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Feedback- 1.
Bardgett, R. D. & van der Putten, W. H. Belowground biodiversity and ecosystem functioning. Nature 515, 505–511 (2014).
- 2.
Bahram, M. et al. Structure and function of the global topsoil microbiome. Nature 560, 233–237 (2018).
- 3.
Luan, L. et al. Coupling bacterial community assembly to microbial metabolism across soil profiles. mSystems 5, e00298–20 (2020).
- 4.
Stegen, J. C. et al. Groundwater–surface water mixing shifts ecological assembly processes and stimulates organic carbon turnover. Nat. Commun. 7, 11237 (2016).
- 5.
Thompson, L. R. et al. A communal catalogue reveals Earth’s multiscale microbial diversity. Nature 551, 457–463 (2017).
- 6.
Tedersoo, L. et al. Global diversity and geography of soil fungi. Science 346, 1256688 (2014).
- 7.
Oliverio, A. M. et al. The global-scale distributions of soil protists and their contributions to belowground systems. Sci. Adv. 6, eaax8787 (2020).
- 8.
van den Hoogen, J. et al. Soil nematode abundance and functional group composition at a global scale. Nature 572, 194–198 (2019).
- 9.
Nemergut, D. R. et al. Patterns and processes of microbial community assembly. Microbiol. Mol. Biol. Rev. 77, 342–356 (2013).
- 10.
Martiny, J. B. H. et al. Microbial biogeography: putting microorganisms on the map. Nat. Rev. Microbiol. 4, 102–112 (2006).
- 11.
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).
- 12.
Vellend, M. Conceptual synthesis in community ecology. Q. Rev. Biol. 85, 183–206 (2010).
- 13.
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).
- 14.
Zhou, J. & Ning, D. Stochastic community assembly: does it matter in microbial ecology? Microbiol. Mol. Biol. Rev. 81, e00002–e00017 (2017).
- 15.
Chave, J. Neutral theory and community ecology. Ecol. Lett. 7, 241–253 (2004).
- 16.
Letten, A. D., Ke, P.-J. & Fukami, T. Linking modern coexistence theory and contemporary niche theory. Ecol. Monogr. 87, 161–177 (2017).
- 17.
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).
- 18.
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).
- 19.
Stearns, S. C. The Evolution of Life Histories (Oxford Univ. Press, Oxford, 1992).
- 20.
Villarino, E. et al. Large-scale ocean connectivity and planktonic body size. Nat. Commun. 9, 142 (2018).
- 21.
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).
- 22.
Soininen, J., Korhonen, J. J. & Luoto, M. Stochastic species distributions are driven by organism size. Ecology 94, 660–670 (2013).
- 23.
Farjalla, V. F. et al. Ecological determinism increases with organism size. Ecology 93, 1752–1759 (2012).
- 24.
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).
- 25.
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).
- 26.
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).
- 27.
Foissner, W. Protist diversity and distribution: some basic considerations. Biodivers. Conserv. 17, 235–242 (2008).
- 28.
Pimm, S. L., Jones, H. L. & Diamond, J. On the risk of extinction. Am. Nat. 132, 757–785 (1988).
- 29.
Jiang, Y. et al. Crop rotations alter bacterial and fungal diversity in paddy soils across East Asia. Soil Biol. Biochem. 95, 250–261 (2016).
- 30.
Li, P. et al. Spatial variation in soil fungal communities across paddy fields in subtropical China. mSystems 5, e00704–e00719 (2020).
- 31.
Peay, K. G., Kennedy, P. G. & Talbot, J. M. Dimensions of biodiversity in the Earth mycobiome. Nat. Rev. Microbiol. 14, 434–447 (2016).
- 32.
Geisen, S. et al. Soil protists: a fertile frontier in soil biology research. FEMS Microbiol. Rev. 42, 293–323 (2018).
- 33.
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).
- 34.
Doledec, S., Chessel, D. & Gimaret-Carpentier, C. Niche separation in community analysis: a new method. Ecology 81, 2914–2927 (2000).
- 35.
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).
- 36.
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).
- 37.
Zinger, L. et al. Body size determines soil community assembly in a tropical forest. Mol. Ecol. 28, 528–543 (2019).
- 38.
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).
- 39.
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).
- 40.
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).
- 41.
Lowe, W. H. & McPeek, M. A. Is dispersal neutral? Trends Ecol. Evol. 29, 444–450 (2014).
- 42.
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).
- 43.
Brown, J. H. Why are there so many species in the tropics? J. Biogeogr. 41, 8–22 (2014).
- 44.
Li, X. et al. Agriculture erases climate constraints on soil nematode communities across large spatial scales. Glob. Change Biol. 26, 919–930 (2020).
- 45.
Briones, M. J. I. Soil fauna and soil functions: a jigsaw puzzle. Front. Environ. Sci. 22, 7 (2014).
- 46.
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).
- 47.
Pansu, M. & Gautheyrou, J. Handbook of Soil Analysis: Mineralogical, Organic, and Inorganic Methods. (Springer, 2006).
- 48.
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).
- 49.
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).
- 50.
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).
- 51.
Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7, 335–336 (2010).
- 52.
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).
- 53.
Zhang, Y. & Sun, Y. HMM-FRAME: accurate protein domain classification for metagenomic sequences containing frameshift errors. BMC Bioinform. 12, 198 (2011).
- 54.
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).
- 55.
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).
- 56.
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).
- 57.
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).
- 58.
Zhao, J. et al. Size spectra of soil nematode assemblages under different land use types. Soil Biol. Biochem. 85, 130–136 (2015).
- 59.
Soininen, J., McDonald, R. & Hillebrand, H. The distance decay of similarity in ecological communities. Ecography 30, 3–12 (2007).
- 60.
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).
- 61.
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).
- 62.
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).
- 63.
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).
- 64.
Harrell, F. E. Jr. Hmisc: harrell miscellaneous. R. package version 3.0−12 (2013). .
- 65.
Davison, J. et al. Global assessment of arbuscular mycorrhizal fungus diversity reveals very low endemism. Science 349, 970–973 (2015).
- 66.
Fiore-Donno, A. M., Weinert, J., Wubet, T. & Bonkowski, M. Metacommunity analysis of amoeboid protists in grassland soils. Sci. Rep. 6, 19068 (2016).
- 67.
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).
- 68.
Oksanen, J. et al. Vegan: community ecology package. R. package version 2.5−4 (2019).
- 69.
Field, A., Miles, J. & Field, Z. Discovering Statistics Using R. London (Sage publications, 2012).
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Source: https://www.nature.com/articles/s41467-020-20271-4
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Original Text (This is the original text for your reference.)
- 1.
Bardgett, R. D. & van der Putten, W. H. Belowground biodiversity and ecosystem functioning. Nature 515, 505–511 (2014).
- 2.
Bahram, M. et al. Structure and function of the global topsoil microbiome. Nature 560, 233–237 (2018).
- 3.
Luan, L. et al. Coupling bacterial community assembly to microbial metabolism across soil profiles. mSystems 5, e00298–20 (2020).
- 4.
Stegen, J. C. et al. Groundwater–surface water mixing shifts ecological assembly processes and stimulates organic carbon turnover. Nat. Commun. 7, 11237 (2016).
- 5.
Thompson, L. R. et al. A communal catalogue reveals Earth’s multiscale microbial diversity. Nature 551, 457–463 (2017).
- 6.
Tedersoo, L. et al. Global diversity and geography of soil fungi. Science 346, 1256688 (2014).
- 7.
Oliverio, A. M. et al. The global-scale distributions of soil protists and their contributions to belowground systems. Sci. Adv. 6, eaax8787 (2020).
- 8.
van den Hoogen, J. et al. Soil nematode abundance and functional group composition at a global scale. Nature 572, 194–198 (2019).
- 9.
Nemergut, D. R. et al. Patterns and processes of microbial community assembly. Microbiol. Mol. Biol. Rev. 77, 342–356 (2013).
- 10.
Martiny, J. B. H. et al. Microbial biogeography: putting microorganisms on the map. Nat. Rev. Microbiol. 4, 102–112 (2006).
- 11.
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).
- 12.
Vellend, M. Conceptual synthesis in community ecology. Q. Rev. Biol. 85, 183–206 (2010).
- 13.
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).
- 14.
Zhou, J. & Ning, D. Stochastic community assembly: does it matter in microbial ecology? Microbiol. Mol. Biol. Rev. 81, e00002–e00017 (2017).
- 15.
Chave, J. Neutral theory and community ecology. Ecol. Lett. 7, 241–253 (2004).
- 16.
Letten, A. D., Ke, P.-J. & Fukami, T. Linking modern coexistence theory and contemporary niche theory. Ecol. Monogr. 87, 161–177 (2017).
- 17.
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).
- 18.
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).
- 19.
Stearns, S. C. The Evolution of Life Histories (Oxford Univ. Press, Oxford, 1992).
- 20.
Villarino, E. et al. Large-scale ocean connectivity and planktonic body size. Nat. Commun. 9, 142 (2018).
- 21.
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).
- 22.
Soininen, J., Korhonen, J. J. & Luoto, M. Stochastic species distributions are driven by organism size. Ecology 94, 660–670 (2013).
- 23.
Farjalla, V. F. et al. Ecological determinism increases with organism size. Ecology 93, 1752–1759 (2012).
- 24.
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).
- 25.
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).
- 26.
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).
- 27.
Foissner, W. Protist diversity and distribution: some basic considerations. Biodivers. Conserv. 17, 235–242 (2008).
- 28.
Pimm, S. L., Jones, H. L. & Diamond, J. On the risk of extinction. Am. Nat. 132, 757–785 (1988).
- 29.
Jiang, Y. et al. Crop rotations alter bacterial and fungal diversity in paddy soils across East Asia. Soil Biol. Biochem. 95, 250–261 (2016).
- 30.
Li, P. et al. Spatial variation in soil fungal communities across paddy fields in subtropical China. mSystems 5, e00704–e00719 (2020).
- 31.
Peay, K. G., Kennedy, P. G. & Talbot, J. M. Dimensions of biodiversity in the Earth mycobiome. Nat. Rev. Microbiol. 14, 434–447 (2016).
- 32.
Geisen, S. et al. Soil protists: a fertile frontier in soil biology research. FEMS Microbiol. Rev. 42, 293–323 (2018).
- 33.
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).
- 34.
Doledec, S., Chessel, D. & Gimaret-Carpentier, C. Niche separation in community analysis: a new method. Ecology 81, 2914–2927 (2000).
- 35.
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).
- 36.
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).
- 37.
Zinger, L. et al. Body size determines soil community assembly in a tropical forest. Mol. Ecol. 28, 528–543 (2019).
- 38.
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).
- 39.
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).
- 40.
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).
- 41.
Lowe, W. H. & McPeek, M. A. Is dispersal neutral? Trends Ecol. Evol. 29, 444–450 (2014).
- 42.
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).
- 43.
Brown, J. H. Why are there so many species in the tropics? J. Biogeogr. 41, 8–22 (2014).
- 44.
Li, X. et al. Agriculture erases climate constraints on soil nematode communities across large spatial scales. Glob. Change Biol. 26, 919–930 (2020).
- 45.
Briones, M. J. I. Soil fauna and soil functions: a jigsaw puzzle. Front. Environ. Sci. 22, 7 (2014).
- 46.
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).
- 47.
Pansu, M. & Gautheyrou, J. Handbook of Soil Analysis: Mineralogical, Organic, and Inorganic Methods. (Springer, 2006).
- 48.
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).
- 49.
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).
- 50.
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).
- 51.
Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7, 335–336 (2010).
- 52.
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).
- 53.
Zhang, Y. & Sun, Y. HMM-FRAME: accurate protein domain classification for metagenomic sequences containing frameshift errors. BMC Bioinform. 12, 198 (2011).
- 54.
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).
- 55.
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).
- 56.
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).
- 57.
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).
- 58.
Zhao, J. et al. Size spectra of soil nematode assemblages under different land use types. Soil Biol. Biochem. 85, 130–136 (2015).
- 59.
Soininen, J., McDonald, R. & Hillebrand, H. The distance decay of similarity in ecological communities. Ecography 30, 3–12 (2007).
- 60.
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).
- 61.
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).
- 62.
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).
- 63.
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).
- 64.
Harrell, F. E. Jr. Hmisc: harrell miscellaneous. R. package version 3.0−12 (2013). .
- 65.
Davison, J. et al. Global assessment of arbuscular mycorrhizal fungus diversity reveals very low endemism. Science 349, 970–973 (2015).
- 66.
Fiore-Donno, A. M., Weinert, J., Wubet, T. & Bonkowski, M. Metacommunity analysis of amoeboid protists in grassland soils. Sci. Rep. 6, 19068 (2016).
- 67.
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).
- 68.
Oksanen, J. et al. Vegan: community ecology package. R. package version 2.5−4 (2019).
- 69.
Field, A., Miles, J. & Field, Z. Discovering Statistics Using R. London (Sage publications, 2012).
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