Bardgett, R. D. & van der Putten, W. H. Belowground biodiversity and ecosystem functioning. Nature 515, 505–511 (2014).
Gessner, M. O. et al. Diversity meets decomposition. Trends Ecol Evol 25, 372–380 (2010).
Delavaux, C. S. et al. Mycorrhizal feedbacks influence global forest structure and diversity. Commun Biol 6 (2023).
Delavaux, C. S. et al. Mycorrhizal fungi influence global plant biogeography. Nat Ecol Evol 3, 424–429 (2019).
Anthony, M. A. et al. Forest tree growth is linked to mycorrhizal fungal composition and function across Europe. ISME J 16 (2022).
Luo, S. et al. Higher productivity in forests with mixed mycorrhizal strategies. Nat Commun 14, 1377 (2023).
van der Heijden, M. G. A., Martin, F. M., Selosse, M. A. & Sanders, I. R. Mycorrhizal ecology and evolution: The past, the present, and the future. New Phytol 205, 1406–1423 (2015).
Singh, B. K. et al. Climate change impacts on plant pathogens, food security and paths forward. Nat Rev Microbiol 21, 640–656 (2023).
Fisher, M. C. et al. Emerging fungal threats to animal, plant and ecosystem health. Nature 484, 186–194 (2012).
van Ruijven, J., Ampt, E., Francioli, D. & Mommer, L. Do soil‐borne fungal pathogens mediate plant diversity–productivity relationships? Evidence and future opportunities. J Ecol 108, 1810–1821 (2020).
Sarmiento, C. et al. Soilborne fungi have host affinity and host-specific effects on seed germination and survival in a lowland tropical forest. Proc Natl Acad Sci USA 114, 11458–11463 (2017).
Liu, S. et al. Phylotype diversity within soil fungal functional groups drives ecosystem stability. Nat Ecol Evol 6, 900–909 (2022).
Averill, C. et al. Defending Earth’s terrestrial microbiome. Nat Microbiol 7, 1717–1725 (2022).
Lutz, S. et al. Soil microbiome indicators can predict crop growth response to large-scale inoculation with arbuscular mycorrhizal fungi. Nat Microbiol 8, 2277–2289 (2023).
Ryberg, M. & Nilsson, R. H. New light on names and naming of dark taxa. MycoKeys 30, 31–39 (2018).
Lücking, R. et al. Fungal taxonomy and sequence-based nomenclature. Nat Microbiol 6, 540–548 (2021).
Niskanen, T. et al. Pushing the Frontiers of Biodiversity Research: Unveiling the Global Diversity, Distribution, and Conservation of Fungi. Annu Rev Environ Resour 48, 149–176 (2023).
Gonçalves, S. C., Haelewaters, D., Furci, G. & Mueller, G. M. Include all fungi in biodiversity goals. Science (1979) 373, 403–403 (2021).
Mikryukov, V. et al. Connecting the multiple dimensions of global soil fungal diversity. Sci Adv 9, eadj8016 (2023).
Tedersoo, L. et al. Global diversity and geography of soil fungi. Science 346, 1052–1053 (2014).
Bissett, A. et al. Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database. Gigascience 5, s13742–016 (2016).
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).
Midgley, D. J., Greenfield, P., Bissett, A. & Tran-Dinh, N. First evidence of Pezoloma ericae in Australia: using the Biomes of Australia Soil Environments (BASE) to explore the Australian phylogeography of known ericoid mycorrhizal and root-associated fungi. Mycorrhiza 27, 587–594 (2017).
Davoodian, N., Jackson, C. J., Holmes, G. D. & Lebel, T. Continental‐scale metagenomics, BLAST searches, and herbarium specimens: The Australian Microbiome Initiative and the National Herbarium of Victoria. Appl Plant Sci 8 (2020).
Freestone, M. W. et al. Continental-scale distribution and diversity of Ceratobasidium orchid mycorrhizal fungi in Australia. Ann Bot 128, 329–343 (2021).
Yan, D. et al. High-throughput eDNA monitoring of fungi to track functional recovery in ecological restoration. Biol Conserv 217, 113–120 (2018).
Mills, J. G. et al. Revegetation of urban green space rewilds soil microbiotas with implications for human health and urban design. Restor Ecol 28, S322–S334 (2020).
Liddicoat, C. et al. Ambient soil cation exchange capacity inversely associates with infectious and parasitic disease risk in regional Australia. Sci Total Environ 626, 117–125 (2018).
Egidi, E. et al. Delving into the dark ecology: A continent-wide assessment of patterns of composition in soil fungal communities from Australian tussock grasslands. Fungal Ecol 39, 356–370 (2019).
Delgado-Baquerizo, M. et al. Ecological drivers of soil microbial diversity and soil biological networks in the Southern Hemisphere. Ecology 99, 583–596 (2018).
Li, J., Nie, M., Powell, J. R., Bissett, A. & Pendall, E. Soil physico-chemical properties are critical for predicting carbon storage and nutrient availability across Australia. Environ Res Lett 15, 094088 (2020).
Viscarra Rossel, R. A. et al. Environmental controls of soil fungal abundance and diversity in Australia’s diverse ecosystems. Soil Biol Biochem 170, 108694 (2022).
Yang, Y., Shen, Z., Bissett, A. & Viscarra Rossel, R. A. Estimating soil fungal abundance and diversity at a macroecological scale with deep learning spectrotransfer functions. SOIL 8, 223–235 (2022).
Bowd, E. J. et al. Direct and indirect effects of fire on microbial communities in a pyrodiverse dry‐sclerophyll forest. J Ecol 110, 1687–1703 (2022).
Bowd, E. J., Banks, S. C., Bissett, A., May, T. W. & Lindenmayer, D. B. Disturbance alters the forest soil microbiome. Mol Ecol 31, 419–447 (2022).
Waymouth, V. et al. Riparian fungal communities respond to land-use mediated changes in soil properties and vegetation structure. Plant Soil 475, 491–513 (2022).
Waymouth, V., Miller, R. E., Ede, F., Bissett, A. & Aponte, C. Variation in soil microbial communities: elucidating relationships with vegetation and soil properties, and testing sampling effectiveness. Plant Ecol 221, 837–851 (2020).
Tedersoo, L. et al. Best practices in metabarcoding of fungi: From experimental design to results. Mol Ecol 31, 2769–2795 (2022).
Egidi, E. et al. A few Ascomycota taxa dominate soil fungal communities worldwide. Nat Commun 10, 2369 (2019).
Větrovský, T. et al. A meta-analysis of global fungal distribution reveals climate-driven patterns. Nat Commun 10, 5142 (2019).
George, P. B. L. et al. Divergent national-scale trends of microbial and animal biodiversity revealed across diverse temperate soil ecosystems. Nat Commun 10, 1107 (2019).
Hakimzadeh, A. et al. A pile of pipelines: An overview of the bioinformatics software for metabarcoding data analyses. Mol Ecol Resour 00, 1–17 (2023).
Gardes, M. & Bruns, T. D. ITS primers with enhanced specificity for basidiomycetes ‐ application to the identification of mycorrhizae and rusts. Mol Ecol 2, 113–118 (1993).
White, T. J., Bruns, T., Lee, S. & Taylor, J. Amplification and direct sequencing of fungal ribosomal rna genes for phylogenetics. in PCR Protocols: A Guide to Methods and Applications 315–322, https://doi.org/10.1016/B978-0-12-372180-8.50042-1 (Academic Press, San Diego, CA, 1990).
Manter, D. K. & Vivanco, J. M. Use of the ITS primers, ITS1F and ITS4, to characterize fungal abundance and diversity in mixed-template samples by qPCR and length heterogeneity analysis. J Microbiol Methods 71, 7–14 (2007).
Větrovský, T. et al. GlobalFungi, a global database of fungal occurrences from high-throughput-sequencing metabarcoding studies. Sci Data 7, 1–14 (2020).
Tedersoo, L. et al. The Global Soil Mycobiome consortium dataset for boosting fungal diversity research. Fungal Divers 111, 573–588 (2021).
Bissett, A. & Brown, M. V. Alpha-diversity is strongly influenced by the composition of other samples when using multiplexed sequencing approaches. Soil Biol Biochem 127, 79–81 (2018).
Belbin, L., Wallis, E., Hobern, D. & Zerger, A. The Atlas of Living Australia: History, current state and future directions. Biodivers Data J 9 (2021).
Lebel, T. et al. Confirming the presence of five exotic species of Amanita in Australia and New Zealand. Swainsona 44, 1–44 (2024).
Atlas of Living Australia occurrence download for Biome of Australia Soil Environments https://doi.org/10.26197/ala.17104622-e3ef-4f3f-b0ad-2e83743c0dcd (Accessed 8 April 2024).
GBIF occurrence download for Biome of Australia Soil Environments https://doi.org/10.15468/hn7xl9 (Accessed 8 April 2024).
Colesie, C., Walshaw, C. V., Sancho, L. G., Davey, M. P. & Gray, A. Antarctica’s vegetation in a changing climate. WIREs Climate Change 14 (2023).
GBIF occurrence download for Antarctica https://doi.org/10.15468/dl.68djdq (Accessed 8 April 2024).
Kauserud, H. ITS alchemy: On the use of ITS as a DNA marker in fungal ecology. Fungal Ecol 65, 101274 (2023).
Drake, L. E. et al. An assessment of minimum sequence copy thresholds for identifying and reducing the prevalence of artefacts in dietary metabarcoding data. Methods Ecol Evol 13, 694–710 (2022).
Florence, L. et al. A curated soil fungal dataset to advance fungal ecology and conservation research in Australia and Antarctica, figshare, https://doi.org/10.6084/m9.figshare.27938037 (2025).
Vu, D., Nilsson, R. H. & Verkley, G. J. M. Dnabarcoder: An open-source software package for analysing and predicting DNA sequence similarity cutoffs for fungal sequence identification. Mol Ecol Resour 22, 2793–2809 (2022).
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).
Rivers, A. R., Weber, K. C., Gardner, T. G., Liu, S. & Armstrong, S. D. ITSxpress: Software to rapidly trim internally transcribed spacer sequences with quality scores for marker gene analysis. F1000Res 7, 1418 (2018).
Rognes, T., Flouri, T., Nichols, B., Quince, C. & Mahé, F. VSEARCH: a versatile open source tool for metagenomics. PeerJ 4, e2584 (2016).
Callahan, B. J. et al. DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods 13, 581–583 (2016).
Abarenkov, K. et al. Full UNITE + INSD fasta release for eukaryotes. Version 04.04.2024. UNITE Community https://doi.org/10.15156/BIO/2959331 (2024).
Edgar, R. C. UCHIME2: improved chimera prediction for amplicon sequencing. biorxiv 074252 (2016).
Calderón-Sanou, I., Münkemüller, T., Boyer, F., Zinger, L. & Thuiller, W. From environmental DNA sequences to ecological conclusions: How strong is the influence of methodological choices? J Biogeogr 47, 193–206 (2020).
Nilsson, R. H. et al. Introducing guidelines for publishing DNA-derived occurrence data through biodiversity data platforms. Metabarcoding Metagenom 6 (2022).
Abarenkov, K. et al. Full UNITE + INSD fasta release for fungi. Version 04.04.2024. UNITE Community https://doi.org/10.15156/BIO/2959330 (2024).
Camacho, C. et al. BLAST + : architecture and applications. BMC Bioinformatics 10, 421 (2009).
Põlme, S. et al. FungalTraits: a user-friendly traits database of fungi and fungus-like stramenopiles. Fungal Divers 105 (2020).
Tedersoo, L. et al. High-level classification of the Fungi and a tool for evolutionary ecological analyses. Fungal Divers 90, 135–159 (2018).
Bradshaw, M. J. et al. Extensive intragenomic variation in the internal transcribed spacer region of fungi. iScience 26, 107317 (2023).
Ovaskainen, O. et al. Global Spore Sampling Project: A global, standardized dataset of airborne fungal DNA. Sci Data 11, 1–17 (2024).
Furneaux, B., Bahram, M., Rosling, A., Yorou, N. S. & Ryberg, M. Long- and short-read metabarcoding technologies reveal similar spatiotemporal structures in fungal communities. Mol Ecol Resour 21, 1833–1849 (2021).
Burg, S. et al. Experimental evidence that root‐associated fungi improve plant growth at high altitude. Mol Ecol 33 (2024).
Dondoshansky, I. & Wolf, Y. BLASTCLUST-BLAST score-based singlelinkage clustering. (2000).
Harwood, T. 9 s climatology for continental Australia 1976-2005: BIOCLIM variable suite. v1. https://doi.org/10.25919/5dce30cad79a8 (2019).
Lembrechts, J. J. et al. Global maps of soil temperature. Glob Chang Biol 28, 3110–3144 (2022).
Malone, B. & Searle, R. Soil and Landscape Grid National Soil Attribute Maps – Sand (3” Resolution) – Release 2. v3. Data Collection. https://doi.org/10.25919/rjmy-pa10 (2022).
Malone, B. & Searle, R. Soil and Landscape Grid National Soil Attribute Maps – Clay (3” Resolution) – Release 2. v4. Data Collection. https://doi.org/10.25919/hc4s-3130 (2022).
Malone, B. & Searle, R. Soil and Landscape Grid National Soil Attribute Maps – Silt (3” Resolution) – Release 2. v2. Data Collection. https://doi.org/10.25919/2ew1-0w57 (2022).
Malone, B. & Searle, R. Soil and Landscape Grid National Soil Attribute Maps – Soil Depth (3” Resolution) – Release 2. v3. Data Collection. https://doi.org/10.25919/djdn-5×77 (2020).
Viscarra Rossel, R., Chen, C., Grundy, M., Searle, R. & Clifford, D. Soil and Landscape Grid Australia-Wide 3D Soil Property Maps (3” Resolution) – Release 1. v3. Data Collection. https://doi.org/10.4225/08/5aaf553b63215 (2014).
Wadoux, A. et al. Soil and Landscape Grid National Soil Attribute Maps – Organic Carbon (3” Resolution) – Release 2. v2.Data Collection. https://doi.org/10.25919/ejhm-c070 (2022).
Zund, P. Soil and Landscape Grid National Soil Attribute Maps – Available Phosphorus (3” Resolution) – Release 1. v1. Data Collection. https://doi.org/10.25919/6qzh-b979 (2022).
Malone, B. Soil and Landscape Grid National Soil Attribute Maps – Cation Exchange Capacity (3” Resolution) – Release 1. v1. Data Collection. https://doi.org/10.25919/pkva-gf85 (2022).
Roman Dobarco, M. et al. Soil and Landscape Grid National Soil Attribute Maps – Soil Organic Carbon Fractions (3” Resolution) – Release 1. v5. Data Collection. https://doi.org/10.25919/fa46-ey49 (2022).
Malone, B. Soil and Landscape Grid National Soil Attribute Maps – PH (Water) (3” Resolution) – Release 1. v1. Data Collection. https://doi.org/10.25919/37z2-0q10 (2022).
Scarth, P., Armston, J., Lucas, R. & Bunting, P. Vegetation Height and Structure – Derived from ALOS-1 PALSAR, Landsat and ICESat/GLAS, Australia Coverage. V1. https://portal.tern.org.au/metadata/TERN/de1c2fef-b129-485e-9042-8b22ee616e66 (2023).
Mokany, K. et al. Plant Diversity Spatial Layers for Australia. v2.Data Collection https://doi.org/10.25919/mk24-1792 (2022).
Harwood, T. et al. 9 Arcsecond Gridded HCAS 2.1 (2001-2018) Base Model Estimation of Habitat Condition for Terrestrial Biodiversity, 18-Year Trend and 2010-2015 Epoch Change for Continental Australia. v7. Data Collection. https://doi.org/10.25919/nkjf-f088 (2021).
Gallant, J., Wilson, N., Tickle, P. K., Dowling, T. & Read, A. 3 Second SRTM Derived Digital Elevation Model (DEM). Version 1.0. https://pid.geoscience.gov.au/dataset/ga/69888 (2009).
Yang, R.-H. et al. Evaluation of the ribosomal DNA internal transcribed spacer (ITS), specifically ITS1 and ITS2, for the analysis of fungal diversity by deep sequencing. PLoS One 13, e0206428 (2018).
Nilsson, R. H., Ryberg, M., Abarenkov, K., Sjökvist, E. & Kristiansson, E. The ITS region as a target for characterization of fungal communities using emerging sequencing technologies. FEMS Microbiol Lett 296, 97–101 (2009).
Lindahl, B. D. et al. Fungal community analysis by high-throughput sequencing of amplified markers – a user’s guide. New Phytologist 199, 288–299 (2013).
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. Methods Ecol Evol 4, 914–919 (2013).
Amses, K. R. et al. Diploid-dominant life cycles characterize the early evolution of Fungi. Proc Natl Acad Sci USA 119, 1–10 (2022).
Tedersoo, L. et al. Regional-Scale In-Depth Analysis of Soil Fungal Diversity Reveals Strong pH and Plant Species Effects in Northern Europe. Front Microbiol 11, 1–31 (2020).
Hao, T., Elith, J., Guillera-Arroita, G., Lahoz-Monfort, J. J. & May, T. W. Enhancing repository fungal data for biogeographic analyses. Fungal Ecol 53, 101097 (2021).
May, T. Biogeography of Australasian Fungi: From Mycogeography to the Mycobiome. in Handbook of Australasian Biogeography 156–213 https://doi.org/10.1201/9781315373096 (CRC Press, Boca Raton, FL, 2017).
Phillips, S. J., Anderson, R. P. & Schapire, R. E. Maximum entropy modeling of species geographic distributions. Ecol Modell 190, 231–259 (2006).
Phillips, S. J. & Dudík, M. Modeling of species distributions with Maxent: new extensions and a comprehensive evaluation. Ecography 31, 161–175 (2008).
Hijmans, R. J., Phillips, S., Leathwick, J., Elith, J. & Hijmans, M. R. J. Package ‘dismo’. Circles 9, 1–68 (2017).
Bougoure, J., Ludwig, M., Brundrett, M. & Grierson, P. Identity and specificity of the fungi forming mycorrhizas with the rare mycoheterotrophic orchid Rhizanthella gardneri. Mycol Res 113, 1097–1106 (2009).
van der Linde, S. et al. Environment and host as large-scale controls of ectomycorrhizal fungi. Nature 558, 243–248 (2018).
Veldre, V. et al. Evolution of nutritional modes of Ceratobasidiaceae (Cantharellales, Basidiomycota) as revealed from publicly available ITS sequences. Fungal Ecol 6, 256–268 (2013).
Martos, F. et al. Independent recruitment of saprotrophic fungi as mycorrhizal partners by tropical achlorophyllous orchids. New Phytol 184, 668–681 (2009).
Suetsugu, K., Yamato, M., Matsubayashi, J. & Tayasu, I. Comparative study of nutritional mode and mycorrhizal fungi in green and albino variants of Goodyera velutina, an orchid mainly utilizing saprotrophic rhizoctonia. Mol Ecol 28, 4290–4299 (2019).
Yagame, T., Orihara, T., Selosse, M., Yamato, M. & Iwase, K. Mixotrophy of Platanthera minor, an orchid associated with ectomycorrhiza‐forming Ceratobasidiaceae fungi. New Phytol 193, 178–187 (2012).
Sánchez‐Ramírez, S., Tulloss, R. E., Amalfi, M. & Moncalvo, J. Palaeotropical origins, boreotropical distribution and increased rates of diversification in a clade of edible ectomycorrhizal mushrooms (Amanita section Caesareae). J Biogeogr 42, 351–363 (2015).