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Plant Microbiota: Diversity, Transmission and Function

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Extended Biocontrol

Abstract

Plants host a wide range of viruses and microorganisms collectively referred to as the plant microbiota. This chapter outlines the state of knowledge on the diversity of these communities of microorganisms within different plant compartments, including the rhizosphere and the phyllosphere. The ecological processes (selection, diversification, dispersal and ecological drift) involved in the assembly of the plant microbiota are also briefly introduced. Finally in the last section of this chapter, the associations between plant traits and microbiota structure are highlighted with a specific emphasis on plant adaptation to biotic stresses.

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References

  • Bai, Y., D.B. Müller, G. Srinivas, R. Garrido-Oter, E. Potthoff, M. Rott, N. Dombrowski, P.C. Münch, S. Spaepen, M. Remus-Emsermann, B. Hüttel, A.C. McHardy, J.A. Vorholt, and P. Schulze-Lefert. 2015. Functional overlap of the Arabidopsis leaf and root microbiota. Nature 528 (7582): 364–369.

    Article  CAS  PubMed  Google Scholar 

  • Bonito, G., K. Hameed, R. Ventura, J. Krishnan, C.W. Schadt, and R. Vilgalys. 2016. Isolating a functionally relevant guild of fungi from the root microbiome of Populus. Fungal Ecology 22: 35–42.

    Article  Google Scholar 

  • Brundrett, M.C. 2006. Understanding the roles of multifunctional mycorrhizal and endophytic fungi. In Microbial Root Endophytes, ed. B.J.E. Schulz, C.J.C. Boyle, and T.N. Sieber, 281–298. Dordrecht: Springer.

    Chapter  Google Scholar 

  • Bulgarelli, D., K. Schlaeppi, S. Spaepen, Ver Loren, E. van Themaat, and P. Schulze-Lefert. 2013. Structure and functions of the bacterial microbiota of plants. Annual Review of Plant Biology 64: 807–838.

    Article  CAS  PubMed  Google Scholar 

  • Coince, A., T. Cordier, J. Lengellé, E. Defossez, C. Vacher, C. Robin, M. Buée, and B. Marçais. 2014. Leaf and root-associated fungal assemblages do not follow similar elevational diversity patterns. PLoS One 9 (6): e100668.

    Article  PubMed  PubMed Central  Google Scholar 

  • Egamberdieva, D., F. Kamilova, S. Validov, L. Gafurova, Z. Kucharova, and B. Lugtenberg. 2008. High incidence of plant growth-stimulating bacteria associated with the rhizosphere of wheat grown on salinated soil in Uzbekistan. Environmental Microbiology 10 (1): 1–9.

    CAS  PubMed  Google Scholar 

  • Guidot, A., W. Jiang, J.-B. Ferdy, C. Thébaud, P. Barberis, J. Gouzy, and S. Genin. 2014. Multihost experimental evolution of the pathogen Ralstonia solanacearum unveils genes involved in adaptation to plants. Molecular Biology and Evolution 31 (11): 2913–2928.

    Article  CAS  PubMed  Google Scholar 

  • Hacquard, S., S. Spaepen, R. Garrido-Oter, and P. Schulze-Lefert. 2017. Interplay between innate immunity and the plant microbiota. Annual Review of Phytopathology 55: 565–589.

    Article  CAS  PubMed  Google Scholar 

  • Hermosa, R., A. Viterbo, I. Chet, and E. Monte. 2012. Plant-beneficial effects of Trichoderma and of its genes. Microbiology 158 (1): 17–25.

    Article  CAS  PubMed  Google Scholar 

  • Horton, M.W., N. Bodenhausen, K. Beilsmith, D. Meng, B.D. Muegge, S. Subramanian, M.M. Vetter, B.J. Vilhjálmsson, M. Nordborg, J.I. Gordon, and J. Bergelson. 2014. Genome-wide association study of Arabidopsis thaliana leaf microbial community. Nature Communications 10 (5): 5320.

    Article  Google Scholar 

  • Hoveland, C.S. 1993. Importance and economic significance of the Acremonium endophytes to performance of animals and grass plant. Agriculture, Ecosystems & Environment 44 (1–4): 3–12.

    Article  Google Scholar 

  • Innerebner, G., C. Knief, and J.A. Vorholt. 2011. Protection of Arabidopsis thaliana against leaf-pathogenic Pseudomonas syringae by Sphingomonas strains in a controlled model system. Applied and Environmental Microbiology 77 (10): 3202–3210.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Khasa, D., Y. Piché, and A.P. Coughlan. 2009. Advances in Mycorrhizal Science and Technology. Ottawa: NRC Research Press.

    Google Scholar 

  • Lau, J.A., and J.T. Lennon. 2012. Rapid responses of soil microorganisms improve plant fitness in novel environments. Proceedings of the National Academy of Sciences of the United States of America 109 (35): 14058–14062.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Leach, J.E., L.R. Triplett, C.T. Argueso, and P. Trivedi. 2017. Communication in the phytobiome. Cell 169 (4): 587–596.

    Article  CAS  PubMed  Google Scholar 

  • Maignien, L., E.A. DeForce, M.E. Chafee, A.M. Eren, and S.L. Simmons. 2014. Ecological succession and stochastic variation in the assembly of Arabidopsis thaliana phyllosphere communities. MBio 5 (1): e00682–e00613.

    Article  PubMed  PubMed Central  Google Scholar 

  • Müller, D.B., C. Vogel, Y. Bai, and J.A. Vorholt. 2016. The plant microbiota: Systems-level insights and perspectives. Annual Review of Genetics 50: 211–234.

    Article  PubMed  Google Scholar 

  • Naylor, D., and D. Coleman-Derr. 2018. Drought stress and root-associated bacterial communities. Frontiers in Plant Science 8: 2223.

    Article  PubMed  PubMed Central  Google Scholar 

  • Nelson, E.B. 2018. The seed microbiome: Origins, interactions, and impacts. Plant and Soil 422 (1–2): 7–34.

    Article  CAS  Google Scholar 

  • Nemergut, D.R., S.K. Schmidt, T. Fukami, S.P. O’Neill, T.M. Bilinski, L.F. Stanish, J.E. Knelman, J.L. Darcy, R.C. Lynch, P. Wickey, and S. Ferrenberg. 2013. Patterns and processes of microbial community assembly. Microbiology and Molecular Biology Reviews 77 (3): 342–356.

    Article  PubMed  PubMed Central  Google Scholar 

  • Panke-Buisse, K., A.C. Poole, J.K. Goodrich, R.E. Ley, and J. Kao-Kniffin. 2015. Selection on soil microbiomes reveals reproducible impacts on plant function. The ISME Journal 9 (4): 980–989.

    Article  CAS  PubMed  Google Scholar 

  • Peay, K.G., M.G. Schubert, N.H. Nguyen, and T.D. Bruns. 2012. Measuring ectomycorrhizal fungal dispersal: Macroecological patterns driven by microscopic propagules. Molecular Ecology 21–16: 4122–4136.

    Article  Google Scholar 

  • Philippot, L., J.M. Raaijmakers, P. Lemanceau, and W.H. van der Putten. 2013. Going back to the roots: The microbial ecology of the rhizosphere. Nature Reviews Microbiology 11 (11): 789–799.

    Article  CAS  PubMed  Google Scholar 

  • Pieterse, C.M.J., C. Zamioudis, R.L. Berendsen, D.M. Weller, S.C.M. Van Wees, and P.A.H.M. Bakker. 2014. Induced systemic resistance by beneficial microbes. Annual Review of Phytopathology 52: 347–375.

    Article  CAS  PubMed  Google Scholar 

  • Porras-Alfaro, A., and P. Bayman. 2011. Hidden fungi, emergent properties: Endophytes and microbiomes. Annual Review of Phytopathology 49: 291–315.

    Article  CAS  PubMed  Google Scholar 

  • Rezki, S., C. Campion, P. Simoneau, M.-A. Jacques, A. Shade, and M. Barret. 2018. Assembly of seed-associated microbial communities within and across successive plant generations. Plant and Soil 422 (1–2): 67–79.

    Article  CAS  Google Scholar 

  • Ritpitakphong, U., L. Falquet, A. Vimoltust, A. Berger, J.P. Métraux, and F. L’Haridon. 2016. The microbiome of the leaf surface of Arabidopsis protects against a fungal pathogen. New Phytologist 210 (3): 1033–1043.

    Article  CAS  PubMed  Google Scholar 

  • Schardl, C.L., A. Leuchtmann, and M.J. Spiering. 2004. Symbioses of grasses with seedborne fungal endophytes. Annual Review of Plant Biology 55: 315–340.

    Article  CAS  PubMed  Google Scholar 

  • Shade, A., M.-A. Jacques, and M. Barret. 2017. Ecological patterns of seed microbiome diversity, transmission, and assembly. Current Opinion in Microbiology 37: 15–22.

    Article  PubMed  Google Scholar 

  • Sugiyama, A., M.G. Bakker, D.V. Badri, D.K. Manter, and J.M. Vivanco. 2013. Relationships between Arabidopsis genotype-specific biomass accumulation and associated soil microbial communities. Botany 91 (2): 123–126.

    Article  CAS  Google Scholar 

  • Vacher, C., A. Hampe, A.J. Porté, U. Sauer, S. Compant, and C.E. Morris. 2016. The phyllosphere: Microbial jungle at the plant-climate interface. Annual Review of Ecology, Evolution, and Systematics 47: 1–24.

    Article  Google Scholar 

  • Vorholt, J.A. 2012. Microbial life in the phyllosphere. Nature Reviews Microbiology 10: 828–840.

    Article  CAS  PubMed  Google Scholar 

  • Wagner, M.R., D.S. Lundberg, T.G. del Rio, S.G. Tringe, J.L. Dangl, and T. Mitchell-Olds. 2016. Host genotype and age shape the leaf and root microbiomes of a wild perennial plant. Nature Communications 7: 12151.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Walters, W.A., Z. Jin, N. Youngblut, J.G. Wallace, J. Sutter, W. Zhang, A. González-Peña, J. Peiffer, O. Koren, Q. Shi, R. Knight, T.G. del Rio, S.G. Tringe, E.S. Buckler, J.L. Dangl, and R.E. Ley. 2018. Large-scale replicated field study of maize rhizosphere identifies heritable microbes. Proceedings of the National Academy of Sciences of the United States of America 115 (28): 7368–7373.

    Article  PubMed  PubMed Central  Google Scholar 

  • Weller, D.M., J.M. Raaijmakers, B.B. McSpadden Gardener, and L.S. Thomashow. 2002. Microbial populations responsible for specific soil suppressiveness to plant pathogens. Annual Review of Phytopathology 40: 309–348.

    Article  CAS  PubMed  Google Scholar 

  • Zgadzaj, R., R. Garrido-Oter, D.B. Jensen, A. Koprivova, P. Schulze-Lefert, and S. Radutoiu. 2016. Root nodule symbiosis in Lotus japonicus drives the establishment of distinctive rhizosphere, root, and nodule bacterial communities. Proceedings of the National Academy of Sciences of the United States of America 113 (49): E7996–E8005.

    CAS  PubMed  PubMed Central  Google Scholar 

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Correspondence to Matthieu Barret .

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Barret, M., Buée, M., Mougel, C., Vacher, C. (2022). Plant Microbiota: Diversity, Transmission and Function. In: Fauvergue, X., et al. Extended Biocontrol. Springer, Dordrecht. https://doi.org/10.1007/978-94-024-2150-7_9

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