GlobalAMFungi: a global database of arbuscular mycorrhizal fungal occurrences from high-throughput sequencing metabarcoding studies

. 2023 Dec ; 240 (5) : 2151-2163. [epub] 20231002

Jazyk angličtina Země Anglie, Velká Británie Médium print-electronic

Typ dokumentu časopisecké články

Perzistentní odkaz   https://www.medvik.cz/link/pmid37781910

Grantová podpora
LM2023055 ELIXIR CZ Research Infrastructure Project (MEYS Grant)
PRG1065 Estonian Research Council
PRG1789 Estonian Research Council
21-17749S Grantová Agentura České Republiky
RVO 67985939 Institute of Botany of the Czech Academy of Sciences
European Regional Development Fund

Arbuscular mycorrhizal (AM) fungi are crucial mutualistic symbionts of the majority of plant species, with essential roles in plant nutrient uptake and stress mitigation. The importance of AM fungi in ecosystems contrasts with our limited understanding of the patterns of AM fungal biogeography and the environmental factors that drive those patterns. This article presents a release of a newly developed global AM fungal dataset (GlobalAMFungi database, https://globalamfungi.com) that aims to reduce this knowledge gap. It contains almost 50 million observations of Glomeromycotinian AM fungal amplicon DNA sequences across almost 8500 samples with geographical locations and additional metadata obtained from 100 original studies. The GlobalAMFungi database is built on sequencing data originating from AM fungal taxon barcoding regions in: i) the small subunit rRNA (SSU) gene; ii) the internal transcribed spacer 2 (ITS2) region; and iii) the large subunit rRNA (LSU) gene. The GlobalAMFungi database is an open source and open access initiative that compiles the most comprehensive atlas of AM fungal distribution. It is designed as a permanent effort that will be continuously updated by its creators and through the collaboration of the scientific community. This study also documented applicability of the dataset to better understand ecology of AM fungal taxa.

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Albornoz FE, Ryan MH, Bending GD, Hilton S, Dickie IA, Gleeson DB, Standish RJ. 2022. Agricultural land-use favours Mucoromycotinian, but not Glomeromycotinian, arbuscular mycorrhizal fungi across ten biomes. New Phytologist 233: 1369-1382.

Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. 1997. Gapped Blast and Psi-Blast: a new generation of protein database search programs. Nucleic Acids Research 25: 3389-3402.

Averill C, Anthony MA, Baldrian P, Finkbeiner F, Hoogen J, Kiers T, Kohout P, Hirt E, Smith GR, Crowther TW. 2022. Defending Earth's terrestrial microbiome. Nature Microbiology 2022: 1717-1725.

Baldrian P, Bell-Dereske L, Lepinay C, Větrovský T, Kohout P. 2022a. Fungal communities in soils under global change. Studies in Mycology 103: 1-24.

Baldrian P, Větrovský T, Lepinay C, Kohout P. 2022b. High-throughput sequencing view on the magnitude of global fungal diversity. Fungal Diversity 114: 539-547.

Bengtsson-Palme J, Ryberg M, Hartmann M, Branco S, Wang Z, Godhe A, de Wit P, Sánchez-García M, Ebersberger I, de Sousa F et al. 2013. 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 in Ecology and Evolution 4: 914-919.

Brundrett MC, Tedersoo L. 2018. Evolutionary history of mycorrhizal symbioses and global host plant diversity. New Phytologist 220: 1108-1115.

Canty A, Ripley BD. 2022. boot: bootstrap R (S-Plus) Functions. R package version 1.3-28.1. [WWW document] URL https://cran.r-project.org/web/packages/boot/index.html [accessed 15 May 2023].

Chagnon PL, Bradley RL, Maherali H, Klironomos JN. 2013. A trait-based framework to understand life history of mycorrhizal fungi. Trends in Plant Science 18: 484-491.

Clavel J, Lembrechts J, Alexander J, Haider S, Lenoir J, Milbau A, Nuñez MA, Pauchard A, Nijs I, Verbruggen E. 2021. The role of arbuscular mycorrhizal fungi in nonnative plant invasion along mountain roads. New Phytologist 230: 1156-1168.

Davison J, de Leon DG, Zobel M, Moora M, Bueno CG, Barceló M, Gerz M, León D, Meng Y, Pillar VD et al. 2020. Plant functional groups associate with distinct arbuscular mycorrhizal fungal communities. New Phytologist 226: 1117-1128.

Davison J, Moora M, Öpik M, Adholeya A, Ainsaar L, Bâ A, Burla S, Diedhiou AG, Hiiesalu I, Jairus T et al. 2015. Global assessment of arbuscular mycorrhizal fungus diversity reveals very low endemism. Science 349: 970-973.

Davison J, Moora M, Semchenko M, Adenan SB, Ahmed T, Akhmetzhanova AA, Alatalo JM, al-Quraishy S, Andriyanova E, Anslan S et al. 2021. Temperature and pH define the realised niche space of arbuscular mycorrhizal fungi. New Phytologist 231: 763-776.

Davison J, Öpik M, Zobel M, Vasar M, Metsis M, Moora M. 2012. Communities of arbuscular mycorrhizal fungi detected in forest soil are spatially heterogeneous but do not vary throughout the growing season. PLoS ONE 7: e41938.

Delavaux CS, Ramos RJ, Sturmer SL, Bever JD. 2022. Environmental identification of arbuscular mycorrhizal fungi using the LSU rDNA gene region: an expanded database and improved pipeline. Mycorrhiza 32: 145-153.

Delavaux CS, Sturmer SL, Wagner MR, Schütte U, Morton JB, Bever JD. 2021. Utility of large subunit for environmental sequencing of arbuscular mycorrhizal fungi: a new reference database and pipeline. New Phytologist 229: 3048-3052.

Delgado-Baquerizo M, Oliverio AM, Brewer TE, Benavent-González A, Eldridge DJ, Bardgett RD, Maestre FT, Singh BK, Fierer N. 2018. A global atlas of the dominant bacteria found in soil. Science 359: 320-325.

Fan K, Delgado-Baquerizo M, Yguan Z, Chu H. 2020. Crop production correlates with soil multitrophic communities at the large spatial scale. Soil Biology and Biochemistry 151: 108047.

Hart M, Reader RJ. 2002. Taxonomic basis for variation in the colonization strategy of arbuscular mycorrhizal fungi. New Phytologist 153: 335-344.

Hengl T, De Jesus JM, Heuvelink GBM, Gonzalez MR, Kilibarda M, Blagotić A, Shangguan W, Wright MN, Geng X, Bauer-Marschallinger B et al. 2017. SoilGrids250m: global gridded soil information based on machine learning. PLoS ONE 12: e0169748.

House GL, Bever JD. 2020. Biochar soil amendments in prairie restorations do not interfere with benefits from inoculation with native arbuscular mycorrhizal fungi. Restoration Ecology 28: 785-795.

Hoysted GA, Field KJ, Sinanaj B, Bell CA, Bidartondo MI, Pressel S. 2023. Direct nitrogen, phosphorus and carbon exchanges between Mucoromycotina ‘fine root endophyte’ fungi and a flowering plant in novel monoxenic cultures. New Phytologist 238: 70-79.

Jetz W, Mcpherson JM, Guralnick RP. 2012. Integrating biodiversity distribution knowledge: toward a global map of life. Trends in Ecology & Evolution 27: 151-159.

Jiang S, Liu Y, Luo J, Qin M, Johnson NC, Öpik M, Vasar M, Chai Y, Zhou X, Mao L et al. 2018. Dynamics of arbuscular mycorrhizal fungal community structure and functioning along a nitrogen enrichment gradient in an alpine meadow ecosystem. New Phytologist 220: 1222-1235.

Kakouridis A, Hagen JA, Kan MP, Mambelli S, Feldman LJ, Herman DJ, Weber PK, Pett-Ridge J, Firestone MK. 2022. Routes to roots: direct evidence of water transport by arbuscular mycorrhizal fungi to host plants. New Phytologist 236: 210-221.

Karger DN, Conrad O, Böhner J, Kawohl T, Kreft H, Soria-Auza RW, Zimmermann NE, Linder HP, Kessler M. 2017. Climatologies at high resolution for the earth's land surface areas. Scientific Data 4: 1-20.

Kiers ET, Duhamel M, Beesetty Y, Mensah JA, Franken O, Verbruggen E, Fellbaum CR, Kowalchuk GA, Hart MM, Bago A et al. 2011. Reciprocal rewards stabilize cooperation in the mycorrhizal symbiosis. Science 333: 880-882.

van Kleunen M, Pyšek P, Dawson W, Essl F, Kreft H, Pergl J, Weigelt P, Stein A, Dullinger S, König C et al. 2019. The Global Naturalized Alien Flora (GloNAF) database. Ecology 100: e02542.

Koch AM, Antunes PM, Maherali H, Hart MM, Klironomos JN. 2017. Evolutionary asymmetry in the arbuscular mycorrhizal symbiosis: conservatism in fungal morphology does not predict host plant growth. New Phytologist 214: 1330-1337.

Kohout P, Doubková P, Bahram M, Suda J, Tedersoo L, Voříšková J, Sudová R. 2015. Niche partitioning in arbuscular mycorrhizal communities in temperate grasslands: a lesson from adjacent serpentine and nonserpentine habitats. Molecular Ecology 24: 1831-1843.

Kohout P, Sudová R, Janoušková M, Čtvrtlíková M, Hejda M, Pánková H, Slavíková R, Štajerová K, Vosátka M, Sýkorová Z. 2014. Comparison of commonly used primer sets for evaluating arbuscular mycorrhizal fungal communities: is there a universal solution? Soil Biology and Biochemistry 68: 482-493.

Kolaříková Z, Slavíková R, Krüger C, Krüger M, Kohout P. 2021. PacBio sequencing of Glomeromycota rDNA: a novel amplicon covering all widely used ribosomal barcoding regions and its applicability in taxonomy and ecology of arbuscular mycorrhizal fungi. New Phytologist 231: 490-499.

Kõljalg U, Nilsson RH, Abarenkov K, Tedersoo L, Taylor AFS, Bahram M, Bates ST, Bruns TD, Bengtsson-Palme J, Callaghan TM et al. 2013. Towards a unified paradigm for sequence-based identification of fungi. Molecular Ecology 22: 5271-5277.

Kreft H, Jetz W. 2007. Global patterns and determinants of vascular plant diversity. Proceedings of the National Academy of Sciences, USA 104: 5925-5930.

Krüger M, Teste FP, Laliberté E, Lambers H, Coghlan M, Zemunik G, Bunce M. 2015. The rise and fall of arbuscular mycorrhizal fungal diversity during ecosystem retrogression. Molecular Ecology 24: 4912-4930.

Lahti L, Shetty S. 2018. Introduction to the microbiome R package. [WWW document] URL https://microbiome.github.io/tutorials/ [accessed 13 December 2021].

Lekberg Y, Gibbons SM, Rosendahl S, Ramsey PW. 2013. Severe plant invasions can increase mycorrhizal fungal abundance and diversity. The ISME Journal 7: 1424-1433.

Lekberg Y, Vasar M, Bullington LS, Sepp SK, Antunes PM, Bunn R, Larkin BG, Öpik M. 2018. More bang for the buck? Can arbuscular mycorrhizal fungal communities be characterized adequately alongside other fungi using general fungal primers? New Phytologist 220: 971-976.

Maestre FT, Delgado-Baquerizo M, Jeffries TC, Eldridge DJ, Ochoa V, Gozalo B, Quero JL, García-Gómez M, Gallardo A, Ulrich W et al. 2015. Increasing aridity reduces soil microbial diversity and abundance in global drylands. Proceedings of the National Academy of Sciences, USA 112: 15684-15689.

Moulíková Š, Kolařík M, Lorch JM, Kolarczyková D, Hubka V, Čmoková A. 2023. Wild rodents harbour high diversity of Arthroderma. Persoonia - Molecular Phylogeny and Evolution of Fungi 50: 27-47.

Mozzachiodi S, Bai FY, Baldrian P, Bell G, Boundy-Mills K, Buzzini P, Čadež N, Cubillos FA, Dashko S, Dimitrov R et al. 2022. Yeasts from temperate forests. Yeast 39: 4-24.

Nilsson RH, Anslan S, Bahram M, Wurzbacher C, Baldrian P, Tedersoo L. 2019a. Mycobiome diversity: high-throughput sequencing and identification of fungi. Nature Reviews. Microbiology 17: 95-109.

Nilsson RH, Larsson KH, Taylor AFS, Bengtsson-Palme J, Jeppesen TS, Schigel D, Kennedy P, Picard K, Glöckner FO, Tedersoo L et al. 2019b. The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications. Nucleic Acids Research 47: D259-D264.

Nilsson RH, Ryberg M, Wurzbacher C, Tedersoo L, Anslan S, Põlme S, Spirin V, Mikryukov V, Svantesson S, Hartmann M et al. 2023. What mycologists should talk about when they are talking about the International Code of Nomenclature for algae, fungi, and plants. bioRxiv. doi: 10.1101/2023.02.25.529721.

Ohsowski BM, Zaitsoff PD, Öpik M, Hart MM. 2014. Where the wild things are: looking for uncultured Glomeromycota. New Phytologist 204: 171-179.

Oliveira BF, Machac A, Costa GC, Brooks TM, Davidson AD, Rondinini C, Graham CH. 2016. Species and functional diversity accumulate differently in mammals. Global Ecology and Biogeography 25: 1119-1130.

Öpik M, Davison J. 2016. Uniting species- and community-oriented approaches to understand arbuscular mycorrhizal fungal diversity. Fungal Ecology 24: 106-113.

Öpik M, Davison J, Moora M, Zobel M. 2014. DNA-based detection and identification of Glomeromycota: the virtual taxonomy of environmental sequences. Botany 92: 135-147.

Öpik M, Vanatoa A, Vanatoa E, Moora M, Davison J, Kalwij JM, Reier Ü, Zobel M. 2010. The online database MaarjAM reveals global and ecosystemic distribution patterns in arbuscular mycorrhizal fungi (Glomeromycota). New Phytologist 188: 223-241.

Öpik M, Zobel M, Cantero JJ, Davison J, Facelli JM, Hiiesalu I, Jairus T, Kalwij JM, Koorem K, Leal ME et al. 2013. Global sampling of plant roots expands the described molecular diversity of arbuscular mycorrhizal fungi. Mycorrhiza 23: 411-430.

Orchard S, Hilton S, Bending GR, Dickie IA, Standish RJ, Gleeson DB, Jeffery RP, Powell JR, Walker C, Bass D et al. 2017. Fine endophytes (Glomus tenue) are related to Mucoromycotina, not Glomeromycota. New Phytologist 213: 481-486.

Qiu Q, Bender SF, Mgelwa AS, Hu Y. 2022. Arbuscular mycorrhizal fungi mitigate soil nitrogen and phosphorus losses: a meta-analysis. Science of the Total Environment 807: 150857.

Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO. 2012. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Research 41: D590-D596.

Réblová M, Kolařík M, Nekvindová J, Réblová K, Sklenář F, Miller AN, Hernández-Restrepo M. 2021. Phylogenetic reassessment, taxonomy, and biogeography of Codinaea and similar fungi. Journal of Fungi 20: 1097.

Rodriguez-Ramos JC, Cale JA, Cahill JF, Simard SW, Karst J, Erbilgin N. 2021. Changes in soil fungal community composition depend on functional group and forest disturbance type. New Phytologist 229: 1105-1117.

Sato K, Suyama Y, Saito M, Sugawara K. 2005. A new primer for discrimination of arbuscular mycorrhizal fungi with polymerase chain reaction-denature gradient gel electrophoresis. Grassland Science 51: 179-181.

Schoch CL, Seifert KA, Huhndorf S, Robert V, Spouge JL, Levesque CA, Chen W, Fungal Barcoding Consortium. 2012. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for fungi. Proceedings of the National Academy of Sciences, USA 109: 6241-6246.

Scholtz R, Twidwell D. 2022. The last continuous grasslands on Earth: identification and conservation importance. Conservation Science and Practice 4: e626.

Smith S, Read D. 2008. Mycorrhizal symbiosis. Cambridge, UK: Academic Press.

Spatafora JW, Chang Y, Benny GL, Lazarus K, Smith ME, Berbee ML, Bonito G, Corradi N, Grigoriev I, Gryganskyi A et al. 2016. A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data. Mycologia 108: 1028-1046.

Stürmer SL, Bever JD, Morton JB. 2018. Biogeography of arbuscular mycorrhizal fungi (Glomeromycota): a phylogenetic perspective on species distribution patterns. Mycorrhiza 28: 587-603.

Stürmer SL, Bever JD, Schultz PA, Bentivenga SP. 2021. Celebrating INVAM: 35 years of the largest living culture collection of arbuscular mycorrhizal fungi. Mycorrhiza 31: 117-126.

Sugiyama Y, Sato H. 2021. The limited establishment of native ectomycorrhizal fungi in exotic Eucalyptus spp. stands in Japan. Frontiers in Microbiology 12: 376.

Tedersoo L, Bahram M, Polme S, Kõljalg U, Yorou NS, Wijesundera R, Ruiz LV, Vasco-Palacios AM, Thu PQ, Suija A et al. 2014. Global diversity and geography of soil fungi. Science 346: 1256688.

Tedersoo L, Mikryukov V, Anslan S, Bahram M, Khalid AN, Corrales A, Agan A, Vasco-Palacios AM, Saitta A, Antonelli A et al. 2021. The Global Soil Mycobiome consortium dataset for boosting fungal diversity research. Fungal Diversity 111: 573-588.

Tedersoo L, Mikryukov V, Zizka A, Bahram M, Hagh-Doust N, Anslan S, Prylutskyi O, Delgado-Baquerizo M, Maestre FT, Pärn J et al. 2022. Global patterns in endemicity and vulnerability of soil fungi. Global Change Biology 28: 6696-6710.

Van Geel M, Busschaert P, Honnay O, Lievens B. 2014. Evaluation of six primer pairs targeting the nuclear rRNA operon for characterization of arbuscular mycorrhizal fungal (AMF) communities using 454 pyrosequencing. Journal of Microbiological Methods 106: 93-100.

Vasar M, Andreson R, Davison J, Jairus T, Moora M, Remm M, Young JPW, Zobel M, Öpik M. 2017. Increased sequencing depth does not increase captured diversity of arbuscular mycorrhizal fungi. Mycorrhiza 27: 761-773.

Vasar M, Davison J, Sepp SK, Öpik M, Moora M, Koorem K, Meng Y, Oja J, Akhmetzhanova AA, al-Quraishy S et al. 2021. Arbuscular mycorrhizal fungal communities in the soils of desert habitats. Microorganisms 9: 1-14.

Větrovský T, Baldrian P, Morais D. 2018. Seed 2: a user-friendly platform for amplicon high-throughput sequencing data analyses. Bioinformatics 34: 2292-2294.

Větrovský T, Kohout P, Kopecký M, Machac A, Man M, Bahnmann BD, Brabcová V, Choi J, Meszárošová L, Human ZR et al. 2019. A meta-analysis of global fungal distribution reveals climate-driven patterns. Nature Communications 10: 5142.

Větrovský T, Morais D, Kohout P, Lepinay C, Algora C, Awokunle Hollá S, Bahnmann BD, Bílohnědá K, Brabcová V, D'Alò F et al. 2020. GlobalFungi, a global database of fungal occurrences from high-throughput-sequencing metabarcoding studies. Scientific Data 7: 1-14.

Vlk L, Tedersoo L, Antl T, Větrovský T, Abarenkov K, Pergl J, Albrechtová J, Vosátka M, Baldrian P, Pyšek P et al. 2020a. Alien ectomycorrhizal plants differ in their ability to interact with co-introduced and native ectomycorrhizal fungi in novel sites. The ISME Journal 14: 2336-2346.

Vlk L, Tedersoo L, Antl T, Větrovský T, Abarenkov K, Pergl J, Albrechtová J, Vosátka M, Baldrian P, Pyšek P et al. 2020b. Early successional ectomycorrhizal fungi are more likely to naturalize outside their native range than other ectomycorrhizal fungi. New Phytologist 227: 1289-1293.

Wijayawardene NN, Hyde KD, Al-Ani LKT, Tedersoo L, Haelewaters D, Rajeshkumar KC, Zhao RL, Aptroot A, Leontyev DV, Saxena RK et al. 2020. Outline of fungi and fungus-like taxa. Mycosphere 11: 1060-1456.

Wu H, Yang J, Fu W, Rillig MC, Cao Z, Zhao A, Hao Z, Zhang X, Chen B, Han X. 2023. Identifying thresholds of nitrogen enrichment for substantial shifts in arbuscular mycorrhizal fungal community metrics in a temperate grassland of northern China. New Phytologist 237: 279-294.

Xiang D, Verbruggen E, Hu Y, Veresoglou SD, Rillig MC, Zhou W, Xu T, Li H, Hao Z, Chen Y et al. 2014. Land use influences arbuscular mycorrhizal fungal communities in the farming-pastoral ecotone of northern China. New Phytologist 204: 968-978.

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