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

Tomáš Větrovský, Daniel Morais, Petr Kohout and 30 more

Scientific Data · 2020 · CC BY

doi:10.1101/2020.04.24.060384

Abstract

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.

Full text

From PubMed Central, U.S. National Library of Medicine, as current on Oct 22, 2026. Paragraph numbers are ours, so an answer can point at one.

Background & Summary

1Fungi 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,. 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 health.

2It is of high importance to determine how environmental factors affect the diversity and distribution of fungal communities. So far, only a few studies have focused on fungal distribution and diversity on global scale–. Importantly, these single survey studies focused either on a limited number of biomes,, fairly narrow groups within the fungal kingdom, or were restricted only to fungi inhabiting soil. Although individual studies have 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 combined. 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 fungi. 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 pathogens and helped to identify which fungi tend to follow alien plants invading new environments.

3Here, 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 variants (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 fungi.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 hypotheses, 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.

Data selection

4We 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). In total, 178 publications contained samples that matched our criteria.

Processing of sequencing data

5For 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 v1.0.11. 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 BLASTn, using the SH created considering a 98.5% similarity threshold (BLASTDBv5, general release 8.1 from 2.2.2019). A sequence was classified to the best best hit SH only when the following thresholds were met: e-value < 10e−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

6Sample 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.

7In addition to the metadata provided by the authors of each study, we also extracted bioclimatic variables from the global CHELSA and WorldClim 2 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 sites.

8For each sequence variant that was classified to SH, fungal species name and genus name was retrieved from the UNITE database, when available.

Data Records

9The raw sequencing reads used to create the database are available at different locations (see Table 2).

10The 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 Figshare (GlobalFungi_ITS_variants.zip, GlobalFungi_metadata.xlsx). All database content is accessible using a public graphical user interface at https://globalfungi.com.

Technical Validation

11The 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),. 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 software were removed. All representative sequences where the BLASTn search against the UNITE database resulted in a nonfungal organism, were discarded.

12For 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.

Usage Notes

13The 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 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.

14In 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.

15It 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).

16Importantly, 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.

17Among 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. 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.

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Delgado‐Baquerizo M, et al. Soil microbial communities drive the resistance of ecosystem multifunctionality to global change in drylands across the globe. Ecol. Lett. 2017;20:1295-1305.
Not in our library10.1111/ele.12826
117.
NCBI Sequence Read Archive. 2017.
Not in our library
118.
Cross H, et al. Fungal diversity and seasonal succession in ash leaves infected by the invasive ascomycete Hymenoscyphus fraxineus. New Phytol. 2017;213:1405-1417.
Not in our library10.1111/nph.14204
119.
NCBI Sequence Read Archive. 2016.
Not in our library
120.
Zhang T, Wang NF, Liu HY, Zhang YQ, Yu LY. Soil pH is a key determinant of soil fungal community composition in the Ny-Alesund region, Svalbard (High Arctic). Front. Microbiol. 2016;7:227.
Not in our library10.3389/fmicb.2016.00227
121.
NCBI Sequence Read Archive. 2016.
Not in our library
122.
Gehring CA, et al. Cheatgrass invasion alters the abundance and composition of dark septate fungal communities in sagebrush steppe. Botany. 2016;94:481-491.
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123.
NCBI Sequence Read Archive. 2016.
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124.
Li Y, et al. Changes of soil microbial community under different degraded gradients of alpine meadow. Agric. Ecosyst. Environ. 2016;222:213-222.
Not in our library
125.
NCBI Sequence Read Archive. 2016.
Not in our library
126.
Temperature mediates continental-scale diversity of microbes in forest soils · 2016
No notice
127.
NCBI Sequence Read Archive. 2016.
Not in our library
128.
Cox F, Newsham KK, Bol R, Dungait JA, Robinson CH. Not poles apart: Antarctic soil fungal communities show similarities to those of the distant Arctic. Ecol. Lett. 2016;19:528-536.
Not in our library10.1111/ele.12587
129.
NCBI Sequence Read Archive. 2017.
Not in our library
130.
Bergottini VM, et al. Exploring the diversity of the root-associated microbiome of Ilex paraguariensis St. Hil. (Yerba Mate). Appl. Soil Ecol. 2017;109:23-31.
Not in our library
131.
NCBI Sequence Read Archive. 2017.
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132.
Moussa TA, Al-Zahrani HS, Almaghrabi OA, Abdelmoneim TS, Fuller MP. Comparative metagenomics approaches to characterize the soil fungal communities of western coastal region, Saudi Arabia. PLoS One. 2017;12:e0185096.
Not in our library10.1371/journal.pone.0185096
133.
NCBI Sequence Read Archive. 2016.
Not in our library
134.
Goldmann K, et al. Divergent habitat filtering of root and soil fungal communities in temperate beech forests. Sci. Rep. 2016;11:31439.
Not in our library10.1038/srep31439
135.
NCBI Sequence Read Archive. 2016.
Not in our library
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. 2016;76:9-18.
Not in our library
137.
NCBI Sequence Read Archive. 2017.
Not in our library
138.
Smith ME, et al. Investigating niche partitioning of ectomycorrhizal fungi in specialized rooting zones of the monodominant leguminous tree Dicymbe corymbosa. New Phytol. 2017;215:443-453.
Not in our library10.1111/nph.14570
139.
NCBI Sequence Read Archive. 2016.
Not in our library
140.
Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database · 2016
No notice
141.
NCBI Sequence Read Archive. 2016.
Not in our library
142.
Vannette RL, Leopold DR, Fukami T. Forest area and connectivity influence root-associated fungal communities in a fragmented landscape. Ecology. 2016;97:2374-2383.
Not in our library10.1002/ecy.1472
143.
NCBI Sequence Read Archive. 2017.
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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. 2017;57:1055-1064.
Not in our library10.1002/jobm.201700312
145.
NCBI Sequence Read Archive. 2017.
Not in our library
146.
Glassman SI, Wang IJ, Bruns TD. Environmental filtering by pH and soil nutrients drives community assembly in fungi at fine spatial scales. Mol. Ecol. 2017;26:6960-6973.
Not in our library10.1111/mec.14414
147.
NCBI Sequence Read Archive. 2018.
Not in our library
148.
Cline LC, Schilling JS, Menke J, Groenhof E, Kennedy PG. Ecological and functional effects of fungal endophytes on wood decomposition. Funct. Ecol. 2018;32:181-191.
Not in our library
149.
NCBI Sequence Read Archive. 2016.
Not in our library
150.
Johansen RB, et al. A native and an invasive dune grass share similar, patchily distributed, root-associated fungal communities. Fungal Ecol. 2016;23:141-155.
Not in our library
151.
NCBI Sequence Read Archive. 2017.
Not in our library
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. 2017;10:73-83.
Not in our library
153.
NCBI Sequence Read Archive. 2017.
Not in our library
154.
Fernandez CW, et al. Ectomycorrhizal fungal response to warming is linked to poor host performance at the boreal-temperate ecotone. Glob. Change Biol. 2017;23:1598-1609.
Not in our library10.1111/gcb.13510
155.
NCBI Sequence Read Archive. 2017.
Not in our library
156.
Zhang Z, et al. Fungal communities in ancient peatlands developed from different periods in the Sanjiang Plain, China. PLoS One. 2017;12:e0187575.
Not in our library10.1371/journal.pone.0187575
157.
NCBI Sequence Read Archive. 2017.
Not in our library
158.
Gomes SI, Merckx VS, Saavedra S. Fungal-host diversity among mycoheterotrophic plants increases proportionally to their fungal-host overlap. Ecol. Evol. 2017;7:3623-3630.
Not in our library10.1002/ece3.2974
159.
NCBI Sequence Read Archive. 2017.
Not in our library
160.
Zhou X, et al. Conversion from long-term cultivated wheat field to Jerusalem artichoke plantation changed soil fungal communities. Sci. Rep. 2017;7:41502.
Not in our library10.1038/srep41502
161.
NCBI Sequence Read Archive. 2017.
Not in our library
162.
NCBI Sequence Read Archive. 2017.
Not in our library
163.
Gomes SI, Aguirre‐Gutiérrez J, Bidartondo MI, Merckx VS. Arbuscular mycorrhizal interactions of mycoheterotrophic Thismia are more specialized than in autotrophic plants. New Phytol. 2017;213:1418-1427.
Not in our library10.1111/nph.14249
164.
NCBI Sequence Read Archive. 2017.
Not in our library
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. 2017;12:e0184223.
Not in our library10.1371/journal.pone.0184223
166.
NCBI Sequence Read Archive. 2016.
Not in our library
167.
Gourmelon V, et al. Environmental and geographical factors structure soil microbial diversity in New Caledonian ultramafic substrates: a metagenomic approach. PLoS One. 2016;11:e0167405.
Not in our library10.1371/journal.pone.0167405
168.
NCBI Sequence Read Archive. 2017.
Not in our library
169.
Younginger BS, Ballhorn DJ. Fungal endophyte communities in the temperate fern Polystichum munitum show early colonization and extensive temporal turnover. Am. J. Bot. 2017;104:1188-1194.
Not in our library10.3732/ajb.1700149
170.
NCBI Sequence Read Archive. 2017.
Not in our library
171.
Kamutando CN, et al. Soil nutritional status and biogeography influence rhizosphere microbial communities associated with the invasive tree Acacia dealbata. Sci. Rep. 2017;7:6472.
Not in our library10.1038/s41598-017-07018-w
172.
NCBI Sequence Read Archive. 2017.
Not in our library
173.
Anthony MA, Frey SD, Stinson KA. Fungal community homogenization, shift in dominant trophic guild, and appearance of novel taxa with biotic invasion. Ecosphere. 2017;8:e01951.
Not in our library
174.
NCBI Sequence Read Archive. 2017.
Not in our library
175.
Ge ZW, Brenneman T, Bonito G, Smith ME. Soil pH and mineral nutrients strongly influence truffles and other ectomycorrhizal fungi associated with commercial pecans (Carya illinoinensis). Plant Soil. 2017;418:493-505.
Not in our library
176.
NCBI Sequence Read Archive. 2018.
Not in our library
177.
Mirmajlessi SM, et al. Survey of soil fungal communities in Strawberry fields by Illumina amplicon sequencing. Eurasian Soil Sci. 2018;51:682-691.
Not in our library
178.
NCBI Sequence Read Archive. 2016.
Not in our library
179.
Harrison JG, Forister ML, Parchman TL, Koch GW. Vertical stratification of the foliar fungal community in the world’s tallest trees. Am. J. Bot. 2016;103:2087-2095.
Not in our library10.3732/ajb.1600277
180.
NCBI Sequence Read Archive. 2019.
Not in our library
181.
Semenova‐Nelsen TA, Platt WJ, Patterson TR, Huffman J, Sikes BA. Frequent fire reorganizes fungal communities and slows decomposition across a heterogeneous pine savanna landscape. New Phytol. 2019;224:916-927.
Not in our library10.1111/nph.16096
182.
NCBI Sequence Read Archive. 2017.
Not in our library
183.
Dean SL, et al. A study of Glycine max (soybean) fungal communities under different agricultural practices. Plant Gene. 2017;11:8-16.
Not in our library
184.
NCBI Sequence Read Archive. 2017.
Not in our library
185.
Kyaschenko J, Clemmensen KE, Hagenbo A, Karltun E, Lindahl BD. Shift in fungal communities and associated enzyme activities along an age gradient of managed Pinus sylvestris stands. ISME J. 2017;11:863-874.
Not in our library10.1038/ismej.2016.184
186.
NCBI Sequence Read Archive. 2017.
Not in our library
187.
Tian J, et al. Ecological succession pattern of fungal community in soil along a retreating glacier. Front. Microbiol. 2017;8:1028.
Not in our library10.3389/fmicb.2017.01028
188.
NCBI Sequence Read Archive. 2017.
Not in our library
189.
Oono R, Rasmussen A, Lefèvre E. Distance decay relationships in foliar fungal endophytes are driven by rare taxa. Environ. Microbiol. 2017;19:2794-2805.
Not in our library10.1111/1462-2920.13799
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. 2017;12:e0189796.
Not in our library10.1371/journal.pone.0189796
191.
NCBI Sequence Read Archive. 2017.
Not in our library
192.
Marín C, et al. Functional land-use change effects on soil fungal communities in Chilean temperate rainforests. J. Soil Sci. Plant Nut. 2017;17:985-1002.
Not in our library
193.
NCBI Sequence Read Archive. 2017.
Not in our library
194.
Siles JA, Margesin R. Seasonal soil microbial responses are limited to changes in functionality at two Alpine forest sites differing in altitude and vegetation. Sci. Rep. 2017;7:2204.
Not in our library10.1038/s41598-017-02363-2
195.
NCBI Sequence Read Archive. 2018.
Not in our library
196.
Kazartsev I, Shorohova E, Kapitsa E, Kushnevskaya H. Decaying Picea abies log bark hosts diverse fungal communities. Fungal Ecol. 2018;33:1-12.
Not in our library
197.
NCBI Sequence Read Archive. 2017.
Not in our library
198.
Peay KG, et al. Convergence and contrast in the community structure of bacteria, fungi and archaea along a tropical elevation-climate gradient. FEMS Microbiol. Ecol. 2017;93:fix045.
Not in our library10.1093/femsec/fix045
199.
NCBI Sequence Read Archive. 2018.
Not in our library
200.
Coleine C, et al. Antarctic cryptoendolithic fungal communities are highly adapted and dominated by Lecanoromycetes and Dothideomycetes. Front. Microbiol. 2018;9:1392.
Not in our library10.3389/fmicb.2018.01392
201.
NCBI Sequence Read Archive. 2018.
Not in our library
202.
Park MS, et al. Diversity of fungi associated with roots of Calanthe orchid species in Korea. J. Microbiol. 2018;56:49-55.
Not in our library10.1007/s12275-018-7319-9
203.
NCBI Sequence Read Archive. 2018.
Not in our library
204.
Glynou K, Nam B, Thines M, Maciá‐Vicente JG. Facultative root-colonizing fungi dominate endophytic assemblages in roots of nonmycorrhizal Microthlaspi species. New Phytol. 2018;217:1190-1202.
Not in our library10.1111/nph.14873
205.
NCBI Sequence Read Archive. 2018.
Not in our library
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. 2018;28:39-47.
Not in our library10.1007/s00572-017-0806-8
207.
NCBI Sequence Read Archive. 2017.
Not in our library
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. 2017;114:E9403-E9412.
Not in our library10.1073/pnas.1710455114
209.
NCBI Sequence Read Archive. 2017.
Not in our library
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. 2017;26:4811-4830.
Not in our library10.1111/mec.14244
211.
NCBI Sequence Read Archive. 2017.
Not in our library
212.
Varenius K, Lindahl BD, Dahlberg A. Retention of seed trees fails to lifeboat ectomycorrhizal fungal diversity in harvested Scots pine forests. FEMS Microbiol. Ecol. 2017;93:fix105.
Not in our library10.1093/femsec/fix105
213.
NCBI Sequence Read Archive. 2017.
Not in our library
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. 2017;115:499-510.
Not in our library
215.
NCBI Sequence Read Archive. 2017.
Not in our library
216.
Mendoza JR, Kok CR, Stratton J, Bianchini A, Hallen-Adams HE. Understanding the mycobiota of maize from the highlands of Guatemala, and implications for maize quality and safety. Crop Prot. 2017;101:5-11.
Not in our library
217.
NCBI Sequence Read Archive. 2017.
Not in our library
218.
Miura T, Sánchez R, Castañeda LE, Godoy K, Barbosa O. Is microbial terroir related to geographic distance between vineyards? Environ. Microbiol. Rep. 2017;9:742-749.
Not in our library10.1111/1758-2229.12589
219.
NCBI Sequence Read Archive. 2018.
Not in our library
220.
Zhang J, et al. Distinct large-scale biogeographic patterns of fungal communities in bulk soil and soybean rhizosphere in China. Sci. Total Environ. 2018;644:791-800.
Not in our library10.1016/j.scitotenv.2018.07.016
221.
NCBI Sequence Read Archive. 2017.
Not in our library
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. 2017;12:e0184611.
Not in our library10.1371/journal.pone.0184611
223.
NCBI Sequence Read Archive. 2018.
Not in our library
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. 2018;610:750-758.
Not in our library10.1016/j.scitotenv.2017.08.110
225.
NCBI Sequence Read Archive. 2018.
Not in our library
226.
Schneider-Maunoury L, et al. Is Tuber melanosporum colonizing the roots of herbaceous, non-ectomycorrhizal plants? Fungal Ecol. 2018;31:59-68.
Not in our library
227.
NCBI Sequence Read Archive. 2018.
Not in our library
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. 2018;257:120-131.
Not in our library
229.
NCBI Sequence Read Archive. 2018.
Not in our library
230.
Schroeder JW, et al. Community composition and diversity of Neotropical root‐associated fungi in common and rare trees. Biotropica. 2018;50:694-703.
Not in our library
231.
NCBI Sequence Read Archive. 2018.
Not in our library
232.
Fan K, Weisenhorn P, Gilbert JA, Chu H. Wheat rhizosphere harbors a less complex and more stable microbial co-occurrence pattern than bulk soil. Soil Biol. Biochem. 2018;125:251-260.
Not in our library
233.
NCBI Sequence Read Archive. 2018.
Not in our library
234.
Montagna M, et al. Differential biodiversity responses between kingdoms (plants, fungi, bacteria and metazoa) along an Alpine succession gradient. Mol. Ecol. 2018;27:3671-3685.
Not in our library10.1111/mec.14817
235.
NCBI Sequence Read Archive. 2018.
Not in our library
236.
Schön ME, Nieselt K, Garnica S. Belowground fungal community diversity and composition associated with Norway spruce along an altitudinal gradient. PLoS One. 2018;13:e0208493.
Not in our library10.1371/journal.pone.0208493
237.
NCBI Sequence Read Archive. 2017.
Not in our library
238.
Thiem D, Piernik A, Hrynkiewicz K. Ectomycorrhizal and endophytic fungi associated with Alnus glutinosa growing in a saline area of central Poland. Symbiosis. 2017;75:17-28.
Not in our library10.1007/s13199-017-0512-5
239.
NCBI Sequence Read Archive. 2016.
Not in our library
240.
Barnes CJ, Maldonado C, Frøslev TG, Antonelli A, Rønsted N. Unexpectedly high beta-diversity of root-associated fungal communities in the Bolivian Andes. Front. Microbiol. 2016;7:1377.
Not in our library10.3389/fmicb.2016.01377
241.
NCBI Sequence Read Archive. 2018.
Not in our library
242.
Schlatter DC, Kahl K, Carlson B, Huggins DR, 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. 2018;94:fiy098.
Not in our library10.1093/femsec/fiy098
243.
NCBI Sequence Read Archive. 2018.
Not in our library
244.
Rasmussen PU, 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. 2018;220:1248-1261.
Not in our library10.1111/nph.15088
245.
NCBI Sequence Read Archive. 2018.
Not in our library
246.
NCBI Sequence Read Archive. 2012.
Not in our library
247.
Guo J, et al. Soil fungal assemblage complexity is dependent on soil fertility and dominated by deterministic processes. New Phytol. 2019;226:232-243.
Not in our library10.1111/nph.16345
248.
NCBI Sequence Read Archive. 2019.
Not in our library
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. 2019;95:fiz092.
Not in our library10.1093/femsec/fiz092
250.
NCBI Sequence Read Archive. 2018.
Not in our library
251.
Rogers TJ, et al. Exploring variation in phyllosphere microbial communities across four hemlock species. Ecosphere. 2018;9:e02524.
Not in our library
252.
NCBI Sequence Read Archive. 2018.
Not in our library
253.
The Endophytic Mycobiome of European Ash and Sycamore Maple Leaves – Geographic Patterns, Host Specificity and Influence of Ash Dieback · 2018
Not checked
254.
NCBI Sequence Read Archive. 2019.
Not in our library
255.
Truong C, et al. Ectomycorrhizal fungi and soil enzymes exhibit contrasting patterns along elevation gradients in southern Patagonia. New Phytol. 2019;222:1936-1950.
Not in our library10.1111/nph.15714
256.
NCBI Sequence Read Archive. 2018.
Not in our library
257.
Soil microbiomes with distinct assemblies through vertical soil profiles drive the cycling of multiple nutrients in reforested ecosystems · 2018
No notice
258.
NCBI Sequence Read Archive. 2018.
Not in our library
259.
Marasco R, et al. Rhizosheath microbial community assembly of sympatric desert speargrasses is independent of the plant host. Microbiome. 2018;6:215.
Not in our library10.1186/s40168-018-0597-y
260.
NCBI Sequence Read Archive. 2018.
Not in our library
261.
Bickford WA, Goldberg DE, Kowalski KP, Zak DR. Root endophytes and invasiveness: no difference between native and non‐native Phragmites in the Great Lakes region. Ecosphere. 2018;9:e02526.
Not in our library
262.
NCBI Sequence Read Archive. 2018.
Not in our library
263.
Si P, et al. Rhizosphere microenvironments of eight common deciduous fruit trees were shaped by microbes in Northern China. Front. Microbiol. 2018;9:3147.
Not in our library10.3389/fmicb.2018.03147
264.
NCBI Sequence Read Archive. 2019.
Not in our library
265.
Purahong W, Wu YT, Chen CT, 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. 2019;10:983.
Not in our library10.3389/fmicb.2019.00983
266.
European Nucleotide Archive. 2014.
Not in our library
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. 2014;9:e99852.
Not in our library10.1371/journal.pone.0099852
268.
European Nucleotide Archive. 2013.
Not in our library
269.
Schmidt PA, et al. Illumina metabarcoding of a soil fungal community. Soil Biol. Biochem. 2013;65:128-132.
Not in our library
270.
European Nucleotide Archive. 2015.
Not in our library
271.
van der Wal A, Ottosson E, De Boer W. Neglected role of fungal community composition in explaining variation in wood decay rates. Ecology. 2015;96:124-133.
Not in our library10.1890/14-0242.1
272.
European Nucleotide Archive. 2015.
Not in our library
273.
Muller LA, Hilger HH. Insights into the effects of serpentine soil conditions on the community composition of fungal symbionts in the roots of Onosma echioides. Soil Biol. Biochem. 2015;81:1-8.
Not in our library
274.
European Nucleotide Archive. 2015.
Not in our library
275.
Sun H, et al. Fungal community shifts in structure and function across a boreal forest fire chronosequence. Appl. Environ. Microbiol. 2015;81:7869-7880.
Not in our library10.1128/aem.02063-15
276.
European Nucleotide Archive. 2015.
Not in our library
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. 2015;18:48-55.
Not in our library
278.
European Nucleotide Archive. 2017.
Not in our library
279.
Purahong W, et al. Characterization of unexplored deadwood mycobiome in highly diverse subtropical forests using culture-independent molecular technique. Front. Microbiol. 2017;8:574.
Not in our library10.3389/fmicb.2017.00574
280.
European Nucleotide Archive. 2016.
Not in our library
281.
van der Wal A, Gunnewiek PJK, Cornelissen JHC, Crowther TW, de Boer W. Patterns of natural fungal community assembly during initial decay of coniferous and broadleaf tree logs. Ecosphere. 2016;7:e01393.
Not in our library
282.
European Nucleotide Archive. 2016.
Not in our library
283.
Reese AT, et al. Urban stress is associated with variation in microbial species composition-but not richness-in Manhattan. ISME J. 2016;10:751-760.
Not in our library10.1038/ismej.2015.152
284.
European Nucleotide Archive. 2016.
Not in our library
285.
Kielak AM, Scheublin TR, Mendes LW, Van Veen JA, Kuramae EE. Bacterial community succession in Pine-wood decomposition. Front. Microbiol. 2016;7:231.
Not in our library10.3389/fmicb.2016.00231
286.
European Nucleotide Archive. 2016.
Not in our library
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).
Not in our library10.1093/femsec/fiw170
288.
European Nucleotide Archive. 2016.
Not in our library
289.
Frey B, et al. Microbial diversity in European alpine permafrost and active layers. FEMS Microbiol. Ecol. 2016;92:fiw018.
Not in our library10.1093/femsec/fiw018
290.
European Nucleotide Archive. 2017.
Not in our library
291.
Wilhelm RC, et al. A metagenomic survey of forest soil microbial communities more than a decade after timber harvesting. Sci. Data. 2017;4:170092.
Not in our library10.1038/sdata.2017.92
292.
European Nucleotide Archive. 2016.
Not in our library
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. 2016;6:28257.
Not in our library10.1038/srep28257
294.
European Nucleotide Archive. 2018.
Not in our library
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. 2018;20:1693-1710.
Not in our library10.1111/1462-2920.14081
296.
European Nucleotide Archive. 2017.
Not in our library
297.
Yang T, et al. Soil fungal diversity in natural grasslands of the Tibetan Plateau: associations with plant diversity and productivity. New Phytol. 2017;215:756-765.
Not in our library10.1111/nph.14606
298.
European Nucleotide Archive. 2017.
Not in our library
299.
Nguyen D, et al. Foliar fungi of Betula pendula: impact of tree species mixtures and assessment methods. Sci. Rep. 2017;7:41801.
Not in our library10.1038/srep41801
300.
European Nucleotide Archive. 2017.
Not in our library
301.
Tu B, et al. Microbial diversity in chinese temperate steppe: unveiling the most influential environmental drivers. FEMS Microbiol. Ecol. 2017;93:fix031.
Not in our library10.1093/femsec/fix031
302.
European Nucleotide Archive. 2017.
Not in our library
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. 2017;115:393-402.
Not in our library
304.
European Nucleotide Archive. 2017.
Not in our library
305.
van der Wal A, Gunnewiek PK, de Hollander M, de Boer W. Fungal diversity and potential tree pathogens in decaying logs and stumps. Forest Ecol. Manag. 2017;406:266-273.
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306.
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307.
Alzarhani AK, et al. Are drivers of root-associated fungal community structure context specific? ISME J. 2019;13:1330-1344.
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308.
European Nucleotide Archive. 2017.
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309.
van der Wal A, Gunnewiek PK, de Boer W. Soil-wood interactions: Influence of decaying coniferous and broadleaf logs on composition of soil fungal communities. Fungal Ecol. 2017;30:132-134.
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310.
European Nucleotide Archive. 2018.
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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. 2018;9:2120.
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312.
European Nucleotide Archive. 2018.
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313.
Sun R, et al. Tillage changes vertical distribution of soil bacterial and fungal communities. Front. Microbiol. 2018;9:699.
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314.
European Nucleotide Archive. 2018.
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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. 2018;132:74-82.
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316.
European Nucleotide Archive. 2018.
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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. 2018;9:76.
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318.
European Nucleotide Archive. 2019.
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319.
Ramirez KS, et al. Range-expansion effects on the belowground plant microbiome. Nat. Ecol. Evol. 2019;3:604.
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320.
European Nucleotide Archive. 2019.
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321.
European Nucleotide Archive. 2019.
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322.
George PB, et al. Divergent national-scale trends of microbial and animal biodiversity revealed across diverse temperate soil ecosystems. Nat. Commun. 2019;10:1107.
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323.
European Nucleotide Archive. 2019.
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324.
Álvarez-Garrido L, Viñegla B, Hortal S, Powell JR, Carreira JA. Distributional shifts in ectomycorrizhal fungal communities lag behind climate-driven tree upward migration in a conifer forest-high elevation shrubland ecotone. Soil Biol. Biochem. 2019;137:107545.
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325.
DNA Data Bank of Japan. 2014.
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326.
Yamamoto S, et al. Spatial segregation and aggregation of ectomycorrhizal and root-endophytic fungi in the seedlings of two Quercus species. PLoS One. 2014;9:e96363.
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327.
DNA Data Bank of Japan. 2014.
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328.
Kadowaki K, et al. Detection of the horizontal spatial structure of soil fungal communities in a natural forest. Popul. Ecol. 2014;56:301-310.
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329.
DNA Data Bank of Japan. 2016.
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330.
Izuno A, et al. Structure of phyllosphere fungal communities in a tropical dipterocarp plantation: A massively parallel next-generation sequencing analysis. Mycoscience. 2016;57:171-180.
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331.
DNA Data Bank of Japan. 2016.
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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. 2016;92:fiw061.
Not in our library10.1093/femsec/fiw061
333.
DNA Data Bank of Japan. 2016.
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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. 2016;11:e0166669.
Not in our library10.1371/journal.pone.0166669
335.
DNA Data Bank of Japan. 2016.
Not in our library
336.
Matsuoka S, Mori AS, 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. 2016;92:fiw044.
Not in our library10.1093/femsec/fiw044
337.
DNA Data Bank of Japan. 2016.
Not in our library
338.
Toju H, Yamamoto S, Tanabe AS, Hayakawa T, Ishii HS. Network modules and hubs in plant-root fungal biomes. J. R. Soc. Interface. 2016;13:20151097.
Not in our library10.1098/rsif.2015.1097
339.
DNA Data Bank of Japan. 2017.
Not in our library
340.
Shen Z, et al. Banana Fusarium Wilt disease incidence is influenced by shifts of soil microbial communities under different monoculture spans. Microb. Ecol. 2017;75:739-750.
Not in our library10.1007/s00248-017-1052-5
341.
DNA Data Bank of Japan. 2018.
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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. 2018;21:165-171.
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343.
DNA Data Bank of Japan. 2015.
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344.
Fukasawa Y, Matsuoka S. Communities of wood-inhabiting fungi in dead pine logs along a geographical gradient in Japan. Fungal Ecol. 2015;18:75-82.
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345.
DNA Data Bank of Japan. 2016.
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346.
Toju H, Tanabe AS, Ishii HS. Ericaceous plant-fungus network in a harsh alpine-subalpine environment. Mol. Ecol. 2016;25:3242-3257.
Not in our library10.1111/mec.13680
347.
DNA Data Bank of Japan. 2019.
Not in our library
348.
Shigyo N, Umeki K, Hirao T. Seasonal dynamics of soil fungal and bacterial communities in cool-temperate montane forests. Front. Microbiol. 2019;10:1944.
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349.
Dryad. 2014.
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350.
Geml J, et al. Long-term warming alters richness and composition of taxonomic and functional groups of arctic fungi. FEMS Microbiol. Ecol. 2015;91:fiv095.
Not in our library10.1093/femsec/fiv095
351.
Arctic. Dryad. 2017.
Not in our library10.5061/dryad.n82g9
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. 2017;26:4798-4810.
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353.
Dryad. 2015.
Not in our library10.5061/dryad.2343k
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. 2015;205:1587-1597.
Not in our library10.1111/nph.13216
355.
Dryad. 2014.
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356.
Rime T, et al. Vertical distribution of the soil microbiota along a successional gradient in a glacier forefield. Mol. Ecol. 2015;24:1091-1108.
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357.
Dryad. 2017.
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358.
Semenova TA, et al. Compositional and functional shifts in arctic fungal communities in response to experimentally increased snow depth. Soil Biol. Biochem. 2016;100:201-209.
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359.
Dryad. 2014.
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360.
Wicaksono CY, et al. Contracting montane cloud forests: a case study of the Andean alder (Alnusacuminata) and associated fungi in the Yungas. Biotropica. 2017;49:141-152.
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361.
Dryad. 2013.
Not in our library10.5061/dryad.216tp
362.
Yao F, et al. Substantial compositional turnover of fungal communities in an alpine ridge-to-snowbed gradient. Mol. Ecol. 2013;22:5040-5052.
Not in our library10.1111/mec.12437
363.
GenBank. 2017.
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364.
Schappe T, et al. The role of soil chemistry and plant neighbourhoods in structuring fungal communities in three Panamanian rainforests. J. Ecol. 2017;105:569-579.
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365.
GenBank. 2017.
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366.
GenBank. 2017.
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367.
BioSample. 2017.
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368.
Vaz AB, et al. Using Next-Generation Sequencing (NGS) to uncover diversity of wood-decaying fungi in neotropical atlantic forests. Phytotaxa. 2017;295:1-21.
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369.
BioSample. 2017.
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370.
Australian Antarctic Data Centre. 2014.
Not in our library10.4225/15/526f42ada05b1
371.
Ji M, et al. Microbial diversity at Mitchell Peninsula, Eastern Antarctica: a potential biodiversity “hotspot”. Polar Biol. 2016;39:237-249.
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372.
Hartmann M, et al. Significant and persistent impact of timber harvesting on soil microbial communities in Northern coniferous forests. ISME J. 2012;6:2199-2218.
Not in our library10.1038/ismej.2012.84
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. 2016;10:1625-1641.
Not in our library10.1038/ismej.2015.238

Cited by papers we hold 3

Defining Soilborne Pathogen Complexes Provides a New Foundation for the Effective Management of Faba Bean Root Diseases in Ethiopia · 2025
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Metagenomes, metatranscriptomes and microbiomes of naturally decomposing deadwood · 2021
Not checked
Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding? · 2020
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