Tomáš Větrovský, Daniel Morais, Petr Kohout, Clémentine Lepinay. ✉e-mail: baldrian@biomed.cas.cz</footnote>
SCIENTIFIC DATA

110110
0111101
11011110
011101101

<figure><img src="image_2.png" /></figure>

Check for updates

OPEN
DATA DESCRIPTOR

GlobalFungi, a global database
of fungal occurrences from
high-throughput-sequencing
metabarcoding studies

Tomáš Větrovský<fnref n="1" />,<fnref n="6" />, Daniel Morais<fnref n="1" />,<fnref n="6" />, Petr Kohout<fnref n="1" />,<fnref n="6" />, Clémentine Lepinay<fnref n="1" />,<fnref n="6" />, Camelia Algora<fnref n="1" />, Sandra Awokunle Hollá<fnref n="1" />, Barbara Doreen Bahnmann<fnref n="1" />, Květa Bílohnědá<fnref n="1" />, Vendula Brabcová<fnref n="1" />, Federica D'Alò<fnref n="2" />, Zander Rainier Human<fnref n="1" />, Mayuko Jomura ID ³, Miroslav Kolařík<fnref n="1" />, Jana Kvasničková<fnref n="1" />, Salvador Lladó<fnref n="1" />, Rubén López-Mondéjar<fnref n="1" />, Tijana Martinović<fnref n="1" />, Tereza Mašínová<fnref n="1" />, Lenka Meszárošová<fnref n="1" />, Lenka Michalčíková<fnref n="1" />, Tereza Michalová<fnref n="1" />, Sunil Mundra⁴,⁵, Diana Navrátilová<fnref n="1" />, Iňaki Odriozola ID <fnref n="1" />, Sarah Piché-Choquette ID <fnref n="1" />, Martina Štursová<fnref n="1" />, Karel Švec<fnref n="1" />, Vojtěch Kláškal ID <fnref n="1" />, Michaela Urbanová<fnref n="1" />, Lukáš Vlk<fnref n="1" />, Jana Voříšková<fnref n="1" />, Lucia Žifčáková<fnref n="1" /> & Petr Baldrian ID <fnref n="1" />✉

Fungi are key players in vital ecosystem services, spanning carbon cycling, decomposition, symbiotic associations with cultivated and wild plants and pathogenicity. The high importance of fungi in ecosystem processes contrasts with the incompleteness of our understanding of the patterns of fungal biogeography and the environmental factors that drive those patterns. To reduce this gap of knowledge, we collected and validated data published on the composition of soil fungal communities in terrestrial environments including soil and plant-associated habitats and made them publicly accessible through a user interface at https://globalfungi.com. The GlobalFungi database contains over 600 million observations of fungal sequences across > 17 000 samples with geographical locations and additional metadata contained in 178 original studies with millions of unique nucleotide sequences (sequence variants) of the fungal internal transcribed spacers (ITS) 1 and 2 representing fungal species and genera. The study represents the most comprehensive atlas of global fungal distribution, and it is framed in such a way that third-party data addition is possible.

Background & Summary

Fungi play fundamental roles in the ecosystem processes across all terrestrial biomes. As plant symbionts, pathogens or major decomposers of organic matter they substantially influence plant primary production, carbon mineralization and sequestration, and act as crucial regulators of the soil carbon balance<fnref n="1" />,<fnref n="2" />. The activities of fungal communities contribute to the production of clean water, food, and air and the suppression of disease-causing soil organisms. Soil fungal biodiversity is thus increasingly recognized to provide services critical to food safety and human health³.

It is of high importance to determine how environmental factors affect the diversity and distribution of fun-
gal communities. So far, only a few studies have focused on fungal distribution and diversity on global scale⁴⁻<fnref n="6" />.
Importantly, these single survey studies focused either on a limited number of biomes⁴,⁵, fairly narrow groups
within the fungal kingdom<fnref n="6" />, or were restricted only to fungi inhabiting soil. Although individual studies have

<footnote n="1">¹Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic.</footnote>

<footnote n="2">²Laboratory of Systematic Botany and Mycology, University of Tuscia, Largo dell'Università snc, Viterbo, 01100, Italy.
³Department of Forest Science and Resources, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, Japan.
⁴Department of Biology, United Arab Emirates University, Al Ain, Abu Dhabi, United Arab Emirates.
⁵Section for Genetics and Evolutionary Biology, University of Oslo, Blindernveien 31, 0316, Oslo, Norway.</footnote>

<footnote n="6">⁶These authors contributed equally: Tomáš Větrovský, Daniel Morais, Petr Kohout, Clémentine Lepinay. ✉e-mail: baldrian@biomed.cas.cz</footnote>
<figure><img src="image_4.png" /><figcaption>**Fig. 1** Map of locations of samples contained in the GlobalFungi database. Each point represents one or several samples where fungal community composition was reported using high-throughput-sequencing methods targeting the ITS1 or ITS2 marker of fungi. The background map image where the samples are represented is the intellectual property of Esri and used herein under license. Copyright © 2019 Esri and its licensors. All rights reserved.</figcaption></figure>

the advantage of standardized methodology across their whole dataset, their limitation is in the limited sampling efforts in space and time that do not allow general conclusions on distribution of fungal taxa. On the other hand, since the advent of high-throughput-sequencing methods, large amounts of sequencing data on fungi from terrestrial environments accumulated along with metadata across numerous studies and allow interesting analyses when combined⁷. As an example of this approach, the meta-analysis of 36 papers made it possible to map global diversity of soil fungi collected in >3000 samples and indicated that climate is an important factor for the global distribution of soil fungi⁸. This approach clearly demonstrated the utility of a meta-study approach to address fungal biogeography, ecology and diversity. In addition, the compilation of these data demonstrated the fact that symbiotic mycorrhizal fungi that aid cultivated and wild plants to access nutrients, are more likely to be affected by rapid changes of climate than other guilds of fungi, including plant pathogens⁸ and helped to identify which fungi tend to follow alien plants invading new environments⁹.

Here, we have undertaken a comprehensive collection and validation of data published on the composition of fungal communities in terrestrial environments including soil and plant-associated habitats. This approach enabled us to construct the GlobalFungi database containing, on March 16, 2020, over 110 million unique sequence variants¹⁰ (i.e., unique nucleotide sequences) of the fungal nuclear ribosomal internal transcribed spacers (ITS) 1 and 2, covering > 17 000 samples contained in 178 original studies (Fig. 1). The ITS region has been used as molecular marker because it is a universal barcode for fungi¹¹. The dataset of sequence variant frequencies across samples, accompanied by metadata retrieved from published papers and in global climate databases is made publicly available at https://globalfungi.com. To achieve the goal to make published data findable, accessible, interoperable and reusable, the user interface at the above address allows the users to search for individual sequences, fungal species hypotheses¹², species or genera, to get a visual representation of their distribution in the environment and to access and download sequence data and metadata. In addition, the user interface also allows authors to submit data from studies not yet covered and in this way to help to build the resource for the community of researchers in systematics, biogeography, and ecology of fungi.
<figure><img src="image_3.png" /><figcaption>**Fig. 1** Map of locations of samples contained in the GlobalFungi database. Each point represents one or several samples where fungal community composition was reported using high-throughput-sequencing methods targeting the ITS1 or ITS2 marker of fungi. The background map image where the samples are represented is the intellectual property of Esri and used herein under license. Copyright © 2019 Esri and its licensors. All rights reserved.</figcaption></figure>

the advantage of standardized methodology across their whole dataset, their limitation is in the limited sampling efforts in space and time that do not allow general conclusions on distribution of fungal taxa. On the other hand, since the advent of high-throughput-sequencing methods, large amounts of sequencing data on fungi from terrestrial environments accumulated along with metadata across numerous studies and allow interesting analyses when combined⁷. As an example of this approach, the meta-analysis of 36 papers made it possible to map global diversity of soil fungi collected in >3000 samples and indicated that climate is an important factor for the global distribution of soil fungi⁸. This approach clearly demonstrated the utility of a meta-study approach to address fungal biogeography, ecology and diversity. In addition, the compilation of these data demonstrated the fact that symbiotic mycorrhizal fungi that aid cultivated and wild plants to access nutrients, are more likely to be affected by rapid changes of climate than other guilds of fungi, including plant pathogens⁸ and helped to identify which fungi tend to follow alien plants invading new environments⁹.

Here, we have undertaken a comprehensive collection and validation of data published on the composition of fungal communities in terrestrial environments including soil and plant-associated habitats. This approach enabled us to construct the GlobalFungi database containing, on March 16, 2020, over 110 million unique sequence variants¹⁰ (i.e., unique nucleotide sequences) of the fungal nuclear ribosomal internal transcribed spacers (ITS) 1 and 2, covering > 17 000 samples contained in 178 original studies (Fig. 1). The ITS region has been used as molecular marker because it is a universal barcode for fungi¹¹. The dataset of sequence variant frequencies across samples, accompanied by metadata retrieved from published papers and in global climate databases is made publicly available at https://globalfungi.com. To achieve the goal to make published data findable, accessible, interoperable and reusable, the user interface at the above address allows the users to search for individual sequences, fungal species hypotheses¹², species or genera, to get a visual representation of their distribution in the environment and to access and download sequence data and metadata. In addition, the user interface also allows authors to submit data from studies not yet covered and in this way to help to build the resource for the community of researchers in systematics, biogeography, and ecology of fungi.
## Methods

**Data selection.** We explored papers fitting with a main criterion, i.e., high-throughput sequencing for the analysis of fungal communities thanks to the ITS region, and that were published up to the beginning of 2019; in total, we explored 843 papers. The following selection criteria were used for the inclusion of samples (and, consequently, studies) into the dataset: (1) samples came from terrestrial biomes of soil, dead or live plant material (e.g., soil, litter, rhizosphere soil, topsoil, lichen, deadwood, root, and shoot) and were not subject to experimental treatment that artificially modifies the fungal community composition (e.g., temperature or nitrogen increase experiment, greenhouse controlled experiment were excluded); (2) the precise geographic location of each sample was recorded and released using GPS coordinates; (3) the whole fungal community was subject to amplicon sequencing (studies using group-specific primers were excluded); (4) the internal transcribed spacer regions (ITS1, ITS2, or both) were subject to amplification; (5) sequencing data (either in fasta with phred scores reported or fastq format) were publicly available or provided by the authors of the study upon request, and the sequences were unambiguously assigned to samples; (6) the samples could be assigned to biomes according to the Environment Ontology (http://www.ontobee.org/ontology/ENVO)⁸. In total, 178 publications contained samples that matched our criteria.

**Processing of sequencing data.** For the processing of data, see Fig. 2 and Code Availability section. Raw datasets from 178 studies, covering 17 242 individual samples were quality filtered by removing all sequences with the mean quality phred scores below 20. Each sequence was labelled using the combination of a sample ID and sequence ID, and the full ITS1 or ITS2 fungal region was extracted using Perl script ITSx v1.0.11¹³. ITS extraction resulted in a total of 416 291 533 full ITS1 and 231 278 756 full ITS2 sequences. The extracted ITS sequences were classified according to the representative sequence of the closest UNITE species hypothesis (SH) using BLASTn¹⁴, using the SH created considering a 98.5% similarity threshold (BLASTDBv5, general release 8.1 from 2.2.2019¹²). A sequence was classified to the best best hit SH only when the following thresholds were met: e-value < 10⁻⁵⁰, sequence similarity > = 98.5%. All representative sequences annotated as nonfungal were discarded. All representative sequences classified to any fungal SH and all unclassified sequences were used to build database library of unique nucleotide sequences (sequence variants). The number of sequence variants accessible through the database is 113 423 871.

**Sample metadata.** Sample metadata were collected from the published papers and/or public repositories where they were submitted by the authors. In some cases, metadata were obtained from the authors of individual studies upon request. The samples were assigned to continents, countries, and specific locations when available, and all sites were categorized into biomes following the classification of Environment Ontology to a maximum achievable depth for each sample. The complete list of metadata included in the database is presented in Table 1.

In addition to the metadata provided by the authors of each study, we also extracted bioclimatic variables from the global CHELSA¹⁵ and WorldClim 2¹⁶ databases for each sample based on its GPS location. Since the results based on CHELSA and WorldClim 2 were comparable, we decided to include those from CHELSA, because precipitation patterns are better captured in the CHELSA dataset, in particular for mountain sites¹⁵.

For each sequence variant that was classified to SH, fungal species name and genus name was retrieved from the UNITE database¹², when available.

## Data Records

The raw sequencing reads used to create the database are available at different locations (see Table 2).

The database contains two data types: sequence variants (individual nucleotide sequences) and samples. For each sequence variant, the following information is stored: sequence variant code, identification of samples where sequence variant occurs and the number of observations, the SH of best hit (when available), fungal species name (when available), fungal genus name (when available). For each sample, metadata information is stored (Table 1). Sequence data and metadata are accessible at Figshare¹⁷ (GlobalFungi ITS variants.zip, GlobalFungi_metadata.xlsx). All database content is accessible using a public graphical user interface at https://globalfungi.com.

## Technical Validation

The technical validation included the screening of the data sources, sequencing data and data reliability. Regarding the data source screening, the data sources (published papers) were screened to fulfil the criteria outlined in the Methods section. The dataset was thoroughly checked for duplicates, and for all records that appeared in multiple publications, only the first original publication of the dataset was considered as a data source. Considering sequence quality, we have only utilized those primer pairs that are generally accepted to target general fungi (see Online-Only Table 1)⁷,¹⁸. Sequences were quality filtered by removing all sequences with the mean quality phred scores below 20 and sequences that did not represent complete ITS1 or ITS2 after extraction or those that were identified as chimeric by the ITS extraction software¹³ were removed. All representative sequences where the BLASTn search against the UNITE database¹² resulted in a nonfungal organism, were discarded.

For data reliability, the geographic location represented by the GPS coordinates was validated first. For each sample set, the geographic location of the sample described in the text of the study was confronted with the location on the map. For those samples where disagreement was recorded (e.g., terrestrial samples positioned in the ocean or located in another region than described in the text), the authors of each study were asked for correction. Studies or samples that could not be reconciled in this way were excluded from the database. The quality of sample metadata was checked and if they were outside the acceptable range (such as content of elements or organic matter > 100%), these invalid metadata were removed.
## Methods

**Data selection.** We explored papers fitting with a main criterion, i.e., high-throughput sequencing for the analysis of fungal communities thanks to the ITS region, and that were published up to the beginning of 2019; in total, we explored 843 papers. The following selection criteria were used for the inclusion of samples (and, consequently, studies) into the dataset: (1) samples came from terrestrial biomes of soil, dead or live plant material (e.g., soil, litter, rhizosphere soil, topsoil, lichen, deadwood, root, and shoot) and were not subject to experimental treatment that artificially modifies the fungal community composition (e.g., temperature or nitrogen increase experiment, greenhouse controlled experiment were excluded); (2) the precise geographic location of each sample was recorded and released using GPS coordinates; (3) the whole fungal community was subject to amplicon sequencing (studies using group-specific primers were excluded); (4) the internal transcribed spacer regions (ITS1, ITS2, or both) were subject to amplification; (5) sequencing data (either in fasta with phred scores reported or fastq format) were publicly available or provided by the authors of the study upon request, and the sequences were unambiguously assigned to samples; (6) the samples could be assigned to biomes according to the Environment Ontology (http://www.ontobee.org/ontology/ENVO)⁸. In total, 178 publications contained samples that matched our criteria.

**Processing of sequencing data.** For the processing of data, see Fig. 2 and Code Availability section. Raw datasets from 178 studies, covering 17 242 individual samples were quality filtered by removing all sequences with the mean quality phred scores below 20. Each sequence was labelled using the combination of a sample ID and sequence ID, and the full ITS1 or ITS2 fungal region was extracted using Perl script ITSx v1.0.11¹³. ITS extraction resulted in a total of 416 291 533 full ITS1 and 231 278 756 full ITS2 sequences. The extracted ITS sequences were classified according to the representative sequence of the closest UNITE species hypothesis (SH) using BLASTn¹⁴, using the SH created considering a 98.5% similarity threshold (BLASTDBv5, general release 8.1 from 2.2.2019¹²). A sequence was classified to the best best hit SH only when the following thresholds were met: e-value < 10⁻⁵⁰, sequence similarity > = 98.5%. All representative sequences annotated as nonfungal were discarded. All representative sequences classified to any fungal SH and all unclassified sequences were used to build database library of unique nucleotide sequences (sequence variants). The number of sequence variants accessible through the database is 113 423 871.

**Sample metadata.** Sample metadata were collected from the published papers and/or public repositories where they were submitted by the authors. In some cases, metadata were obtained from the authors of individual studies upon request. The samples were assigned to continents, countries, and specific locations when available, and all sites were categorized into biomes following the classification of Environment Ontology to a maximum achievable depth for each sample. The complete list of metadata included in the database is presented in Table 1.

In addition to the metadata provided by the authors of each study, we also extracted bioclimatic variables from the global CHELSA¹⁵ and WorldClim 2¹⁶ databases for each sample based on its GPS location. Since the results based on CHELSA and WorldClim 2 were comparable, we decided to include those from CHELSA, because precipitation patterns are better captured in the CHELSA dataset, in particular for mountain sites¹⁵.

For each sequence variant that was classified to SH, fungal species name and genus name was retrieved from the UNITE database¹², when available.

## Data Records

The raw sequencing reads used to create the database are available at different locations (see Table 2).

The database contains two data types: sequence variants (individual nucleotide sequences) and samples. For each sequence variant, the following information is stored: sequence variant code, identification of samples where sequence variant occurs and the number of observations, the SH of best hit (when available), fungal species name (when available), fungal genus name (when available). For each sample, metadata information is stored (Table 1). Sequence data and metadata are accessible at Figshare¹⁷ (GlobalFungi ITS variants.zip, GlobalFungi_metadata.xlsx). All database content is accessible using a public graphical user interface at https://globalfungi.com.

## Technical Validation

The technical validation included the screening of the data sources, sequencing data and data reliability. Regarding the data source screening, the data sources (published papers) were screened to fulfil the criteria outlined in the Methods section. The dataset was thoroughly checked for duplicates, and for all records that appeared in multiple publications, only the first original publication of the dataset was considered as a data source. Considering sequence quality, we have only utilized those primer pairs that are generally accepted to target general fungi (see Online-Only Table 1)⁷,¹⁸. Sequences were quality filtered by removing all sequences with the mean quality phred scores below 20 and sequences that did not represent complete ITS1 or ITS2 after extraction or those that were identified as chimeric by the ITS extraction software¹³ were removed. All representative sequences where the BLASTn search against the UNITE database¹² resulted in a nonfungal organism, were discarded.

For data reliability, the geographic location represented by the GPS coordinates was validated first. For each sample set, the geographic location of the sample described in the text of the study was confronted with the location on the map. For those samples where disagreement was recorded (e.g., terrestrial samples positioned in the ocean or located in another region than described in the text), the authors of each study were asked for correction. Studies or samples that could not be reconciled in this way were excluded from the database. The quality of sample metadata was checked and if they were outside the acceptable range (such as content of elements or organic matter > 100%), these invalid metadata were removed.
<figure><img src="image_5.png" /><figcaption>**Fig. 2** Processing of raw sequencing data for the GlobalFungi database. Workflow of processing of sequencing data included in the GlobalFungi database.</figcaption></figure>

## Usage Notes

The user interface at https://globalfungi.com enables the users to access the database in several ways (Fig. 3). In the taxon search, it is possible to search for genera or species of fungi or for the 98.5% SH species hypotheses of UNITE, contained in the general release 8.1 from 2.2.2019. The search results open the options to download the
<figure><img src="image_4.png" /><figcaption>**Fig. 2** Processing of raw sequencing data for the GlobalFungi database. Workflow of processing of sequencing data included in the GlobalFungi database.</figcaption></figure>

## Usage Notes

The user interface at https://globalfungi.com enables the users to access the database in several ways (Fig. 3). In the taxon search, it is possible to search for genera or species of fungi or for the 98.5% SH species hypotheses of UNITE, contained in the general release 8.1 from 2.2.2019. The search results open the options to download the
<table><caption>**Table 1.** List of metadata contained in the GlobalFungi database. The table lists identifiers, units and sources of metadata contained in the database with the description of their content. The data source “original paper” may also represent additional metadata provided by the authors of the paper.</caption><thead><tr><th>Metadata identifier</th><th>Unit</th><th>Description of content</th><th>Source</th></tr></thead><tbody><tr><td>Sample ID</td><td></td><td>unique identifier</td><td>generated</td></tr><tr><td>Longitude</td><td>degrees</td><td>Geographical longitude</td><td>original paper</td></tr><tr><td>Latitude</td><td>degrees</td><td>Geographical latitude</td><td>original paper</td></tr><tr><td>Continent</td><td></td><td>One of the following: Africa/Antarctica/Asia/Australia/Europe/North America/ South America</td><td>original paper</td></tr><tr><td>Sample type</td><td></td><td>One of the following: soil/rhizosphere soil/litter/litter + humus/deadwood/ lichen/shoot/root</td><td>original paper</td></tr><tr><td>Biome</td><td></td><td>One of the following: forest biome/woodland biome/shrubland biome/grassland biome/desert biome/tundra biome/mangrove biome/anthropogenic terrestrial biome/marine biome/freshwater biome/polar desert biome</td><td>original paper</td></tr><tr><td>Sampling year</td><td></td><td>Year of sample collection</td><td>original paper</td></tr><tr><td>Primers</td><td></td><td>Primers used</td><td>original paper</td></tr><tr><td>pH</td><td></td><td>pH</td><td>original paper</td></tr><tr><td>ITS total</td><td></td><td>Number of full ITS sequences extracted</td><td>generated</td></tr><tr><td>MAT (°C)</td><td>°C</td><td>Mean annual temperature from CHELSA database</td><td>CHELSA</td></tr><tr><td>MAP (mm)</td><td>mm</td><td>Mean annual precipitation from CHELSA database</td><td>CHELSA</td></tr></tbody></table>

<table><caption>**Table 2.** List of identifiers and source database of the raw sequencing datasets used.</caption><thead><tr><th>Database</th><th>Accession Identifiers (in superscripts, respectively: dataset reference, study reference(s))</th></tr></thead><tbody><tr><td>National Center for Biotechnology Information Sequence Read Archive</td><td>SRP001058<sup>19,20</sup>, SRP001175<sup>21,22</sup>, SRP006078<sup>23,24</sup>, SRP012868<sup>25,26</sup>, SRP013695<sup>27,28</sup>, SRP013944<sup>29,30</sup>, SRP015735<sup>31,32</sup>, SRP016090<sup>33,34</sup>, SRP026207<sup>35,36</sup>, SRP028404<sup>37,38</sup>, SRP033719<sup>39,40</sup>, SRP035356<sup>41,42</sup>, SRP040314<sup>43,44</sup>, SRP040786<sup>45,46</sup>, SRP041347<sup>47,48</sup>, SRP043106<sup>49,50</sup>, SRP043706<sup>4,51-53</sup>, SRP043982<sup>54,55</sup>, SRP044665<sup>56,57</sup>, SRP045166<sup>58,59</sup>, SRP045587<sup>60,61</sup>, SRP045746<sup>62,63</sup>, SRP045933<sup>64,65</sup>, SRP046049<sup>66,67</sup>, SRP048036<sup>68-70</sup>, SRP048856<sup>71,72</sup>, SRP049544<sup>73,74</sup>, SRP051033<sup>75,76</sup>, SRP052222<sup>77,78</sup>, SRP052716<sup>79,80</sup>, SRP055957<sup>81,82</sup>, SRP057433<sup>83,84</sup>, SRP057541<sup>85,86</sup>, SRP058508<sup>87,88</sup>, SRP058555<sup>89,90</sup>, SRP058851<sup>91,92</sup>, SRP059280<sup>93,94</sup>, SRP060838<sup>95,96</sup>, SRP061179<sup>97,98</sup>, SRP061305<sup>99,100</sup>, SRP061904<sup>101,102</sup>, SRP062647<sup>103,104</sup>, SRP063711<sup>105,106</sup>, SRP064158<sup>107,108</sup>, SRP065817<sup>109,110</sup>, SRP066030<sup>111,112</sup>, SRP066284<sup>113,114</sup>, SRP066331<sup>115,116</sup>, SRP067301<sup>117,118</sup>, SRP067367<sup>119,120</sup>, SRP068514<sup>121,122</sup>, SRP068608<sup>123,124</sup>, SRP068620<sup>125,126</sup>, SRP068654<sup>127,128</sup>, SRP069065<sup>129,130</sup>, SRP069742<sup>131,132</sup>, SRP070568<sup>133,134</sup>, SRP073070<sup>135,136</sup>, SRP073265<sup>137,138</sup>, SRP074055<sup>139,140</sup>, SRP074496<sup>141,142</sup>, SRP075989<sup>143,144</sup>, SRP079403<sup>145,146</sup>, SRP079521<sup>147,148</sup>, SRP080210<sup>149,150</sup>, SRP080428<sup>151,152</sup>, SRP080680<sup>153,154</sup>, SRP082472<sup>155,156</sup>, SRP082976<sup>157,158</sup>, SRP083394<sup>159,160</sup>, SRP083434<sup>160,161</sup>, SRP083901<sup>162,163</sup>, SRP087715<sup>164,165</sup>, SRP090261<sup>166,167</sup>, SRP090335<sup>168,169</sup>, SRP090490<sup>170,171</sup>, SRP090651<sup>172,173</sup>, SRP091741<sup>174,175</sup>, SRP091855<sup>176,177</sup>, SRP091867<sup>178,179</sup>, SRP092609<sup>180,181</sup>, SRP092777<sup>182,183</sup>, SRP093592<sup>184,185</sup>, SRP093928<sup>186,187</sup>, SRP094708<sup>188-190</sup>, SRP097883<sup>191,192</sup>, SRP101553<sup>193,194</sup>, SRP101605<sup>195,196</sup>, SRP102378<sup>197,198</sup>, SRP102417<sup>199,200</sup>, SRP102775<sup>201,202</sup>, SRP106137<sup>203,204</sup>, SRP106774<sup>205,206</sup>, SRP109773<sup>213,214</sup>, SRP110522<sup>215,216</sup>, SRP110810<sup>217,218</sup>, SRP113348<sup>219,220</sup>, SRP114697<sup>221,222</sup>, SRP114821<sup>223,224</sup>, SRP115350<sup>225,226</sup>, SRP115464<sup>227,228</sup>, SRP115599<sup>229,230</sup>, SRP117302<sup>231,232</sup>, SRP118875<sup>233,234</sup>, SRP118960<sup>235,236</sup>, SRP119174<sup>237,238</sup>, SRP125864<sup>239,240</sup>, SRP132277<sup>241,242</sup>, SRP132591<sup>243,244</sup>, SRP132598<sup>244,245</sup>, SRP136886<sup>246,247</sup>, SRP139483<sup>248,249</sup>, SRP142723<sup>250,251</sup>, SRP148813<sup>252,253</sup>, SRP150527<sup>254,255</sup>, SRP151262<sup>256,257</sup>, SRP153934<sup>258,259</sup>, SRP160913<sup>260,261</sup>, SRP161632<sup>262,263</sup>, SRP195764<sup>264,265</sup></td></tr><tr><td>European Nucleotide Archive Sequence Read Archive</td><td>ERP001713<sup>266,267</sup>, ERP003251<sup>268,269</sup>, ERP003790<sup>270,271</sup>, ERP005177<sup>272,273</sup>, ERP005905<sup>274,275</sup>, ERP009341<sup>276,277</sup>, ERP010027<sup>278,279</sup>, ERP010084<sup>280,281</sup>, ERP010743<sup>282,283</sup>, ERP011924<sup>284,285</sup>, ERP012017<sup>286,287</sup>, ERP013208<sup>288,289</sup>, ERP013987<sup>290,291</sup>, ERP014227<sup>292,293</sup>, ERP017480<sup>294,295</sup>, ERP017851<sup>296,297</sup>, ERP017915<sup>298,299</sup>, ERP019580<sup>300,301</sup>, ERP019924<sup>302,303</sup>, ERP020657<sup>304,305</sup>, ERP022511<sup>306,307</sup>, ERP022742<sup>308,309</sup>, ERP023275<sup>310,311</sup>, ERP023718<sup>312,313</sup>, ERP023855<sup>314,315</sup>, ERP106131<sup>316,317</sup>, ERP107634<sup>318,319</sup>, ERP107636<sup>319,320</sup>, ERP110188<sup>321,322</sup>, ERP112007<sup>323,324</sup></td></tr><tr><td>DNA Data Bank of Japan</td><td>DRA000926<sup>325,326</sup>, DRA000937<sup>327,328</sup>, DRA001737<sup>329,330</sup>, DRA002424<sup>331,332</sup>, DRA002469<sup>333,334</sup>, DRA003024<sup>335,336</sup>, DRA003730<sup>337,338</sup>, DRA004913<sup>339,340</sup>, DRA006519<sup>341,342</sup>, DRP002783<sup>343,344</sup>, DRP003138<sup>345,346</sup>, DRP005365<sup>347,348</sup></td></tr><tr><td>Dryad Digital Repository</td><td>10.5061/dryad.2fc32<sup>349,350</sup>, 10.5061/dryad.n82g9<sup>351,352</sup>, 10.5061/dryad.2343k<sup>353,354</sup>, 10.5061/dryad.gp302<sup>355,356</sup>, 10.5061/dryad.cq2rb<sup>357,358</sup>, 10.5061/dryad.8fn8j<sup>359,360</sup>, 10.5061/dryad.216p<sup>361,362</sup></td></tr><tr><td>GenBank</td><td>KAYV0000000.1<sup>363,364</sup>, KAYU0000000.1<sup>364,365</sup>, KAYT0000000.1<sup>364,366</sup>, SAMN02934078<sup>367,368</sup>, SAMN02934079<sup>368,369</sup></td></tr><tr><td>Australian Antarctic Data Center database</td><td>10.4225/15/526f42ada05b1<sup>370,371</sup></td></tr><tr><td>Supplemental Data</td><td>Hartmann et al. (2012)Supplementary_Data2,372, Rime et al. (2016)Fungi_SeqID,373</td></tr></tbody></table>

corresponding SH or the corresponding sequence variants. It is also possible to view a breakdown of samples by type, biome, mean annual temperature, mean annual precipitation, pH, and continents. The results also contain an interactive map of the taxon distribution with relative abundances of sequences of the taxon across samples and a list of samples with metadata. Several modes of filtering of results are available as well.

In the sequence search, it is possible to search for multiple nucleotide sequences by choosing if the result will be the exact match or a BLAST result. The BLAST option gives the possibility to retrieve the sequence variant best hit in the database, or, when only one sequence is submitted, it is possible to display multiple ranked high score hits among the sequence variants.
<table><caption>**Table 1.** List of metadata contained in the GlobalFungi database. The table lists identifiers, units and sources of metadata contained in the database with the description of their content. The data source “original paper” may also represent additional metadata provided by the authors of the paper.</caption><thead><tr><th>Metadata identifier</th><th>Unit</th><th>Description of content</th><th>Source</th></tr></thead><tbody><tr><td>Sample ID</td><td></td><td>unique identifier</td><td>generated</td></tr><tr><td>Longitude</td><td>degrees</td><td>Geographical longitude</td><td>original paper</td></tr><tr><td>Latitude</td><td>degrees</td><td>Geographical latitude</td><td>original paper</td></tr><tr><td>Continent</td><td></td><td>One of the following: Africa/Antarctica/Asia/Australia/Europe/North America/ South America</td><td>original paper</td></tr><tr><td>Sample type</td><td></td><td>One of the following: soil/rhizosphere soil/litter/litter + humus/deadwood/ lichen/shoot/root</td><td>original paper</td></tr><tr><td>Biome</td><td></td><td>One of the following: forest biome/woodland biome/shrubland biome/grassland biome/desert biome/tundra biome/mangrove biome/anthropogenic terrestrial biome/marine biome/freshwater biome/polar desert biome</td><td>original paper</td></tr><tr><td>Sampling year</td><td></td><td>Year of sample collection</td><td>original paper</td></tr><tr><td>Primers</td><td></td><td>Primers used</td><td>original paper</td></tr><tr><td>pH</td><td></td><td>pH</td><td>original paper</td></tr><tr><td>ITS total</td><td></td><td>Number of full ITS sequences extracted</td><td>generated</td></tr><tr><td>MAT (°C)</td><td>°C</td><td>Mean annual temperature from CHELSA database</td><td>CHELSA</td></tr><tr><td>MAP (mm)</td><td>mm</td><td>Mean annual precipitation from CHELSA database</td><td>CHELSA</td></tr></tbody></table>

<table><caption>**Table 2.** List of identifiers and source database of the raw sequencing datasets used.</caption><thead><tr><th>Database</th><th>Accession Identifiers (in superscripts, respectively: dataset reference, study reference(s))</th></tr></thead><tbody><tr><td>National Center for<br>Biotechnology Information<br>Sequence Read Archive</td><td>SRP001058<sup>19,20</sup>, SRP001175<sup>21,22</sup>, SRP006078<sup>23,24</sup>, SRP012868<sup>25,26</sup>, SRP013695<sup>27,28</sup>, SRP013944<sup>29,30</sup>,<br>SRP015735<sup>31,32</sup>, SRP016090<sup>33,34</sup>, SRP026207<sup>35,36</sup>, SRP028404<sup>37,38</sup>, SRP033719<sup>39,40</sup>, SRP035356<sup>41,42</sup>,<br>SRP040314<sup>43,44</sup>, SRP040786<sup>45,46</sup>, SRP041347<sup>47,48</sup>, SRP043106<sup>49,50</sup>, SRP043706<sup>4,51-53</sup>, SRP043982<sup>54,55</sup>,<br>SRP044665<sup>56,57</sup>, SRP045166<sup>58,59</sup>, SRP045587<sup>60,61</sup>, SRP045746<sup>62,63</sup>, SRP045933<sup>64,65</sup>, SRP046049<sup>66,67</sup>,<br>SRP048036<sup>68-70</sup>, SRP048856<sup>71,72</sup>, SRP049544<sup>73,74</sup>, SRP051033<sup>75,76</sup>, SRP052222<sup>77,78</sup>, SRP052716<sup>79,80</sup>,<br>SRP055957<sup>81,82</sup>, SRP057433<sup>83,84</sup>, SRP057541<sup>85,86</sup>, SRP058508<sup>87,88</sup>, SRP058555<sup>89,90</sup>, SRP058851<sup>91,92</sup>,<br>SRP059280<sup>93,94</sup>, SRP060838<sup>95,96</sup>, SRP061179<sup>97,98</sup>, SRP061305<sup>99,100</sup>, SRP061904<sup>101,102</sup>, SRP062647<sup>103,104</sup>,<br>SRP063711<sup>105,106</sup>, SRP064158<sup>107,108</sup>, SRP065817<sup>109,110</sup>, SRP066030<sup>111,112</sup>, SRP066284<sup>113,114</sup>, SRP066331<sup>115,116</sup>,<br>SRP067301<sup>117,118</sup>, SRP067367<sup>119,120</sup>, SRP068514<sup>121,122</sup>, SRP068608<sup>123,124</sup>, SRP068620<sup>125,126</sup>, SRP068654<sup>127,128</sup>,<br>SRP069065<sup>129,130</sup>, SRP069742<sup>131,132</sup>, SRP070568<sup>133,134</sup>, SRP073070<sup>135,136</sup>, SRP073265<sup>137,138</sup>, SRP074055<sup>139,140</sup>,<br>SRP074496<sup>141,142</sup>, SRP075989<sup>143,144</sup>, SRP079403<sup>145,146</sup>, SRP079521<sup>147,148</sup>, SRP080210<sup>149,150</sup>, SRP080428<sup>151,152</sup>,<br>SRP080680<sup>153,154</sup>, SRP082472<sup>155,156</sup>, SRP082976<sup>157,158</sup>, SRP083394<sup>159,160</sup>, SRP083434<sup>160,161</sup>, SRP083901<sup>162,163</sup>,<br>SRP087715<sup>164,165</sup>, SRP090261<sup>166,167</sup>, SRP090335<sup>168,169</sup>, SRP090490<sup>170,171</sup>, SRP090651<sup>172,173</sup>, SRP091741<sup>174,175</sup>,<br>SRP091855<sup>176,177</sup>, SRP091867<sup>178,179</sup>, SRP092609<sup>180,181</sup>, SRP092777<sup>182,183</sup>, SRP093592<sup>184,185</sup>, SRP093928<sup>186,187</sup>,<br>SRP094708<sup>188-190</sup>, SRP097883<sup>191,192</sup>, SRP101553<sup>193,194</sup>, SRP101605<sup>195,196</sup>, SRP102378<sup>197,198</sup>, SRP102417<sup>199,200</sup>,<br>SRP102775<sup>201,202</sup>, SRP106137<sup>203,204</sup>, SRP106774<sup>205,206</sup>, SRP107174<sup>207,208</sup>, SRP107743<sup>209,210</sup>, SRP109164<sup>211,212</sup>,<br>SRP109773<sup>213,214</sup>, SRP110522<sup>215,216</sup>, SRP110810<sup>217,218</sup>, SRP113348<sup>219,220</sup>, SRP114697<sup>221,222</sup>, SRP114821<sup>223,224</sup>,<br>SRP115350<sup>225,226</sup>, SRP115464<sup>227,228</sup>, SRP115599<sup>229,230</sup>, SRP117302<sup>231,232</sup>, SRP118875<sup>233,234</sup>, SRP118960<sup>235,236</sup>,<br>SRP119174<sup>237,238</sup>, SRP125864<sup>239,240</sup>, SRP132277<sup>241,242</sup>, SRP132591<sup>243,244</sup>, SRP132598<sup>244,245</sup>, SRP136886<sup>246,247</sup>,<br>SRP139483<sup>248,249</sup>, SRP142723<sup>250,251</sup>, SRP148813<sup>252,253</sup>, SRP150527<sup>254,255</sup>, SRP151262<sup>256,257</sup>, SRP153934<sup>258,259</sup>,<br>SRP160913<sup>260,261</sup>, SRP161632<sup>262,263</sup>, SRP195764<sup>264,265</sup></td></tr><tr><td>European Nucleotide Archive<br>Sequence Read Archive</td><td>ERP001713<sup>266,267</sup>, ERP003251<sup>268,269</sup>, ERP003790<sup>270,271</sup>, ERP005177<sup>272,273</sup>, ERP005905<sup>274,275</sup>,<br>ERP009341<sup>276,277</sup>, ERP010027<sup>278,279</sup>, ERP010084<sup>280,281</sup>, ERP010743<sup>282,283</sup>, ERP011924<sup>284,285</sup>,<br>ERP012017<sup>286,287</sup>, ERP013208<sup>288,289</sup>, ERP013987<sup>290,291</sup>, ERP014227<sup>292,293</sup>, ERP017480<sup>294,295</sup>,<br>ERP017851<sup>296,297</sup>, ERP017915<sup>298,299</sup>, ERP019580<sup>300,301</sup>, ERP019924<sup>302,303</sup>, ERP020657<sup>304,305</sup>,<br>ERP022511<sup>306,307</sup>, ERP022742<sup>308,309</sup>, ERP023275<sup>310,311</sup>, ERP023718<sup>312,313</sup>, ERP023855<sup>314,315</sup>,<br>ERP106131<sup>316,317</sup>, ERP107634<sup>318,319</sup>, ERP107636<sup>319,320</sup>, ERP110188<sup>321,322</sup>, ERP112007<sup>323,324</sup></td></tr><tr><td>DNA Data Bank of Japan</td><td>DRA000926<sup>325,326</sup>, DRA000937<sup>327,328</sup>, DRA001737<sup>329,330</sup>, DRA002424<sup>331,332</sup>, DRA002469<sup>333,334</sup>,<br>DRA003024<sup>335,336</sup>, DRA003730<sup>337,338</sup>, DRA004913<sup>339,340</sup>, DRA006519<sup>341,342</sup>, DRP002783<sup>343,344</sup>,<br>DRP003138<sup>345,346</sup>, DRP005365<sup>347,348</sup></td></tr><tr><td>Dryad Digital Repository</td><td>10.5061/dryad.2fc32<sup>349,350</sup>, 10.5061/dryad.n82g9<sup>351,352</sup>, 10.5061/dryad.2343k<sup>353,354</sup>, 10.5061/dryad.gp302<sup>355,356</sup>, 10.5061/dryad.cq2rb<sup>357,358</sup>, 10.5061/dryad.8fn8j<sup>359,360</sup>, 10.5061/dryad.216p<sup>361,362</sup></td></tr><tr><td>GenBank</td><td>KAYV0000000.1<sup>363,364</sup>, KAYU0000000.1<sup>364,365</sup>, KAYT0000000.1<sup>364,366</sup>, SAMN02934078<sup>367,368</sup>,<br>SAMN02934079<sup>368,369</sup></td></tr><tr><td>Australian Antarctic Data<br>Center database</td><td>10.4225/15/526f42ada05b1<sup>370,371</sup></td></tr><tr><td>Supplemental Data</td><td>Hartmann et al. (2012)<sup>Supplementary_Data2,372</sup>, Rime et al. (2016)<sup>Fungi_SeqID,373</sup></td></tr></tbody></table>

corresponding SH or the corresponding sequence variants. It is also possible to view a breakdown of samples by type, biome, mean annual temperature, mean annual precipitation, pH, and continents. The results also contain an interactive map of the taxon distribution with relative abundances of sequences of the taxon across samples and a list of samples with metadata. Several modes of filtering of results are available as well.

In the sequence search, it is possible to search for multiple nucleotide sequences by choosing if the result will be the exact match or a BLAST result. The BLAST option gives the possibility to retrieve the sequence variant best hit in the database, or, when only one sequence is submitted, it is possible to display multiple ranked high score hits among the sequence variants.
<figure><img src="image_6.png" /><figcaption>Fig. 3 User interface to access the GlobalFungi database.</figcaption></figure>

It is also possible to open individual studies and access their content. Finally, in the Geosearch, users can select a group of samples on the map, with a range of tools, and retrieve data for these samples (such as the FASTA file with all occurring sequence variants).

Importantly, the database is intended to grow, both by the continuing activity of the authors and by using the help of the scientific community. For that, the “Submit your study” section of the web interface enabling the submission of studies not yet represented is available to users. The submission tool guides the submitting person through the steps where details about the publication, samples, sample metadata and sequences are sequentially submitted. The submitted data will be used to update the database twice a year after processing and validation by the authors. Thus, users submitting their data, besides a precious contribution to mycological progress, will benefit from making their data accessible to the international scientific community in an easily accessible form and increasing the visibility of their results. Users can also maximize their visibility by approving to add their name and affiliation to the online list of collaborators and/or to the GlobalFungi Group Author' list that will be mentioned in future publications describing the database content, its development, or metastudies using the whole database.

Among the possible uses of the GlobalFungi Database, fungal ecologists will be able to link fungal diversity data with the panel of collected metadata, which should allow them to determine the environmental factors driving the fungal diversity. This kind of study can be done at different geographic levels, from country scale up to the entire world, and for all the fungal communities or by focusing on some ecosystem compartments. This should lead to a better understanding of the biogeography of the fungal diversity. Větrovský et al.⁸ brought interesting findings by doing this for soil fungal communities at the scale of the globe. The evolutionary biologists could study, for example, the effect of global change on the fungal diversity by comparing the natural versus anthropogenic biomes. In addition to focus on the fungal diversity, some studies could trigger specific fungi. Thus, mycologists could determine the biogeography of one specific fungal species. They could also determine the composition of the fungal communities associated with the focused species and detect some potential recurrent fungal associations. The GlobalFungi Database could also speed up the progress in fungal taxonomy by highlighting the existence of a high number of fungal sequences not currently assigned to species along with environmental metadata promoting thus the interest in their description.

## Code availability

The workflow included several custom made python scripts (labelled by star in the Fig. 2) which are accessible here: https://github.com/VetrovskyTomas/GlobalFungi.

Received: 6 April 2020; Accepted: 5 June 2020;

Published: 13 July 2020

## References

1. Crowther, T. W. et al. Quantifying global soil carbon losses in response to warming. *Nature* **540**, 104–108 (2016).

2. Peay, K. G., Kennedy, P. G. & Talbot, J. M. Dimensions of biodiversity in the Earth mycobiome. *Nature Rev. Microbiol.* **14**, 434–447 (2016).

3. Wall, D. H., Nielsen, U. N. & Six, J. Soil biodiversity and human health. *Nature* **528**, 69–76 (2015).

4. Tedersoo, L. et al. Global diversity and geography of soil fungi. *Science* **346**, 1256–688 (2014).

5. Bahram, M. et al. Structure and function of the global topsoil microbiome. *Nature* **560**, 233–237 (2018).

6. Egidi, E. et al. A few Ascomycota taxa dominate soil fungal communities worldwide. *Nature Commun.* **10**, 2369 (2019).
<figure><img src="image_5.png" /><figcaption>Fig. 3 User interface to access the GlobalFungi database.</figcaption></figure>

It is also possible to open individual studies and access their content. Finally, in the Geosearch, users can select a group of samples on the map, with a range of tools, and retrieve data for these samples (such as the FASTA file with all occurring sequence variants).

Importantly, the database is intended to grow, both by the continuing activity of the authors and by using the help of the scientific community. For that, the “Submit your study” section of the web interface enabling the submission of studies not yet represented is available to users. The submission tool guides the submitting person through the steps where details about the publication, samples, sample metadata and sequences are sequentially submitted. The submitted data will be used to update the database twice a year after processing and validation by the authors. Thus, users submitting their data, besides a precious contribution to mycological progress, will benefit from making their data accessible to the international scientific community in an easily accessible form and increasing the visibility of their results. Users can also maximize their visibility by approving to add their name and affiliation to the online list of collaborators and/or to the GlobalFungi Group Author' list that will be mentioned in future publications describing the database content, its development, or metastudies using the whole database.

Among the possible uses of the GlobalFungi Database, fungal ecologists will be able to link fungal diversity data with the panel of collected metadata, which should allow them to determine the environmental factors driving the fungal diversity. This kind of study can be done at different geographic levels, from country scale up to the entire world, and for all the fungal communities or by focusing on some ecosystem compartments. This should lead to a better understanding of the biogeography of the fungal diversity. Větrovský et al.⁸ brought interesting findings by doing this for soil fungal communities at the scale of the globe. The evolutionary biologists could study, for example, the effect of global change on the fungal diversity by comparing the natural versus anthropogenic biomes. In addition to focus on the fungal diversity, some studies could trigger specific fungi. Thus, mycologists could determine the biogeography of one specific fungal species. They could also determine the composition of the fungal communities associated with the focused species and detect some potential recurrent fungal associations. The GlobalFungi Database could also speed up the progress in fungal taxonomy by highlighting the existence of a high number of fungal sequences not currently assigned to species along with environmental metadata promoting thus the interest in their description.

## Code availability

The workflow included several custom made python scripts (labelled by star in the Fig. 2) which are accessible here: https://github.com/VetrovskyTomas/GlobalFungi.

Received: 6 April 2020; Accepted: 5 June 2020;

Published: 13 July 2020

## References

1. Crowther, T. W. et al. Quantifying global soil carbon losses in response to warming. *Nature* **540**, 104–108 (2016).

2. Peay, K. G., Kennedy, P. G. & Talbot, J. M. Dimensions of biodiversity in the Earth mycobiome. *Nature Rev. Microbiol.* **14**, 434–447 (2016).

3. Wall, D. H., Nielsen, U. N. & Six, J. Soil biodiversity and human health. *Nature* **528**, 69–76 (2015).

4. Tedersoo, L. et al. Global diversity and geography of soil fungi. *Science* **346**, 1256–688 (2014).

5. Bahram, M. et al. Structure and function of the global topsoil microbiome. *Nature* **560**, 233–237 (2018).

6. Egidi, E. et al. A few Ascomycota taxa dominate soil fungal communities worldwide. *Nature Commun.* **10**, 2369 (2019).
7. Nilsson, R. H. et al. Mycobiome diversity: high-throughput sequencing and identification of fungi. *Nature Rev. Microbiol.* **17**, 95–109 (2019).

8. Větrovský, T. et al. A meta-analysis of global fungal distribution reveals climate-driven patterns. *Nature Commun.* **10**, 5142 (2019).

9. Vlk, L. et al. Early successional ectomycorrhizal fungi are more likely to naturalize outside their native range than other ectomycorrhizal fungi. *New Phytol.*, https://doi.org/10.1111/nph.16557 (2020).

10. Thompson, L. R. et al. A communal catalogue reveals Earth's multiscale microbial diversity. *Nature* **551**, 457–463 (2017).

11. Schoch, C. L. et al. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. *Proc. Natl. Acad. Sci. USA.* **109**, 6241–6246 (2012).

12. Nilsson, R. H. et al. The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications. *Nucleic Acids Res.* **47**, D259–D264 (2019).

13. Bengtsson-Palme, J. et al. Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data. *Meth. Ecol. Evol.* **4**, 914–919 (2013).

14. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. *J. Mol. Biol.* **215**, 403–410 (1990).

15. Karger, D. N. et al. Data Descriptor: Climatologies at high resolution for the earth's land surface areas. *Scientific Data* **4**, 170122 (2017).

16. Fick, S. E. & Hijmans, R. J. WorldClim 2: new 1-km spatial resolution climate surfaces for global land areas. *Int. J. Climatol.* **37**, 4302–4315 (2017).

17. Baldrian, P. et al. GlobalFungi: Global database of fungal records from high-throughput-sequencing metabarcoding studies. figshare https://doi.org/10.6084/m9.f figshare.c.4915392 (2020).

18. Anslan, S. et al. Great differences in performance and outcome of high-throughput sequencing data analysis platforms for fungal metabarcoding. *Myckeys* **39**, 29–40 (2018).

19. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP001058 (2010).

20. Jumpponen, A. & Jones, K. L. Seasonally dynamic fungal communities in the Quercus macrocarpa phyllosphere differ between urban and nonurban environments. *New Phytol.* **186**, 496–513 (2010).

21. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP001175 (2010).

22. Jumpponen, A., Jones, K. L., Mattox, J. D. & Yaege, C. Massively parallel 454-sequencing of fungal communities in Quercus spp ectomycorrhizas indicates seasonal dynamics in urban and rural sites. *Mol. Ecol.* **19**, 41–53 (2010).

23. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP006078 (2011).

24. Mello, A. et al. ITS-1 versus ITS-2 pyrosequencing: a comparison of fungal populations in truffle grounds. *Mycologia* **103**, 1184–1193 (2011).

25. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP012868 (2012).

26. Ihrmark, K. et al. New primers to amplify the fungal ITS2 region - evaluation by 454-sequencing of artificial and natural communities. *FEMS Microbiol. Ecol.* **82**, 666–677 (2012).

27. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP013695 (2012).

28. Zimmerman, N. B. & Vitousek, P. M. Fungal endophyte communities reflect environmental structuring across a Hawaiian landscape. *Proc. Natl. Acad. Sci. USA* **109**, 13022–13027 (2012).

29. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP013944 (2016).

30. Uroz, S. et al. Specific impacts of beech and Norway spruce on the structure and diversity of the rhizosphere and soil microbial communities. *Sci. Rep.* **6**, 27756 (2016).

31. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP015735 (2015).

32. Gao, C. et al. Community assembly of ectomycorrhizal fungi along a subtropical secondary forest succession. *New Phytol.* **205**, 771–785 (2015).

33. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP016090 (2015).

34. Clemmensen, K. E. et al. Carbon sequestration is related to mycorrhizal fungal community shifts during long-term succession in boreal forests. *New Phytol.* **205**, 1525–1536 (2015).

35. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP026207 (2014).

36. De Beeck, M. O. et al. Comparison and validation of some ITS primer pairs useful for fungal metabarcoding studies. *PLoS One* **9**, e97629 (2014).

37. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP028404 (2015).

38. De Beeck, M. O. et al. Impact of metal pollution on fungal diversity and community structures. *Environ. Microbiol.* **17**, 2035–2047 (2015).

39. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP033719 (2015).

40. Chaput, D. L., Hansel, C. M., Burgos, W. D. & Santelli, C. M. Profiling microbial communities in manganese remediation systems treating coal mine drainage. *Appl. Environ. Microbiol.* **81**, 2189–2198 (2015).

41. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP035356 (2015).

42. Sterkenburg, E., Bahr, A., Brandström Durling, M., Clemmensen, K. E. & Lindahl, B. D. Changes in fungal communities along a boreal forest soil fertility gradient. *New Phytol.* **207**, 1145–1158 (2015).

43. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP040314 (2014).

44. Talbot, J. M. et al. Endemism and functional convergence across the North American soil mycobiome. *Proc. Natl. Acad. Sci. USA.* **111**, 6341–6346 (2014).

45. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP040786 (2015).

46. Saravesi, K. et al. Moth outbreaks alter root-associated fungal communities in subarctic mountain birch forests. *Microb. Ecol.* **69**, 788–797 (2015).

47. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP041347 (2015).

48. Liu, J. et al. Soil carbon content drives the biogeographical distribution of fungal communities in the black soil zone of northeast China. *Soil Biol. Biochem.* **83**, 29–39 (2015).

49. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP043106 (2015).

50. Hoppe, B. et al. Linking molecular deadwood-inhabiting fungal diversity and community dynamics to ecosystem functions and processes in Central European forests. *Fungal Divers.* **77**, 367–379 (2015).

51. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP043706 (2017).

52. Hiiesalu, I., Bahram, M. & Tedersoo, L. Plant species richness and productivity determine the diversity of soil fungal guilds in temperate coniferous forest and bog habitats. *Mol. Ecol.* **26**, 4846–4858 (2017).

53. Tedersoo, L. et al. Tree diversity and species identity effects on soil fungi, protists and animals are context dependent. *ISME J.* **10**, 346–362 (2016).

54. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP043982 (2015).

55. Jarvis, S. G., Woodward, S. & Taylor, A. F. Strong altitudinal partitioning in the distributions of ectomycorrhizal fungi along a short (300 m) elevation gradient. *New Phytol.* **206**, 1145–1155 (2015).

56. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP044665 (2016).

57. Nacke, H. et al. Fine spatial scale variation of soil microbial communities under European Beech and Norway Spruce. *Front. Microbiol.* **7**, 2067 (2016).

58. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP045166 (2015).
7. Nilsson, R. H. et al. Mycobiome diversity: high-throughput sequencing and identification of fungi. *Nature Rev. Microbiol.* **17**, 95–109 (2019).

8. Větrovský, T. et al. A meta-analysis of global fungal distribution reveals climate-driven patterns. *Nature Commun.* **10**, 5142 (2019).

9. Vlk, L. et al. Early successional ectomycorrhizal fungi are more likely to naturalize outside their native range than other ectomycorrhizal fungi. *New Phytol.*, https://doi.org/10.1111/nph.16557 (2020).

10. Thompson, L. R. et al. A communal catalogue reveals Earth's multiscale microbial diversity. *Nature* **551**, 457–463 (2017).

11. Schoch, C. L. et al. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. *Proc. Natl. Acad. Sci. USA.* **109**, 6241–6246 (2012).

12. Nilsson, R. H. et al. The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications. *Nucleic Acids Res.* **47**, D259–D264 (2019).

13. Bengtsson-Palme, J. et al. Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data. *Meth. Ecol. Evol.* **4**, 914–919 (2013).

14. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. *J. Mol. Biol.* **215**, 403–410 (1990).

15. Karger, D. N. et al. Data Descriptor: Climatologies at high resolution for the earth's land surface areas. *Scientific Data* **4**, 170122 (2017).

16. Fick, S. E. & Hijmans, R. J. WorldClim 2: new 1-km spatial resolution climate surfaces for global land areas. *Int. J. Climatol.* **37**, 4302–4315 (2017).

17. Baldrian, P. et al. GlobalFungi: Global database of fungal records from high-throughput-sequencing metabarcoding studies. figshare https://doi.org/10.6084/m9.f figshare.c.4915392 (2020).

18. Anslan, S. et al. Great differences in performance and outcome of high-throughput sequencing data analysis platforms for fungal metabarcoding. *Myckeys* **39**, 29–40 (2018).

19. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP001058 (2010).

20. Jumpponen, A. & Jones, K. L. Seasonally dynamic fungal communities in the Quercus macrocarpa phyllosphere differ between urban and nonurban environments. *New Phytol.* **186**, 496–513 (2010).

21. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP001175 (2010).

22. Jumpponen, A., Jones, K. L., Mattox, J. D. & Yaege, C. Massively parallel 454-sequencing of fungal communities in Quercus spp ectomycorrhizas indicates seasonal dynamics in urban and rural sites. *Mol. Ecol.* **19**, 41–53 (2010).

23. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP006078 (2011).

24. Mello, A. et al. ITS-1 versus ITS-2 pyrosequencing: a comparison of fungal populations in truffle grounds. *Mycologia* **103**, 1184–1193 (2011).

25. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP012868 (2012).

26. Ihrmark, K. et al. New primers to amplify the fungal ITS2 region - evaluation by 454-sequencing of artificial and natural communities. *FEMS Microbiol. Ecol.* **82**, 666–677 (2012).

27. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP013695 (2012).

28. Zimmerman, N. B. & Vitousek, P. M. Fungal endophyte communities reflect environmental structuring across a Hawaiian landscape. *Proc. Natl. Acad. Sci. USA* **109**, 13022–13027 (2012).

29. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP013944 (2016).

30. Uroz, S. et al. Specific impacts of beech and Norway spruce on the structure and diversity of the rhizosphere and soil microbial communities. *Sci. Rep.* **6**, 27756 (2016).

31. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP015735 (2015).

32. Gao, C. et al. Community assembly of ectomycorrhizal fungi along a subtropical secondary forest succession. *New Phytol.* **205**, 771–785 (2015).

33. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP016090 (2015).

34. Clemmensen, K. E. et al. Carbon sequestration is related to mycorrhizal fungal community shifts during long-term succession in boreal forests. *New Phytol.* **205**, 1525–1536 (2015).

35. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP026207 (2014).

36. De Beeck, M. O. et al. Comparison and validation of some ITS primer pairs useful for fungal metabarcoding studies. *PLoS One* **9**, e97629 (2014).

37. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP028404 (2015).

38. De Beeck, M. O. et al. Impact of metal pollution on fungal diversity and community structures. *Environ. Microbiol.* **17**, 2035–2047 (2015).

39. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP033719 (2015).

40. Chaput, D. L., Hansel, C. M., Burgos, W. D. & Santelli, C. M. Profiling microbial communities in manganese remediation systems treating coal mine drainage. *Appl. Environ. Microbiol.* **81**, 2189–2198 (2015).

41. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP035356 (2015).

42. Sterkenburg, E., Bahr, A., Brandström Durling, M., Clemmensen, K. E. & Lindahl, B. D. Changes in fungal communities along a boreal forest soil fertility gradient. *New Phytol.* **207**, 1145–1158 (2015).

43. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP040314 (2014).

44. Talbot, J. M. et al. Endemism and functional convergence across the North American soil mycobiome. *Proc. Natl. Acad. Sci. USA.* **111**, 6341–6346 (2014).

45. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP040786 (2015).

46. Saravesi, K. et al. Moth outbreaks alter root-associated fungal communities in subarctic mountain birch forests. *Microb. Ecol.* **69**, 788–797 (2015).

47. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP041347 (2015).

48. Liu, J. et al. Soil carbon content drives the biogeographical distribution of fungal communities in the black soil zone of northeast China. *Soil Biol. Biochem.* **83**, 29–39 (2015).

49. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP043106 (2015).

50. Hoppe, B. et al. Linking molecular deadwood-inhabiting fungal diversity and community dynamics to ecosystem functions and processes in Central European forests. *Fungal Divers.* **77**, 367–379 (2015).

51. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP043706 (2017).

52. Hiiesalu, I., Bahram, M. & Tedersoo, L. Plant species richness and productivity determine the diversity of soil fungal guilds in temperate coniferous forest and bog habitats. *Mol. Ecol.* **26**, 4846–4858 (2017).

53. Tedersoo, L. et al. Tree diversity and species identity effects on soil fungi, protists and animals are context dependent. *ISME J.* **10**, 346–362 (2016).

54. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP043982 (2015).

55. Jarvis, S. G., Woodward, S. & Taylor, A. F. Strong altitudinal partitioning in the distributions of ectomycorrhizal fungi along a short (300 m) elevation gradient. *New Phytol.* **206**, 1145–1155 (2015).

56. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP044665 (2016).

57. Nacke, H. et al. Fine spatial scale variation of soil microbial communities under European Beech and Norway Spruce. *Front. Microbiol.* **7**, 2067 (2016).

58. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP045166 (2015).
59. Rincón, A. et al. Compartmentalized and contrasted response of ectomycorrhizal and soil fungal communities of Scots pine forests along elevation gradients in France and Spain. *Environ. Microbiol.* **17**, 3009–3024 (2015).

60. *NCBI Sequence Read Archive* https://identifiers.org/ncbi/insdc.sra:SRP045587 (2016).

61. Bahram, M. et al. Stochastic distribution of small soil eukaryotes resulting from high dispersal and drift in a local environment. *ISME J.* **10**, 885–896 (2016).

62. *NCBI Sequence Read Archive* https://identifiers.org/ncbi/insdc.sra:SRP045746 (2014).

63. Walker, D. M. et al. A metagenomics-based approach to the top-down effect on the detritivore food web: a salamanders influence on fungal communities within a deciduous forest. *Ecol. Evol.* **4**, 4106–4116 (2014).

64. *NCBI Sequence Read Archive* https://identifiers.org/ncbi/insdc.sra:SRP045933 (2015).

65. Zhang, T., Wei, X. L., Zhang, Y. Q., Liu, H. Y. & Yu, L. Y. Diversity and distribution of lichen-associated fungi in the Ny-Alesund Region (Svalbard, High Arctic) as revealed by 454 pyrosequencing. *Sci. Rep.* **5**, 14850 (2015).

66. *NCBI Sequence Read Archive* https://identifiers.org/ncbi/insdc.sra:SRP046049 (2016).

67. Oh, S. Y., Fong, J. J., Park, M. S. & Lim, Y. W. Distinctive feature of microbial communities and bacterial functional profiles in Tricholoma matsutake dominant soil. *PLoS One* **11**, e0168573 (2016).

68. *NCBI Sequence Read Archive* https://identifiers.org/ncbi/insdc.sra:SRP048036 (2016).

69. Yang, T. et al. Carbon constrains fungal endophyte assemblages along the timberline. *Environ. Microbiol.* **18**, 2455–2469 (2016).

70. Yang, T., Sun, H., Shen, C. & Chu, H. Fungal assemblages in different habitats in an Erman's Birch forest. *Front. Microbiol.* **7**, 1368 (2016).

71. *NCBI Sequence Read Archive* https://identifiers.org/ncbi/insdc.sra:SRP048856 (2015).

72. Elliott, D. R., Caporn, S. J., Nwaishi, F., Nilsson, R. H. & Sen, R. Bacterial and fungal communities in a degraded ombrotrophic peatland undergoing natural and managed re-vegetation. *PLoS One* **10**, e0124726 (2015).

73. *NCBI Sequence Read Archive* https://identifiers.org/ncbi/insdc.sra:SRP049544 (2015).

74. Goldmann, K., Schöning, I., Buscot, F. & Wubet, T. Forest management type influences diversity and community composition of soil fungi across temperate forest ecosystems. *Front. Microbiol.* **6**, 1300 (2015).

75. *NCBI Sequence Read Archive* https://identifiers.org/ncbi/insdc.sra:SRP051033 (2016).

76. Roy-Bolduc, A., Laliberté, E., Boudreau, S. & Hijri, M. Strong linkage between plant and soil fungal communities along a successional coastal dune system. *FEMS Microbiol. Ecol.* **92**, fiv156 (2016).

77. *NCBI Sequence Read Archive* https://identifiers.org/ncbi/insdc.sra:SRP052222 (2017).

78. Fernández-Martinez, M. A. et al. Microbial succession dynamics along glacier forefield chronosequences in Tierra del Fuego (Chile). *Polar Biol.* **40**, 1939–1957 (2017).

79. *NCBI Sequence Read Archive* https://identifiers.org/ncbi/insdc.sra:SRP052716 (2015).

80. Leff, J. W. et al. Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe. *Proc. Natl. Acad. Sci. USA* **112**, 10967–10972 (2015).

81. *NCBI Sequence Read Archive* https://identifiers.org/ncbi/insdc.sra:SRP055957 (2015).

82. Tedersoo, L. et al. Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi. *MycKeYs* **10**, 1–43 (2015).

83. *NCBI Sequence Read Archive* https://identifiers.org/ncbi/insdc.sra:SRP057433 (2016).

84. Wang, W., Zhai, Y., Cao, L., Tan, H. & Zhang, R. Endophytic bacterial and fungal microbiota in sprouts, roots and stems of rice (Oryza sativa L.). *Microbiol. Res.* **188**, 1–8 (2016).

85. *NCBI Sequence Read Archive* https://identifiers.org/ncbi/insdc.sra:SRP057541 (2016).

86. Waring, B. G., Adams, R., Branco, S. & Powers, J. S. Scale-dependent variation in nitrogen cycling and soil fungal communities along gradients of forest composition and age in regenerating tropical dry forests. *New Phytol.* **209**, 845–854 (2016).

87. *NCBI Sequence Read Archive* https://identifiers.org/ncbi/insdc.sra:SRP058508 (2016).

88. Glassman, S. I., Levine, C. R., DiRocco, A. M., Battles, J. J. & Bruns, T. D. Ectomycorrhizal fungal spore bank recovery after a severe forest fire: some like it hot. *ISME J.* **10**, 1228–1239 (2016).

89. *NCBI Sequence Read Archive* https://identifiers.org/ncbi/insdc.sra:SRP058555 (2016).

90. De Gannes, V. et al. Microbial community structure and function of soil following ecosystem conversion from native forests to Teak plantation forests. *Front. Microbiol.* **7**, 1976 (2016).

91. *NCBI Sequence Read Archive* https://identifiers.org/ncbi/insdc.sra:SRP058851 (2018).

92. Bach, E. M., Williams, R. J., Hargreaves, S. K., Yang, F. & Hofmockel, K. S. Greatest soil microbial diversity found in micro-habitats. *Soil Biol. Biochem.* **118**, 217–226 (2018).

93. *NCBI Sequence Read Archive* https://identifiers.org/ncbi/insdc.sra:SRP059280 (2016).

94. Roy-Bolduc, A., Laliberté, E. & Hijri, M. High richness of ectomycorrhizal fungi and low host specificity in a coastal sand dune ecosystem revealed by network analysis. *Ecol. Evol.* **6**, 349–362 (2016).

95. *NCBI Sequence Read Archive* https://identifiers.org/ncbi/insdc.sra:SRP060838 (2016).

96. He, F. et al. Changes in composition and diversity of fungal communities along Quercus mongolica forests developments in Northeast China. *Appl. Soil Ecol.* **100**, 162–171 (2016).

97. *NCBI Sequence Read Archive* https://identifiers.org/ncbi/insdc.sra:SRP061179 (2016).

98. Valverde, A. et al. Specific microbial communities associate with the rhizosphere of Welwitschia mirabilis, a living fossil. *PLoS One* **11**, e0153353 (2016).

99. *NCBI Sequence Read Archive* https://identifiers.org/ncbi/insdc.sra:SRP061305 (2017).

100. Yao, F. et al. Microbial taxa distribution is associated with ecological trophic cascades along an elevation gradient. *Front. Microbiol.* **8**, 2071 (2017).

101. *NCBI Sequence Read Archive* https://identifiers.org/ncbi/insdc.sra:SRP061904 (2015).

102. Veach, A. M., Dodds, W. K. & Jumpponen, A. Woody plant encroachment, and its removal, impact bacterial and fungal communities across stream and terrestrial habitats in a tallgrass prairie ecosystem. *FEMS Microbiol. Ecol.* **91**, fiv109 (2015).

103. *NCBI Sequence Read Archive* https://identifiers.org/ncbi/insdc.sra:SRP062647 (2016).

104. Newsham, K. K. et al. Relationship between soil fungal diversity and temperature in the maritime Antarctic. *Nat. Clim. Change* **6**, 182 (2016).

105. *NCBI Sequence Read Archive* https://identifiers.org/ncbi/insdc.sra:SRP063711 (2017).

106. Poosakkannu, A., Nissinen, R., Männistö, M. & Kytöviita, M. M. Microbial community composition but not diversity changes along succession in arctic sand dunes. *Environ. Microbiol.* **19**, 698–709 (2017).

107. *NCBI Sequence Read Archive* https://identifiers.org/ncbi/insdc.sra:SRP064158 (2017).

108. Tian, J. et al. Patterns and drivers of fungal diversity along an altitudinal gradient on Mount Gongga, China. *J. Soil. Sediment.* **17**, 2856–2865 (2017).

109. *NCBI Sequence Read Archive* https://identifiers.org/ncbi/insdc.sra:SRP065817 (2017).

110. Zhang, W., Lu, Z., Yang, K. & Zhu, J. Impacts of conversion from secondary forests to larch plantations on the structure and function of microbial communities. *Appl. Soil Ecol.* **111**, 73–83 (2017).

111. *NCBI Sequence Read Archive* https://identifiers.org/ncbi/insdc.sra:SRP066030 (2016).

112. Porter, T. M., Shokralla, S., Baird, D., Golding, G. B. & Hajibabaei, M. Ribosomal DNA and plastid markers used to sample fungal and plant communities from wetland soils reveals complementary biotas. *PLoS One* **11**, e0142759 (2016).
59. Rincón, A. et al. Compartmentalized and contrasted response of ectomycorrhizal and soil fungal communities of Scots pine forests along elevation gradients in France and Spain. *Environ. Microbiol.* **17**, 3009–3024 (2015).

60. *NCBI Sequence Read Archive* https://identifiers.org/ncbi/insdc.sra:SRP045587 (2016).

61. Bahram, M. et al. Stochastic distribution of small soil eukaryotes resulting from high dispersal and drift in a local environment. *ISME J.* **10**, 885–896 (2016).

62. *NCBI Sequence Read Archive* https://identifiers.org/ncbi/insdc.sra:SRP045746 (2014).

63. Walker, D. M. et al. A metagenomics-based approach to the top-down effect on the detritivore food web: a salamanders influence on fungal communities within a deciduous forest. *Ecol. Evol.* **4**, 4106–4116 (2014).

64. *NCBI Sequence Read Archive* https://identifiers.org/ncbi/insdc.sra:SRP045933 (2015).

65. Zhang, T., Wei, X. L., Zhang, Y. Q., Liu, H. Y. & Yu, L. Y. Diversity and distribution of lichen-associated fungi in the Ny-Alesund Region (Svalbard, High Arctic) as revealed by 454 pyrosequencing. *Sci. Rep.* **5**, 14850 (2015).

66. *NCBI Sequence Read Archive* https://identifiers.org/ncbi/insdc.sra:SRP046049 (2016).

67. Oh, S. Y., Fong, J. J., Park, M. S. & Lim, Y. W. Distinctive feature of microbial communities and bacterial functional profiles in Tricholoma matsutake dominant soil. *PLoS One* **11**, e0168573 (2016).

68. *NCBI Sequence Read Archive* https://identifiers.org/ncbi/insdc.sra:SRP048036 (2016).

69. Yang, T. et al. Carbon constrains fungal endophyte assemblages along the timberline. *Environ. Microbiol.* **18**, 2455–2469 (2016).

70. Yang, T., Sun, H., Shen, C. & Chu, H. Fungal assemblages in different habitats in an Erman's Birch forest. *Front. Microbiol.* **7**, 1368 (2016).

71. *NCBI Sequence Read Archive* https://identifiers.org/ncbi/insdc.sra:SRP048856 (2015).

72. Elliott, D. R., Caporn, S. J., Nwaishi, F., Nilsson, R. H. & Sen, R. Bacterial and fungal communities in a degraded ombrotrophic peatland undergoing natural and managed re-vegetation. *PLoS One* **10**, e0124726 (2015).

73. *NCBI Sequence Read Archive* https://identifiers.org/ncbi/insdc.sra:SRP049544 (2015).

74. Goldmann, K., Schöning, I., Buscot, F. & Wubet, T. Forest management type influences diversity and community composition of soil fungi across temperate forest ecosystems. *Front. Microbiol.* **6**, 1300 (2015).

75. *NCBI Sequence Read Archive* https://identifiers.org/ncbi/insdc.sra:SRP051033 (2016).

76. Roy-Bolduc, A., Laliberté, E., Boudreau, S. & Hijri, M. Strong linkage between plant and soil fungal communities along a successional coastal dune system. *FEMS Microbiol. Ecol.* **92**, fiv156 (2016).

77. *NCBI Sequence Read Archive* https://identifiers.org/ncbi/insdc.sra:SRP052222 (2017).

78. Fernández-Martinez, M. A. et al. Microbial succession dynamics along glacier forefield chronosequences in Tierra del Fuego (Chile). *Polar Biol.* **40**, 1939–1957 (2017).

79. *NCBI Sequence Read Archive* https://identifiers.org/ncbi/insdc.sra:SRP052716 (2015).

80. Leff, J. W. et al. Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe. *Proc. Natl. Acad. Sci. USA* **112**, 10967–10972 (2015).

81. *NCBI Sequence Read Archive* https://identifiers.org/ncbi/insdc.sra:SRP055957 (2015).

82. Tedersoo, L. et al. Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi. *MycKeYs* **10**, 1–43 (2015).

83. *NCBI Sequence Read Archive* https://identifiers.org/ncbi/insdc.sra:SRP057433 (2016).

84. Wang, W., Zhai, Y., Cao, L., Tan, H. & Zhang, R. Endophytic bacterial and fungal microbiota in sprouts, roots and stems of rice (Oryza sativa L.). *Microbiol. Res.* **188**, 1–8 (2016).

85. *NCBI Sequence Read Archive* https://identifiers.org/ncbi/insdc.sra:SRP057541 (2016).

86. Waring, B. G., Adams, R., Branco, S. & Powers, J. S. Scale-dependent variation in nitrogen cycling and soil fungal communities along gradients of forest composition and age in regenerating tropical dry forests. *New Phytol.* **209**, 845–854 (2016).

87. *NCBI Sequence Read Archive* https://identifiers.org/ncbi/insdc.sra:SRP058508 (2016).

88. Glassman, S. I., Levine, C. R., DiRocco, A. M., Battles, J. J. & Bruns, T. D. Ectomycorrhizal fungal spore bank recovery after a severe forest fire: some like it hot. *ISME J.* **10**, 1228–1239 (2016).

89. *NCBI Sequence Read Archive* https://identifiers.org/ncbi/insdc.sra:SRP058555 (2016).

90. De Gannes, V. et al. Microbial community structure and function of soil following ecosystem conversion from native forests to Teak plantation forests. *Front. Microbiol.* **7**, 1976 (2016).

91. *NCBI Sequence Read Archive* https://identifiers.org/ncbi/insdc.sra:SRP058851 (2018).

92. Bach, E. M., Williams, R. J., Hargreaves, S. K., Yang, F. & Hofmockel, K. S. Greatest soil microbial diversity found in micro-habitats. *Soil Biol. Biochem.* **118**, 217–226 (2018).

93. *NCBI Sequence Read Archive* https://identifiers.org/ncbi/insdc.sra:SRP059280 (2016).

94. Roy-Bolduc, A., Laliberté, E. & Hijri, M. High richness of ectomycorrhizal fungi and low host specificity in a coastal sand dune ecosystem revealed by network analysis. *Ecol. Evol.* **6**, 349–362 (2016).

95. *NCBI Sequence Read Archive* https://identifiers.org/ncbi/insdc.sra:SRP060838 (2016).

96. He, F. et al. Changes in composition and diversity of fungal communities along Quercus mongolica forests developments in Northeast China. *Appl. Soil Ecol.* **100**, 162–171 (2016).

97. *NCBI Sequence Read Archive* https://identifiers.org/ncbi/insdc.sra:SRP061179 (2016).

98. Valverde, A. et al. Specific microbial communities associate with the rhizosphere of Welwitschia mirabilis, a living fossil. *PLoS One* **11**, e0153353 (2016).

99. *NCBI Sequence Read Archive* https://identifiers.org/ncbi/insdc.sra:SRP061305 (2017).

100. Yao, F. et al. Microbial taxa distribution is associated with ecological trophic cascades along an elevation gradient. *Front. Microbiol.* **8**, 2071 (2017).

101. *NCBI Sequence Read Archive* https://identifiers.org/ncbi/insdc.sra:SRP061904 (2015).

102. Veach, A. M., Dodds, W. K. & Jumpponen, A. Woody plant encroachment, and its removal, impact bacterial and fungal communities across stream and terrestrial habitats in a tallgrass prairie ecosystem. *FEMS Microbiol. Ecol.* **91**, fiv109 (2015).

103. *NCBI Sequence Read Archive* https://identifiers.org/ncbi/insdc.sra:SRP062647 (2016).

104. Newsham, K. K. et al. Relationship between soil fungal diversity and temperature in the maritime Antarctic. *Nat. Clim. Change* **6**, 182 (2016).

105. *NCBI Sequence Read Archive* https://identifiers.org/ncbi/insdc.sra:SRP063711 (2017).

106. Poosakkannu, A., Nissinen, R., Männistö, M. & Kytöviita, M. M. Microbial community composition but not diversity changes along succession in arctic sand dunes. *Environ. Microbiol.* **19**, 698–709 (2017).

107. *NCBI Sequence Read Archive* https://identifiers.org/ncbi/insdc.sra:SRP064158 (2017).

108. Tian, J. et al. Patterns and drivers of fungal diversity along an altitudinal gradient on Mount Gongga, China. *J. Soil. Sediment.* **17**, 2856–2865 (2017).

109. *NCBI Sequence Read Archive* https://identifiers.org/ncbi/insdc.sra:SRP065817 (2017).

110. Zhang, W., Lu, Z., Yang, K. & Zhu, J. Impacts of conversion from secondary forests to larch plantations on the structure and function of microbial communities. *Appl. Soil Ecol.* **111**, 73–83 (2017).

111. *NCBI Sequence Read Archive* https://identifiers.org/ncbi/insdc.sra:SRP066030 (2016).

112. Porter, T. M., Shokralla, S., Baird, D., Golding, G. B. & Hajibabaei, M. Ribosomal DNA and plastid markers used to sample fungal and plant communities from wetland soils reveals complementary biotas. *PLoS One* **11**, e0142759 (2016).
113. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP066284 (2017).

114. Wang, M. et al. Influence of Peanut cultivars and environmental conditions on the diversity and community composition of Pod Rot soil fungi in China. *Mycobiology* **45**, 392–400 (2017).

115. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP066331 (2017).

116. Delgado-Baquerizo, M. et al. Soil microbial communities drive the resistance of ecosystem multifunctionality to global change in drylands across the globe. *Ecol. Lett.* **20**, 1295–1305 (2017).

117. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP067301 (2017).

118. Cross, H. et al. Fungal diversity and seasonal succession in ash leaves infected by the invasive ascomycete Hymenoscyphus fraxineus. *New Phytol.* **213**, 1405–1417 (2017).

119. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP067367 (2016).

120. Zhang, T., Wang, N. F., Liu, H. Y., Zhang, Y. Q. & Yu, L. Y. Soil pH is a key determinant of soil fungal community composition in the Ny-Alesund region, Svalbard (High Arctic). *Front. Microbiol.* **7**, 227 (2016).

121. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP068514 (2016).

122. Gehring, C. A. et al. Cheatgrass invasion alters the abundance and composition of dark septate fungal communities in sagebrush steppe. *Botany* **94**, 481–491 (2016).

123. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP068608 (2016).

124. Li, Y. et al. Changes of soil microbial community under different degraded gradients of alpine meadow. *Agric. Ecosyst. Environ.* **222**, 213–222 (2016).

125. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP068620 (2016).

126. Zhou, J. et al. Temperature mediates continental-scale diversity of microbes in forest soils. *Nat. Commun.* **7**, 12083 (2016).

127. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP068654 (2016).

128. Cox, F., Newsham, K. K., Bol, R., Dungait, J. A. & Robinson, C. H. Not poles apart: Antarctic soil fungal communities show similarities to those of the distant Arctic. *Ecol. Lett.* **19**, 528–536 (2016).

129. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP069065 (2017).

130. Bergottini, V. M. et al. Exploring the diversity of the root-associated microbiome of Ilex paraguariensis St. Hil. (Yerba Mate). *Appl. Soil Ecol.* **109**, 23–31 (2017).

131. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP069742 (2017).

132. Moussa, T. A., Al-Zahrani, H. S., Almaghrabi, O. A., Abdelmoneim, T. S. & Fuller, M. P. Comparative metagenomics approaches to characterize the soil fungal communities of western coastal region, Saudi Arabia. *PLoS One* **12**, e0185096 (2017).

133. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP070568 (2016).

134. Goldmann, K. et al. Divergent habitat filtering of root and soil fungal communities in temperate beech forests. *Sci. Rep.* **11**, 31439 (2016).

135. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP073070 (2016).

136. Liu, C. et al. The influence of soil properties on the size and structure of bacterial and fungal communities along a paddy soil chronosequence. *Eur. J. Soil Biol.* **76**, 9–18 (2016).

137. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP073265 (2017).

138. Smith, M. E. et al. Investigating niche partitioning of ectomycorrhizal fungi in specialized rooting zones of the monodominant leguminous tree Dicymbe corymbosa. *New Phytol.* **215**, 443–453 (2017).

139. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP074055 (2016).

140. Bissett, A. et al. Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database. *GigaScience* **5**, 21 (2016).

141. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP074496 (2016).

142. Vannette, R. L., Leopold, D. R. & Fukami, T. Forest area and connectivity influence root-associated fungal communities in a fragmented landscape. *Ecology* **97**, 2374–2383 (2016).

143. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP075989 (2017).

144. Zhou, X. et al. Rhizospheric fungi and their link with the nitrogen-fixing Frankia harbored in host plant Hippophae rhamnoides L. *J. Basic Microbiol.* **57**, 1055–1064 (2017).

145. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP079403 (2017).

146. Glassman, S. I., Wang, I. J. & Bruns, T. D. Environmental filtering by pH and soil nutrients drives community assembly in fungi at fine spatial scales. *Mol. Ecol.* **26**, 6960–6973 (2017).

147. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP079521 (2018).

148. Cline, L. C., Schilling, J. S., Menke, J., Groenhof, E. & Kennedy, P. G. Ecological and functional effects of fungal endophytes on wood decomposition. *Funct. Ecol.* **32**, 181–191 (2018).

149. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP080210 (2016).

150. Johansen, R. B. et al. A native and an invasive dune grass share similar, patchily distributed, root-associated fungal communities. *Fungal Ecol.* **23**, 141–155 (2016).

151. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP080428 (2017).

152. Zhang, S., Chen, X., Zhong, Q., Huang, Z. & Bai, Z. Relations among epiphytic microbial communities from soil, leaves and grapes of the grapevine. *Front. Life Sci.* **10**, 73–83 (2017).

153. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP080680 (2017).

154. Fernandez, C. W. et al. Ectomycorrhizal fungal response to warming is linked to poor host performance at the boreal-temperate ecotone. *Glob. Change Biol.* **23**, 1598–1609 (2017).

155. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP082472 (2017).

156. Zhang, Z. et al. Fungal communities in ancient peatlands developed from different periods in the Sanjiang Plain, China. *PLoS One* **12**, e0187575 (2017).

157. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP082976 (2017).

158. Gomes, S. I., Merckx, V. S. & Saavedra, S. Fungal-host diversity among mycoheterotrophic plants increases proportionally to their fungal-host overlap. *Ecol. Evol.* **7**, 3623–3630 (2017).

159. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP083394 (2017).

160. Zhou, X. et al. Conversion from long-term cultivated wheat field to Jerusalem artichoke plantation changed soil fungal communities. *Sci. Rep.* **7**, 41502 (2017).

161. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP083434 (2017).

162. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP083901 (2017).

163. Gomes, S. I., Aguirre-Gutiérrez, J., Bidartondo, M. I. & Merckx, V. S. Arbuscular mycorrhizal interactions of mycoheterotrophic Thismia are more specialized than in autotrophic plants. *New Phytol.* **213**, 1418–1427 (2017).

164. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP087715 (2017).

165. Tian, H. et al. Changes in soil microbial communities after 10 years of winter wheat cultivation versus fallow in an organic-poor soil in the Loess Plateau of China. *PLoS One* **12**, e0184223 (2017).

166. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP090261 (2016).

167. Gourmelon, V. et al. Environmental and geographical factors structure soil microbial diversity in New Caledonian ultramafic substrates: a metagenomic approach. *PLoS One* **11**, e0167405 (2016).
113. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP066284 (2017).

114. Wang, M. et al. Influence of Peanut cultivars and environmental conditions on the diversity and community composition of Pod Rot soil fungi in China. *Mycobiology* **45**, 392–400 (2017).

115. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP066331 (2017).

116. Delgado-Baquerizo, M. et al. Soil microbial communities drive the resistance of ecosystem multifunctionality to global change in drylands across the globe. *Ecol. Lett.* **20**, 1295–1305 (2017).

117. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP067301 (2017).

118. Cross, H. et al. Fungal diversity and seasonal succession in ash leaves infected by the invasive ascomycete Hymenoscyphus fraxineus. *New Phytol.* **213**, 1405–1417 (2017).

119. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP067367 (2016).

120. Zhang, T., Wang, N. F., Liu, H. Y., Zhang, Y. Q. & Yu, L. Y. Soil pH is a key determinant of soil fungal community composition in the Ny-Alesund region, Svalbard (High Arctic). *Front. Microbiol.* **7**, 227 (2016).

121. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP068514 (2016).

122. Gehring, C. A. et al. Cheatgrass invasion alters the abundance and composition of dark septate fungal communities in sagebrush steppe. *Botany* **94**, 481–491 (2016).

123. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP068608 (2016).

124. Li, Y. et al. Changes of soil microbial community under different degraded gradients of alpine meadow. *Agric. Ecosyst. Environ.* **222**, 213–222 (2016).

125. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP068620 (2016).

126. Zhou, J. et al. Temperature mediates continental-scale diversity of microbes in forest soils. *Nat. Commun.* **7**, 12083 (2016).

127. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP068654 (2016).

128. Cox, F., Newsham, K. K., Bol, R., Dungait, J. A. & Robinson, C. H. Not poles apart: Antarctic soil fungal communities show similarities to those of the distant Arctic. *Ecol. Lett.* **19**, 528–536 (2016).

129. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP069065 (2017).

130. Bergottini, V. M. et al. Exploring the diversity of the root-associated microbiome of Ilex paraguariensis St. Hil. (Yerba Mate). *Appl. Soil Ecol.* **109**, 23–31 (2017).

131. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP069742 (2017).

132. Moussa, T. A., Al-Zahrani, H. S., Almaghrabi, O. A., Abdelmoneim, T. S. & Fuller, M. P. Comparative metagenomics approaches to characterize the soil fungal communities of western coastal region, Saudi Arabia. *PLoS One* **12**, e0185096 (2017).

133. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP070568 (2016).

134. Goldmann, K. et al. Divergent habitat filtering of root and soil fungal communities in temperate beech forests. *Sci. Rep.* **11**, 31439 (2016).

135. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP073070 (2016).

136. Liu, C. et al. The influence of soil properties on the size and structure of bacterial and fungal communities along a paddy soil chronosequence. *Eur. J. Soil Biol.* **76**, 9–18 (2016).

137. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP073265 (2017).

138. Smith, M. E. et al. Investigating niche partitioning of ectomycorrhizal fungi in specialized rooting zones of the monodominant leguminous tree Dicymbe corymbosa. *New Phytol.* **215**, 443–453 (2017).

139. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP074055 (2016).

140. Bissett, A. et al. Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database. *GigaScience* **5**, 21 (2016).

141. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP074496 (2016).

142. Vannette, R. L., Leopold, D. R. & Fukami, T. Forest area and connectivity influence root-associated fungal communities in a fragmented landscape. *Ecology* **97**, 2374–2383 (2016).

143. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP075989 (2017).

144. Zhou, X. et al. Rhizospheric fungi and their link with the nitrogen-fixing Frankia harbored in host plant Hippophae rhamnoides L. *J. Basic Microbiol.* **57**, 1055–1064 (2017).

145. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP079403 (2017).

146. Glassman, S. I., Wang, I. J. & Bruns, T. D. Environmental filtering by pH and soil nutrients drives community assembly in fungi at fine spatial scales. *Mol. Ecol.* **26**, 6960–6973 (2017).

147. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP079521 (2018).

148. Cline, L. C., Schilling, J. S., Menke, J., Groenhof, E. & Kennedy, P. G. Ecological and functional effects of fungal endophytes on wood decomposition. *Funct. Ecol.* **32**, 181–191 (2018).

149. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP080210 (2016).

150. Johansen, R. B. et al. A native and an invasive dune grass share similar, patchily distributed, root-associated fungal communities. *Fungal Ecol.* **23**, 141–155 (2016).

151. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP080428 (2017).

152. Zhang, S., Chen, X., Zhong, Q., Huang, Z. & Bai, Z. Relations among epiphytic microbial communities from soil, leaves and grapes of the grapevine. *Front. Life Sci.* **10**, 73–83 (2017).

153. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP080680 (2017).

154. Fernandez, C. W. et al. Ectomycorrhizal fungal response to warming is linked to poor host performance at the boreal-temperate ecotone. *Glob. Change Biol.* **23**, 1598–1609 (2017).

155. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP082472 (2017).

156. Zhang, Z. et al. Fungal communities in ancient peatlands developed from different periods in the Sanjiang Plain, China. *PLoS One* **12**, e0187575 (2017).

157. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP082976 (2017).

158. Gomes, S. I., Merckx, V. S. & Saavedra, S. Fungal-host diversity among mycoheterotrophic plants increases proportionally to their fungal-host overlap. *Ecol. Evol.* **7**, 3623–3630 (2017).

159. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP083394 (2017).

160. Zhou, X. et al. Conversion from long-term cultivated wheat field to Jerusalem artichoke plantation changed soil fungal communities. *Sci. Rep.* **7**, 41502 (2017).

161. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP083434 (2017).

162. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP083901 (2017).

163. Gomes, S. I., Aguirre-Gutiérrez, J., Bidartondo, M. I. & Merckx, V. S. Arbuscular mycorrhizal interactions of mycoheterotrophic Thismia are more specialized than in autotrophic plants. *New Phytol.* **213**, 1418–1427 (2017).

164. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP087715 (2017).

165. Tian, H. et al. Changes in soil microbial communities after 10 years of winter wheat cultivation versus fallow in an organic-poor soil in the Loess Plateau of China. *PLoS One* **12**, e0184223 (2017).

166. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP090261 (2016).

167. Gourmelon, V. et al. Environmental and geographical factors structure soil microbial diversity in New Caledonian ultramafic substrates: a metagenomic approach. *PLoS One* **11**, e0167405 (2016).
168. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP090335 (2017).

169. Younginger, B. S. & Ballhorn, D. J. Fungal endophyte communities in the temperate fern Polystichum munitum show early colonization and extensive temporal turnover. *Am. J. Bot.* **104**, 1188–1194 (2017).

170. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP090490 (2017).

171. Kamutando, C. N. et al. Soil nutritional status and biogeography influence rhizosphere microbial communities associated with the invasive tree Acacia dealbata. *Sci. Rep.* **7**, 6472 (2017).

172. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP090651 (2017).

173. Anthony, M. A., Frey, S. D. & Stinson, K. A. Fungal community homogenization, shift in dominant trophic guild, and appearance of novel taxa with biotic invasion. *Ecosphere* **8**, e01951 (2017).

174. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP091741 (2017).

175. Ge, Z. W., Brenneman, T., Bonito, G. & Smith, M. E. Soil pH and mineral nutrients strongly influence truffles and other ectomycorrhizal fungi associated with commercial pecans (Carya illinoinensis). *Plant Soil* **418**, 493–505 (2017).

176. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP091855 (2018).

177. Mirmajlessi, S. M. et al. Survey of soil fungal communities in Strawberry fields by Illumina amplicon sequencing. *Eurasian Soil Sci.* **51**, 682–691 (2018).

178. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP091867 (2016).

179. Harrison, J. G., Forister, M. L., Parchman, T. L. & Koch, G. W. Vertical stratification of the foliar fungal community in the world's tallest trees. *Am. J. Bot.* **103**, 2087–2095 (2016).

180. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP092609 (2019).

181. Semenova-Nelsen, T. A., Platt, W. J., Patterson, T. R., Huffman, J. & Sikes, B. A. Frequent fire reorganizes fungal communities and slows decomposition across a heterogeneous pine savanna landscape. *New Phytol.* **224**, 916–927 (2019).

182. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP092777 (2017).

183. Dean, S. L. et al. A study of Glycine max (soybean) fungal communities under different agricultural practices. *Plant Gene* **11**, 8–16 (2017).

184. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP093592 (2017).

185. Kyaschenko, J., Clemmensen, K. E., Hagenbo, A., Karl tun, E. & Lindahl, B. D. Shift in fungal communities and associated enzyme activities along an age gradient of managed Pinus sylvestris stands. *ISME J.* **11**, 863–874 (2017).

186. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP093928 (2017).

187. Tian, J. et al. Ecological succession pattern of fungal community in soil along a retreating glacier. *Front. Microbiol.* **8**, 1028 (2017).

188. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP094708 (2017).

189. Oono, R., Rasmussen, A. & Lefèvre, E. Distance decay relationships in foliar fungal endophytes are driven by rare taxa. *Environ. Microbiol.* **19**, 2794–2805 (2017).

190. Oono, R. A confidence interval analysis of sampling effort, sequencing depth, and taxonomic resolution of fungal community ecology in the era of high-throughput sequencing. *PLoS One* **12**, e0189796 (2017).

191. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP097883 (2017).

192. Marín, C. et al. Functional land-use change effects on soil fungal communities in Chilean temperate rainforests. *J. Soil Sci. Plant Nut.* **17**, 985–1002 (2017).

193. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP101553 (2017).

194. Siles, J. A. & Margesin, R. Seasonal soil microbial responses are limited to changes in functionality at two Alpine forest sites differing in altitude and vegetation. *Sci. Rep.* **7**, 2204 (2017).

195. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP101605 (2018).

196. Kazartsev, I., Shorohova, E., Kapitsa, E. & Kushnevskaya, H. Decaying Picea abies log bark hosts diverse fungal communities. *Fungal Ecol.* **33**, 1–12 (2018).

197. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP102378 (2017).

198. Peay, K. G. et al. Convergence and contrast in the community structure of bacteria, fungi and archaea along a tropical elevation-climate gradient. *FEMS Microbiol. Ecol.* **93**, fix045 (2017).

199. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP102417 (2018).

200. Coleine, C. et al. Antarctic cryptoendolithic fungal communities are highly adapted and dominated by Lecanoromycetes and Dothideomycetes. *Front. Microbiol.* **9**, 1392 (2018).

201. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP102775 (2018).

202. Park, M. S. et al. Diversity of fungi associated with roots of Calanthe orchid species in Korea. *J. Microbiol.* **56**, 49–55 (2018).

203. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP106137 (2018).

204. Glynou, K., Nam, B., Thines, M. & Maciá-Vicente, J. G. Facultative root-colonizing fungi dominate endophytic assemblages in roots of nonmycorrhizal Microthlaspi species. *New Phytol.* **217**, 1190–1202 (2018).

205. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP106774 (2018).

206. Saitta, A., Anslan, S., Bahram, M., Brocca, L. & Tedersoo, L. Tree species identity and diversity drive fungal richness and community composition along an elevational gradient in a Mediterranean ecosystem. *Mycorrhiza* **28**, 39–47 (2018).

207. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP107174 (2017).

208. Almario, J. et al. Root-associated fungal microbiota of nonmycorrhizal Arabis alpina and its contribution to plant phosphorus nutrition. *Proc. Natl. Acad. Sci. USA.* **114**, E9403–E9412 (2017).

209. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP107743 (2017).

210. Fernández-Mendoza, F., Fleischhacker, A., Kopun, T., Grube, M. & Muggia, L. ITS1 metabarcoding highlights low specificity of lichen mycobiomes at a local scale. *Mol. Ecol.* **26**, 4811–4830 (2017).

211. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP109164 (2017).

212. Varenius, K., Lindahl, B. D. & Dahlberg, A. Retention of seed trees fails to lifeboat ectomycorrhizal fungal diversity in harvested Scots pine forests. *FEMS Microbiol. Ecol.* **93**, fix105 (2017).

213. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP109773 (2017).

214. He, D. et al. Diversity and co-occurrence network of soil fungi are more responsive than those of bacteria to shifts in precipitation seasonality in a subtropical forest. *Soil Biol. Biochem.* **115**, 499–510 (2017).

215. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP110522 (2017).

216. Mendoza, J. R., Kok, C. R., Stratton, J., Bianchini, A. & Hallen-Adams, H. E. Understanding the mycobiota of maize from the highlands of Guatemala, and implications for maize quality and safety. *Crop Prot.* **101**, 5–11 (2017).

217. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP110810 (2017).

218. Miura, T., Sánchez, R., Castañeda, L. E., Godoy, K. & Barbosa, O. Is microbial terroir related to geographic distance between vineyards? *Environ. Microbiol. Rep.* **9**, 742–749 (2017).

219. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP113348 (2018).

220. Zhang, J. et al. Distinct large-scale biogeographic patterns of fungal communities in bulk soil and soybean rhizosphere in China. *Sci. Total Environ.* **644**, 791–800 (2018).

221. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP114697 (2017).

222. Sharma-Poudyal, D., Schlatter, D., Yin, C., Hulbert, S. & Paulitz, T. Long-term no-till: A major driver of fungal communities in dryland wheat cropping systems. *PLoS One* **12**, e0184611 (2017).
168. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP090335 (2017).

169. Younginger, B. S. & Ballhorn, D. J. Fungal endophyte communities in the temperate fern Polystichum munitum show early colonization and extensive temporal turnover. *Am. J. Bot.* **104**, 1188–1194 (2017).

170. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP090490 (2017).

171. Kamutando, C. N. et al. Soil nutritional status and biogeography influence rhizosphere microbial communities associated with the invasive tree Acacia dealbata. *Sci. Rep.* **7**, 6472 (2017).

172. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP090651 (2017).

173. Anthony, M. A., Frey, S. D. & Stinson, K. A. Fungal community homogenization, shift in dominant trophic guild, and appearance of novel taxa with biotic invasion. *Ecosphere* **8**, e01951 (2017).

174. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP091741 (2017).

175. Ge, Z. W., Brenneman, T., Bonito, G. & Smith, M. E. Soil pH and mineral nutrients strongly influence truffles and other ectomycorrhizal fungi associated with commercial pecans (Carya illinoinensis). *Plant Soil* **418**, 493–505 (2017).

176. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP091855 (2018).

177. Mirmajlessi, S. M. et al. Survey of soil fungal communities in Strawberry fields by Illumina amplicon sequencing. *Eurasian Soil Sci.* **51**, 682–691 (2018).

178. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP091867 (2016).

179. Harrison, J. G., Forister, M. L., Parchman, T. L. & Koch, G. W. Vertical stratification of the foliar fungal community in the world's tallest trees. *Am. J. Bot.* **103**, 2087–2095 (2016).

180. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP092609 (2019).

181. Semenova-Nelsen, T. A., Platt, W. J., Patterson, T. R., Huffman, J. & Sikes, B. A. Frequent fire reorganizes fungal communities and slows decomposition across a heterogeneous pine savanna landscape. *New Phytol.* **224**, 916–927 (2019).

182. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP092777 (2017).

183. Dean, S. L. et al. A study of Glycine max (soybean) fungal communities under different agricultural practices. *Plant Gene* **11**, 8–16 (2017).

184. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP093592 (2017).

185. Kyaschenko, J., Clemmensen, K. E., Hagenbo, A., Karl tun, E. & Lindahl, B. D. Shift in fungal communities and associated enzyme activities along an age gradient of managed Pinus sylvestris stands. *ISME J.* **11**, 863–874 (2017).

186. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP093928 (2017).

187. Tian, J. et al. Ecological succession pattern of fungal community in soil along a retreating glacier. *Front. Microbiol.* **8**, 1028 (2017).

188. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP094708 (2017).

189. Oono, R., Rasmussen, A. & Lefèvre, E. Distance decay relationships in foliar fungal endophytes are driven by rare taxa. *Environ. Microbiol.* **19**, 2794–2805 (2017).

190. Oono, R. A confidence interval analysis of sampling effort, sequencing depth, and taxonomic resolution of fungal community ecology in the era of high-throughput sequencing. *PLoS One* **12**, e0189796 (2017).

191. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP097883 (2017).

192. Marín, C. et al. Functional land-use change effects on soil fungal communities in Chilean temperate rainforests. *J. Soil Sci. Plant Nut.* **17**, 985–1002 (2017).

193. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP101553 (2017).

194. Siles, J. A. & Margesin, R. Seasonal soil microbial responses are limited to changes in functionality at two Alpine forest sites differing in altitude and vegetation. *Sci. Rep.* **7**, 2204 (2017).

195. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP101605 (2018).

196. Kazartsev, I., Shorohova, E., Kapitsa, E. & Kushnevskaya, H. Decaying Picea abies log bark hosts diverse fungal communities. *Fungal Ecol.* **33**, 1–12 (2018).

197. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP102378 (2017).

198. Peay, K. G. et al. Convergence and contrast in the community structure of bacteria, fungi and archaea along a tropical elevation-climate gradient. *FEMS Microbiol. Ecol.* **93**, fix045 (2017).

199. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP102417 (2018).

200. Coleine, C. et al. Antarctic cryptoendolithic fungal communities are highly adapted and dominated by Lecanoromycetes and Dothideomycetes. *Front. Microbiol.* **9**, 1392 (2018).

201. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP102775 (2018).

202. Park, M. S. et al. Diversity of fungi associated with roots of Calanthe orchid species in Korea. *J. Microbiol.* **56**, 49–55 (2018).

203. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP106137 (2018).

204. Glynou, K., Nam, B., Thines, M. & Maciá-Vicente, J. G. Facultative root-colonizing fungi dominate endophytic assemblages in roots of nonmycorrhizal Microthlaspi species. *New Phytol.* **217**, 1190–1202 (2018).

205. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP106774 (2018).

206. Saitta, A., Anslan, S., Bahram, M., Brocca, L. & Tedersoo, L. Tree species identity and diversity drive fungal richness and community composition along an elevational gradient in a Mediterranean ecosystem. *Mycorrhiza* **28**, 39–47 (2018).

207. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP107174 (2017).

208. Almario, J. et al. Root-associated fungal microbiota of nonmycorrhizal Arabis alpina and its contribution to plant phosphorus nutrition. *Proc. Natl. Acad. Sci. USA.* **114**, E9403–E9412 (2017).

209. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP107743 (2017).

210. Fernández-Mendoza, F., Fleischhacker, A., Kopun, T., Grube, M. & Muggia, L. ITS1 metabarcoding highlights low specificity of lichen mycobiomes at a local scale. *Mol. Ecol.* **26**, 4811–4830 (2017).

211. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP109164 (2017).

212. Varenius, K., Lindahl, B. D. & Dahlberg, A. Retention of seed trees fails to lifeboat ectomycorrhizal fungal diversity in harvested Scots pine forests. *FEMS Microbiol. Ecol.* **93**, fix105 (2017).

213. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP109773 (2017).

214. He, D. et al. Diversity and co-occurrence network of soil fungi are more responsive than those of bacteria to shifts in precipitation seasonality in a subtropical forest. *Soil Biol. Biochem.* **115**, 499–510 (2017).

215. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP110522 (2017).

216. Mendoza, J. R., Kok, C. R., Stratton, J., Bianchini, A. & Hallen-Adams, H. E. Understanding the mycobiota of maize from the highlands of Guatemala, and implications for maize quality and safety. *Crop Prot.* **101**, 5–11 (2017).

217. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP110810 (2017).

218. Miura, T., Sánchez, R., Castañeda, L. E., Godoy, K. & Barbosa, O. Is microbial terroir related to geographic distance between vineyards? *Environ. Microbiol. Rep.* **9**, 742–749 (2017).

219. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP113348 (2018).

220. Zhang, J. et al. Distinct large-scale biogeographic patterns of fungal communities in bulk soil and soybean rhizosphere in China. *Sci. Total Environ.* **644**, 791–800 (2018).

221. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP114697 (2017).

222. Sharma-Poudyal, D., Schlatter, D., Yin, C., Hulbert, S. & Paulitz, T. Long-term no-till: A major driver of fungal communities in dryland wheat cropping systems. *PLoS One* **12**, e0184611 (2017).
223. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP114821 (2018).

224. Ren, C. et al. Differential responses of soil microbial biomass, diversity, and compositions to altitudinal gradients depend on plant and soil characteristics. *Sci. Total Environ.* **610**, 750–758 (2018).

225. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP115350 (2018).

226. Schneider-Maunoury, L. et al. Is Tuber melanosporum colonizing the roots of herbaceous, non-ectomycorrhizal plants? *Fungal Ecol.* **31**, 59–68 (2018).

227. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP115464 (2018).

228. Sapkota, R. & Nicolaisen, M. Cropping history shapes fungal, oomycete and nematode communities in arable soils and affects cavity spot in carrot. *Agric. Ecosyst. Environ.* **257**, 120–131 (2018).

229. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP115599 (2018).

230. Schroeder, J. W. et al. Community composition and diversity of Neotropical root-associated fungi in common and rare trees. *Biotropica* **50**, 694–703 (2018).

231. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP117302 (2018).

232. Fan, K., Weisenhorn, P., Gilbert, J. A. & Chu, H. Wheat rhizosphere harbors a less complex and more stable microbial co-occurrence pattern than bulk soil. *Soil Biol. Biochem.* **125**, 251–260 (2018).

233. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP118875 (2018).

234. Montagna, M. et al. Differential biodiversity responses between kingdoms (plants, fungi, bacteria and metazoa) along an Alpine succession gradient. *Mol. Ecol.* **27**, 3671–3685 (2018).

235. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP118960 (2018).

236. Schön, M. E., Nieselt, K. & Garnica, S. Belowground fungal community diversity and composition associated with Norway spruce along an altitudinal gradient. *PLoS One* **13**, e0208493 (2018).

237. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP119174 (2017).

238. Thiem, D., Piernik, A. & Hrynkiewicz, K. Ectomycorrhizal and endophytic fungi associated with Alnus glutinosa growing in a saline area of central Poland. *Symbiosis* **75**, 17–28 (2017).

239. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP125864 (2016).

240. Barnes, C. J., Maldonado, C., Frošlev, T. G., Antonelli, A. & Ronsted, N. Unexpectedly high beta-diversity of root-associated fungal communities in the Bolivian Andes. *Front. Microbiol.* **7**, 1377 (2016).

241. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP132277 (2018).

242. Schlatter, D. C., Kahl, K., Carlson, B., Huggins, D. R. & Paulitz, T. Fungal community composition and diversity vary with soil depth and landscape position in a no-till wheat-based cropping system. *FEMS Microbiol. Ecol.* **94**, fiy098 (2018).

243. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP132591 (2018).

244. Rasmussen, P. U. et al. Multiscale patterns and drivers of arbuscular mycorrhizal fungal communities in the roots and root-associated soil of a wild perennial herb. *New Phytol.* **220**, 1248–1261 (2018).

245. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP132598 (2018).

246. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP136886 (2012).

247. Guo, J. et al. Soil fungal assemblage complexity is dependent on soil fertility and dominated by deterministic processes. *New Phytol.* **226**, 232–243 (2019).

248. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP139483 (2019).

249. Song, H. et al. Tropical forest conversion to rubber plantation in southwest China results in lower fungal beta diversity and reduced network complexity. *FEMS Microbiol. Ecol.* **95**, fiz092 (2019).

250. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP142723 (2018).

251. Rogers, T. J. et al. Exploring variation in phyllosphere microbial communities across four hemlock species. *Ecosphere* **9**, e02524 (2018).

252. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP148813 (2018).

253. Schlegel, M., Queloz, V. & Sieber, T. N. The endophytic mycobiome of European Ash and Sycamore Maple leaves - geographic patterns, host specificity and influence of Ash Dieback. *Front. Microbiol.* **9**, 2345 (2018).

254. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP150527 (2019).

255. Truong, C. et al. Ectomycorrhizal fungi and soil enzymes exhibit contrasting patterns along elevation gradients in southern Patagonia. *New Phytol.* **222**, 1936–1950 (2019).

256. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP151262 (2018).

257. Jiao, S. et al. Soil microbiomes with distinct assemblies through vertical soil profiles drive the cycling of multiple nutrients in reforested ecosystems. *Microbiome* **6**, 146 (2018).

258. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP153934 (2018).

259. Marasco, R. et al. Rhizosheath microbial community assembly of sympatric desert speargrasses is independent of the plant host. *Microbiome* **6**, 215 (2018).

260. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP160913 (2018).

261. Bickford, W. A., Goldberg, D. E., Kowalski, K. P. & Zak, D. R. Root endophytes and invasiveness: no difference between native and non-native Phragmites in the Great Lakes region. *Ecosphere* **9**, e02526 (2018).

262. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP161632 (2018).

263. Si, P. et al. Rhizosphere microenvironments of eight common deciduous fruit trees were shaped by microbes in Northern China. *Front. Microbiol.* **9**, 3147 (2018).

264. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP195764 (2019).

265. Purahong, W., Wu, Y. T., Chen, C. T. & Mapook, A. Characterization of the Castanopsis carlesii deadwood mycobiome by Pacbio sequencing of the full-length fungal nuclear ribosomal internal transcribed spacer (ITS). *Front. Microbiol.* **10**, 983 (2019).

266. European Nucleotide Archive https://identifiers.org/ena:embl:ERP001713 (2014).

267. Geml, J. et al. The contribution of DNA metabarcoding to fungal conservation: diversity assessment, habitat partitioning and mapping red-listed fungi in protected coastal Salix repens communities in the Netherlands. *PLoS One* **9**, e99852 (2014).

268. European Nucleotide Archive https://identifiers.org/ena:embl:ERP003251 (2013).

269. Schmidt, P. A. et al. Illumina metabarcoding of a soil fungal community. *Soil Biol. Biochem.* **65**, 128–132 (2013).

270. European Nucleotide Archive https://identifiers.org/ena:embl:ERP003790 (2015).

271. van der Wal, A., Ottosson, E. & De Boer, W. Neglected role of fungal community composition in explaining variation in wood decay rates. *Ecology* **96**, 124–133 (2015).

272. European Nucleotide Archive https://identifiers.org/ena:embl:ERP005177 (2015).

273. Muller, L. A. & Hilger, H. H. Insights into the effects of serpentine soil conditions on the community composition of fungal symbionts in the roots of Onosma echioides. *Soil Biol. Biochem.* **81**, 1–8 (2015).

274. European Nucleotide Archive https://identifiers.org/ena:embl:ERP005905 (2015).

275. Sun, H. et al. Fungal community shifts in structure and function across a boreal forest fire chronosequence. *Appl. Environ. Microbiol.* **81**, 7869–7880 (2015).

276. European Nucleotide Archive https://identifiers.org/ena:embl:ERP009341 (2015).

277. Rajala, T., Tuomivirta, T., Pennanen, T. & Mäkipää, R. Habitat models of wood-inhabiting fungi along a decay gradient of Norway spruce logs. *Fungal Ecol.* **18**, 48–55 (2015).
223. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP114821 (2018).

224. Ren, C. et al. Differential responses of soil microbial biomass, diversity, and compositions to altitudinal gradients depend on plant and soil characteristics. *Sci. Total Environ.* **610**, 750–758 (2018).

225. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP115350 (2018).

226. Schneider-Maunoury, L. et al. Is Tuber melanosporum colonizing the roots of herbaceous, non-ectomycorrhizal plants? *Fungal Ecol.* **31**, 59–68 (2018).

227. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP115464 (2018).

228. Sapkota, R. & Nicolaisen, M. Cropping history shapes fungal, oomycete and nematode communities in arable soils and affects cavity spot in carrot. *Agric. Ecosyst. Environ.* **257**, 120–131 (2018).

229. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP115599 (2018).

230. Schroeder, J. W. et al. Community composition and diversity of Neotropical root-associated fungi in common and rare trees. *Biotropica* **50**, 694–703 (2018).

231. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP117302 (2018).

232. Fan, K., Weisenhorn, P., Gilbert, J. A. & Chu, H. Wheat rhizosphere harbors a less complex and more stable microbial co-occurrence pattern than bulk soil. *Soil Biol. Biochem.* **125**, 251–260 (2018).

233. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP118875 (2018).

234. Montagna, M. et al. Differential biodiversity responses between kingdoms (plants, fungi, bacteria and metazoa) along an Alpine succession gradient. *Mol. Ecol.* **27**, 3671–3685 (2018).

235. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP118960 (2018).

236. Schön, M. E., Nieselt, K. & Garnica, S. Belowground fungal community diversity and composition associated with Norway spruce along an altitudinal gradient. *PLoS One* **13**, e0208493 (2018).

237. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP119174 (2017).

238. Thiem, D., Piernik, A. & Hrynkiewicz, K. Ectomycorrhizal and endophytic fungi associated with Alnus glutinosa growing in a saline area of central Poland. *Symbiosis* **75**, 17–28 (2017).

239. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP125864 (2016).

240. Barnes, C. J., Maldonado, C., Frošlev, T. G., Antonelli, A. & Ronsted, N. Unexpectedly high beta-diversity of root-associated fungal communities in the Bolivian Andes. *Front. Microbiol.* **7**, 1377 (2016).

241. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP132277 (2018).

242. Schlatter, D. C., Kahl, K., Carlson, B., Huggins, D. R. & Paulitz, T. Fungal community composition and diversity vary with soil depth and landscape position in a no-till wheat-based cropping system. *FEMS Microbiol. Ecol.* **94**, fiy098 (2018).

243. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP132591 (2018).

244. Rasmussen, P. U. et al. Multiscale patterns and drivers of arbuscular mycorrhizal fungal communities in the roots and root-associated soil of a wild perennial herb. *New Phytol.* **220**, 1248–1261 (2018).

245. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP132598 (2018).

246. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP136886 (2012).

247. Guo, J. et al. Soil fungal assemblage complexity is dependent on soil fertility and dominated by deterministic processes. *New Phytol.* **226**, 232–243 (2019).

248. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP139483 (2019).

249. Song, H. et al. Tropical forest conversion to rubber plantation in southwest China results in lower fungal beta diversity and reduced network complexity. *FEMS Microbiol. Ecol.* **95**, fiz092 (2019).

250. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP142723 (2018).

251. Rogers, T. J. et al. Exploring variation in phyllosphere microbial communities across four hemlock species. *Ecosphere* **9**, e02524 (2018).

252. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP148813 (2018).

253. Schlegel, M., Queloz, V. & Sieber, T. N. The endophytic mycobiome of European Ash and Sycamore Maple leaves – geographic patterns, host specificity and influence of Ash Dieback. *Front. Microbiol.* **9**, 2345 (2018).

254. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP150527 (2019).

255. Truong, C. et al. Ectomycorrhizal fungi and soil enzymes exhibit contrasting patterns along elevation gradients in southern Patagonia. *New Phytol.* **222**, 1936–1950 (2019).

256. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP151262 (2018).

257. Jiao, S. et al. Soil microbiomes with distinct assemblies through vertical soil profiles drive the cycling of multiple nutrients in reforested ecosystems. *Microbiome* **6**, 146 (2018).

258. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP153934 (2018).

259. Marasco, R. et al. Rhizosheath microbial community assembly of sympatric desert speargrasses is independent of the plant host. *Microbiome* **6**, 215 (2018).

260. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP160913 (2018).

261. Bickford, W. A., Goldberg, D. E., Kowalski, K. P. & Zak, D. R. Root endophytes and invasiveness: no difference between native and non-native Phragmites in the Great Lakes region. *Ecosphere* **9**, e02526 (2018).

262. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP161632 (2018).

263. Si, P. et al. Rhizosphere microenvironments of eight common deciduous fruit trees were shaped by microbes in Northern China. *Front. Microbiol.* **9**, 3147 (2018).

264. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP195764 (2019).

265. Purahong, W., Wu, Y. T., Chen, C. T. & Mapook, A. Characterization of the Castanopsis carlesii deadwood mycobiome by Pacbio sequencing of the full-length fungal nuclear ribosomal internal transcribed spacer (ITS). *Front. Microbiol.* **10**, 983 (2019).

266. European Nucleotide Archive https://identifiers.org/ena:embl:ERP001713 (2014).

267. Geml, J. et al. The contribution of DNA metabarcoding to fungal conservation: diversity assessment, habitat partitioning and mapping red-listed fungi in protected coastal Salix repens communities in the Netherlands. *PLoS One* **9**, e99852 (2014).

268. European Nucleotide Archive https://identifiers.org/ena:embl:ERP003251 (2013).

269. Schmidt, P. A. et al. Illumina metabarcoding of a soil fungal community. *Soil Biol. Biochem.* **65**, 128–132 (2013).

270. European Nucleotide Archive https://identifiers.org/ena:embl:ERP003790 (2015).

271. van der Wal, A., Ottosson, E. & De Boer, W. Neglected role of fungal community composition in explaining variation in wood decay rates. *Ecology* **96**, 124–133 (2015).

272. European Nucleotide Archive https://identifiers.org/ena:embl:ERP005177 (2015).

273. Muller, L. A. & Hilger, H. H. Insights into the effects of serpentine soil conditions on the community composition of fungal symbionts in the roots of Onosma echioides. *Soil Biol. Biochem.* **81**, 1–8 (2015).

274. European Nucleotide Archive https://identifiers.org/ena:embl:ERP005905 (2015).

275. Sun, H. et al. Fungal community shifts in structure and function across a boreal forest fire chronosequence. *Appl. Environ. Microbiol.* **81**, 7869–7880 (2015).

276. European Nucleotide Archive https://identifiers.org/ena:embl:ERP009341 (2015).

277. Rajala, T., Tuomivirta, T., Pennanen, T. & Mäkipää, R. Habitat models of wood-inhabiting fungi along a decay gradient of Norway spruce logs. *Fungal Ecol.* **18**, 48–55 (2015).
278. *European Nucleotide Archive* https://identifiers.org/ena.embl:ERP010027 (2017).

279. Purahong, W. *et al.* Characterization of unexplored deadwood mycobiome in highly diverse subtropical forests using culture-independent molecular technique. *Front. Microbiol.* **8**, 574 (2017).

280. *European Nucleotide Archive* https://identifiers.org/ena.embl:ERP010084 (2016).

281. van der Wal, A., Gunnewiek, P. J. K., Cornelissen, J. H. C., Crowther, T. W. & de Boer, W. Patterns of natural fungal community assembly during initial decay of coniferous and broadleaf tree logs. *Ecosphere* **7**, e01393 (2016).

282. *European Nucleotide Archive* https://identifiers.org/ena.embl:ERP010743 (2016).

283. Reese, A. T. *et al.* Urban stress is associated with variation in microbial species composition-but not richness-in Manhattan. *ISME J.* **10**, 751–760 (2016).

284. *European Nucleotide Archive* https://identifiers.org/ena.embl:ERP011924 (2016).

285. Kielak, A. M., Scheublin, T. R., Mendes, L. W., Van Veen, J. A. & Kuramae, E. E. Bacterial community succession in Pine-wood decomposition. *Front. Microbiol.* **7**, 231 (2016).

286. *European Nucleotide Archive* https://identifiers.org/ena.embl:ERP012017 (2016).

287. Santalahti, M., Sun, H., Jumpponen, A., Pennanen, T. & Heinonsalo, J. Vertical and seasonal dynamics of fungal communities in boreal Scots pine forest soil. *FEMS Microbiol. Ecol.* **92**, fiw170 (2016).

288. *European Nucleotide Archive* https://identifiers.org/ena.embl:ERP013208 (2016).

289. Frey, B. *et al.* Microbial diversity in European alpine permafrost and active layers. *FEMS Microbiol. Ecol.* **92**, fiw018 (2016).

290. *European Nucleotide Archive* https://identifiers.org/ena.embl:ERP013987 (2017).

291. Wilhelm, R. C. *et al.* A metagenomic survey of forest soil microbial communities more than a decade after timber harvesting. *Sci. Data* **4**, 170092 (2017).

292. *European Nucleotide Archive* https://identifiers.org/ena.embl:ERP014227 (2016).

293. Lanzén, A. *et al.* Multi-targeted metagenetic analysis of the influence of climate and environmental parameters on soil microbial communities along an elevational gradient. *Sci. Rep.* **6**, 28257 (2016).

294. *European Nucleotide Archive* https://identifiers.org/ena.embl:ERP017480 (2018).

295. Purahong, W. *et al.* Increasing N deposition impacts neither diversity nor functions of deadwood-inhabiting fungal communities, but adaptation and functional redundancy ensure ecosystem function. *Environ. Microbiol.* **20**, 1693–1710 (2018).

296. *European Nucleotide Archive*, https://identifiers.org/ena.embl:ERP017851 (2017).

297. Yang, T. *et al.* Soil fungal diversity in natural grasslands of the Tibetan Plateau: associations with plant diversity and productivity. *New Phytol.* **215**, 756–765 (2017).

298. *European Nucleotide Archive* https://identifiers.org/ena.embl:ERP017915 (2017).

299. Nguyen, D. *et al.* Foliar fungi of Betula pendula: impact of tree species mixtures and assessment methods. *Sci. Rep.* **7**, 41801 (2017).

300. *European Nucleotide Archive* https://identifiers.org/ena.embl:ERP019580 (2017).

301. Tu, B. *et al.* Microbial diversity in chinese temperate steppe: unveiling the most influential environmental drivers. *FEMS Microbiol. Ecol.* **93**, fix031 (2017).

302. *European Nucleotide Archive* https://identifiers.org/ena.embl:ERP019924 (2017).

303. Yang, T. *et al.* Fungal community assemblages in a high elevation desert environment: absence of dispersal limitation and edaphic effects in surface soil. *Soil Biol. Biochem.* **115**, 393–402 (2017).

304. *European Nucleotide Archive* https://identifiers.org/ena.embl:ERP020657 (2017).

305. van der Wal, A., Gunnewiek, P. K., de Hollander, M. & de Boer, W. Fungal diversity and potential tree pathogens in decaying logs and stumps. *Forest Ecol. Manag.* **406**, 266–273 (2017).

306. *European Nucleotide Archive* https://identifiers.org/ena.embl:ERP022511 (2019).

307. Alzarhani, A. K. *et al.* Are drivers of root-associated fungal community structure context specific? *ISME J.* **13**, 1330–1344 (2019).

308. *European Nucleotide Archive* https://identifiers.org/ena.embl:ERP022742 (2017).

309. van der Wal, A., Gunnewiek, P. K. & de Boer, W. Soil-wood interactions: Influence of decaying coniferous and broadleaf logs on composition of soil fungal communities. *Fungal Ecol.* **30**, 132–134 (2017).

310. *European Nucleotide Archive* https://identifiers.org/ena.embl:ERP023275 (2018).

311. Purahong, W. *et al.* Determinants of deadwood-inhabiting fungal communities in temperate forests: molecular evidence from a large scale deadwood decomposition experiment. *Front. Microbiol.* **9**, 2120 (2018).

312. *European Nucleotide Archive* https://identifiers.org/ena.embl:ERP023718 (2018).

313. Sun, R. *et al.* Tillage changes vertical distribution of soil bacterial and fungal communities. *Front. Microbiol.* **9**, 699 (2018).

314. *European Nucleotide Archive* https://identifiers.org/ena.embl:ERP023855 (2018).

315. Santalahti, M. *et al.* Reindeer grazing alter soil fungal community structure and litter decomposition related enzyme activities in boreal coniferous forests in finnish lapland. *Appl. Soil Ecol.* **132**, 74–82 (2018).

316. *European Nucleotide Archive* https://identifiers.org/ena.embl:ERP106131 (2018).

317. Gałązka, A. & Grządziel, J. Fungal genetics and functional diversity of microbial communities in the soil under long-term monoculture of Maize using different cultivation techniques. *Front. Microbiol.* **9**, 76 (2018).

318. *European Nucleotide Archive* https://identifiers.org/ena.embl:ERP107634 (2019).

319. Ramirez, K. S. *et al.* Range-expansion effects on the belowground plant microbiome. *Nat. Ecol. Evol.* **3**, 604 (2019).

320. *European Nucleotide Archive* https://identifiers.org/ena.embl:ERP107636 (2019).

321. *European Nucleotide Archive* https://identifiers.org/ena.embl:ERP110188 (2019).

322. George, P. B. *et al.* Divergent national-scale trends of microbial and animal biodiversity revealed across diverse temperate soil ecosystems. *Nat. Commun.* **10**, 1107 (2019).

323. *European Nucleotide Archive* https://identifiers.org/ena.embl:ERP112007 (2019).

324. Álvarez-Garrido, L., Viñegla, B., Hortal, S., Powell, J. R. & Carreira, J. A. Distributional shifts in ectomycorrhizal fungal communities lag behind climate-driven tree upward migration in a conifer forest-high elevation shrubland ecotone. *Soil Biol. Biochem.* **137**, 107545 (2019).

325. *DNA Data Bank of Japan* https://identifiers.org/ncbi/insdc.sra:DRA000926 (2014).

326. Yamamoto, S. *et al.* Spatial segregation and aggregation of ectomycorrhizal and root-endophytic fungi in the seedlings of two Quercus species. *PLoS One* **9**, e96363 (2014).

327. *DNA Data Bank of Japan* https://identifiers.org/ncbi/insdc.sra:DRA000937 (2014).

328. Kadowaki, K. *et al.* Detection of the horizontal spatial structure of soil fungal communities in a natural forest. *Popul. Ecol.* **56**, 301–310 (2014).

329. *DNA Data Bank of Japan* https://identifiers.org/ncbi/insdc.sra:DRA001737 (2016).

330. Izuno, A. *et al.* Structure of phyllosphere fungal communities in a tropical dipterocarp plantation: A massively parallel next-generation sequencing analysis. *Mycoscience* **57**, 171–180 (2016).

331. *DNA Data Bank of Japan* https://identifiers.org/ncbi/insdc.sra:DRA002424 (2016).

332. Matsuoka, S., Kawaguchi, E. & Osono, T. Temporal distance decay of similarity of ectomycorrhizal fungal community composition in a subtropical evergreen forest in Japan. *FEMS Microbiol. Ecol.* **92**, fiw061 (2016).

333. *DNA Data Bank of Japan* https://identifiers.org/ncbi/insdc.sra:DRA002469 (2016).

334. Izuno, A., Kanzaki, M., Artchawakom, T., Wachrinrat, C. & Isagi, Y. Vertical structure of phyllosphere fungal communities in a tropical forest in Thailand uncovered by high-throughput sequencing. *PLoS One* **11**, e0166669 (2016).
278. *European Nucleotide Archive* https://identifiers.org/ena.embl:ERP010027 (2017).

279. Purahong, W. et al. Characterization of unexplored deadwood mycobiome in highly diverse subtropical forests using culture-independent molecular technique. *Front. Microbiol.* **8**, 574 (2017).

280. *European Nucleotide Archive* https://identifiers.org/ena.embl:ERP010084 (2016).

281. van der Wal, A., Gunnewiek, P. J. K., Cornelissen, J. H. C., Crowther, T. W. & de Boer, W. Patterns of natural fungal community assembly during initial decay of coniferous and broadleaf tree logs. *Ecosphere* **7**, e01393 (2016).

282. *European Nucleotide Archive* https://identifiers.org/ena.embl:ERP010743 (2016).

283. Reese, A. T. et al. Urban stress is associated with variation in microbial species composition-but not richness-in Manhattan. *ISME J.* **10**, 751–760 (2016).

284. *European Nucleotide Archive* https://identifiers.org/ena.embl:ERP011924 (2016).

285. Kielak, A. M., Scheublin, T. R., Mendes, L. W., Van Veen, J. A. & Kuramae, E. E. Bacterial community succession in Pine-wood decomposition. *Front. Microbiol.* **7**, 231 (2016).

286. *European Nucleotide Archive* https://identifiers.org/ena.embl:ERP012017 (2016).

287. Santalahti, M., Sun, H., Jumpponen, A., Pennanen, T. & Heinonsalo, J. Vertical and seasonal dynamics of fungal communities in boreal Scots pine forest soil. *FEMS Microbiol. Ecol.* **92**, fiw170 (2016).

288. *European Nucleotide Archive* https://identifiers.org/ena.embl:ERP013208 (2016).

289. Frey, B. et al. Microbial diversity in European alpine permafrost and active layers. *FEMS Microbiol. Ecol.* **92**, fiw018 (2016).

290. *European Nucleotide Archive* https://identifiers.org/ena.embl:ERP013987 (2017).

291. Wilhelm, R. C. et al. A metagenomic survey of forest soil microbial communities more than a decade after timber harvesting. *Sci. Data* **4**, 170092 (2017).

292. *European Nucleotide Archive* https://identifiers.org/ena.embl:ERP014227 (2016).

293. Lanzén, A. et al. Multi-targeted metagenetic analysis of the influence of climate and environmental parameters on soil microbial communities along an elevational gradient. *Sci. Rep.* **6**, 28257 (2016).

294. *European Nucleotide Archive* https://identifiers.org/ena.embl:ERP017480 (2018).

295. Purahong, W. et al. Increasing N deposition impacts neither diversity nor functions of deadwood-inhabiting fungal communities, but adaptation and functional redundancy ensure ecosystem function. *Environ. Microbiol.* **20**, 1693–1710 (2018).

296. *European Nucleotide Archive*, https://identifiers.org/ena.embl:ERP017851 (2017).

297. Yang, T. et al. Soil fungal diversity in natural grasslands of the Tibetan Plateau: associations with plant diversity and productivity. *New Phytol.* **215**, 756–765 (2017).

298. *European Nucleotide Archive* https://identifiers.org/ena.embl:ERP017915 (2017).

299. Nguyen, D. et al. Foliar fungi of Betula pendula: impact of tree species mixtures and assessment methods. *Sci. Rep.* **7**, 41801 (2017).

300. *European Nucleotide Archive* https://identifiers.org/ena.embl:ERP019580 (2017).

301. Tu, B. et al. Microbial diversity in chinese temperate steppe: unveiling the most influential environmental drivers. *FEMS Microbiol. Ecol.* **93**, fix031 (2017).

302. *European Nucleotide Archive* https://identifiers.org/ena.embl:ERP019924 (2017).

303. Yang, T. et al. Fungal community assemblages in a high elevation desert environment: absence of dispersal limitation and edaphic effects in surface soil. *Soil Biol. Biochem.* **115**, 393–402 (2017).

304. *European Nucleotide Archive* https://identifiers.org/ena.embl:ERP020657 (2017).

305. van der Wal, A., Gunnewiek, P. K., de Hollander, M. & de Boer, W. Fungal diversity and potential tree pathogens in decaying logs and stumps. *Forest Ecol. Manag.* **406**, 266–273 (2017).

306. *European Nucleotide Archive* https://identifiers.org/ena.embl:ERP022511 (2019).

307. Alzarhani, A. K. et al. Are drivers of root-associated fungal community structure context specific? *ISME J.* **13**, 1330–1344 (2019).

308. *European Nucleotide Archive* https://identifiers.org/ena.embl:ERP022742 (2017).

309. van der Wal, A., Gunnewiek, P. K. & de Boer, W. Soil-wood interactions: Influence of decaying coniferous and broadleaf logs on composition of soil fungal communities. *Fungal Ecol.* **30**, 132–134 (2017).

310. *European Nucleotide Archive* https://identifiers.org/ena.embl:ERP023275 (2018).

311. Purahong, W. et al. Determinants of deadwood-inhabiting fungal communities in temperate forests: molecular evidence from a large scale deadwood decomposition experiment. *Front. Microbiol.* **9**, 2120 (2018).

312. *European Nucleotide Archive* https://identifiers.org/ena.embl:ERP023718 (2018).

313. Sun, R. et al. Tillage changes vertical distribution of soil bacterial and fungal communities. *Front. Microbiol.* **9**, 699 (2018).

314. *European Nucleotide Archive* https://identifiers.org/ena.embl:ERP023855 (2018).

315. Santalahti, M. et al. Reindeer grazing alter soil fungal community structure and litter decomposition related enzyme activities in boreal coniferous forests in finnish lapland. *Appl. Soil Ecol.* **132**, 74–82 (2018).

316. *European Nucleotide Archive* https://identifiers.org/ena.embl:ERP106131 (2018).

317. Gałązka, A. & Grządziel, J. Fungal genetics and functional diversity of microbial communities in the soil under long-term monoculture of Maize using different cultivation techniques. *Front. Microbiol.* **9**, 76 (2018).

318. *European Nucleotide Archive* https://identifiers.org/ena.embl:ERP107634 (2019).

319. Ramirez, K. S. et al. Range-expansion effects on the belowground plant microbiome. *Nat. Ecol. Evol.* **3**, 604 (2019).

320. *European Nucleotide Archive* https://identifiers.org/ena.embl:ERP107636 (2019).

321. *European Nucleotide Archive* https://identifiers.org/ena.embl:ERP110188 (2019).

322. George, P. B. et al. Divergent national-scale trends of microbial and animal biodiversity revealed across diverse temperate soil ecosystems. *Nat. Commun.* **10**, 1107 (2019).

323. *European Nucleotide Archive* https://identifiers.org/ena.embl:ERP112007 (2019).

324. Álvarez-Garrido, L., Viñegla, B., Hortal, S., Powell, J. R. & Carreira, J. A. Distributional shifts in ectomycorrhizal fungal communities lag behind climate-driven tree upward migration in a conifer forest-high elevation shrubland ecotone. *Soil Biol. Biochem.* **137**, 107545 (2019).

325. *DNA Data Bank of Japan* https://identifiers.org/ncbi/insdc.sra:DRA000926 (2014).

326. Yamamoto, S. et al. Spatial segregation and aggregation of ectomycorrhizal and root-endophytic fungi in the seedlings of two Quercus species. *PLoS One* **9**, e96363 (2014).

327. *DNA Data Bank of Japan* https://identifiers.org/ncbi/insdc.sra:DRA000937 (2014).

328. Kadowaki, K. et al. Detection of the horizontal spatial structure of soil fungal communities in a natural forest. *Popul. Ecol.* **56**, 301–310 (2014).

329. *DNA Data Bank of Japan* https://identifiers.org/ncbi/insdc.sra:DRA001737 (2016).

330. Izuno, A. et al. Structure of phyllosphere fungal communities in a tropical dipterocarp plantation: A massively parallel next-generation sequencing analysis. *Mycoscience* **57**, 171–180 (2016).

331. *DNA Data Bank of Japan* https://identifiers.org/ncbi/insdc.sra:DRA002424 (2016).

332. Matsuoka, S., Kawaguchi, E. & Osono, T. Temporal distance decay of similarity of ectomycorrhizal fungal community composition in a subtropical evergreen forest in Japan. *FEMS Microbiol. Ecol.* **92**, fiw061 (2016).

333. *DNA Data Bank of Japan* https://identifiers.org/ncbi/insdc.sra:DRA002469 (2016).

334. Izuno, A., Kanzaki, M., Artchawakom, T., Wachrinrat, C. & Isagi, Y. Vertical structure of phyllosphere fungal communities in a tropical forest in Thailand uncovered by high-throughput sequencing. *PLoS One* **11**, e0166669 (2016).
335. DNA Data Bank of Japan https://identifiers.org/ncbi/insdc.sra:DRA003024 (2016).

336. Matsuoka, S., Mori, A. S., Kawaguchi, E., Hobara, S. & Osono, T. Disentangling the relative importance of host tree community, abiotic environment and spatial factors on ectomycorrhizal fungal assemblages along an elevation gradient. *FEMS Microbiol. Ecol.* **92**, fw044 (2016).

337. DNA Data Bank of Japan https://identifiers.org/ncbi/insdc.sra:DRA003730 (2016).

338. Toju, H., Yamamoto, S., Tanabe, A. S., Hayakawa, T. & Ishii, H. S. Network modules and hubs in plant-root fungal biomes. *J. R. Soc. Interface* **13**, 20151097 (2016).

339. DNA Data Bank of Japan https://identifiers.org/ncbi/insdc.sra:DRA004913 (2017).

340. Shen, Z. et al. Banana Fusarium Wilt disease incidence is influenced by shifts of soil microbial communities under different monoculture spans. *Microb. Ecol.* **75**, 739–750 (2017).

341. DNA Data Bank of Japan https://identifiers.org/ncbi/insdc.sra:DRA006519 (2018).

342. Matsuoka, S., Ogisu, Y., Sakoh, S., Hobara, S. & Osono, T. Taxonomic, functional, and phylogenetic diversity of fungi along primary successional and elevational gradients near Mount Robson, British Columbia. *Polar Sci.* **21**, 165–171 (2018).

343. DNA Data Bank of Japan https://identifiers.org/ncbi/insdc.sra:DRP002783 (2015).

344. Fukasawa, Y. & Matsuoka, S. Communities of wood-inhabiting fungi in dead pine logs along a geographical gradient in Japan. *Fungal Ecol.* **18**, 75–82 (2015).

345. DNA Data Bank of Japan https://identifiers.org/ncbi/insdc.sra:DRP003138 (2016).

346. Toju, H., Tanabe, A. S. & Ishii, H. S. Ericaceous plant-fungus network in a harsh alpine-subalpine environment. *Mol. Ecol.* **25**, 3242–3257 (2016).

347. DNA Data Bank of Japan https://identifiers.org/ncbi/insdc.sra:DRP005365 (2019).

348. Shigyo, N., Umeki, K. & Hirao, T. Seasonal dynamics of soil fungal and bacterial communities in cool-temperate montane forests. *Front. Microbiol.* **10**, 1944 (2019).

349. Semenova, T. A. et al. Data from: Long-term experimental warming alters community composition of ascomycetes in Alaskan moist and dry arctic tundra. *Dryad* https://doi.org/10.5061/dryad.2fc32 (2014).

350. Geml, J. et al. Long-term warming alters richness and composition of taxonomic and functional groups of arctic fungi. *FEMS Microbiol. Ecol.* **91**, fiv095 (2015).

351. Oriol, G. et al. Data from: Abrupt changes in the composition and function of fungal communities along an environmental gradient in the High. *Arctic. Dryad* https://doi.org/10.5061/dryad.n82g9 (2017).

352. Grau, O. et al. Abrupt changes in the composition and function of fungal communities along an environmental gradient in the high Arctic. *Mol. Ecol.* **26**, 4798–4810 (2017).

353. Mundra, S. et al. Data from: Arctic fungal communities associated with roots of Bistorta vivipara do not respond to the same fine-scale edaphic gradients as the above-ground vegetation. *Dryad* https://doi.org/10.5061/dryad.2343k (2015).

354. Mundra, S. et al. Arctic fungal communities associated with roots of Bistorta vivipara do not respond to the same fine-scale edaphic gradients as the aboveground vegetation. *New Phytol.* **205**, 1587–1597 (2015).

355. Rime, T. et al. Data from: Vertical distribution of the soil microbiota along a successional gradient in a glacier forefield. *Dryad* https://doi.org/10.5061/dryad.gp302 (2014).

356. Rime, T. et al. Vertical distribution of the soil microbiota along a successional gradient in a glacier forefield. *Mol. Ecol.* **24**, 1091–1108 (2015).

357. Semenova, T. A. et al. Data from: Compositional and functional shifts in arctic fungal communities in response to experimentally increased snow depth. *Dryad* https://doi.org/10.5061/dryad.cq2rb (2017).

358. Semenova, T. A. et al. Compositional and functional shifts in arctic fungal communities in response to experimentally increased snow depth. *Soil Biol. Biochem.* **100**, 201–209 (2016).

359. Geml, J. et al. Data from: Large-scale fungal diversity assessment in the Andean Yungas forests reveals strong community turnover among forest types along an altitudinal gradient. *Dryad* https://doi.org/10.5061/dryad.8fn8j (2014).

360. Wicaksono, C. Y. et al. Contracting montane cloud forests: a case study of the Andean alder (Alnusacuminata) and associated fungi in the Yungas. *Biotropica* **49**, 141–152 (2017).

361. Yao, F. et al. Data from: Substantial compositional turnover of fungal communities in an alpine ridge-to-snowbed gradient. *Dryad* https://doi.org/10.5061/dryad.216tp (2013).

362. Yao, F. et al. Substantial compositional turnover of fungal communities in an alpine ridge-to-snowbed gradient. *Mol. Ecol.* **22**, 5040–5052 (2013).

363. Schappe, T. et al. Uncultured fungus internal transcribed spacer 1, targeted locus study. *GenBank* https://identifiers.org/ncbi/insdc:KAYV00000000.1 (2017).

364. Schappe, T. et al. The role of soil chemistry and plant neighbourhoods in structuring fungal communities in three Panamanian rainforests. *J. Ecol.* **105**, 569–579 (2017).

365. Schappe, T. et al. Uncultured fungus internal transcribed spacer 1, targeted locus study. *GenBank* https://identifiers.org/ncbi/insdc:KAYU00000000.1 (2017).

366. Schappe, T. et al. Uncultured fungus internal transcribed spacer 1, targeted locus study. *GenBank* https://identifiers.org/ncbi/insdc:KAYT00000000.1 (2017).

367. Vaz, A. B. et al. MIMS Environmental/Metagenome sample from biofilm metagenome. *BioSample* https://identifiers.org/biosample:SAMN02934078 (2017).

368. Vaz, A. B. et al. Using Next-Generation Sequencing (NGS) to uncover diversity of wood-decaying fungi in neotropical atlantic forests. *Phytotaxa* **295**, 1–21 (2017).

369. Vaz, A. B. et al. MIMS Environmental/Metagenome sample from biofilm metagenome. *BioSample* https://identifiers.org/biosample:SAMN02934079 (2017).

370. Siciliano, S. et al. Polar soil bacterial and fungal biodiversity survey. *Australian Antarctic Data Centre* https://doi.org/10.4225/15/526f42ada05b1 (2014).

371. Ji, M. et al. Microbial diversity at Mitchell Peninsula, Eastern Antarctica: a potential biodiversity “hotspot”. *Polar Biol.* **39**, 237–249 (2016).

372. Hartmann, M. et al. Significant and persistent impact of timber harvesting on soil microbial communities in Northern coniferous forests. *ISME J.* **6**, 2199–2218 (2012).

373. Rime, T., Hartmann, M. & Frey, B. Potential sources of microbial colonizers in an initial soil ecosystem after retreat of an alpine glacier. *ISME J.* **10**, 1625–1641 (2016).

## Acknowledgements

We acknowledge funding from the Czech Science Foundation Grant No 18–26191S. ELIXIR CZ research infrastructure project LM2015047 by the Ministry of Education, Youth and Sports of the Czech Republic is acknowledged for hosting the database. All corresponding authors of published studies that provided additional information on the samples included in the database are gratefully acknowledged.
335. DNA Data Bank of Japan https://identifiers.org/ncbi/insdc.sra:DRA003024 (2016).

336. Matsuoka, S., Mori, A. S., Kawaguchi, E., Hobara, S. & Osono, T. Disentangling the relative importance of host tree community, abiotic environment and spatial factors on ectomycorrhizal fungal assemblages along an elevation gradient. *FEMS Microbiol. Ecol.* **92**, fw044 (2016).

337. DNA Data Bank of Japan https://identifiers.org/ncbi/insdc.sra:DRA003730 (2016).

338. Toju, H., Yamamoto, S., Tanabe, A. S., Hayakawa, T. & Ishii, H. S. Network modules and hubs in plant-root fungal biomes. *J. R. Soc. Interface* **13**, 20151097 (2016).

339. DNA Data Bank of Japan https://identifiers.org/ncbi/insdc.sra:DRA004913 (2017).

340. Shen, Z. et al. Banana Fusarium Wilt disease incidence is influenced by shifts of soil microbial communities under different monoculture spans. *Microb. Ecol.* **75**, 739–750 (2017).

341. DNA Data Bank of Japan https://identifiers.org/ncbi/insdc.sra:DRA006519 (2018).

342. Matsuoka, S., Ogisu, Y., Sakoh, S., Hobara, S. & Osono, T. Taxonomic, functional, and phylogenetic diversity of fungi along primary successional and elevational gradients near Mount Robson, British Columbia. *Polar Sci.* **21**, 165–171 (2018).

343. DNA Data Bank of Japan https://identifiers.org/ncbi/insdc.sra:DRP002783 (2015).

344. Fukasawa, Y. & Matsuoka, S. Communities of wood-inhabiting fungi in dead pine logs along a geographical gradient in Japan. *Fungal Ecol.* **18**, 75–82 (2015).

345. DNA Data Bank of Japan https://identifiers.org/ncbi/insdc.sra:DRP003138 (2016).

346. Toju, H., Tanabe, A. S. & Ishii, H. S. Ericaceous plant-fungus network in a harsh alpine-subalpine environment. *Mol. Ecol.* **25**, 3242–3257 (2016).

347. DNA Data Bank of Japan https://identifiers.org/ncbi/insdc.sra:DRP005365 (2019).

348. Shigyo, N., Umeki, K. & Hirao, T. Seasonal dynamics of soil fungal and bacterial communities in cool-temperate montane forests. *Front. Microbiol.* **10**, 1944 (2019).

349. Semenova, T. A. et al. Data from: Long-term experimental warming alters community composition of ascomycetes in Alaskan moist and dry arctic tundra. *Dryad* https://doi.org/10.5061/dryad.2fc32 (2014).

350. Geml, J. et al. Long-term warming alters richness and composition of taxonomic and functional groups of arctic fungi. *FEMS Microbiol. Ecol.* **91**, fiv095 (2015).

351. Oriol, G. et al. Data from: Abrupt changes in the composition and function of fungal communities along an environmental gradient in the High. *Arctic. Dryad* https://doi.org/10.5061/dryad.n82g9 (2017).

352. Grau, O. et al. Abrupt changes in the composition and function of fungal communities along an environmental gradient in the high Arctic. *Mol. Ecol.* **26**, 4798–4810 (2017).

353. Mundra, S. et al. Data from: Arctic fungal communities associated with roots of Bistorta vivipara do not respond to the same fine-scale edaphic gradients as the above-ground vegetation. *Dryad* https://doi.org/10.5061/dryad.2343k (2015).

354. Mundra, S. et al. Arctic fungal communities associated with roots of Bistorta vivipara do not respond to the same fine-scale edaphic gradients as the aboveground vegetation. *New Phytol.* **205**, 1587–1597 (2015).

355. Rime, T. et al. Data from: Vertical distribution of the soil microbiota along a successional gradient in a glacier forefield. *Dryad* https://doi.org/10.5061/dryad.gp302 (2014).

356. Rime, T. et al. Vertical distribution of the soil microbiota along a successional gradient in a glacier forefield. *Mol. Ecol.* **24**, 1091–1108 (2015).

357. Semenova, T. A. et al. Data from: Compositional and functional shifts in arctic fungal communities in response to experimentally increased snow depth. *Dryad* https://doi.org/10.5061/dryad.cq2rb (2017).

358. Semenova, T. A. et al. Compositional and functional shifts in arctic fungal communities in response to experimentally increased snow depth. *Soil Biol. Biochem.* **100**, 201–209 (2016).

359. Geml, J. et al. Data from: Large-scale fungal diversity assessment in the Andean Yungas forests reveals strong community turnover among forest types along an altitudinal gradient. *Dryad* https://doi.org/10.5061/dryad.8fn8j (2014).

360. Wicaksono, C. Y. et al. Contracting montane cloud forests: a case study of the Andean alder (Alnusacuminata) and associated fungi in the Yungas. *Biotropica* **49**, 141–152 (2017).

361. Yao, F. et al. Data from: Substantial compositional turnover of fungal communities in an alpine ridge-to-snowbed gradient. *Dryad* https://doi.org/10.5061/dryad.216tp (2013).

362. Yao, F. et al. Substantial compositional turnover of fungal communities in an alpine ridge-to-snowbed gradient. *Mol. Ecol.* **22**, 5040–5052 (2013).

363. Schappe, T. et al. Uncultured fungus internal transcribed spacer 1, targeted locus study. *GenBank* https://identifiers.org/ncbi/insdc:KAYV00000000.1 (2017).

364. Schappe, T. et al. The role of soil chemistry and plant neighbourhoods in structuring fungal communities in three Panamanian rainforests. *J. Ecol.* **105**, 569–579 (2017).

365. Schappe, T. et al. Uncultured fungus internal transcribed spacer 1, targeted locus study. *GenBank* https://identifiers.org/ncbi/insdc:KAYU00000000.1 (2017).

366. Schappe, T. et al. Uncultured fungus internal transcribed spacer 1, targeted locus study. *GenBank* https://identifiers.org/ncbi/insdc:KAYT00000000.1 (2017).

367. Vaz, A. B. et al. MIMS Environmental/Metagenome sample from biofilm metagenome. *BioSample* https://identifiers.org/biosample:SAMN02934078 (2017).

368. Vaz, A. B. et al. Using Next-Generation Sequencing (NGS) to uncover diversity of wood-decaying fungi in neotropical atlantic forests. *Phytotaxa* **295**, 1–21 (2017).

369. Vaz, A. B. et al. MIMS Environmental/Metagenome sample from biofilm metagenome. *BioSample* https://identifiers.org/biosample:SAMN02934079 (2017).

370. Siciliano, S. et al. Polar soil bacterial and fungal biodiversity survey. *Australian Antarctic Data Centre* https://doi.org/10.4225/15/526f42ada05b1 (2014).

371. Ji, M. et al. Microbial diversity at Mitchell Peninsula, Eastern Antarctica: a potential biodiversity “hotspot”. *Polar Biol.* **39**, 237–249 (2016).

372. Hartmann, M. et al. Significant and persistent impact of timber harvesting on soil microbial communities in Northern coniferous forests. *ISME J.* **6**, 2199–2218 (2012).

373. Rime, T., Hartmann, M. & Frey, B. Potential sources of microbial colonizers in an initial soil ecosystem after retreat of an alpine glacier. *ISME J.* **10**, 1625–1641 (2016).

## Acknowledgements

We acknowledge funding from the Czech Science Foundation Grant No 18–26191S. ELIXIR CZ research infrastructure project LM2015047 by the Ministry of Education, Youth and Sports of the Czech Republic is acknowledged for hosting the database. All corresponding authors of published studies that provided additional information on the samples included in the database are gratefully acknowledged.
## Author contributions

T.V., P.K. and P.B. jointly conceived the study. C.L. and coordinated data acquisition, T.V., D.M., M.K. and P.B. designed the database, T.V. and D.M. developed the database and created the user interface. C.A.G., S.A.H., B.D.B., K.B., V.B., F.D., R.Z.H., M.J., J.K., C.L., S.L., R.L.M., T. Mar., T. Maš., L. Me., L. Mi., T. Mi., S.M., D.N., I.O., S.P.C., M.Š., K.Š., V.T., M.U., L.V., J.V. and L.Ž. identified data sources, processed and analysed sequencing information, collated and analysed metadata. P.B. drafted the manuscript along with T.V., C.L. and P.K. All authors wrote and reviewed the manuscript.

## Competing interests

The authors declare no competing interests.

## Additional information

**Correspondence** and requests for materials should be addressed to P.B.

**Reprints and permissions information** is available at www.nature.com/reprints.

**Publisher's note** Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

<figure><img src="image_7.png" /></figure>

**Open Access** This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

The Creative Commons Public Domain Dedication waiver http://creativecommons.org/publicdomain/zero/1.0/ applies to the metadata files associated with this article.

© The Author(s) 2020
## Author contributions

T.V., P.K. and P.B. jointly conceived the study. C.L. and coordinated data acquisition, T.V., D.M., M.K. and P.B. designed the database, T.V. and D.M. developed the database and created the user interface. C.A.G., S.A.H., B.D.B., K.B., V.B., F.D., R.Z.H., M.J., J.K., C.L., S.L., R.L.M., T. Mar., T. Maš., L. Me., L. Mi., T. Mi., S.M., D.N., I.O., S.P.C., M.Š., K.Š., V.T., M.U., L.V., J.V. and L.Ž. identified data sources, processed and analysed sequencing information, collated and analysed metadata. P.B. drafted the manuscript along with T.V., C.L. and P.K. All authors wrote and reviewed the manuscript.

## Competing interests

The authors declare no competing interests.

## Additional information

**Correspondence** and requests for materials should be addressed to P.B.

**Reprints and permissions information** is available at www.nature.com/reprints.

**Publisher's note** Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

<figure><img src="image_6.png" /></figure>

**Open Access** This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

The Creative Commons Public Domain Dedication waiver http://creativecommons.org/publicdomain/zero/1.0/ applies to the metadata files associated with this article.

© The Author(s) 2020