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Dissection of plant microbiota and plant-microbiome interactions

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  • Omics in Microbial Ecology
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Abstract

Plants rooted in soil have intimate associations with a diverse array of soil microorganisms. While the microbial diversity of soil is enormous, the predominant bacterial phyla associated with plants include Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, and Verrucomicrobia. Plants supply nutrient niches for microbes, and microbes support plant functions such as plant growth, development, and stress tolerance. The interdependent interaction between the host plant and its microbes sculpts the plant microbiota. Plant and microbiome interactions are a good model system for understanding the traits in eukaryotic organisms from a holobiont perspective. The holobiont concept of plants, as a consequence of co-evolution of plant host and microbiota, treats plants as a discrete ecological unit assembled with their microbiota. Dissection of plant-microbiome interactions is highly complicated; however, some reductionist approaches are useful, such as the synthetic community method in a gnotobiotic system. Deciphering the interactions between plant and microbiome by this reductionist approach could lead to better elucidation of the functions of microbiota in plants. In addition, analysis of microbial communities’ interactions would further enhance our understanding of coordinated plant microbiota functions. Ultimately, better understanding of plantmicrobiome interactions could be translated to improvements in plant productivity.

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References

  • Akasaka, H., Izawa, T., Ueki, K., and Ueki, A. 2003. Phylogeny of numerically abundant culturable anaerobic bacteria associated with degradation of rice plant residue in Japanese paddy field soil. FEMS Microbiol. Ecol. 43, 149–161.

    Article  CAS  PubMed  Google Scholar 

  • Artursson, V., Finlay, R.D., and Jansson, J.K. 2006. Interactions between arbuscular mycorrhizal fungi and bacteria and their potential for stimulating plant growth. Environ. Microbiol. 8, 1–10.

    Article  CAS  PubMed  Google Scholar 

  • Baas, P., Bell, C., Mancini, L.M., Lee, M.N., Conant, R.T., and Wallenstein, M.D. 2016. Phosphorus mobilizing consortium Mammoth P™ enhances plant growth. Peer J. 4, e2121.

    Article  PubMed  PubMed Central  Google Scholar 

  • Badri, D.V., Quintana, N., El Kassis, E.G., Kim, H.K., Choi, Y.H., Sugiyama, A., Verpoorte, R., Martinoia, E., Manter, D.K., and Vivanco, J.M. 2009. An ABC transporter mutation alters root exudation of phytochemicals that provoke an overhaul of natural soil microbiota. Plant Physiol. 151, 2006–2017.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Badri, D.V., Zolla, G., Bakker, M.G., Manter, D.K., and Vivanco, J.M. 2013. Potential impact of soil microbiomes on the leaf metabolome and on herbivore feeding behavior. New Phytol. 198, 264–273.

    Article  CAS  PubMed  Google Scholar 

  • Bai, Y., Müller, D.B., Srinivas, G., Garrido-Oter, R., Potthoff, E., Rott, M., Dombrowski, N., Münch, P.C., Spaepen, S., Remus-Emsermann, M., et al. 2015. Functional overlap of the Arabidopsis leaf and root microbiota. Nature 528, 364–369.

    Article  CAS  PubMed  Google Scholar 

  • Berendsen, R.L., Bakker, P.A., Feussner, I., and Pieterse, C.M. 2018. MYB72-dependent coumarin exudation shapes root microbiome assembly to promote plant health. Proc. Natl. Acad. Sci. USA 115, 5213–5222.

    CAS  Google Scholar 

  • Berendsen, R.L., Vismans, G., Yu, K., Song, Y., de Jonge, R., Burgman, W.P., Burmølle, M., Herschend, J., Bakker, P.A., and Pieterse, C.M. 2018. Disease-induced assemblage of a plant-beneficial bacterial consortium. ISME J. 12, 1496–1507.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Berg, G., Krechel, A., Ditz, M., Sikora, R.A., Ulrich, A., and Hallmann, J. 2005. Endophytic and ectophytic potato-associated bacterial communities differ in structure and antagonistic function against plant pathogenic fungi. FEMS Microbiol. Ecol. 51, 215–229.

    Article  CAS  PubMed  Google Scholar 

  • Bonfante, P. and Anca, I.A. 2009. Plants, mycorrhizal fungi, and bacteria: a network of interactions. Annu. Rev. Microbiol. 63, 363–383.

    Article  CAS  PubMed  Google Scholar 

  • Bonito, G., Reynolds, H., Robeson, M.S., Nelson, J., Hodkinson, B.P., Tuskan, G., Schadt, C.W., and Vilgalys, R. 2014. Plant host and soil origin influence fungal and bacterial assemblages in the roots of woody plants. Mol. Ecol. 23, 3356–3370.

    Article  PubMed  Google Scholar 

  • Brader, G., Compant, S., Vescio, K., Mitter, B., Trognitz, F., Ma, L.J., and Sessitsch, A. 2017. Ecology and genomic insights into plantpathogenic and plant-nonpathogenic endophytes. Annu. Rev. Phytopathol. 55, 61–83.

    Article  CAS  PubMed  Google Scholar 

  • Bulgarelli, D., Rott, M., Schlaeppi, K., van Themaat, E.V.L., Ahmadinejad, N., Assenza, F., Rauf, P., Huettel, B., Reinhardt, R., Schmelzer, E., et al. 2012. Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota. Nature 488, 91–95.

    Article  CAS  PubMed  Google Scholar 

  • Bulgarelli, D., Schlaeppi, K., Spaepen, S., Van Themaat, E.V.L., and Schulze-Lefert, P. 2013. Structure and functions of the bacterial microbiota of plants. Annu. Rev. Plant Biol. 64, 807–838.

    Article  CAS  PubMed  Google Scholar 

  • Carrión, V.J., Perez-Jaramillo, J., Cordovez, V., Tracanna, V., De Hollander, M., Ruiz-Buck, D., Mendes, L.W., van Ijcken, W.F., Gomez-Exposito, R., and Elsayed, S.S. 2019. Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome. Science 366, 606–612.

    Article  PubMed  CAS  Google Scholar 

  • Castrillo, G., Teixeira, P.J.P.L., Paredes, S.H., Law, T.F., de Lorenzo, L., Feltcher, M.E., Finkel, O.M., Breakfield, N.W., Mieczkowski, P., Jones, C.D., et al. 2017. Root microbiota drive direct integration of phosphate stress and immunity. Nature 543, 513–518.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cha, J.Y., Han, S., Hong, H.J., Cho, H., Kim, D., Kwon, Y., Kwon, S.K., Crüsemann, M., Lee, Y.B., Kim, J.F., et al. 2016. Microbial and biochemical basis of a Fusarium wilt-suppressive soil. ISME J. 10, 119–129.

    Article  CAS  PubMed  Google Scholar 

  • Chanway, C.P., Shishido, M., Nairn, J., Jungwirth, S., Markham, J., Xiao, G., and Holl, F.B. 2000. Endophytic colonization and field responses of hybrid spruce seedlings after inoculation with plant growth-promoting rhizobacteria. For. Ecol. Manag. 133, 81–88.

    Article  Google Scholar 

  • Chapelle, E., Mendes, R., Bakker, P.A.H., and Raaijmakers, J.M. 2016. Fungal invasion of the rhizosphere microbiome. ISME J. 10, 265–268.

    Article  CAS  PubMed  Google Scholar 

  • Chen, T., Nomura, K., Wang, X., Sohrabi, R., Xu, J., Yao, L., Paasch, B.C., Ma, L., Kremer, J., Cheng, Y., et al. 2020. A plant genetic network for preventing dysbiosis in the phyllosphere. Nature 580, 653–657.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chen, Y., Wang, J., Yang, N., Wen, Z., Sun, X., Chai, Y., and Ma, Z. 2018. Wheat microbiome bacteria can reduce virulence of a plant pathogenic fungus by altering histone acetylation. Nat. Commun. 9, 1–14.

    CAS  Google Scholar 

  • Chialva, M., Salvioli di Fossalunga, A., Daghino, S., Ghignone, S., Bagnaresi, P., Chiapello, M., Novero, M., Spadaro, D., Perotto, S., and Bonfante, P. 2018. Native soils with their microbiotas elicit a state of alert in tomato plants. New Phytol. 220, 1296–1308.

    Article  CAS  PubMed  Google Scholar 

  • Choi, K., Choi, J., Lee, P.A., Roy, N., Khan, R., Lee, H.J., Weon, H.Y., Kong, H.G., and Lee, S.W. 2020. Alteration of bacterial wilt resistance in tomato plant by microbiota transplant. Front. Plant Sci. 11, 1186.

    Article  PubMed  PubMed Central  Google Scholar 

  • Compant, S., Clément, C., and Sessitsch, A. 2010. Plant growthromoting bacteria in the rhizo- and endosphere of plants: their role, colonization, mechanisms involved and prospects for utilization. Soil Biol. Biochem. 42, 669–678.

    Article  CAS  Google Scholar 

  • Compant, S., Reiter, B., Sessitsch, A., Nowak, J., Clément, C., and Ait Barka, E. 2005. Endophytic colonization of Vitis vinifera L. by plant growth-promoting bacterium Burkholderia sp. strain PsJN. Appl. Environ. Microbiol. 71, 1685–1693.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Conn, K.L., Nowak, J., and Lazarovitz, G. 1997. A gnotobiotic bioassay for studying interactions between potato and plant growthpromoting rhizobacteria. Can. J. Microbiol. 43, 801–808.

    Article  CAS  Google Scholar 

  • Correa-Galeote, D., Bedmar, E.J., and Arone, G.J. 2018. Maize endophytic bacterial diversity as affected by soil cultivation history. Front. Microbiol. 9, 484.

    Article  PubMed  PubMed Central  Google Scholar 

  • Dal Cortivo, C., Barion, G., Ferrari, M., Visioli, G., Dramis, L., Panozzo, A., and Vamerali, T. 2018. Effects of field inoculation with VAM and bacteria consortia on root growth and nutrients uptake in common wheat. Sustainability 10, 3286.

    Article  CAS  Google Scholar 

  • Delmotte, N., Knief, C., Chaffron, S., Innerebner, G., Roschitzki, B., Schlapbach, R., von Mering, C., and Vorholt, J.A. 2009. Community proteogenomics reveals insights into the physiology of phyllosphere bacteria. Proc. Natl. Acad. Sci. USA 106, 16428–16433.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dennis, P.G., Miller, A.J., and Hirsch, P.R. 2010. Are root exudates more important than other sources of rhizodeposits in structuring rhizosphere bacterial communities? FEMS Microbiol. Ecol. 72, 313–327.

    Article  CAS  PubMed  Google Scholar 

  • Ding, L.J., Cui, H.L., Nie, S.A., Long, X.E., Duan, G.L., and Zhu, Y.G. 2019. Microbiomes inhabiting rice roots and rhizosphere. FEMS Microbiol. Ecol. 95, fiz040.

    Article  CAS  PubMed  Google Scholar 

  • Durán, P., Thiergart, T., Garrido-Oter, R., Agler, M., Kemen, E., Schulze-Lefert, P., and Hacquard, S. 2018. Microbial interkingdom interactions in roots promote Arabidopsis survival. Cell 175, 973–983.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Edwards, J., Johnson, C., Santos-Medellín, C., Lurie, E., Podishetty, N.K., Bhatnagar, S., Eisen, J.A., and Sundaresan, V. 2015. Structure, variation, and assembly of the root-associated microbiomes of rice. Proc. Natl. Acad. Sci. USA 112, 911–920.

    Article  CAS  Google Scholar 

  • Farag, M.A., Song, G.C., Park, Y.S., Audrain, B., Lee, S., Ghigo, J.M., Kloepper, J.W., and Ryu, C.M. 2017. Biological and chemical strategies for exploring inter-and intra-kingdom communication mediated via bacterial volatile signals. Nat. Protoc. 12, 1359–1377.

    Article  CAS  PubMed  Google Scholar 

  • Farré-Armengol, G., Filella, I., Llusia, J., and Peñuelas, J. 2016. Bidirectional interaction between phyllospheric microbiotas and plant volatile emissions. Trends Plant Sci. 21, 854–860.

    Article  PubMed  CAS  Google Scholar 

  • Finkel, O.M., Burch, A.Y., Lindow, S.E., Post, A.F., and Belkin, S. 2011. Geographical location determines the population structure in phyllosphere microbial communities of a salt-excreting desert tree. Appl. Environ. Microbiol. 77, 7647–7655.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Finkel, O.M., Castrillo, G., Herrera Paredes, S., Salas González, I., and Dangl, J.L. 2017. Understanding and exploiting plant beneficial microbes. Curr. Opin. Plant Biol. 38, 155–163.

    Article  PubMed  PubMed Central  Google Scholar 

  • Finkel, O.M., Salas-González, I., Castrillo, G., Conway, J.M., Law, T.F., Teixeira, P.J.P.L., Wilson, E.D., Fitzpatrick, C.R., Jones, C.D., and Dangl, J.L. 2020. A single bacterial genus maintains root growth in a complex microbiome. Nature 587, 103–108.

    Article  CAS  PubMed  Google Scholar 

  • Fitzpatrick, C.R., Copeland, J., Wang, P.W., Guttman, D.S., Kotanen, P.M., and Johnson, M.T. 2018. Assembly and ecological function of the root microbiome across angiosperm plant species. Proc. Natl. Acad. Sci. USA 115, 1157–1165.

    Article  CAS  Google Scholar 

  • French, E., Tran, T., and Iyer-Pascuzzi, A.S. 2020. Tomato genotype modulates selection and responses to root microbiota. Phytobiomes J. 4, 314–326.

    Article  Google Scholar 

  • Frey-Klett, P., Garbaye, J., and Tarkka, M. 2007. The mycorrhiza helper bacteria revisited. New Phytol. 176, 22–36.

    Article  CAS  PubMed  Google Scholar 

  • Garbaye, J. 1994. Tansley review no. 76 helper bacteria: a new dimension to the mycorrhizal symbiosis. New Phytol. 128, 197–210.

    Article  PubMed  Google Scholar 

  • Garrido-Oter, R., Nakano, R.T., Dombrowski, N., Ma, K.W., Team, T.A., McHardy, A.C., and Schulze-Lefert, P. 2018. Modular traits of the Rhizobiales root microbiota and their evolutionary relationship with symbiotic rhizobia. Cell Host Microbe 24, 155–167.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gilbert, J.A., Jansson, J.K., and Knight, R. 2014. The earth microbiome project: successes and aspirations. BMC Biol. 12, 69.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Glaeser, S.P., Imani, J., Alabid, I., Guo, H., Kumar, N., Kämpfer, P., Hardt, M., Blom, J., Goesmann, A., Rothballer, M., et al. 2016. Non-pathogenic Rhizobium radiobacter F4 deploys plant beneficial activity independent of its host Piriformospora indica. ISME J. 10, 871–884.

    Article  PubMed  Google Scholar 

  • Gottel, N.R., Castro, H.F., Kerley, M., Yang, Z., Pelletier, D.A., Podar, M., Karpinets, T., Uberbacher, E.D., Tuskan, G.A., Vilgalys, R., et al. 2011. Distinct microbial communities within the endosphere and rhizosphere of Populus deltoides roots across contrasting soil types. Appl. Environ. Microbiol. 77, 5934–5944.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Guerrero, R., Margulis, L., and Berlanga, M. 2013. Symbiogenesis: the holobiont as a unit of evolution. Int. J. Microbiol. 16, 133–143.

    Google Scholar 

  • Guttman, D.S., McHardy, A.C., and Schulze-Lefert, P. 2014. Microbial genome-enabled insights into plant-microorganism interactions. Nat. Rev. Genet. 15, 797–813.

    Article  CAS  PubMed  Google Scholar 

  • Hallmann, J. 2001. Plant interactions with endophytic bacteria. In Jeger, M.J. and Spence, N.J. (eds.), Biotic Interactions in Plante Pathogen Associations, pp. 87–119. CABI Publishing, Wallingford, United Kingdom.

    Chapter  Google Scholar 

  • Ham, B.K., Chen, J., Yan, Y., and Lucas, W.J. 2018. Insights into plant phosphate sensing and signaling. Curr. Opin. Biotechnol. 49, 1–9.

    Article  CAS  PubMed  Google Scholar 

  • Hammerbacher, A., Coutinho, T.A., and Gershenzon, J. 2019. Roles of plant volatiles in defence against microbial pathogens and microbial exploitation of volatiles. Plant Cell Environ. 42, 2827–2843.

    Article  CAS  PubMed  Google Scholar 

  • Haney, C.H., Samuel, B.S., Bush, J., and Ausubel, F.M. 2015. Associations with rhizosphere bacteria can confer an adaptive advantage to plants. Nat. Plants 1, 1–9.

    Article  CAS  Google Scholar 

  • Hardoim, P.R., van Overbeek, L.S., and Elsas, J.D. 2008. Properties of bacterial endophytes and their proposed role in plant growth. Trends Microbiol. 16, 463–471.

    Article  CAS  PubMed  Google Scholar 

  • Hart, M.M., Antunes, P.M., Chaudhary, V.B., and Abbott, L.K. 2018. Fungal inoculants in the field: Is the reward greater than the risk? Funct. Ecol. 32, 126–135.

    Article  Google Scholar 

  • Hartmann, A., Schmid, M., van Tuinen, D., and Berg, G. 2009. Plantdriven selection of microbes. Plant Soil 321, 235–257.

    Article  CAS  Google Scholar 

  • Hassani, M.A., Durán, P., and Hacquard, S. 2018. Microbial interactions within the plant holobiont. Microbiome 6, 58.

    Article  PubMed  PubMed Central  Google Scholar 

  • Hirsch, P.R. and Mauchline, T.H. 2012. Who’s who in the plant root microbiome? Nat. Biotechnol. 30, 961–962.

    Article  CAS  PubMed  Google Scholar 

  • Idris, R., Trifonova, R., Puschenreiter, M., Wenzel, W.W., and Sessitsch, A. 2004. Bacterial communities associated with flowering plants of the Ni hyperaccumulator Thlaspi goesingense. Appl. Environ. Microbiol. 70, 2667–2677.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kandel, S.L., Joubert, P.M., and Doty, S.L. 2017. Bacterial endophyte colonization and distribution within plants. Microorganisms 5, 77.

    Article  PubMed Central  CAS  Google Scholar 

  • Kim, H. and Lee, Y.H. 2020. The rice microbiome: A model platform for crop holobiome. Phytobiomes J. 4, 5–18.

    Article  Google Scholar 

  • Kim, H., Lee, K.K., Jeon, J., Harris, W.A., and Lee, Y.H. 2020. Domestication of Oryza species eco-evolutionarily shapes bacterial and fungal communities in rice seed. Microbiome 8, 1–17.

    Article  Google Scholar 

  • Kim, M., Singh, D., Lai-Hoe, A., Go, R., Rahim, R.A., Ainuddin, A.N., Chun, J., and Adams, J.M. 2012. Distinctive phyllosphere bacterial communities in tropical trees. Microb. Ecol. 63, 674–681.

    Article  PubMed  Google Scholar 

  • Knief, C., Delmotte, N., Chaffron, S., Stark, M., Innerebner, G., Wassmann, R., Von Mering, C., and Vorholt, J.A. 2012. Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice. ISME J. 6, 1378–1390.

    Article  CAS  PubMed  Google Scholar 

  • Knief, C., Ramette, A., Frances, L., Alonso-Blanco, C., and Vorholt, J.A. 2010. Site and plant species are important determinants of the Methylobacterium community composition in the plant phyllosphere. ISME J. 4, 719–728.

    Article  CAS  PubMed  Google Scholar 

  • Kong, H.G., Song, G.C., Sim, H.J., and Ryu, C.M. 2021. Achieving similar root microbiota composition in neighbouring plants through airborne signaling. ISME J. 15, 397–408.

    Article  CAS  PubMed  Google Scholar 

  • Kour, D., Rana, K.L., Yadav, N., Yadav, A.N., Kumar, A., Meena, V.S., Singh, B., Chauhan, V.S., Dhaliwal, H.S., and Saxena, A.K. 2019. Rhizospheric microbiomes: biodiversity, mechanisms of plant growth promotion, and biotechnological applications for sustainable agriculture, pp. 19–65. In Plant Growth Promoting Rhizobacteria for Agricultural Sustainability. Springer, Singapore.

    Chapter  Google Scholar 

  • Krechel, A., Ditz, M., Ulrich, A., Faupel, A., Hallmann, J., and Berg, G. 2004. Bacterial life inside and outside potato roots and leaves. IOBC/WPRS Bulletin 27, 157–163.

    Google Scholar 

  • Kwak, M.J., Kong, H.G., Choi, K., Kwon, S.K., Song, J.Y., Lee, J., Lee, P.A., Choi, S.Y., Seo, M., Lee, H.J., et al. 2018. Rhizosphere microbiome structure alters to enable wilt resistance in tomato. Nat. Biotechnol. 36, 1100–1109.

    Article  CAS  Google Scholar 

  • Labbé, J.L., Weston, D.J., Dunkirk, N., Pelletier, D.A., and Tuskan, G.A. 2014. Newly identified helper bacteria stimulate ectomycorrhizal formation in Populus. Front. Plant Sci. 5, 579.

    PubMed  PubMed Central  Google Scholar 

  • Lareen, A., Burton, F., and Schäfer, P. 2016. Plant root-microbe communication in shaping root microbiomes. Plant Mol. Biol. 90, 575–587.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lau, J.A. and Lennon, J.T. 2012. Rapid responses of soil microorganisms improve plant fitness in novel environments. Proc. Natl. Acad. Sci. USA 109, 14058–14062.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Lebeis, S.L., Paredes, S.H., Lundberg, D.S., Breakfield, N., Gehring, J., McDonald, M., Malfatti, S., Del Rio, T.G., Jones, C.D., Tringe, S.G., et al. 2015. Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa. Science 349, 860–864.

    Article  CAS  PubMed  Google Scholar 

  • Lee, S.M., Kong, H.G., Song, G.C., and Ryu, C.M. 2020. Disruption of Firmicutes and Actinobacteria abundance in tomato rhizosphere causes the incidence of bacterial wilt disease. ISME J. 15, 330–347.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Lee, B., Lee, S., and Ryu, C.M. 2012. Foliar aphid feeding recruits rhizosphere bacteria and primes plant immunity against pathogenic and non-pathogenic bacteria in pepper. Ann. Bot. 110, 281–290.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Leifert, C., Waites, W.M., and Nicholas, J.R. 1989. Bacterial contaminants of micropropagated plant cultures. J. Appl. Bacteriol. 67, 353–361.

    Article  Google Scholar 

  • Lindow, S.E. and Brandl, M.T. 2003. Microbiology of the phyllosphere. Appl. Environ. Microbiol. 69, 1875–1883.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu, H. and Brettell, L.E. 2019. Plant defense by VOC-induced microbial priming. Trends Plant Sci. 24, 187–189.

    Article  CAS  PubMed  Google Scholar 

  • Lombardi, N., Vitale, S., Turrà, D., Reverberi, M., Fanelli, C., Vinale, F., Marra, R., Ruocco, M., Pascale, A., d’Errico, G., et al. 2018. Root exudates of stressed plants stimulate and attract Trichoderma soil fungi. Mol. Plant-Microbe Interact. 31, 982–994.

    Article  CAS  PubMed  Google Scholar 

  • Lundberg, D.S., Lebeis, S.L., Paredes, S.H., Yourstone, S., Gehring, J., Malfatti, S., Tremblay, J., Engelbrektson, A., Kunin, V., Del Rio, T.G., et al. 2012. Defining the core Arabidopsis thaliana root microbiome. Nature 488, 86–90.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Malusà, E., Pinzari, F., and Canfora, L. 2016. Efficacy of biofertilizers: challenges to improve crop production, pp. 17–40. In Singh, D.P., Singh, H.B., and Prabha, R. (eds.), Microbial inoculants in sustainable agricultural productivity. Springer, New Delhi, India.

    Chapter  Google Scholar 

  • Margulis, L. and Fester, R. 1991. Symbiosis as a source of evolutionary innovation: speciation and morphogenesis. The MIT Press, USA.

    Google Scholar 

  • Martínez-Hidalgo, P. and Hirsch, A.M. 2017. The nodule microbiome: N2-fixing rhizobia do not live alone. Phytobiomes 1, 70–82.

    Article  Google Scholar 

  • McNear, D.H.Jr. 2013. The rhizosphere-roots, soil and everything in between. Nat. Educ. Knowl. 4, 1.

    Google Scholar 

  • Mendes, R., Kruijt, M., De Bruijn, I., Dekkers, E., van der Voort, M., Schneider, J.H., Piceno, Y.M., DeSantis, T.Z., Andersen, G.L., Bakker, P.A., et al. 2011. Deciphering the rhizosphere microbiome for disease-suppressive bacteria. Science 332, 1097–1100.

    Article  CAS  PubMed  Google Scholar 

  • Meng, Q.X., Jiang, H.H., Hanson, L.E., and Hao, J.J. 2012. Characterizing a novel strain of Bacillus amyloliquefaciens BAC 03 for potential biological control application. J. Appl. Microbiol. 113, 1165–1175.

    Article  CAS  PubMed  Google Scholar 

  • Millet, Y.A., Danna, C.H., Clay, N.K., Songnuan, W., Simon, M.D., Werck-Reichhart, D., and Ausubel, F.M. 2010. Innate immune responses activated in Arabidopsis roots by microbe-associated molecular patterns. Plant Cell 22, 973–990.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Molina-Romero, D., Baez, A., Quintero-Hernández, V., Castañeda-Lucio, M., Fuentes-Ramírez, L.E., Bustillos-Cristales, M.D.R., Rodríguez-Andrade, O., Morales-García, Y.E., Munive, A., and Muñoz-Rojas, J. 2017. Compatible bacterial mixture, tolerant to desiccation, improves maize plant growth. PLoS ONE 12, 1–21.

    Article  CAS  Google Scholar 

  • Murphy, K.P. 2012. Machine learning: a probabilistic perspective. The MIT Press, USA.

    Google Scholar 

  • Niu, B., Paulson, J.N., Zheng, X., and Kolter, R. 2017. Simplified and representative bacterial community of maize roots. Proc. Natl. Acad. Sci. USA 114, 2450–2459.

    Article  CAS  Google Scholar 

  • Ottesen, A.R., Peña, A.G., White, J.R., Pettengill, J.B., Li, C., Allard, S., Rideout, S., Allard, M., Hill, T., Evans, P., et al. 2013. Baseline survey of the anatomical microbial ecology of an important food plant: Solanum lycopersicum (tomato). BMC Microbiol. 13, 114.

    Article  PubMed  PubMed Central  Google Scholar 

  • Peiffer, J.A., Spor, A., Koren, O., Jin, Z., Tringe, S.G., Dangl, J.L., Buckler, E.S., and Ley, R.E. 2013. Diversity and heritability of the maize rhizosphere microbiome under field conditions. Proc. Natl. Acad. Sci. USA 110, 6548–6553.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pieterse, C.M., Leon-Reyes, A., Van der Ent, S., and Van Wees, S.C. 2009. Networking by small-molecule hormones in plant immunity. Nat. Chem. Biol. 5, 308–316.

    Article  CAS  PubMed  Google Scholar 

  • Pineda, A., Kaplan, I., and Bezemer, T.M. 2017. Steering soil microbiomes to suppress aboveground insect pests. Trends Plant Sci. 22, 770–778.

    Article  CAS  PubMed  Google Scholar 

  • Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K.S., Manichanh, C., Nielsen, T., Pons, N., Levenez, F., Yamada, T., et al. 2010. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464, 59–65.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Qiu, Y.L., Kuang, X.Z., Shi, X.S., Yuan, X.Z., and Guo, R.B. 2014. Paludibacter jiangxiensis sp. nov., a strictly anaerobic, propionate-producing bacterium isolated from rice paddy field. Arch. Microbiol. 196, 149–155.

    Article  CAS  PubMed  Google Scholar 

  • Raaijmakers, J.M., Bonsall, R.F., and Weller, D.M. 1999. Effect of population density of Pseudomonas fluorescens on production of 2, 4-diacetylphloroglucinol in the rhizosphere of wheat. Phytopathology 89, 470–475.

    Article  CAS  PubMed  Google Scholar 

  • Redford, A.J., Bowers, R.M., Knight, R., Linhart, Y., and Fierer, N. 2010. The ecology of the phyllosphere: geographic and phylogenetic variability in the distribution of bacteria on tree leaves. Environ. Microbiol. 12, 2885–2893.

    Article  PubMed  PubMed Central  Google Scholar 

  • Remus-Emsermann, M.N., Tecon, R., Kowalchuk, G.A., and Leveau, J.H. 2012. Variation in local carrying capacity and the individual fate of bacterial colonizers in the phyllosphere. ISME J. 6, 756–765.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Rolli, E., Marasco, R., Vigani, G., Ettoumi, B., Mapelli, F., Deangelis, M.L., Gandolfi, C., Casati, E., Previtali, F., Gerbino, R., et al. 2015. Improved plant resistance to drought is promoted by the root-associated microbiome as a water stress-dependent trait. Environ. Microbiol. 17, 316–331.

    Article  PubMed  Google Scholar 

  • Roy, N., Choi, K., Khan, R., and Lee, S.W. 2019. Culturing simpler and bacterial wilt suppressive microbial communities from tomato rhizosphere. Plant Pathol. J. 35, 362–371.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Samad, A., Trognitz, F., Compant, S., Antonielli, L., and Sessitsch, A. 2017. Shared and host specific microbiome diversity and functioning of grapevine and accompanying weed plants. Environ. Microbiol. 19, 1407–1424.

    Article  PubMed  Google Scholar 

  • Santos-Medellín, C., Edwards, J., Liechty, Z., Nguyen, B., and Sundaresan, V. 2017. Drought stress results in a compartment-specific restructuring of the rice root-associated microbiomes. mBio 8, e00764–17.

    Article  PubMed  PubMed Central  Google Scholar 

  • Sasse, J., Martinoia, E., and Northen, T. 2018. Feed your friends: do plant exudates shape the root microbiome? Trends Plant Sci. 23, 25–41.

    Article  CAS  PubMed  Google Scholar 

  • Schlaeppi, K. and Bulgarelli, D. 2015. The plant microbiome at work. Mol. Plant-Microbe Interact. 28, 212–217.

    Article  CAS  PubMed  Google Scholar 

  • Schlaeppi, K., Dombrowski, N., Oter, R.G., van Themaat, E.V.L., and Schulze-Lefert, P. 2014. Quantitative divergence of the bacterial root microbiota in Arabidopsis thaliana relatives. Proc. Natl. Acad. Sci. USA 111, 585–592.

    Article  CAS  PubMed  Google Scholar 

  • Schroth, M.N. and Hancock, J.G. 1982. Disease-suppressive soil and root-colonizing bacteria. Science 216, 1376–1381.

    Article  CAS  PubMed  Google Scholar 

  • Sessitsch, A., Reiter, B., Pfeifer, U., and Wilhelm, E. 2002. Cultivation-independent population analysis of bacterial endophytes in three potato varieties based on eubacterial and Actinomycetes-specific PCR of 16S rRNA genes. FEMS Microbiol. Ecol. 39, 23–32.

    Article  CAS  PubMed  Google Scholar 

  • Thapa, S. and Prasanna, R. 2018. Prospecting the characteristics and significance of the phyllosphere microbiome. Ann. Microbiol. 68, 229–245.

    Article  CAS  Google Scholar 

  • Timm, C.M., Carter, K.R., Carrell, A.A., Jun, S.R., Jawdy, S.S., Vélez, J.M., Gunter, L.E., Yang, Z., Nookaew, I., and Engle, N.L. 2018. Abiotic stresses shift belowground Populus-associated bacteria toward a core stress microbiome. mSystems 3, e00070–17.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Toju, H., Peay, K.G., Yamamichi, M., Narisawa, K., Hiruma, K., Naito, K., Fukuda, S., Ushio, M., Nakaoka, S., Onoda, Y., et al. 2018. Core microbiomes for sustainable agroecosystems. Nat. Plants 4, 247–257.

    Article  PubMed  Google Scholar 

  • Tonouchi, A. 2009. Isolation and characterization of a novel facultative anaerobic filamentous fungus from Japanese rice field soil. Int. J. Microbiol. 2009, 1–9.

    Article  CAS  Google Scholar 

  • Turner, T.R., James, E.K., and Poole, P.S. 2013. The plant microbiome. Genome Biol. 14, 1–10.

    Article  CAS  Google Scholar 

  • Uroz, S., Buee, M., Murat, C., Frey-Klett, P., and Martin, F. 2010. Pyrosequencing reveals a contrasted bacterial diversity between oak rhizosphere and surrounding soil. Environ. Microbiol. Rep. 2, 281–288.

    Article  CAS  PubMed  Google Scholar 

  • Van der Ent, S., Van Hulten, M., Pozo, M.J., Czechowski, T., Udvardi, M.K., Pieterse, C.M., and Ton, J. 2009. Priming of plant innate immunity by rhizobacteria and β-aminobutyric acid: differences and similarities in regulation. New Phytol. 183, 419–431.

    Article  CAS  PubMed  Google Scholar 

  • Van Der Heijden, M.G., De Bruin, S., Luckerhoff, L., Van Logtestijn, R.S., and Schlaeppi, K. 2016. A widespread plant-fungal-bacterial symbiosis promotes plant biodiversity, plant nutrition and seedling recruitment. ISME J. 10, 389–399.

    Article  CAS  PubMed  Google Scholar 

  • Vandenkoornhuyse, P., Quaiser, A., Duhamel, M., Le Van, A., and Dufresne, A. 2015. The importance of the microbiome of the plant holobiont. New Phytol. 206, 1196–1206.

    Article  PubMed  Google Scholar 

  • Vorholt, J.A. 2012. Microbial life in the phyllosphere. Nat. Rev. Microbiol. 10, 828–840.

    Article  CAS  PubMed  Google Scholar 

  • Vorholt, J.A., Vogel, C., Carlström, C.I., and Müller, D.B. 2017. Establishing causality: opportunities of synthetic communities for plant microbiome research. Cell Host Microbe 22, 142–155.

    Article  CAS  PubMed  Google Scholar 

  • Weller, D.M., Howie, W.J., and Cook, R.J. 1988. Relationship between in vitro inhibition of Gaeumannomyces graminis var. tritici and suppression of take-all of wheat by fluorescent pseudomonads. Phytopathology 78, 1094–1100.

    Article  Google Scholar 

  • Whipps, J.M., Hand, P., Pink, D., and Bending, G.D. 2008. Phyllosphere microbiology with special reference to diversity and plant genotype. J. Appl. Microbiol. 105, 1744–1755.

    Article  CAS  PubMed  Google Scholar 

  • Xu, L., Naylor, D., Dong, Z., Simmons, T., Pierroz, G., Hixson, K.K., Kim, Y.M., Zink, E.M., Engbrecht, K.M., Wang, Y., et al. 2018. Drought delays development of the sorghum root microbiome and enriches for monoderm bacteria. Proc. Natl. Acad. Sci. USA 115, E4284–E4293.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zamioudis, C., Korteland, J., Van Pelt, J.A., van Hamersveld, M., Dombrowski, N., Bai, Y., Hanson, J., Van Verk, M.C., Ling, H.Q., Schulze-Lefert, P., et al. 2015. Rhizobacterial volatiles and photosynthesis-related signals coordinate MYB72 expression in Arabidopsis roots during onset of induced systemic resistance and irondeficiency responses. Plant J. 84, 309–322.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zgadzaj, R., Garrido-Oter, R., Jensen, D.B., Koprivova, A., Schulze-Lefert, P., and Radutoiu, S. 2016. Root nodule symbiosis in Lotus japonicus drives the establishment of distinctive rhizosphere, root, and nodule bacterial communities. Proc. Natl. Acad. Sci. USA 113, 7996–8005.

    Article  CAS  Google Scholar 

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Acknowledgments

This research was supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MIST) (No. 2020R1A2C3005453, 2020R1A6A1A03047729, and 2020R1G1A1006624), Republic of Korea.

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  1. Department of Applied Bioscience, Dong-A University, Busan, 49315, Republic of Korea

    Kihyuck Choi & Seon-Woo Lee

  2. Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, 46000, Pakistan

    Raees Khan

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  1. Kihyuck Choi
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Choi, K., Khan, R. & Lee, SW. Dissection of plant microbiota and plant-microbiome interactions. J Microbiol. 59, 281–291 (2021). https://doi.org/10.1007/s12275-021-0619-5

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