Bardgett, R. D. & van der Putten, W. H. Belowground biodiversity and ecosystem functioning. Nature 515, 505–511 (2014).
Bahram, M. et al. Structure and function of the global topsoil microbiome. Nature 560, 233–237 (2018).
Luan, L. et al. Coupling bacterial community assembly to microbial metabolism across soil profiles. mSystems 5, e00298–20 (2020).
Stegen, J. C. et al. Groundwater–surface water mixing shifts ecological assembly processes and stimulates organic carbon turnover. Nat. Commun. 7, 11237 (2016).
Thompson, L. R. et al. A communal catalogue reveals Earth’s multiscale microbial diversity. Nature 551, 457–463 (2017).
Tedersoo, L. et al. Global diversity and geography of soil fungi. Science 346, 1256688 (2014).
Oliverio, A. M. et al. The global-scale distributions of soil protists and their contributions to belowground systems. Sci. Adv. 6, eaax8787 (2020).
van den Hoogen, J. et al. Soil nematode abundance and functional group composition at a global scale. Nature 572, 194–198 (2019).
Nemergut, D. R. et al. Patterns and processes of microbial community assembly. Microbiol. Mol. Biol. Rev. 77, 342–356 (2013).
Martiny, J. B. H. et al. Microbial biogeography: putting microorganisms on the map. Nat. Rev. Microbiol. 4, 102–112 (2006).
Hanson, C. A., Fuhrman, J. A., Horner-Devine, M. C. & Martiny, J. B. H. Beyond biogeographic patterns: processes shaping the microbial landscape. Nat. Rev. Microbiol. 10, 497–506 (2012).
Vellend, M. Conceptual synthesis in community ecology. Q. Rev. Biol. 85, 183–206 (2010).
Dini-Andreote, F., Stegen, J. C., Van Elsas, J. D. & Falcão Salles, J. Disentangling mechanisms that mediate the balance between stochastic and deterministic processes in microbial succession. Proc. Natl Acad. Sci. USA 112, E1326–E1332 (2015).
Zhou, J. & Ning, D. Stochastic community assembly: does it matter in microbial ecology? Microbiol. Mol. Biol. Rev. 81, e00002–e00017 (2017).
Chave, J. Neutral theory and community ecology. Ecol. Lett. 7, 241–253 (2004).
Letten, A. D., Ke, P.-J. & Fukami, T. Linking modern coexistence theory and contemporary niche theory. Ecol. Monogr. 87, 161–177 (2017).
Stegen, J. C., Lin, X. J., Fredrickson, J. K. & Konopka, A. E. Estimating and mapping ecological processes influencing microbial community assembly. Front. Microbiol. 6, 370 (2015).
Li, P. et al. Distinct Successions of common and rare bacteria in soil under humic acid amendment – a microcosm study. Front. Microbiol. 10, 2271 (2019).
Stearns, S. C. The Evolution of Life Histories (Oxford Univ. Press, Oxford, 1992).
Villarino, E. et al. Large-scale ocean connectivity and planktonic body size. Nat. Commun. 9, 142 (2018).
Woo, C., An, C., Xu, S., Yi, S. M. & Yamamoto, N. Taxonomic diversity of fungi deposited from the atmosphere. ISME J. 12, 2051–2060 (2018).
Soininen, J., Korhonen, J. J. & Luoto, M. Stochastic species distributions are driven by organism size. Ecology 94, 660–670 (2013).
Farjalla, V. F. et al. Ecological determinism increases with organism size. Ecology 93, 1752–1759 (2012).
Thuiller, W., Lavorel, S. & Araújo, M. B. Niche properties and geographical extent as predictors of species sensitivity to climate change. Glob. Ecol. Biogeogr. 14, 347–357 (2005).
Li, P. et al. Responses of microbial communities to a gradient of pig manure amendment in red paddy soils. Sci. Total Environ. 705, 135884 (2020).
Brown, J. H., Gillooly, J. F., Allen, A. P., Savage, V. M. & West, G. B. Toward a metabolic theory of ecology. Ecology 85, 1771–1789 (2004).
Foissner, W. Protist diversity and distribution: some basic considerations. Biodivers. Conserv. 17, 235–242 (2008).
Pimm, S. L., Jones, H. L. & Diamond, J. On the risk of extinction. Am. Nat. 132, 757–785 (1988).
Jiang, Y. et al. Crop rotations alter bacterial and fungal diversity in paddy soils across East Asia. Soil Biol. Biochem. 95, 250–261 (2016).
Li, P. et al. Spatial variation in soil fungal communities across paddy fields in subtropical China. mSystems 5, e00704–e00719 (2020).
Peay, K. G., Kennedy, P. G. & Talbot, J. M. Dimensions of biodiversity in the Earth mycobiome. Nat. Rev. Microbiol. 14, 434–447 (2016).
Geisen, S. et al. Soil protists: a fertile frontier in soil biology research. FEMS Microbiol. Rev. 42, 293–323 (2018).
Tucker, C. M., Shoemaker, L. G., Davies, K. F., Nemergut, D. R. & Melbourne, B. A. Differentiating between niche and neutral assembly in metacommunities using null models of β-diversity. Oikos 125, 778–789 (2016).
Doledec, S., Chessel, D. & Gimaret-Carpentier, C. Niche separation in community analysis: a new method. Ecology 81, 2914–2927 (2000).
Sloan, W. T., Woodcock, S., Lunn, M., Head, I. M. & Curtis, T. P. Modeling taxa-abundance distributions in microbial communities using environmental sequence data. Microb. Ecol. 53, 443–455 (2007).
De Wit, R. & Bouvier, T. Everything is everywhere, but, the environment selects; what did BaasBecking and Beijerinck really say. Environ. Microbiol. 8, 755–758 (2006).
Zinger, L. et al. Body size determines soil community assembly in a tropical forest. Mol. Ecol. 28, 528–543 (2019).
Chase, J. M. et al. Embracing scale-dependence to achieve a deeper understanding of biodiversity and its change across communities. Ecol. Lett. 21, 1737–1751 (2018).
Zhalnina, K. et al. Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly. Nat. Microbiol. 3, 470–480 (2018).
De Bie, T. et al. Body size and dispersal mode as key traits determining metacommunity structure of aquatic organisms. Ecol. Lett. 15, 740–747 (2012).
Lowe, W. H. & McPeek, M. A. Is dispersal neutral? Trends Ecol. Evol. 29, 444–450 (2014).
O’Brien, E. M., Whittaker, R. J. & Field, R. Climate and woody plant diversity in Southern Africa: relationships at species, genus and family levels. Ecography 21, 495–509 (1998).
Brown, J. H. Why are there so many species in the tropics? J. Biogeogr. 41, 8–22 (2014).
Li, X. et al. Agriculture erases climate constraints on soil nematode communities across large spatial scales. Glob. Change Biol. 26, 919–930 (2020).
Briones, M. J. I. Soil fauna and soil functions: a jigsaw puzzle. Front. Environ. Sci. 22, 7 (2014).
Martiny, J. B. H., Jones, S. E., Lennon, J. T. & Martiny, A. C. Microbiomes in light of traits: a phylogenetic perspective. Science 350, 9323 (2015).
Pansu, M. & Gautheyrou, J. Handbook of Soil Analysis: Mineralogical, Organic, and Inorganic Methods. (Springer, 2006).
Biddle, J. F., Fitz-Gibbon, S., Schuster, S. C., Brenchley, J. E. & House, C. H. Metagenomic signatures of the Peru Margin subseafloor biosphere show a genetically distinct environment. Proc. Natl Acad. Sci. USA 105, 10583–10588 (2008).
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 (2008).
Stoeck, T. et al. Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water. Mol. Ecol. 19, 21–31 (2010).
Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7, 335–336 (2010).
Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C. & Knight, R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27, 2194–2200 (2011).
Zhang, Y. & Sun, Y. HMM-FRAME: accurate protein domain classification for metagenomic sequences containing frameshift errors. BMC Bioinform. 12, 198 (2011).
Li, W. & Godzik, A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22, 1658–1659 (2006).
Quast, C. et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, D590–D596 (2013).
Nilsson, R. H. et al. The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications. Nucleic Acids Res. 47, D259–D264 (2019).
Guillou, L. et al. The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote small sub-unit rRNA sequences with curated taxonomy. Nucleic Acids Res. 41, D597–D604 (2012).
Zhao, J. et al. Size spectra of soil nematode assemblages under different land use types. Soil Biol. Biochem. 85, 130–136 (2015).
Soininen, J., McDonald, R. & Hillebrand, H. The distance decay of similarity in ecological communities. Ecography 30, 3–12 (2007).
Dray, S., Legendre, P. & Peres-Neto, P. R. Spatial modelling: A comprehensive framework for principal coordinate analysis of neighbor matrices (PCNM). Ecol. Model. 196, 483–493 (2006).
Chen, W., Jiao, S., Li, Q. & Du, N. Dispersal limitation relative to environmental filtering governs the vertical small‐scale assembly of soil microbiomes during restoration. J. Appl. Ecol. 57, 402–412 (2020).
Jiao, S., Yang, Y., Xu, Y., Zhang, J. & Lu, Y. Balance between community assembly processes mediates species coexistence in agricultural soil microbiomes across eastern China. ISME J. 14, 202–216 (2020).
Elzhov, T. V., Mullen, K. M., Spiess, A.-N. & Bolker, B. Minpack. lm: R Interface to the levenberg–marquardt nonlinear least-squares algorithm found in MINPACK, plus support for bounds (CRAN Repository, 2016).
Harrell, F. E. Jr. Hmisc: harrell miscellaneous. R. package version 3.0−12 (2013). .
Davison, J. et al. Global assessment of arbuscular mycorrhizal fungus diversity reveals very low endemism. Science 349, 970–973 (2015).
Fiore-Donno, A. M., Weinert, J., Wubet, T. & Bonkowski, M. Metacommunity analysis of amoeboid protists in grassland soils. Sci. Rep. 6, 19068 (2016).
Heger, T. J. et al. High-throughput environmental sequencing reveals high diversity of litter and moss associated protist communities along a gradient of drainage and tree productivity. Environ. Microbiol. 20, 1185–1203 (2018).
Oksanen, J. et al. Vegan: community ecology package. R. package version 2.5−4 (2019).
Field, A., Miles, J. & Field, Z. Discovering Statistics Using R. London (Sage publications, 2012).
Source: Ecology - nature.com
