Articles | Volume 10, issue 1
https://doi.org/10.5194/soil-10-251-2024
© Author(s) 2024. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
https://doi.org/10.5194/soil-10-251-2024
© Author(s) 2024. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Original research article
| Highlight paper
| 
11 Apr 2024
Original research article | Highlight paper |
| 11 Apr 2024
| 11 Apr 2024
Unraveling biogeographical patterns and environmental drivers of soil fungal diversity at the French national scale
Christophe Djemiel
Agroécologie, INRAE, Institut Agro, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
Samuel Dequiedt
Agroécologie, INRAE, Institut Agro, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
Walid Horrigue
Agroécologie, INRAE, Institut Agro, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
Arthur Bailly
Agroécologie, INRAE, Institut Agro, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
Mélanie Lelièvre
Agroécologie, INRAE, Institut Agro, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
Julie Tripied
Agroécologie, INRAE, Institut Agro, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
Charles Guilland
Agroécologie, INRAE, Institut Agro, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
present address: Novasol experts, 21000 Dijon, France
Solène Perrin
Agroécologie, INRAE, Institut Agro, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
Gwendoline Comment
Agroécologie, INRAE, Institut Agro, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
Nicolas P. A. Saby
INRAE, Info&Sols, 45075 Orléans, France
Claudy Jolivet
INRAE, Info&Sols, 45075 Orléans, France
Antonio Bispo
INRAE, Info&Sols, 45075 Orléans, France
Line Boulonne
INRAE, Info&Sols, 45075 Orléans, France
Antoine Pierart
ADEME, Service Agriculture et Forêt, 49004 Angers, France
Patrick Wincker
Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
Corinne Cruaud
Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
Pierre-Alain Maron
Agroécologie, INRAE, Institut Agro, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
Sébastien Terrat
Agroécologie, INRAE, Institut Agro, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
Lionel Ranjard
CORRESPONDING AUTHOR
Agroécologie, INRAE, Institut Agro, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
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Cited articles
Alberdi, A. and Gilbert, M. T. P.: A guide to the application of Hill numbers to DNA-based diversity analyses, Mol. Ecol. Resour., 19, 804–817, https://doi.org/10.1111/1755-0998.13014, 2019.
Bahram, M., Hildebrand, F., Forslund, S. K., Anderson, J. L., Soudzilovskaia, N. A., Bodegom, P. M., Bengtsson-Palme, J., Anslan, S., Coelho, L. P., Harend, H., Huerta-Cepas, J., Medema, M. H., Maltz, M. R., Mundra, S., Olsson, P. A., Pent, M., Põlme, S., Sunagawa, S., Ryberg, M., Tedersoo, L., and Bork, P.: Structure and function of the global topsoil microbiome, Nature, 560, 233–237, https://doi.org/10.1038/s41586-018-0386-6, 2018.
Baldrian, P., Větrovský, T., Lepinay, C., and Kohout, P.: High-throughput sequencing view on the magnitude of global fungal diversity, Fungal Divers., 114, 539–547, https://doi.org/10.1007/s13225-021-00472-y, 2022.
Ballabio, C., Panagos, P., and Monatanarella, L.: Mapping topsoil physical properties at European scale using the LUCAS database, Geoderma, 261, 110–123, https://doi.org/10.1016/j.geoderma.2015.07.006, 2016.
Banos, S., Lentendu, G., Kopf, A., Wubet, T., Glöckner, F. O., and Reich, M.: A comprehensive fungi-specific 18S rRNA gene sequence primer toolkit suited for diverse research issues and sequencing platforms, BMC Microbiol., 18, 190, https://doi.org/10.1186/s12866-018-1331-4, 2018.
Bar-On, Y. M., Phillips, R., and Milo, R.: The biomass distribution on Earth, P. Natl. Acad. Sci., 115, 6506–6511, https://doi.org/10.1073/pnas.1711842115, 2018.
Bastida, F., Eldridge, D. J., García, C., Kenny Png, G., Bardgett, R. D., and Delgado-Baquerizo, M.: Soil microbial diversity–biomass relationships are driven by soil carbon content across global biomes, ISME J., 15, 2081–2091, https://doi.org/10.1038/s41396-021-00906-0, 2021.
Bent, S. J. and Forney, L. J.: The tragedy of the uncommon: understanding limitations in the analysis of microbial diversity, ISME J., 2, 689–695, https://doi.org/10.1038/ismej.2008.44, 2008.
Berbee, M. L., Strullu-Derrien, C., Delaux, P. M., Strother, P. K., Kenrick, P., Selosse, M. A., and Taylor, J. W.: Genomic and fossil windows into the secret lives of the most ancient fungi, Nat. Rev. Microbiol., 18, 717–730, https://doi.org/10.1038/s41579-020-0426-8, 2020.
Bickel, S., Chen, X., Papritz, A., and Or, D.: A hierarchy of environmental covariates control the global biogeography of soil bacterial richness, Sci. Rep., 9, 12129, https://doi.org/10.1038/s41598-019-48571-w, 2019.
Bivand, R., Keitt, T., Rowlingson, B., Pebesma, E., Sumner, M., Hijmans, R., Rouault, E., and Bivand, M. R.: Package “rgdal”, Bindings for the Geospatial Data Abstraction Library, https://cran.r-project.org/web/packages/rgdal/index.html (last access: 15 October 2017), 2015.
Blackwell, M.: The fungi: 1, 2, 3 …5.1 million species?, Am. J. Bot., 98, 426–38, https://doi.org/10.3732/ajb.1000298, 2011.
Bonneville, S., Delpomdor, F., Preat, A., Chevalier, C., Araki, T., Kazemian, M., Steele, A., Schreiber, A., Wirth, R., and Benning, L. G.: Molecular identification of fungi microfossils in a Neoproterozoic shale rock, Sci. Adv., 6, eaax7599, https://doi.org/10.1126/sciadv.aax7599, 2020.
Calabon, M. S., Hyde, K. D., Jones, E. B. G., Luo, Z. L., Dong, W., Hurdeal, V. G., Gentekaki, E., Rossi, W., Leonardi, M., Thiyagaraja, V., Lestari, A. S., Shen, H. W., Bao, D. F., Boonyuen, N., and Zeng, M.: Freshwater fungal numbers, Fungal Divers., 114, 3–235, https://doi.org/10.1007/s13225-022-00503-2, 2022.
Canini, F., Zucconi, L., Pacelli, C., Selbmann, L., Onofri, S., and Geml, J.: Vegetation, pH and Water Content as Main Factors for Shaping Fungal Richness, Community Composition and Functional Guilds Distribution in Soils of Western Greenland, Front. Microbiol., 10, 2348, https://doi.org/10.3389/fmicb.2019.02348, 2019.
Chao, A., Gotelli, N. J., Hsieh, T. C., Sander, E. L., Ma, K. H., Colwell, R. K., and Ellison, A. M.: Rarefaction and extrapolation with Hill numbers: a framework for sampling and estimation in species diversity studies, Ecol. Monogr., 84, 45–67, https://doi.org/10.1890/13-0133.1, 2014.
Chemidlin Prévost-Bouré, N., Christen, R., Dequiedt, S., Mougel, C., Lelièvre, M., Jolivet, C., Shahbazkia, H. R., Guillou, L., Arrouays, D., and Ranjard, L.: Validation and Application of a PCR Primer Set to Quantify Fungal Communities in the Soil Environment by Real-Time Quantitative PCR, PLoS ONE, 6, e24166, https://doi.org/10.1371/journal.pone.0024166, 2011.
Christel, A., Maron, P.-A., and Ranjard, L.: Impact of farming systems on soil ecological quality: a meta-analysis, Environ. Chem. Lett., 19, 4603–4625, https://doi.org/10.1007/s10311-021-01302-y, 2021.
Chu, H., Gao, G.-F., Ma, Y., Fan, K., and Delgado-Baquerizo, M.: Soil Microbial Biogeography in a Changing World: Recent Advances and Future Perspectives, mSystems, 5, e00803-19, https://doi.org/10.1128/mSystems.00803-19, 2020.
Connell, J. H.: Diversity in Tropical Rain Forests and Coral Reefs, Science, 199, 1302–1310, https://doi.org/10.1126/science.199.4335.1302, 1978.
Cordero, O. X. and Datta, M. S.: Microbial interactions and community assembly at microscales, Curr. Opin. Microbiol., 31, 227–234, https://doi.org/10.1016/j.mib.2016.03.015, 2016.
De Boer, W., Folman, L. B., Summerbell, R. C., and Boddy, L.: Living in a fungal world: Impact of fungi on soil bacterial niche development, FEMS Microbiol. Rev., 29, 795–811, https://doi.org/10.1016/j.femsre.2004.11.005, 2005.
Delgado-Baquerizo, M., Oliverio, A. M., Brewer, T. E., Benavent-González, A., Eldridge, D. J., Bardgett, R. D., Maestre, F. T., Singh, B. K., and Fierer, N.: A global atlas of the dominant bacteria found in soil, Science, 359, 320–325, https://doi.org/10.1126/science.aap9516, 2018.
Dequiedt, S., Saby, N. P. A., Lelievre, M., Jolivet, C., Thioulouse, J., Toutain, B., Arrouays, D., Bispo, A., Lemanceau, P., and Ranjard, L.: Biogeographical patterns of soil molecular microbial biomass as influenced by soil characteristics and management, Glob. Ecol. Biogeogr., 20, 641–652, https://doi.org/10.1111/j.1466-8238.2010.00628.x, 2011.
de Vries, F. T., Thébault, E., Liiri, M., Birkhofer, K., Tsiafouli, M. A., Bjørnlund, L., Bracht Jørgensen, H., Brady, M. V., Christensen, S., de Ruiter, P. C., D'Hertefeldt, T., Frouz, J., Hedlund, K., Hemerik, L., Hol, W. H. G., Hotes, S., Mortimer, S. R., Setälä, H., Sgardelis, S. P., Uteseny, K., van der Putten, W. H., Wolters, V., and Bardgett, R. D.: Soil food web properties explain ecosystem services across European land use systems, P. Natl. Acad. Sci. USA, 110, 14296–14301, https://doi.org/10.1073/pnas.1305198110, 2013.
Ding, C., Chen, J., Zhu, F., Chai, L., Lin, Z., Zhang, K., and Shi, Y.: Biological Toxicity of Heavy Metal(loid)s in Natural Environments: From Microbes to Humans, Front. Environ. Sci., 10, 920957, https://doi.org/10.3389/fenvs.2022.920957, 2022.
Dini-Andreote, F., Kowalchuk, G. A., Prosser, J. I., and Raaijmakers, J. M.: Towards meaningful scales in ecosystem microbiome research, Environ. Microbiol., 23, 1–4, https://doi.org/10.1111/1462-2920.15276, 2021.
Djemiel, C., Dequiedt, S., Karimi, B., Cottin, A., Girier, T., El Djoudi, Y., Wincker, P., Lelièvre, M., Mondy, S., Chemidlin Prévost-Bouré, N., Maron, P. A., Ranjard, L., and Terrat, S.: BIOCOM-PIPE: a new user-friendly metabarcoding pipeline for the characterization of microbial diversity from 16S, 18S and 23S rRNA gene amplicons, BMC Bioinformatics, 21, 492, https://doi.org/10.1186/s12859-020-03829-3, 2020.
Djemiel, C., Maron, P. A., Terrat, S., Dequiedt, S., Cottin, A., and Ranjard, L.: Inferring microbiota functions from taxonomic genes: a review, GigaScience, 11, giab090, https://doi.org/10.1093/gigascience/giab090, 2022.
Egidi, E., Delgado-Baquerizo, M., Plett, J. M., Wang, J., Eldridge, D. J., Bardgett, R. D., Maestre, F. T., and Singh, B. K.: A few Ascomycota taxa dominate soil fungal communities worldwide, Nat. Commun., 10, 2369, https://doi.org/10.1038/s41467-019-10373-z, 2019.
Fausto, A., Rodrigues, M. L., and Coelho, C.: The still underestimated problem of fungal diseases worldwide, Front. Microbiol., 10, 214, https://doi.org/10.3389/fmicb.2019.00214, 2019.
Fernandez-Ugalde, O., Scarpa, S., Orgiazzi, A., Panagos, P., Van Liedekerke, M., Marechal, A., and Jones, A.: LUCAS 2018 Soil Module, ISBN 978-92-76-54832-4, 2022.
Fierer, N. and Jackson, R. B.: The diversity and biogeography of soil bacterial communities, P. Natl. Acad. Sci. USA, 103, 626–631, https://doi.org/10.1073/pnas.0507535103, 2006.
Finn, D. R., Lee, S., Lanzén, A., Bertrand, M., Nicol, G. W., and Hazard, C.: Cropping systems impact changes in soil fungal, but not prokaryote, alpha-diversity and community composition stability over a growing season in a long-term field trial, FEMS Microbiol. Ecol., 97, fiab136, https://doi.org/10.1093/femsec/fiab136, 2021.
Frac, M., Hannula, S. E., Belka, M., and Jȩdryczka, M.: Fungal biodiversity and their role in soil health, Front. Microbiol., 9, 1–9, https://doi.org/10.3389/fmicb.2018.00707, 2018.
Geisen, S., Wall, D. H., and van der Putten, W. H.: Challenges and Opportunities for Soil Biodiversity in the Anthropocene, Curr. Biol., 29, R1036–R1044, https://doi.org/10.1016/j.cub.2019.08.007, 2019.
Genre, A., Lanfranco, L., Perotto, S., and Bonfante, P.: Unique and common traits in mycorrhizal symbioses, Nat. Rev. Microbiol., 18, 649–660, https://doi.org/10.1038/s41579-020-0402-3, 2020.
George, P. B. L., Lallias, D., Creer, S., Seaton, F. M., Kenny, J. G., Eccles, R. M., Griffiths, R. I., Lebron, I., Emmett, B. A., Robinson, D. A., and Jones, D. L.: Divergent national-scale trends of microbial and animal biodiversity revealed across diverse temperate soil ecosystems, Nat. Commun., 10, 1107, https://doi.org/10.1038/s41467-019-09031-1, 2019a.
George, P. B. L., Creer, S., Griffiths, R. I., Emmett, B. A., Robinson, D. A., and Jones, D. L.: Primer and Database Choice Affect Fungal Functional but Not Biological Diversity Findings in a National Soil Survey, Front. Environ. Sci., 7, 173, https://doi.org/10.3389/fenvs.2019.00173, 2019b.
Giller, K. E., Witter, E., and Mcgrath, S. P.: Toxicity of heavy metals to microorganisms and microbial processes in agricultural soils: A review, Soil Biol. Biochem., 30, 1389–1414, https://doi.org/10.1016/S0038-0717(97)00270-8, 1998.
Glassman, S. I., Wang, I. J., and Bruns, T. D.: Environmental filtering by pH and soil nutrients drives community assembly in fungi at fine spatial scales, Mol. Ecol., 26, 6960–6973, https://doi.org/10.1111/mec.14414, 2017.
Granger, V., Bez, N., Fromentin, J., Meynard, C., Jadaud, A., and Mérigot, B.: Mapping diversity indices: not a trivial issue, Methods Ecol. Evol., 6, 688–696, https://doi.org/10.1111/2041-210X.12357, 2015.
Griffiths, B. S. and Philippot, L.: Insights into the resistance and resilience of the soil microbial community, FEMS Microbiol. Rev., 37, 112–129, https://doi.org/10.1111/j.1574-6976.2012.00343.x, 2013.
Griffiths, R. I., Thomson, B. C., James, P., Bell, T., Bailey, M., and Whiteley, A. S.: The bacterial biogeography of British soils, Environ. Microbiol., 13, 1642–1654, https://doi.org/10.1111/j.1462-2920.2011.02480.x, 2011.
Le Guillou, C., Chemidlin Prévost-Bouré, N., Karimi, B., Akkal-Corfini, N., Dequiedt, S., Nowak, V., Terrat, S., Menasseri-Aubry, S., Viaud, V., Maron, P., and Ranjard, L.: Tillage intensity and pasture in rotation effectively shape soil microbial communities at a landscape scale, MicrobiologyOpen, 8, e00676, https://doi.org/10.1002/mbo3.676, 2019.
Hage, H. and Rosso, M. N.: Evolution of fungal carbohydrate-active enzyme portfolios and adaptation to plant cell-wall polymers, J. Fungi, 7, 1–16, https://doi.org/10.3390/jof7030185, 2021.
Handcock, M. S., Hunter, D. R., Butts, C. T., Goodreau, S. M., Krivitsky, P. N., Bender-deMoll, S., Morris, M., and Morris, M. M.: Package “statnet”, https://github.com/statnet/statnet (last access: 2 April 2024), 2019.
Hannula, S. E. and Träger, S.: Soil fungal guilds as important drivers of the plant richness–productivity relationship, New Phytol., 226, 947–949, https://doi.org/10.1111/nph.16523, 2020.
Hawksworth, D. L. and Lücking, R.: Fungal Diversity Revisited: 2.2 to 3.8 Million Species, Microbiol. Spectr., 5, 10–128, https://doi.org/10.1128/microbiolspec.funk-0052-2016, 2017.
Hazard, C. and Johnson, D.: Does genotypic and species diversity of mycorrhizal plants and fungi affect ecosystem function?, New Phytol., 220, 1122–1128, https://doi.org/10.1111/nph.15010, 2018.
Hiiesalu, I., Bahram, M., and 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, https://doi.org/10.1111/mec.14246, 2017.
Hsieh, T. C., Ma, K. H., and Chao, A.: iNEXT: an R package for rarefaction and extrapolation of species diversity (Hill numbers), Methods Ecol. Evol., 7, 1451–1456, https://doi.org/10.1111/2041-210X.12613, 2016.
Hyde, K. D.: The numbers of fungi, Fungal Divers., 114, p. 1, https://doi.org/10.1007/s13225-022-00507-y, 2022.
Hyndman, R. J., Athanasopoulos, G., Bergmeir, C., Caceres, G., Chhay, L., O'Hara-Wild, M., Petropoulos, F., Razbash, S., and Wang, E.: Package “forecast”, https://github.com/robjhyndman/forecast (last access: 10 January 2022), 2020.
Jia, X., Dini-Andreote, F., and Falcão Salles, J.: Community Assembly Processes of the Microbial Rare Biosphere, Trends Microbiol., 26, 738–747, https://doi.org/10.1016/j.tim.2018.02.011, 2018.
Jiao, S. and Lu, Y.: Abundant fungi adapt to broader environmental gradients than rare fungi in agricultural fields, Glob. Change Biol., 26, 4506–4520, https://doi.org/10.1111/gcb.15130, 2020.
Jiao, S., Zhang, B., Zhang, G., Chen, W., and Wei, G.: Stochastic community assembly decreases soil fungal richness in arid ecosystems, Mol. Ecol., 30, 4338–4348, https://doi.org/10.1111/mec.16047, 2021.
Jolivet, C., Arrouays, D., Boulonne, L., Ratié, C., and Saby, N.: Le réseau de mesures de la qualité des sols de France (RMQS), Etat D'avancement Prem. Résultats Etude Gest. Sols, 13, 149–164, 2006.
Jolivet, C., Almeida Falcon, J.-L., Berché, P., Boulonne, L., Fontaine, M., Gouny, L., Lehmann, S., Maitre, B., Ratié, C., Schellenberger, E., and Soler-Dominguez, N.: French Soil Quality Monitoring Network Manual RMQS2: second metropolitan campaign 2016–2027, ISBN: 2-7380-1451-8, https://doi.org/10.17180/KC64-NY88, 2022.
Jousset, A., Bienhold, C., Chatzinotas, A., Gallien, L., Gobet, A., Kurm, V., Küsel, K., Rillig, M. C., Rivett, D. W., Salles, J. F., van der Heijden, M. G. A., Youssef, N. H., Zhang, X., Wei, Z., and Hol, W. H. G.: Where less may be more: how the rare biosphere pulls ecosystems strings, ISME J., 11, 853–862, https://doi.org/10.1038/ismej.2016.174, 2017.
Karimi, B., Maron, P. A., Chemidlin-Prevost Boure, N., Bernard, N., Gilbert, D., and Ranjard, L.: Microbial diversity and ecological networks as indicators of environmental quality, Environ. Chem. Lett., 15, 265–281, https://doi.org/10.1007/s10311-017-0614-6, 2017.
Karimi, B., Terrat, S., Dequiedt, S., Saby, N. P. A., Horrigue, W., Lelièvre, M., Nowak, V., Jolivet, C., Arrouays, D., Wincker, P., Cruaud, C., Bispo, A., Maron, P.-A., Bouré, N. C. P., and Ranjard, L.: Biogeography of soil bacteria and archaea across France, Sci. Adv., 4, eaat1808, https://doi.org/10.1126/sciadv.aat1808, 2018.
Karimi, B., Dequiedt, S., Terrat, S., Jolivet, C., Arrouays, D., Wincker, P., Cruaud, C., Bispo, A., Chemidlin Prévost-Bouré, N., and Ranjard, L.: Biogeography of Soil Bacterial Networks along a Gradient of Cropping Intensity, Sci. Rep., 9, 3812, https://doi.org/10.1038/s41598-019-40422-y, 2019.
Karimi, B., Villerd, J., Dequiedt, S., Terrat, S., Chemidlin-Prévost Bouré, N., Djemiel, C., Lelièvre, M., Tripied, J., Nowak, V., Saby, N. P. A., Bispo, A., Jolivet, C., Arrouays, D., Wincker, P., Cruaud, C., and Ranjard, L.: Biogeography of soil microbial habitats across France, Glob. Ecol. Biogeogr., 29, 1399–1411, https://doi.org/10.1111/geb.13118, 2020.
Karimi, B., Masson, V., Guilland, C., Leroy, E., Pellegrinelli, S., Giboulot, E., Maron, P.-A., and Ranjard, L.: Ecotoxicity of copper input and accumulation for soil biodiversity in vineyards, Environ. Chem. Lett., 19, 2013–2030, https://doi.org/10.1007/s10311-020-01155-x, 2021.
Khan, M. A., Khan, S., Khan, A., and Alam, M.: Soil contamination with cadmium, consequences and remediation using organic amendments, Sci. Total Environ., 601/602, 1591–1605, https://doi.org/10.1016/j.scitotenv.2017.06.030, 2017.
Komsta, L. and Komsta, M. L.: Package “outliers”, Med. Univ. Lub. Lub., https://cran.r-project.org/web/packages/outliers/index.html (last access: 26 March 2022), 2011.
Lark, R. M.: Modelling complex soil properties as contaminated regionalized variables, Geoderma, 106, 173–190, https://doi.org/10.1016/S0016-7061(01)00123-9, 2002.
Leckie, S. E., Prescott, C. E., Grayston, S. J., Neufeld, J. D., and Mohn, W. W.: Characterization of Humus Microbial Communities in Adjacent Forest Types That Differ in Nitrogen Availability, Microb. Ecol., 48, 29–40, https://doi.org/10.1007/s00248-003-1020-0, 2004.
Legendre, P.: Numerical ecology, Elsevier, 487–493, https://doi.org/10.1016/B978-0-12-409548-9.10595-0, 2018.
Lehmann, A., Zheng, W., Ryo, M., Soutschek, K., Roy, J., Rongstock, R., Maaß, S., and Rillig, M. C.: Fungal Traits Important for Soil Aggregation, Front. Microbiol., 10, 2904, https://doi.org/10.3389/fmicb.2019.02904, 2020.
Lentendu, G., Wubet, T., Chatzinotas, A., Wilhelm, C., Buscot, F., and Schlegel, M.: Effects of long-term differential fertilization on eukaryotic microbial communities in an arable soil: A multiple barcoding approach, Mol. Ecol., 23, 3341–3355, https://doi.org/10.1111/mec.12819, 2014.
Li, Y., Steenwyk, J. L., Chang, Y., Wang, Y., James, T. Y., Stajich, J. E., Spatafora, J. W., Groenewald, M., Dunn, C. W., Hittinger, C. T., Shen, X. X., and Rokas, A.: A genome-scale phylogeny of the kingdom Fungi, Curr. Biol., 31, 1653–1665, https://doi.org/10.1016/j.cub.2021.01.074, 2021.
Lienhard, P., Tivet, F., Chabanne, A., Dequiedt, S., Lelièvre, M., Sayphoummie, S., Leudphanane, B., Prévost-Bouré, N. C., Séguy, L., Maron, P.-A., and Ranjard, L.: No-till and cover crops shift soil microbial abundance and diversity in Laos tropical grasslands, Agron. Sustain. Dev., 33, 375–384, https://doi.org/10.1007/s13593-012-0099-4, 2013.
Loron, C. C., François, C., Rainbird, R. H., Turner, E. C., Borensztajn, S., and Javaux, E. J.: Early fungi from the Proterozoic era in Arctic Canada, Nature, 570, 232–235, https://doi.org/10.1038/s41586-019-1217-0, 2019.
Lumley, T. and Lumley, M. T.: Package “leaps”, Regres. Subset Sel. Thomas Lumley Based Fortran Code Alan Mill. Available Online HttpCRAN R-Proj. Orgpackage Leaps, https://cran.r-project.org/web/packages/leaps/index.html (last access: 16 January 2020), 2013.
Ma, B., Dai, Z., Wang, H., Dsouza, M., Liu, X., He, Y., Wu, J., Rodrigues, J. L. M., Gilbert, J. A., Brookes, P. C., and Xu, J.: Distinct Biogeographic Patterns for Archaea, Bacteria, and Fungi along the Vegetation Gradient at the Continental Scale in Eastern China, mSystems, 2, 10–128, https://doi.org/10.1128/mSystems.00174-16, 2017.
Maestre, F. T., Delgado-Baquerizo, M., Jeffries, T. C., Eldridge, D. J., Ochoa, V., Gozalo, B., Quero, J. L., García-Gómez, M., Gallardo, A., Ulrich, W., Bowker, M. A., Arredondo, T., Barraza-Zepeda, C., Bran, D., Florentino, A., Gaitán, J., Gutiérrez, J. R., Huber-Sannwald, E., Jankju, M., Mau, R. L., Miriti, M., Naseri, K., Ospina, A., Stavi, I., Wang, D., Woods, N. N., Yuan, X., Zaady, E., and Singh, B. K.: Increasing aridity reduces soil microbial diversity and abundance in global drylands, P. Natl. Acad. Sci. USA, 112, 15684–15689, https://doi.org/10.1073/pnas.1516684112, 2015.
Martin, G., Durand, J.-L., Duru, M., Gastal, F., Julier, B., Litrico, I., Louarn, G., Médiène, S., Moreau, D., Valentin-Morison, M., Novak, S., Parnaudeau, V., Paschalidou, F., Vertès, F., Voisin, A.-S., Cellier, P., and Jeuffroy, M.-H.: Role of ley pastures in tomorrow's cropping systems. A review, Agron. Sustain. Dev., 40, 25 pp., https://doi.org/10.1007/s13593-020-00620-9, 2020.
MetaOMIC-RMQS: Determinism of biogeographical patterns and network interactions of soil fungal diversity across France, Genoscope [data set], https://www.ebi.ac.uk/ena/browser/view/PRJEB57875, last access: 26 March 2024.
Minasny, B., McBratney, A. B., and Hartemink, A. E.: Global pedodiversity, taxonomic distance, and the World Reference Base, Geoderma, 155, 132–139, https://doi.org/10.1016/j.geoderma.2009.04.024, 2010.
Miyauchi, S., Kiss, E., Kuo, A., Drula, E., Kohler, A., Sánchez-García, M., Morin, E., Andreopoulos, B., Barry, K. W., Bonito, G., Buée, M., Carver, A., Chen, C., Cichocki, N., Clum, A., Culley, D., Crous, P. W., Fauchery, L., Girlanda, M., Hayes, R. D., Kéri, Z., LaButti, K., Lipzen, A., Lombard, V., Magnuson, J., Maillard, F., Murat, C., Nolan, M., Ohm, R. A., Pangilinan, J., Pereira, M. de F., Perotto, S., Peter, M., Pfister, S., Riley, R., Sitrit, Y., Stielow, J. B., Szöllősi, G., Žifčáková, L., Štursová, M., Spatafora, J. W., Tedersoo, L., Vaario, L.-M., Yamada, A., Yan, M., Wang, P., Xu, J., Bruns, T., Baldrian, P., Vilgalys, R., Dunand, C., Henrissat, B., Grigoriev, I. V., Hibbett, D., Nagy, L. G., and Martin, F. M.: Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits, Nat. Commun., 11, 5125, https://doi.org/10.1038/s41467-020-18795-w, 2020.
Mo, Y., Zhang, W., Yang, J., Lin, Y., Yu, Z., and Lin, S.: Biogeographic patterns of abundant and rare bacterioplankton in three subtropical bays resulting from selective and neutral processes, ISME J., 12, 2198–2210, https://doi.org/10.1038/s41396-018-0153-6, 2018.
Möller, M. and Stukenbrock, E. H.: Evolution and genome architecture in fungal plant pathogens, Nat. Rev. Microbiol., 15, 756–771, https://doi.org/10.1038/nrmicro.2017.76, 2017.
Mora, C., Tittensor, D. P., Adl, S., Simpson, A. G. B., and Worm, B.: How many species are there on earth and in the ocean?, PLoS Biol., 9, e1001127, https://doi.org/10.1371/journal.pbio.1001127, 2011.
Naimi, B.: USDM: Uncertainty analysis for species distribution models, R package version 1.1–15, R Doc. Httpwww Rdocu-Mentation Orgpackagesusdm, https://github.com/babaknaimi/usdm (last access: 25 June 2017), 2015.
Naranjo-Ortiz, M. A. and Gabaldón, T.: Fungal evolution: major ecological adaptations and evolutionary transitions, Biol. Rev., 94, 1443–1476, https://doi.org/10.1111/brv.12510, 2019.
Nawrocki, E. P. and Eddy, S. R.: Infernal 1.1: 100-fold faster RNA homology searches, Bioinformatics, 29, 2933–2935, https://doi.org/10.1093/bioinformatics/btt509, 2013.
Nilsson, R. H., Tedersoo, L., Abarenkov, K., Ryberg, M., Kristiansson, E., Hartmann, M., Schoch, C. L., Nylander, J. A. A., Bergsten, J., Porter, T. M., Jumpponen, A., Vaishampayan, P., Ovaskainen, O., Hallenberg, N., Bengtsson-Palme, J., Eriksson, K. M., Larsson, K.-H., Larsson, E., and Kõljalg, U.: Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences, MycoKeys, 4, 37–63, https://doi.org/10.3897/mycokeys.4.3606, 2012.
Nilsson, R. H., Wurzbacher, C., Bahram, M., R. M. Coimbra, V., Larsson, E., Tedersoo, L., Eriksson, J., Duarte, C., Svantesson, S., Sánchez-García, M., Ryberg, M. K., Kristiansson, E., and Abarenkov, K.: Top 50 most wanted fungi, MycoKeys, 12, 29–40, https://doi.org/10.3897/mycokeys.12.7553, 2016.
Oksanen, J., Blanchet, F. G., Kindt, R., Legendre, P., Minchin, P. R., and O'Hara, R. B.: Package “vegan”, Community ecology package, version, 2, 1–295, https://github.com/vegandevs/vegan (last access: 11 October 2022), 2013.
Pärtel, M., Öpik, M., Moora, M., Tedersoo, L., Szava-Kovats, R., Rosendahl, S., Rillig, M. C., Lekberg, Y., Kreft, H., Helgason, T., Eriksson, O., Davison, J., Bello, F., Caruso, T., and Zobel, M.: Historical biome distribution and recent human disturbance shape the diversity of arbuscular mycorrhizal fungi, New Phytol., 216, 227–238, https://doi.org/10.1111/nph.14695, 2017.
Pauvert, C., Buée, M., Laval, V., Edel-Hermann, V., Fauchery, L., Gautier, A., Lesur, I., Vallance, J., and Vacher, C.: Bioinformatics matters: The accuracy of plant and soil fungal community data is highly dependent on the metabarcoding pipeline, Fungal Ecol., 41, 23–33, https://doi.org/10.1016/j.funeco.2019.03.005, 2019.
Peng, Y., Li, S. J., Yan, J., Tang, Y., Cheng, J. P., Gao, A. J., Yao, X., Ruan, J. J., and Xu, B. L.: Research Progress on Phytopathogenic Fungi and Their Role as Biocontrol Agents, Front. Microbiol., 12, 670135, https://doi.org/10.3389/fmicb.2021.670135, 2021.
Phukhamsakda, C., Nilsson, R. H., Bhunjun, C. S., de Farias, A. R. G., Sun, Y.-R., Wijesinghe, S. N., Raza, M., Bao, D.-F., Lu, L., Tibpromma, S., Dong, W., Tennakoon, D. S., Tian, X.-G., Xiong, Y.-R., Karunarathna, S. C., Cai, L., Luo, Z.-L., Wang, Y., Manawasinghe, I. S., Camporesi, E., Kirk, P. M., Promputtha, I., Kuo, C.-H., Su, H.-Y., Doilom, M., Li, Y., Fu, Y.-P., and Hyde, K. D.: The numbers of fungi: contributions from traditional taxonomic studies and challenges of metabarcoding, Fungal Divers., 114, 327–386, https://doi.org/10.1007/s13225-022-00502-3, 2022.
Quiquerez, A., Garcia, J.-P., Dequiedt, S., Djemiel, C., Terrat, S., Mathieu, O., Sassi, A., and Ranjard, L.: Legacy of land-cover changes on soil microbiology in Burgundy vineyards (Pernand-Vergelesses, France), OENO One, 56, 223–237, https://doi.org/10.20870/oeno-one.2022.56.2.5432, 2022.
Ranjard, L., Dequiedt, S., Chemidlin Prévost-Bouré, N., Thioulouse, J., Saby, N. P. A., Lelievre, M., Maron, P. A., Morin, F. E. R., Bispo, A., Jolivet, C., Arrouays, D., and Lemanceau, P.: Turnover of soil bacterial diversity driven by wide-scale environmental heterogeneity, Nat. Commun., 4, 1434, https://doi.org/10.1038/ncomms2431, 2013.
Rivett, D. W. and Bell, T.: Abundance determines the functional role of bacterial phylotypes in complex communities, Nat. Microbiol., 3, 767–772, https://doi.org/10.1038/s41564-018-0180-0, 2018.
Roswell, M., Dushoff, J., and Winfree, R.: A conceptual guide to measuring species diversity, Oikos, 130, 321–338, https://doi.org/10.1111/oik.07202, 2021.
Rousk, J., Bååth, E., Brookes, P. C., Lauber, C. L., Lozupone, C., Caporaso, J. G., Knight, R., and Fierer, N.: Soil bacterial and fungal communities across a pH gradient in an arable soil., ISME J., 4, 1340–51, https://doi.org/10.1038/ismej.2010.58, 2010.
Sadet-Bourgeteau, S., Houot, S., Karimi, B., Mathieu, O., Mercier, V., Montenach, D., Morvan, T., Sappin-Didier, V., Watteau, F., Nowak, V., Dequiedt, S., and Maron, P. A.: Microbial communities from different soil types respond differently to organic waste input, Appl. Soil Ecol., 143, 70–79, https://doi.org/10.1016/j.apsoil.2019.05.026, 2019.
Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., and Ideker, T.: Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks, Genome Res., 13, 2498–2504, https://doi.org/10.1101/gr.1239303, 2003.
Shi, L., Dossa, G. G. O., Paudel, E., Zang, H., Xu, J., and Harrison, R. D.: Changes in fungal communities across a forest disturbance gradient, Appl. Environ. Microbiol., 85, e00080-19, https://doi.org/10.1128/AEM.00080-19, 2019.
Sommermann, L., Geistlinger, J., Wibberg, D., Deubel, A., Zwanzig, J., Babin, D., Schlüter, A., and Schellenberg, I.: Fungal community profiles in agricultural soils of a long-term field trial under different tillage, fertilization and crop rotation conditions analyzed by high-throughput ITS-amplicon sequencing, PLOS ONE, 13, e0195345, https://doi.org/10.1371/journal.pone.0195345, 2018.
Spake, R., Ezard, T. H. G., Martin, P. A., Newton, A. C., and Doncaster, C. P.: A meta-analysis of functional group responses to forest recovery outside of the tropics, Conserv. Biol., 29, 1695–1703, https://doi.org/10.1111/cobi.12548, 2015.
Stefan, L., Hartmann, M., Engbersen, N., Six, J., and Schöb, C.: Positive Effects of Crop Diversity on Productivity Driven by Changes in Soil Microbial Composition, Front. Microbiol., 12, 660749, https://doi.org/10.3389/fmicb.2021.660749, 2021.
Sun, H., Shao, C., Jin, Q., Li, M., Zhang, Z., Liang, H., Lei, H., Qian, J., and Zhang, Y.: Effects of cadmium contamination on bacterial and fungal communities in Panax ginseng-growing soil, BMC Microbiol., 22, 77, https://doi.org/10.1186/s12866-022-02488-z, 2022.
Szoboszlay, M., Dohrmann, A. B., Poeplau, C., Don, A., and Tebbe, C. C.: Impact of land-use change and soil organic carbon quality on microbial diversity in soils across Europe, FEMS Microbiol. Ecol., 93, fix146, https://doi.org/10.1093/femsec/fix146, 2017.
Taylor, D. L., Hollingsworth, T. N., McFarland, J. W., Lennon, N. J., Nusbaum, C., and Ruess, R. W.: A first comprehensive census of fungi in soil reveals both hyperdiversity and fine-scale niche partitioning, Ecol. Monogr., 84, 3–20, https://doi.org/10.1890/12-1693.1, 2014.
Tecon, R. and Or, D.: Biophysical processes supporting the diversity of microbial life in soil, FEMS Microbiol. Rev., 41, 599–623, https://doi.org/10.1093/femsre/fux039, 2017.
Tedersoo, L., Bahram, M., Põlme, S., Kõljalg, U., Yorou, N. S., Wijesundera, R., Ruiz, L. V., Vasco-Palacios, A. M., Thu, P. Q., Suija, A., Smith, M. E., Sharp, C., Saluveer, E., Saitta, A., Rosas, M., Riit, T., Ratkowsky, D., Pritsch, K., Põldmaa, K., Piepenbring, M., Phosri, C., Peterson, M., Parts, K., Pärtel, K., Otsing, E., Nouhra, E., Njouonkou, A. L., Nilsson, R. H., Morgado, L. N., Mayor, J., May, T. W., Majuakim, L., Lodge, D. J., Lee, S. S., Larsson, K.-H., Kohout, P., Hosaka, K., Hiiesalu, I., Henkel, T. W., Harend, H., Guo, L., Greslebin, A., Grelet, G., Geml, J., Gates, G., Dunstan, W., Dunk, C., Drenkhan, R., Dearnaley, J., De Kesel, A., Dang, T., Chen, X., Buegger, F., Brearley, F. Q., Bonito, G., Anslan, S., Abell, S., and Abarenkov, K.: Global diversity and geography of soil fungi, Science, 346, 1256688, https://doi.org/10.1126/science.1256688, 2014.
Tedersoo, L., Bahram, M., Cajthaml, T., Põlme, S., Hiiesalu, I., Anslan, S., Harend, H., Buegger, F., Pritsch, K., Koricheva, J., and Abarenkov, K.: Tree diversity and species identity effects on soil fungi, protists and animals are context dependent, ISME J., 10, 346–362, https://doi.org/10.1038/ismej.2015.116, 2016.
Tedersoo, L., Anslan, S., Bahram, M., Drenkhan, R., Pritsch, K., Buegger, F., Padari, A., Hagh-Doust, N., Mikryukov, V., Gohar, D., Amiri, R., Hiiesalu, I., Lutter, R., Rosenvald, R., Rähn, E., Adamson, K., Drenkhan, T., Tullus, H., Jürimaa, K., Sibul, I., Otsing, E., Põlme, S., Metslaid, M., Loit, K., Agan, A., Puusepp, R., Varik, I., Kõljalg, U., and Abarenkov, K.: Regional-Scale In-Depth Analysis of Soil Fungal Diversity Reveals Strong pH and Plant Species Effects in Northern Europe, Front. Microbiol., 11, 1953, https://doi.org/10.3389/fmicb.2020.01953, 2020.
Tedersoo, L., Mikryukov, V., Anslan, S., Bahram, M., Khalid, A. N., Corrales, A., Agan, A., Vasco-Palacios, A.-M., Saitta, A., Antonelli, A., Rinaldi, A. C., Verbeken, A., Sulistyo, B. P., Tamgnoue, B., Furneaux, B., Ritter, C. D., Nyamukondiwa, C., Sharp, C., Marín, C., Dai, D. Q., Gohar, D., Sharmah, D., Biersma, E. M., Cameron, E. K., De Crop, E., Otsing, E., Davydov, E. A., Albornoz, F. E., Brearley, F. Q., Buegger, F., Gates, G., Zahn, G., Bonito, G., Hiiesalu, I., Hiiesalu, I., Zettur, I., Barrio, I. C., Pärn, J., Heilmann-Clausen, J., Ankuda, J., Kupagme, J. Y., Sarapuu, J., Maciá-Vicente, J. G., Fovo, J. D., Geml, J., Alatalo, J. M., Alvarez-Manjarrez, J., Monkai, J., Põldmaa, K., Runnel, K., Adamson, K., Bråthen, K. A., Pritsch, K., Tchan, K. I., Armolaitis, K., Hyde, K. D., Newsham, K. K., Panksep, K., Adebola, L. A., Lamit, L. J., Saba, M., Da Silva Cáceres, M. E., Tuomi, M., Gryzenhout, M., Bauters, M., Bálint, M., Wijayawardene, N., Hagh-Doust, N., Yorou, N. S., Kurina, O., Mortimer, P. E., Meidl, P., Nilsson, R. H., Puusepp, R., Casique-Valdés, R., Drenkhan, R., Garibay-Orijel, R., Godoy, R., Alfarraj, S., Rahimlou, S., Põlme, S., Dudov, S. V., Mundra, S., Ahmed, T., Netherway, T., Henkel, T. W., Roslin, T., Fedosov, V. E., Onipchenko, V. G., Yasanthika, W. A. E., Lim, Y. W., Piepenbring, M., Klavina, D., Kõljalg, U., and Abarenkov, K.: The Global Soil Mycobiome consortium dataset for boosting fungal diversity research, Fungal Divers., 111, 573–588, https://doi.org/10.1007/s13225-021-00493-7, 2021.
Terrat, S., Christen, R., Dequiedt, S., Lelièvre, M., Nowak, V., Regnier, T., Bachar, D., Plassart, P., Wincker, P., Jolivet, C., Bispo, A., Lemanceau, P., Maron, P.-A., Mougel, C., and Ranjard, L.: Molecular biomass and MetaTaxogenomic assessment of soil microbial communities as influenced by soil DNA extraction procedure., Microb. Biotechnol., 5, 135–41, https://doi.org/10.1111/j.1751-7915.2011.00307.x, 2012.
Terrat, S., Plassart, P., Bourgeois, E., Ferreira, S., Dequiedt, S., Adele-Dit-De-Renseville, N., Lemanceau, P., Bispo, A., Chabbi, A., Maron, P. A., and Ranjard, L.: Meta-barcoded evaluation of the ISO standard 11063 DNA extraction procedure to characterize soil bacterial and fungal community diversity and composition, Microb. Biotechnol., 8, 131–142, https://doi.org/10.1111/1751-7915.12162, 2015.
Terrat, S., Horrigue, W., Dequietd, S., Saby, N. P. A., Lelièvre, M., Nowak, V., Tripied, J., Régnier, T., Jolivet, C., Arrouays, D., Wincker, P., Cruaud, C., Karimi, B., Bispo, A., Maron, P. A., Prévost-Bouré, N. C., and Ranjard, L.: Mapping and predictive variations of soil bacterial richness across France, PLoS ONE, 12, 5–8, https://doi.org/10.1371/journal.pone.0186766, 2017.
Terrat, S., Djemiel, C., Journay, C., Karimi, B., Dequiedt, S., Horrigue, W., Maron, P., Chemidlin Prévost-Bouré, N., and Ranjard, L.: ReClustOR: a re-clustering tool using an open-reference method that improves operational taxonomic unit definition, Methods Ecol. Evol., 11, 168–180, https://doi.org/10.1111/2041-210X.13316, 2019.
Thomson, B. C., Tisserant, E., Plassart, P., Uroz, S., Griffiths, R. I., Hannula, S. E., Buée, M., Mougel, C., Ranjard, L., Van Veen, J. A., Martin, F., Bailey, M. J., and Lemanceau, P.: Soil conditions and land use intensification effects on soil microbial communities across a range of European field sites, Soil Biol. Biochem., 88, 403–413, https://doi.org/10.1016/j.soilbio.2015.06.012, 2015.
Treseder, K. K. and Lennon, J. T.: Fungal Traits That Drive Ecosystem Dynamics on Land, Microbiol. Mol. Biol. Rev., 79, 243–262, https://doi.org/10.1128/MMBR.00001-15, 2015.
Tsiafouli, M. A., Thébault, E., Sgardelis, S. P., de Ruiter, P. C., van der Putten, W. H., Birkhofer, K., Hemerik, L., de Vries, F. T., Bardgett, R. D., Brady, M. V., Bjornlund, L., Jørgensen, H. B., Christensen, S., Hertefeldt, T. D., Hotes, S., Gera Hol, W. H., Frouz, J., Liiri, M., Mortimer, S. R., Setälä, H., Tzanopoulos, J., Uteseny, K., Pižl, V., Stary, J., Wolters, V., and Hedlund, K.: Intensive agriculture reduces soil biodiversity across Europe, Glob. Change Biol., 21, 973–985, https://doi.org/10.1111/gcb.12752, 2015.
Vazquez, C., Goede, R. G. M., Korthals, G. W., Rutgers, M., Schouten, A. J., and Creamer, R.: The effects of increasing land use intensity on soil nematodes: A turn towards specialism, Funct. Ecol., 33, 2003–2016, https://doi.org/10.1111/1365-2435.13417, 2019.
Větrovský, T., Kohout, P., Kopecký, M., Machac, A., Man, M., Bahnmann, B. D., Brabcová, V., Choi, J., Meszárošová, L., Human, Z. R., Lepinay, C., Lladó, S., López-Mondéjar, R., Martinović, T., Mašínová, T., Morais, D., Navrátilová, D., Odriozola, I., Štursová, M., Švec, K., Tláskal, V., Urbanová, M., Wan, J., Žifčáková, L., Howe, A., Ladau, J., Peay, K. G., Storch, D., Wild, J., and Baldrian, P.: A meta-analysis of global fungal distribution reveals climate-driven patterns, Nat. Commun., 10, 5142, https://doi.org/10.1038/s41467-019-13164-8, 2019.
Wang, D., Rui, Y., Ding, K., Cui, X., Hao, Y., Tang, L., Pang, Z., Zhang, B., Zhou, S., Wang, K., and Wang, Y.: Precipitation drives the biogeographic distribution of soil fungal community in Inner Mongolian temperate grasslands, J. Soil. Sediment., 18, 222–228, https://doi.org/10.1007/s11368-017-1727-z, 2018.
Wang, J.-T., Shen, J.-P., Zhang, L.-M., Singh, B. K., Delgado-Baquerizo, M., Hu, H.-W., Han, L.-L., Wei, W.-X., Fang, Y.-T., and He, J.-Z.: Generalist Taxa Shape Fungal Community Structure in Cropping Ecosystems, Front. Microbiol., 12, 678290, https://doi.org/10.3389/fmicb.2021.678290, 2021.
Ward, E. B., Duguid, M. C., Kuebbing, S. E., Lendemer, J. C., and Bradford, M. A.: The functional role of ericoid mycorrhizal plants and fungi on carbon and nitrogen dynamics in forests, New Phytol., 235, 1701–1718, https://doi.org/10.1111/nph.18307, 2022.
Wardle, D. A., Bardgett, R. D., Klironomos, J. N., Setälä, H., Van Der Putten, W. H., and Wall, D. H.: Ecological linkages between aboveground and belowground biota, Science, 304, 1629–1633, https://doi.org/10.1126/science.1094875, 2004.
Wilkinson, D. M.: The Disturbing History of Intermediate Disturbance, Oikos, 84, 145–147, https://doi.org/10.2307/3546874, 1999.
Witzgall, K., Vidal, A., Schubert, D. I., Höschen, C., Schweizer, S. A., Buegger, F., Pouteau, V., Chenu, C., and Mueller, C. W.: Particulate organic matter as a functional soil component for persistent soil organic carbon, Nat. Commun., 12, 4115, https://doi.org/10.1038/s41467-021-24192-8, 2021.
Wu, B., Hussain, M., Zhang, W., Stadler, M., Liu, X., and Xiang, M.: Current insights into fungal species diversity and perspective on naming the environmental DNA sequences of fungi, Mycology, 10, 127–140, https://doi.org/10.1080/21501203.2019.1614106, 2019.
Xu, M., Li, X., Cai, X., Li, X., Christie, P., and Zhang, J.: Land use alters arbuscular mycorrhizal fungal communities and their potential role in carbon sequestration on the Tibetan Plateau, Sci. Rep., 7, 3067, https://doi.org/10.1038/s41598-017-03248-0, 2017.
Xu, Q., Vandenkoornhuyse, P., Li, L., Guo, J., Zhu, C., Guo, S., Ling, N., and Shen, Q.: Microbial generalists and specialists differently contribute to the community diversity in farmland soils, J. Adv. Res., 40, 17–27, https://doi.org/10.1016/j.jare.2021.12.003, 2022a.
Xu, Q., Ling, N., Quaiser, A., Guo, J., Ruan, J., Guo, S., Shen, Q., and Vandenkoornhuyse, P.: Rare Bacteria Assembly in Soils Is Mainly Driven by Deterministic Processes, Microb. Ecol., 83, 137–150, https://doi.org/10.1007/s00248-021-01741-8, 2022b.
Xue, P., Minasny, B., and McBratney, A. B.: Land-use affects soil microbial co-occurrence networks and their putative functions, Appl. Soil Ecol., 169, 104184, https://doi.org/10.1016/j.apsoil.2021.104184, 2022.
Yang, T., Tedersoo, L., Soltis, P. S., Soltis, D. E., Gilbert, J. A., Sun, M., Shi, Y., Wang, H., Li, Y., Zhang, J., Chen, Z., Lin, H., Zhao, Y., Fu, C., and Chu, H.: Phylogenetic imprint of woody plants on the soil mycobiome in natural mountain forests of eastern China, ISME J., 13, 686–697, https://doi.org/10.1038/s41396-018-0303-x, 2019.
Zhang, T., Liu, Y., Sui, X., Frey, B., and Song, F.: Effects of Land Conversion on Soil Microbial Community Structure and Diversity in Songnen Plain, Northeast China, Sustain. Switz., 14, 10767, https://doi.org/10.3390/su141710767, 2022.
Zhao, Z., Ma, Y., Feng, T., Kong, X., Wang, Z., Zheng, W., and Zhai, B.: Assembly processes of abundant and rare microbial communities in orchard soil under a cover crop at different periods, Geoderma, 406, 115543, https://doi.org/10.1016/j.geoderma.2021.115543, 2022.
Executive editor
This is one of the first surveys of soil fungal diversity across land uses at the national scale.
Short summary
The fungal kingdom has been diversifying for more than 800 million years by colonizing a large number of habitats on Earth. Based on a unique dataset (18S rDNA meta-barcoding), we described the spatial distribution of fungal diversity at the scale of France and the environmental drivers by tackling biogeographical patterns. We also explored the fungal network interactions across land uses and climate types.
The fungal kingdom has been diversifying for more than 800 million years by colonizing a large...
