Berendsen, R. L., Pieterse, C. M. J. & Bakker, P. A. H. M. The rhizosphere microbiome and plant health. Trends Plant Sci. 17, 478–486 (2012).
Google Scholar
Philippot, L., Raaijmakers, J. M., Lemanceau, P. & Putten, W. Hvander Going back to the roots: the microbial ecology of the rhizosphere. Nat. Rev. Microbiol 11, 789–799 (2013).
Google Scholar
Bais, H. P., Weir, T. L., Perry, L. G., Gilroy, S. & Vivanco, J. M. The role of root exudates in rhizosphere interactions with plants and other organisms. Annu Rev. Plant Biol. 57, 233–266 (2006).
Google Scholar
De Long, J. R., Fry, E. L., Veen, G. F. & Kardol, P. Why are plant–soil feedbacks so unpredictable, and what to do about it? Funct. Ecol. 33, 118–128 (2019).
Google Scholar
Meisner, A., De Deyn, G. B., de Boer, W. & van der Putten, W. H. Soil biotic legacy effects of extreme weather events influence plant invasiveness. Proc. Natl. Acad. Sci. USA. 110, 9835–9838 (2013).
Google Scholar
Kostenko, O., van de Voorde, T. F. J., Mulder, P. P. J., van der Putten, W. H. & Bezemer, T. M. Legacy effects of aboveground-belowground interactions. Ecol. Lett. 15, 813–821 (2012).
Google Scholar
Heinen, R. et al. Plant community composition steers grassland vegetation via soil legacy effects. Ecol. Lett. 23, 973–982 (2020).
Google Scholar
Semchenko, M. et al. Fungal diversity regulates plant-soil feedbacks in temperate grassland. Sci. Adv. 4, eaau4578 (2018).
Google Scholar
Cordovez, V., Dini-Andreote, F., Carrión, V. J. & Raaijmakers, J. M. Ecology and evolution of plant microbiomes. Annu. Rev. Microbiol. 73, 69–88 (2019).
Google Scholar
Bennett, J. A. & Klironomos, J. Mechanisms of plant–soil feedback: interactions among biotic and abiotic drivers. New Phytol. 222, 91–96 (2019).
Google Scholar
van der Putten, W. H. et al. Plant–soil feedbacks: the past, the present and future challenges. J. Ecol. 101, 265–276 (2013).
Google Scholar
Bever, J. D., Platt, T. G. & Morton, E. R. Microbial population and community dynamics on plant roots and their feedbacks on plant communities. Annu. Rev. Microbiol. 66, 265–283 (2012).
Google Scholar
Petermann, J. S., Fergus, A. J. F., Turnbull, L. A. & Schmid, B. Janzen-connell effects are widespread and strong enough to maintain diversity in grasslands. Ecology 89, 2399–2406 (2008).
Google Scholar
Cortois, R., Schröder‐Georgi, T., Weigelt, A., van der Putten, W. H. & De Deyn, G. B. Plant–soil feedbacks: role of plant functional group and plant traits. J. Ecol. 104, 1608–1617 (2016).
Google Scholar
Bezemer, T. M., Jing, J., Bakx‐Schotman, J. M. T. & Bijleveld, E.-J. Plant competition alters the temporal dynamics of plant-soil feedbacks. J. Ecol. 106, 2287–2300 (2018).
Google Scholar
Kardol, P., Deyn, G. B. D., Laliberté, E., Mariotte, P. & Hawkes, C. V. Biotic plant–soil feedbacks across temporal scales. J. Ecol. 101, 309–315 (2013).
Google Scholar
Dudenhöffer, J.-H., Ebeling, A., Klein, A.-M. & Wagg, C. Beyond biomass: Soil feedbacks are transient over plant life stages and alter fitness. J. Ecol. 106, 230–241 (2018).
Google Scholar
Elger, A., Lemoine, D. G., Fenner, M. & Hanley, M. E. Plant ontogeny and chemical defence: older seedlings are better defended. Oikos. 118, 767–773 (2009).
Google Scholar
Nelson, E. B. The seed microbiome: origins, interactions, and impacts. Plant Soil 422, 7–34 (2018).
Google Scholar
Wei, Z. et al. Initial soil microbiome composition and functioning predetermine future plant health. Sci. Adv. 5, eaaw0759 (2019).
Google Scholar
Rosenblueth, M. & Martínez-Romero, E. Bacterial endophytes and their interactions with hosts. Mol. Plant Microbe Interact. 19, 827–837 (2006).
Google Scholar
Lundberg, D. S. et al. Defining core Arabidopsis thaliana root microbiome. Nature 488, 86–90 (2012).
Google Scholar
Gaiero, J. R. et al. Inside the root microbiome: bacterial root endophytes and plant growth promotion. Am. J. Bot. 100, 1738–1750 (2013).
Google Scholar
Rodriguez, R. J. Jr, Arnold, J. F. W. & Redman, A. E. Fungal endophytes: diversity and functional roles. New Phytol. 182, 314–330 (2009).
Google Scholar
Carrión, V. J. et al. Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome. Science 366, 606–612 (2019).
Google Scholar
Fitzpatrick, C. R. et al. Ecological role of the angiosperm root microbiome. Proc. Natl. Acad. Sci. USA. 115, E1157–E1165 (2018).
Google Scholar
Hardoim, P. R., van Overbeek, L. S. & Elsas, J. Dvan Properties of bacterial endophytes and their proposed role in plant growth. Trends Microbiol. 16, 463–471 (2008).
Google Scholar
Bulgarelli, D. et al. Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota. Nature 488, 91–95 (2012).
Google Scholar
Hannula, S. E., Zhu, F., Heinen, R. & Bezemer, T. M. Foliar-feeding insects acquire microbiomes from the soil rather than the host plant. Nat. Commun. 10, 1–9 (2019).
Google Scholar
Sikes, B. A., Hawkes, C. V. & Fukami, T. Plant and root endophyte assembly history: interactive effects on native and exotic plants. Ecology 97, 484–493 (2016).
Google Scholar
Bezemer, T. M. et al. Plant species and functional group effects on abiotic and microbial soil properties and plant–soil feedback responses in two grasslands. J. Ecol. 94, 893–904 (2006).
Google Scholar
van de Voorde, T. F., van der Putten, W. H. & Bezemer, T. M. Intra‐and interspecific plant–soil interactions, soil legacies and priority effects during old‐field succession. J. Ecol. 99, 945–953 (2011).
Google Scholar
Hannula, S. E. et al. Time after time: temporal variation in the effects of grass and forb species on soil bacterial and fungal communities. mBio 10, e02635–19 (2019).
Google Scholar
Mendes, R., Garbeva, P. & Raaijmakers, J. M. The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms. FEMS Microbiol. Rev. 37, 634–663 (2013).
Google Scholar
Ampt, E. A., van Ruijven, J., Raaijmakers, J. M., Termorshuizen, A. J. & Mommer, L. Linking ecology and plant pathology to unravel the importance of soil-borne fungal pathogens in species-rich grasslands. Eur. J. Plant Pathol. 154, 141–156 (2019).
Google Scholar
Allison, S. D. & Martiny, J. B. H. Resistance, resilience, and redundancy in microbial communities. Proc. Natl. Acad. Sci. USA. 105, 11512–11519 (2008).
Google Scholar
Rousk, J. & Bååth, E. Fungal biomass production and turnover in soil estimated using the acetate-in-ergosterol technique. Soil Biol. Biochem. 39, 2173–2177 (2007).
Google Scholar
Phillips, M. L. et al. Fungal community assembly in soils and roots under plant invasion and nitrogen deposition. Fungal Ecol. 40, 107–117 (2019).
Google Scholar
Carini, P., Marsden, P. & Leff, J. E. A. Relic DNA is abundant in soil and obscures estimates of soil microbial diversity. Nat. Microbiol. 2, 16242 (2017).
Google Scholar
Hannula, S. E., Morrien, E., van der Putter, W. H. & de Boer, W. Rhizosphere fungi actively assimilating plant-derived carbon in a grassland soil. Fungal Ecol. 48, 100988 (2020).
Google Scholar
Kulmatiski, A., Beard, K. H., Stevens, J. R. & Cobbold, S. M. Plant–soil feedbacks: a meta‐analytical review. Ecol. Lett. 11, 980–992 (2008).
Google Scholar
Dassen, S. et al. Differential responses of soil bacteria, fungi, archaea and protists to plant species richness and plant functional group identity. Mol. Ecol. 26, 4085–4098 (2017).
Google Scholar
Hannula, S. E. et al. Structure and ecological function of the soil microbiome affecting plant–soil feedbacks in the presence of a soil‐borne pathogen. Environ. Microbiol. 22, 660–676 (2020).
Google Scholar
Francioli, D. et al. Plant functional group drives the community structure of saprophytic fungi in a grassland biodiversity experiment. Plant Soil https://doi.org/10.1007/s11104-020-04454-y (2020).
Craine, J., Froehle, J., Tilman, D., Wedin, D. & Chapin, F. S. III The relationships among root and leaf traits of 76 grassland species and relative abundance along fertility and disturbance gradients. Oikos 93, 274–285 (2001).
Google Scholar
Tjoelker, M., Craine, J. M., Wedin, D., Reich, P. B. & Tilman, D. Linking leaf and root trait syndromes among 39 grassland and savannah species. New Phytol. 167, 493–508 (2005).
Google Scholar
Herz, K. et al. Linking root exudates to functional plant traits. PLoS ONE 13, e0204128 (2018).
Google Scholar
Huberty, M., Choi, Y. H., Heinen, R. & Bezemer, T. M. Above-ground plant metabolomic responses to plant–soil feedbacks and herbivory. J. Ecol. 108, 1703–1712 (2020).
Google Scholar
Edwards, J. et al. Structure, variation, and assembly of the root-associated microbiomes of rice. Proc. Natl. Acad. Sci. USA. 112, E911–E920 (2015).
Google Scholar
Jones, D. L., Nguyen, C. & Finlay, R. D. Carbon flow in the rhizosphere: carbon trading at the soil–root interface. Plant Soil 321, 5–33 (2009).
Google Scholar
Hannula, S. E. et al. Shifts in rhizosphere fungal community during secondary succession following abandonment from agriculture. ISME J. 11, 2294–2304 (2017).
Google Scholar
Koyama, A., Maherali, H. & Antunes, P. M. Plant geographic origin and phylogeny as potential drivers of community structure in root‐inhabiting fungi. J. Ecol. 107, 1720–1736 (2019).
Google Scholar
Wemheuer, F., Wemheuer, B., Daniel, R. & Vidal, S. Deciphering bacterial and fungal endophyte communities in leaves of two maple trees with green islands. Sci. Rep. 9, 1–14 (2019).
Google Scholar
Ma, H. et al. Steering root microbiomes of a commercial horticultural crop with plant-soil feedbacks. Appl. Soil Ecol. 150, 103468 (2020).
Google Scholar
Suárez-Moreno, Z. R. et al. Plant-growth promotion and biocontrol properties of three streptomyces spp. isolates to control bacterial rice pathogens. Front. Microbiol. 10, 290 (2019).
Google Scholar
Treseder, K. K. The extent of mycorrhizal colonization of roots and its influence on plant growth and phosphorus content. Plant Soil 371, 1–13 (2013).
Google Scholar
Liang, M. et al. Arbuscular mycorrhizal fungi counteract the Janzen-Connell effect of soil pathogens. Ecology 96, 562–574 (2015).
Google Scholar
Teste, F. P., Veneklaas, E. J., Dixon, K. W. & Lambers, H. Complementary plant nutrient-acquisition strategies promote growth of neighbour species. Funct. Ecol. 28, 819–828 (2014).
Google Scholar
Mommer, L. et al. Lost in diversity: the interactions between soil-borne fungi, biodiversity and plant productivity. New Phytol. 218, 542–553 (2018).
Google Scholar
Hassani, M. A., Durán, P. & Hacquard, S. Microbial interactions within the plant holobiont. Microbiome 6, 58 (2018).
Google Scholar
De Long, J. R. et al. How plant–soil feedbacks influence the next generation of plants?. Ecol. Res. 36, 32–44 https://doi.org/10.1111/1440-1703.12165 (2021).
Google Scholar
Tedersoo, L. et al. Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi. MycoKeys 10, 1–43 (2015).
Google Scholar
Caporaso, J. G. et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 6, 1621–1624 (2012).
Google Scholar
Parada, A. E., Needham, D. M. & Fuhrman, J. A. Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples. Environ. Microbiol. 18, 1403–1414 (2016).
Google Scholar
Apprill, A., McNally, S., Parsons, R. & Weber, L. Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton. Aquat. Micro. Ecol. 75, 129–137 (2015).
Google Scholar
Callahan, B. J. et al. DADA2: High-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581–583 (2016).
Google Scholar
Gweon, H. S. et al. PIPITS: an automated pipeline for analyses of fungal internal transcribed spacer sequences from the Illumina sequencing platform. Methods Ecol. Evol. 6, 973–980 (2015).
Google Scholar
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).
Google Scholar
Nguyen, N. H. et al. FUNGuild: an open annotation tool for parsing fungal community datasets by ecological guild. Fungal Ecol. 20, 241–248 (2016).
Google Scholar
Paulson, J. N., Stine, O. C., Bravo, H. C. & Pop, M. Robust methods for differential abundance analysis in marker gene surveys. Nat. Methods 10, 1200–1202 (2013).
Google Scholar
Weiss, S. et al. Normalization and microbial differential abundance strategies depend upon data characteristics. Microbiome 5, 27 (2017).
Google Scholar
Oksanen, J. et al. Vegan: Ordination Methods, Diversity Analysis And Other Functions For Community And Vegetation Ecologists (Community Ecol Package Vegan, 2013).
Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B Methodol. 57, 289–300 (1995).
Google Scholar
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