References
de Araujo, A.S.F., Mendes, L.W., Lemos, L.N., Antunes, J.E.L., Beserra, J.E.A., de Lyra, M. do C.C.P., et al. (2018). Protist species richness and soil microbiome complexity increase towards climax vegetation in the Brazilian Cerrado. Commun Biol , 1, 135.
Arribas, P., Andújar, C., Salces‐Castellano, A., Emerson, B.C. & Vogler, A.P. (2021). The limited spatial scale of dispersal in soil arthropods revealed with whole‐community haplotype‐level metabarcoding.Mol Ecol , 30, 48–61.
Bardgett, R.D. & van der Putten, W.H. (2014). Belowground biodiversity and ecosystem functioning. Nature , 515, 505–511.
Baselga, A., Orme, D., Villeger, S., Bortoli, J.D., Leprieur, F., Logez, M., et al. (2022). betapart: Partitioning Beta Diversity into Turnover and Nestedness Components.
Bauer, B., Berti, E., Ryser, R., Gauzens, B., Hirt, M.R., Rosenbaum, B.,et al. (2022). Biotic filtering by species’ interactions constrains food-web variability across spatial and abiotic gradients.Ecol Lett , 25, 1225–1236.
Bonin, A., Guerrieri, A. & Ficetola, G.F. (2023). Optimal sequence similarity thresholds for clustering of molecular operational taxonomic units in DNA metabarcoding studies. Mol Ecol , 23, 368–381.
Boyer, F., Mercier, C., Bonin, A., Le Bras, Y., Taberlet, P. & Coissac, E. (2016). obitools : a unix -inspired software package for DNA metabarcoding. Mol Ecol Resour , 16, 176–182.
van Buuren, S. & Groothuis-Oudshoorn, K. (2011). mice: Multivariate Imputation by Chained Equations in R. J Stat Softw , 45, 1–67.
Calderón‐Sanou, I., Münkemüller, T., Boyer, F., Zinger, L. & Thuiller, W. (2020). From environmental DNA sequences to ecological conclusions: How strong is the influence of methodological choices? J Biogeogr , 47, 193–206.
Calderón‐Sanou, I., Zinger, L., Hedde, M., Martinez‐Almoyna, C., Saillard, A., Renaud, J., et al. (2022). Energy and physiological tolerance explain multi‐trophic soil diversity in temperate mountains.Divers Distrib , 28, 2549–2564.
Caruso, T., Clemente, G.V., Rillig, M.C. & Garlaschelli, D. (2022). Fluctuating ecological networks: A synthesis of maximum‐entropy approaches for pattern detection and process inference. Methods Ecol Evol , 13, 2306–2317.
Choler, P. (2015). Growth response of temperate mountain grasslands to inter-annual variations in snow cover duration. Biogeosciences , 12, 3885–3897.
Compson, Z.G., Monk, W.A., Curry, C.J., Gravel, D., Bush, A., Baker, C.J.O., et al. (2018). Chapter Two - Linking DNA Metabarcoding and Text Mining to Create Network-Based Biomonitoring Tools: A Case Study on Boreal Wetland Macroinvertebrate Communities. In:Advances in Ecological Research , Next Generation Biomonitoring: Part 2 (eds. Bohan, D.A., Dumbrell, A.J., Woodward, G. & Jackson, M.). Academic Press, pp. 33–74.
Crotty, F.V., Blackshaw, R.P., Adl, S.M., Inger, R. & Murray, P.J. (2014). Divergence of feeding channels within the soil food web determined by ecosystem type. Ecol Evol , 4, 1–13.
David, J.-F. & Handa, I.T. (2010). The ecology of saprophagous macroarthropods (millipedes, woodlice) in the context of global change.Biol Rev , 85, 881–895.
Davison, J., Moora, M., Öpik, M., Adholeya, A., Ainsaar, L., Bâ, A.,et al. (2015). Global assessment of arbuscular mycorrhizal fungus diversity reveals very low endemism. Science , 349, 970–973.
Decaëns, T. (2010). Macroecological patterns in soil communities.Glob Ecol Biogeogr , 19, 287–302.
Delgado-Baquerizo, M., Oliverio, A.M., Brewer, T.E., Benavent-González, A., Eldridge, D.J., Bardgett, R.D., et al. (2018). A global atlas of the dominant bacteria found in soil. Science , 359, 320–325.
Delgado-Baquerizo, M., Reich, P.B., Trivedi, C., Eldridge, D.J., Abades, S., Alfaro, F.D., et al. (2020). Multiple elements of soil biodiversity drive ecosystem functions across biomes. Nat Ecol Evol , 4, 210–220.
Dunne, J.A. (2006). The network structure of food webs. In:Ecological networks: linking structure to dynamics in food webs(eds. Pascual, M. & Dunne, J.A.). Oxford University Press, pp. 27–86.
Eisenhauer, N., Bender, S.F., Calderón-Sanou, I., de Vries, F.T., Lembrechts, J.J., Thuiller, W., et al. (2022). Frontiers in soil ecology—Insights from the World Biodiversity Forum 2022. J sustain agric , 1, 245–261.
Eisenhauer, N., Buscot, F., Heintz-Buschart, A., Jurburg, S.D., Küsel, K., Sikorski, J., et al. (2021). The multidimensionality of soil macroecology. Glob Ecol Biogeogr , 30, 4–10.
Eisenhauer, N., Dobies, T., Cesarz, S., Hobbie, S.E., Meyer, R.J., Worm, K., et al. (2013). Plant diversity effects on soil food webs are stronger than those of elevated CO2 and N deposition in a long-term grassland experiment. Proc Natl Acad Sci U S A , 110, 6889–6894.
Elton, C.S. (1927). Animal ecology . Macmillan Co., New York,.
Ettema, C.H. & Wardle, D.A. (2002). Spatial soil ecology. Trends Ecol Evol , 17, 177–183.
Ferrier, S., Manion, G., Elith, J. & Richardson, K. (2007). Using generalized dissimilarity modelling to analyse and predict patterns of beta diversity in regional biodiversity assessment. Divers Distrib , 13, 252–264.
Ficetola, G.F., Coissac, E., Zundel, S., Riaz, T., Shehzad, W., Bessière, J., et al. (2010). An In silico approach for the evaluation of DNA barcodes. BMC Genomics , 11, 434.
Fierer, N. & Jackson, R.B. (2006). The diversity and biogeography of soil bacterial communities. PNAS , 103, 626–631.
Fiore-Donno, A.M., Richter-Heitmann, T. & Bonkowski, M. (2020). Contrasting Responses of Protistan Plant Parasites and Phagotrophs to Ecosystems, Land Management and Soil Properties. Front Microbiol , 11.
Fitzpatrick, M., Mokany, K., Manion, G., Nieto-Lugilde, D., Ferrier, S., Lisk, M., et al. (2022). gdm: Generalized Dissimilarity Modeling.
Ganault, P., Barantal, S., Coq, S., Hättenschwiler, S., Lucas, S., Decaëns, T., et al. (2022). Leaf litter morphological traits, invertebrate body mass and phylogenetic affiliation explain the feeding and feces properties of saprophagous macroarthropods. Eur J Soil Biol , 109, 103383.
Geisen, S., Briones, M.J.I., Gan, H., Behan-Pelletier, V.M., Friman, V.-P., de Groot, G.A., et al. (2019). A methodological framework to embrace soil biodiversity. Soil Biol Biochem , 136, 107536.
Glassman, S.I., Wang, I.J. & Bruns, T.D. (2017). Environmental filtering by pH and soil nutrients drives community assembly in fungi at fine spatial scales. Mol Ecol , 26, 6960–6973.
Gravel, D., Baiser, B., Dunne, J.A., Kopelke, J.-P., Martinez, N.D., Nyman, T., et al. (2019). Bringing Elton and Grinnell Together: a quantitative framework to represent the biogeography of ecological interaction networks. Ecography , 42, 401–620.
Hedde, M., Blight, O., Briones, M.J.I., Bonfanti, J., Brauman, A., Brondani, M., et al. (2022). A common framework for developing robust soil fauna classifications. Geoderma , 426, 116073.
Heděnec, P., Jiménez, J.J., Moradi, J., Domene, X., Hackenberger, D., Barot, S., et al. (2022). Global distribution of soil fauna functional groups and their estimated litter consumption across biomes.Sci Rep , 12, 17362.
Jackson, R.B., Mooney, H.A. & Schulze, E.-D. (1997). A global budget for fine root biomass, surface area, and nutrient contents. Proc. Natl. Acad. Sci. U.S.A. , 94, 7362–7366.
Joimel, S., Cortet, J., Jolivet, C.C., Saby, N.P.A., Chenot, E.D., Branchu, P., et al. (2016). Physico-chemical characteristics of topsoil for contrasted forest, agricultural, urban and industrial land uses in France. Sci Total Environ , 545–546, 40–47.
Jonasson, S. (1988). Evaluation of the Point Intercept Method for the Estimation of Plant Biomass. Oikos , 52, 101–106.
Kang, L., Chen, L., Zhang, D., Peng, Y., Song, Y., Kou, D., et al. (2022). Stochastic processes regulate belowground community assembly in alpine grasslands on the Tibetan Plateau. Environ Microbiol , 24, 179–194.
Kardol, P. & De Long, J.R. (2018). How anthropogenic shifts in plant community composition alter soil food webs. F1000Res , 7, 4.
Kardol, P., De Long, J.R. & Mariotte, P. (2018). Soil Biota as Drivers of Plant Community Assembly. In: Aboveground–Belowground Community Ecology , Ecological Studies (eds. Ohgushi, T., Wurst, S. & Johnson, S.N.). Springer International Publishing, Cham, pp. 293–318.
Keddy, P.A. (1992). Assembly and Response Rules: Two Goals for Predictive Community Ecology. J Veg Sci , 3, 157–164.
Kelly, R.P., Shelton, A.O. & Gallego, R. (2019). Understanding PCR Processes to Draw Meaningful Conclusions from Environmental DNA Studies.Sci Rep , 9, 12133.
Konvalinková, T. & Jansa, J. (2016). Lights Off for Arbuscular Mycorrhiza: On Its Symbiotic Functioning under Light Deprivation.Front Plant Sci , 7.
Landolt, E., Bäumler, B., Ehrhardt, A., Hegg, O., Klötzli, F., Lämmler, W., et al. (2010). Flora indicativa: Okologische Zeigerwerte und biologische Kennzeichen zur Flora der Schweiz und der Alpen . Haupt, Bern.
Le Guillarme, N., Hedde, M., Potapov, A.M., Berg, M.P., Briones, M.J.I., Calderón-Sanou, I., et al. (2023). The Soil Food Web Ontology: aligning trophic groups, processes, and resources to harmonise and automatise soil food web reconstructions.
Le Guillarme, N. & Thuiller, W. (2023). A practical approach to constructing a knowledge graph for soil ecological research. Eur J Soil Biol , 117, 103497.
Louca, S., Parfrey, L.W. & Doebeli, M. (2016). Decoupling function and taxonomy in the global ocean microbiome. Science , 353, 1272–1277.
Maaß, S., Maraun, M., Scheu, S., Rillig, M.C. & Caruso, T. (2015). Environmental filtering vs. resource-based niche partitioning in diverse soil animal assemblages. Soil Biol Biochem , 85, 145–152.
Magneville, C., Loiseau, N., Albouy, C., Casajus, N., Claverie, T., Escalas, A., et al. (2021). mFD: Compute and Illustrate the Multiple Facets of Functional Diversity.
Martinez-Almoyna, C., Saillard, A., Zinger, L., Lionnet, C., Arnoldi, C., Foulquier, A., et al. (2022). Differential effects of soil trophic networks on microbial decomposition activity in mountain ecosystems. Soil Biol Biochem , 172, 108771.
Mason, J.A. & Zanner, C.W. (2005). GRASSLAND SOILS. In:Encyclopedia of Soils in the Environment (ed. Hillel, D.). Elsevier, Oxford, pp. 138–145.
McInnes, L., Healy, J. & Melville, J. (2020). UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction.
Mercier, C., Boyer, F., Bonin, A. & Coissac, E. (2013). SUMATRA and SUMACLUST: fast and exact comparison and clustering of sequences. In:Programs and Abstracts of the SeqBio 2013 workshop. Abstract . Citeseer, pp. 27–29.
Miele, V., Matias, C., Dray, S., Botella, C., Ohlmann, M., Poggiato, G.,et al. (2021). econetwork: Analyzing Ecological Networks.
Mokany, K., Ware, C., Woolley, S.N.C., Ferrier, S. & Fitzpatrick, M.C. (2022). A working guide to harnessing generalized dissimilarity modelling for biodiversity analysis and conservation assessment.Global Ecol Biogeogr , 31, 802–821.
Moore, J.C. & de Ruiter, P.C. (1991). Temporal and spatial heterogeneity of trophic interactions within below-ground food webs.Agric Ecosyst Environ , 34, 371–397.
Münkemüller, T., Gallien, L., Pollock, L.J., Barros, C., Carboni, M., Chalmandrier, L., et al. (2020). Dos and don’ts when inferring assembly rules from diversity patterns. Global Ecol Biogeogr , 29, 1212–1229.
Noguerales, V., Meramveliotakis, E., Castro-Insua, A., Andújar, C., Arribas, P., Creedy, T.J., et al. (2021). Community metabarcoding reveals the relative role of environmental filtering and spatial processes in metacommunity dynamics of soil microarthropods across a mosaic of montane forests. Mol Ecol , 1–19.
O’Brien, S.L., Gibbons, S.M., Owens, S.M., Hampton-Marcell, J., Johnston, E.R., Jastrow, J.D., et al. (2016). Spatial scale drives patterns in soil bacterial diversity. Environ Microbiol , 18, 2039–2051.
Ohlmann, M., Garnier, J. & Vuillon, L. (2023). ‘metanetwork’: a R package dedicated to handling and representing trophic metanetworks.Ecol Evol , in press.
Ohlmann, M., Miele, V., Dray, S., Chalmandrier, L., O’Connor, L. & Thuiller, W. (2019). Diversity indices for ecological networks: a unifying framework using Hill numbers. Ecol Lett , 22, 737–747.
Peay, K.G., Garbelotto, M. & Bruns, T.D. (2010). Evidence of dispersal limitation in soil microorganisms: Isolation reduces species richness on mycorrhizal tree islands. Ecology , 91, 3631–3640.
Poggiato, G., Andréoletti, J., Shirley, L. & Thuiller, W. (2022).Integrating food webs in species distribution models improves ecological niche estimation and predictions (preprint). Preprints.
Potapov, A.M., Beaulieu, F., Birkhofer, K., Bluhm, S.L., Degtyarev, M.I., Devetter, M., et al. (2022). Feeding habits and multifunctional classification of soil‐associated consumers from protists to vertebrates. Biol Rev , brv.12832.
Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P.,et al. (2013). The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res , 41, D590–D596.
R Core Team. (2020). A Language and Environment for Statistical Computing.
Ramirez, K.S., Leff, J.W., Barberán, A., Bates, S.T., Betley, J., Crowther, T.W., et al. (2014). Biogeographic patterns in below-ground diversity in New York City’s Central Park are similar to those observed globally. Proc. R. Soc. B , 281, 20141988.
Schoch, D. (2022). edgebundle: Algorithms for Bundling Edges in Networks and Visualizing Flow and Metro Maps.
Sepp, S.-K., Davison, J., Moora, M., Neuenkamp, L., Oja, J., Roslin, T.,et al. (2021). Woody encroachment in grassland elicits complex changes in the functional structure of above- and belowground biota.Ecosphere , 12, e03512.
Soliveres, S., van der Plas, F., Manning, P., Prati, D., Gossner, M.M., Renner, S.C., et al. (2016). Biodiversity at multiple trophic levels is needed for ecosystem multifunctionality. Nature , 536, 456–459.
Taberlet, P., Bonin, A., Zinger, L. & Coissac, E. (2018).Environmental DNA: for biodiversity research and monitoring . Oxford University Press, New York.
Taberlet, P., Coissac, E., Hajibabaei, M. & Rieseberg, L.H. (2012). Environmental DNA. Mol Ecol , 21, 1789–1793.
Tackenberg, O. & Stöcklin, J. (2008). Wind dispersal of alpine plant species: A comparison with lowland species. J Veg Sci , 19, 109–118.
Tedersoo, L., Bahram, M., Polme, S., Koljalg, U., Yorou, N.S., Wijesundera, R., et al. (2014). Global diversity and geography of soil fungi. Science , 346, 1256688–1256688.
Thakur, M.P. & Geisen, S. (2019). Trophic Regulations of the Soil Microbiome. Trends Microbiol , 27, 771–780.
Thakur, M.P., Phillips, H.R.P., Brose, U., Vries, F.T.D., Lavelle, P., Loreau, M., et al. (2020). Towards an integrative understanding of soil biodiversity. Biol Rev , 95, 350–364.
Thompson, R.M., Brose, U., Dunne, J.A., Hall, R.O., Hladyz, S., Kitching, R.L., et al. (2012). Food webs: reconciling the structure and function of biodiversity. Trends Ecol Evol , 27, 689–697.
Thuiller, W., Münkemüller, T., Lavergne, S., Mouillot, D., Mouquet, N., Schiffers, K., et al. (2013). A road map for integrating eco-evolutionary processes into biodiversity models. Ecol Lett , 16, 94–105.
Vályi, K., Mardhiah, U., Rillig, M.C. & Hempel, S. (2016). Community assembly and coexistence in communities of arbuscular mycorrhizal fungi.ISME J , 10, 2341–2351.
Vernay, M., Lafaysse, M., Monteiro, D., Hagenmuller, P., Nheili, R., Samacoïts, R., et al. (2021). The S2M meteorological and snow cover reanalysis over the French mountainous areas, description and evaluation (1958–2020) (preprint). Cryosphere – Snow and Sea Ice.
Wall, D.H., Nielsen, U.N. & Six, J. (2015). Soil biodiversity and human health. Nature , 528, 69–76.
Wilschut, R.A., van der Putten, W.H., Garbeva, P., Harkes, P., Konings, W., Kulkarni, P., et al. (2019). Root traits and belowground herbivores relate to plant–soil feedback variation among congeners.Nat Commun , 10, 1564.
Zhao, J. & Neher, D.A. (2014). Soil energy pathways of different ecosystems using nematode trophic group analysis: a meta analysis.Nematology , 16, 379–385.
Zinger, L., Lejon, D.P.H., Baptist, F., Bouasria, A., Aubert, S., Geremia, R.A., et al. (2011). Contrasting Diversity Patterns of Crenarchaeal, Bacterial and Fungal Soil Communities in an Alpine Landscape. PLoS ONE , 6, e19950.
Zinger, L., Lionnet, C., Benoiston, A.-S., Donald, J., Mercier, C. & Boyer, F. (2021). metabaR: An r package for the evaluation and improvement of DNA metabarcoding data quality. Methods Ecol Evol , 12, 586–592.
Zinger, L., Taberlet, P., Schimann, H., Bonin, A., Boyer, F., De Barba, M., et al. (2019). Body size determines soil community assembly in a tropical forest. Mol Ecol , 28, 528–543.
Zuo, J., Fonck, M., van Hal, J., Cornelissen, J.H.C. & Berg, M.P. (2014). Diversity of macro-detritivores in dead wood is influenced by tree species, decay stage and environment. Soil Biol Biochem , 78, 288–297.