Savci, S. An agricultural pollutant: chemical fertilizer. Int. J. Environ. Sci. Dev. 3, 77–80 (2012).
Google Scholar
Guo, J. H. et al. Significant acidification in major Chinese croplands. Science 327, 1008–1010 (2010).
Google Scholar
Raza, S. et al. Dramatic loss of inorganic carbon by nitrogen‐induced soil acidification in Chinese croplands. Glob. Change Biol. 26, 3738–3751 (2020).
Google Scholar
Jez, J. M., Lee, S. G. & Sherp, A. M. The next green movement: plant biology for the environment and sustainability. Science 353, 1241–1244 (2016).
Google Scholar
Cordovez, V., Dini-Andreote, F., Carrion, V. J. & Raaijmakers, J. M. Ecology and evolution of plant microbiomes. Annu. Rev. Microbiol. 73, 69–88 (2019).
Google Scholar
Duran, P. et al. Microbial interkingdom interactions in roots promote Arabidopsis survival. Cell 175, 973–983.e914 (2018).
Google Scholar
Dini-Andreote, F. & Raaijmakers, J. M. Embracing community ecology in plant microbiome research. Trends Plant Sci. 23, 467–469 (2018).
Google Scholar
de Vries, F. T., Griffiths, R. I., Knight, C. G., Nicolitch, O. & Williams, A. Harnessing rhizosphere microbiomes for drought-resilient crop production. Science 368, 270–274 (2020).
Google Scholar
Hubbard, C. J. et al. The effect of rhizosphere microbes outweighs host plant genetics in reducing insect herbivory. Mol. Ecol. 28, 1801–1811 (2019).
Google Scholar
Oldroyd, G. E. D. & Leyser, O. A plant’s diet, surviving in a variable nutrient environment. Science 368, eaba0196 (2020).
Google Scholar
Tedersoo, L., Bahram, M. & Zobel, M. How mycorrhizal associations drive plant population and community biology. Science 367, eaba1223 (2020).
Google Scholar
Martín‐Robles, N. et al. Impacts of domestication on the arbuscular mycorrhizal symbiosis of 27 crop species. New Phytol. 218, 322–334 (2018).
Google Scholar
Genre, A., Lanfranco, L., Perotto, S. & Bonfante, P. Unique and common traits in mycorrhizal symbioses. Nat. Rev. Microbiol. 18, 649–660 (2020).
Google Scholar
Liu, X. et al. Partitioning of soil phosphorus among arbuscular and ectomycorrhizal trees in tropical and subtropical forests. Ecol. Lett. 21, 713–723 (2018).
Google Scholar
Varoquaux, N. et al. Transcriptomic analysis of field-droughted sorghum from seedling to maturity reveals biotic and metabolic responses. Proc. Natl Acad. Sci. USA 116, 27124–27132 (2019).
Google Scholar
Lazcano, C., Barrios-Masias, F. H. & Jackson, L. E. Arbuscular mycorrhizal effects on plant water relations and soil greenhouse gas emissions under changing moisture regimes. Soil Biol. Biochem. 74, 184–192 (2014).
Google Scholar
Sprent, J. I. Evolving ideas of legume evolution and diversity: a taxonomic perspective on the occurrence of nodulation. New Phytol. 174, 11–25 (2007).
Google Scholar
Soltis, D. E. et al. Chloroplast gene sequence data suggest a single origin of the predisposition for symbiotic nitrogen fixation in angiosperms. Proc. Natl Acad. Sci. USA 92, 2647–2651 (1995).
Google Scholar
Young, N. D. et al. The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature 480, 520–524 (2011).
Google Scholar
van Velzen, R. et al. Comparative genomics of the nonlegume Parasponia reveals insights into evolution of nitrogen-fixing Rhizobium symbioses. Proc. Natl Acad. Sci. USA 115, E4700–E4709 (2018).
Google Scholar
Smil, V. Nitrogen in crop production: an account of global flows. Glob. Biogeochem. Cycles 13, 647–662 (1999).
Google Scholar
O’Hara, G. W. The role of nitrogen fixation in crop production. J. Crop Prod. 1, 115–138 (1998).
Google Scholar
Remigi, P., Zhu, J., Young, J. P. W. & Masson-Boivin, C. Symbiosis within symbiosis: evolving nitrogen-fixing legume symbionts. Trends Microbiol. 24, 63–75 (2016).
Google Scholar
Garcia, K., Delaux, P. M., Cope, K. R. & Ané, J. M. Molecular signals required for the establishment and maintenance of ectomycorrhizal symbioses. New Phytol. 208, 79–87 (2015).
Google Scholar
Fisher, R. F. & Long, S. R. Rhizobium–plant signal exchange. Nature 357, 655–660 (1992).
Google Scholar
Cao, Y., Halane, M. K., Gassmann, W. & Stacey, G. The role of plant innate immunity in the legume–Rhizobium symbiosis. Annu. Rev. Plant Biol. 68, 535–561 (2017).
Google Scholar
Ferguson, B. J. et al. Legume nodulation: the host controls the party. Plant Cell Environ. 42, 41–51 (2019).
Google Scholar
Remans, R. et al. Effect of Rhizobium–Azospirillum coinoculation on nitrogen fixation and yield of two contrasting Phaseolus vulgaris L. genotypes cultivated across different environments in Cuba. Plant Soil 312, 25–37 (2008).
Google Scholar
Cassán, F. & Diaz-Zorita, M. Azospirillum sp. in current agriculture: from the laboratory to the field. Soil Biol. Biochem. 103, 117–130 (2016).
Google Scholar
Han, Q. et al. Variation in rhizosphere microbial communities and its association with the symbiotic efficiency of rhizobia in soybean. ISME J. 14, 1915–1928 (2020).
Google Scholar
Saharan, B. S. & Nehra, V. Plant growth promoting rhizobacteria: a critical review. Life Sci. Med. Res. 21, 30 (2011).
Cheng, Y. T., Zhang, L. & He, S. Y. Plant–microbe interactions facing environmental challenge. Cell Host Microbe 26, 183–192 (2019).
Google Scholar
Dini-Andreote, F. Endophytes: the second layer of plant defense. Trends Plant Sci. 25, 319–322 (2020).
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
Sieber, M. et al. Neutrality in the metaorganism. PLoS Biol. 17, e3000298 (2019).
Google Scholar
Trivedi, P., Leach, J. E., Tringe, S. G., Sa, T. & Singh, B. K. Plant–microbiome interactions: from community assembly to plant health. Nat. Rev. Microbiol. 18, 607–621 (2020).
Google Scholar
Burns, A. R. et al. Contribution of neutral processes to the assembly of gut microbial communities in the zebrafish over host development. ISME J. 10, 655–664 (2016).
Google Scholar
Sloan, W. T. et al. Quantifying the roles of immigration and chance in shaping prokaryote community structure. Environ. Microbiol. 8, 732–740 (2006).
Google Scholar
Ning, D., Deng, Y., Tiedje, J. M. & Zhou, J. A general framework for quantitatively assessing ecological stochasticity. Proc. Natl Acad. Sci. USA 116, 16892–16898 (2019).
Google Scholar
Carlström, C. I. et al. Synthetic microbiota reveal priority effects and keystone strains in the Arabidopsis phyllosphere. Nat. Ecol. Evol. 3, 1445–1454 (2019).
Google Scholar
Purugganan, M. D. & Fuller, D. Q. The nature of selection during plant domestication. Nature 457, 843–848 (2009).
Google Scholar
Chen, Y. H., Gols, R. & Benrey, B. Crop domestication and its impact on naturally selected trophic interactions. Annu. Rev. Entomol. 60, 35–58 (2015).
Google Scholar
Szoboszlay, M. et al. Comparison of root system architecture and rhizosphere microbial communities of Balsas teosinte and domesticated corn cultivars. Soil Biol. Biochem. 80, 34–44 (2015).
Google Scholar
Perez-Jaramillo, J. E., Mendes, R. & Raaijmakers, J. M. Impact of plant domestication on rhizosphere microbiome assembly and functions. Plant Mol. Biol. 90, 635–644 (2016).
Google Scholar
Perez-Jaramillo, J. E., Carrion, V. J., de Hollander, M. & Raaijmakers, J. M. The wild side of plant microbiomes. Microbiome 6, 143 (2018).
Google Scholar
Emmett, B. D., Buckley, D. H., Smith, M. E. & Drinkwater, L. E. Eighty years of maize breeding alters plant nitrogen acquisition but not rhizosphere bacterial community composition. Plant Soil 431, 53–69 (2018).
Google Scholar
Mutch, L. A. & Young, J. P. W. Diversity and specificity of Rhizobium leguminosarum biovar viciae on wild and cultivated legumes. Mol. Ecol. 13, 2435–2444 (2004).
Google Scholar
Kiers, E. T., Hutton, M. G. & Denison, R. F. Human selection and the relaxation of legume defences against ineffective rhizobia. Proc. R. Soc. B 274, 3119–3126 (2007).
Google Scholar
Pérez-Jaramillo, J. E. et al. Linking rhizosphere microbiome composition of wild and domesticated Phaseolus vulgaris to genotypic and root phenotypic traits. ISME J. 11, 2244–2257 (2017).
Google Scholar
Zachow, C., Müller, H., Tilcher, R. & Berg, G. Differences between the rhizosphere microbiome of Beta vulgaris ssp. maritima—ancestor of all beet crops—and modern sugar beets. Front. Microbiol. 5, 415 (2014).
Google Scholar
Coleman‐Derr, D. et al. Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species. New Phytol. 209, 798–811 (2016).
Google Scholar
Warschefsky, E., Penmetsa, R. V., Cook, D. R. & von Wettberg, E. J. Back to the wilds: tapping evolutionary adaptations for resilient crops through systematic hybridization with crop wild relatives. Am. J. Bot. 101, 1791–1800 (2014).
Google Scholar
Brozynska, M., Furtado, A. & Henry, R. J. Genomics of crop wild relatives: expanding the gene pool for crop improvement. Plant Biotechnol. J. 14, 1070–1085 (2016).
Google Scholar
Zhang, H., Mittal, N., Leamy, L. J., Barazani, O. & Song, B. H. Back into the wild—apply untapped genetic diversity of wild relatives for crop improvement. Evol. Appl. 10, 5–24 (2017).
Google Scholar
Maxted, N. & Kell, S. P. Establishment of a Global Network for the In Situ Conservation of Crop Wild Relatives: Status and Needs (FAO Commission on Genetic Resources for Food and Agriculture, 2009).
Stenberg, J. A., Heil, M., Åhman, I. & Björkman, C. Optimizing crops for biocontrol of pests and disease. Trends Plant Sci. 20, 698–712 (2015).
Google Scholar
Heil, M. & Baldwin, I. T. Fitness costs of induced resistance: emerging experimental support for a slippery concept. Trends Plant Sci. 7, 61–67 (2002).
Google Scholar
Liu, H. & Brettell, L. E. Plant defense by VOC-induced microbial priming. Trends Plant Sci. 24, 187–189 (2019).
Google Scholar
Schulz-Bohm, K. et al. Calling from distance: attraction of soil bacteria by plant root volatiles. ISME J. 12, 1252–1262 (2018).
Google Scholar
Ehlers, B. K. et al. Plant secondary compounds in soil and their role in belowground species interactions. Trends Ecol. Evol. 35, 716–730 (2020).
Google Scholar
Preece, C. & Penuelas, J. A return to the wild: root exudates and food security. Trends Plant Sci. 25, 14–21 (2020).
Google Scholar
Rasmann, S. et al. Recruitment of entomopathogenic nematodes by insect-damaged maize roots. Nature 434, 732–737 (2005).
Google Scholar
Köllner, T. G. et al. A maize (E)-β-caryophyllene synthase implicated in indirect defense responses against herbivores is not expressed in most American maize varieties. Plant Cell 20, 482–494 (2008).
Google Scholar
Lebeis, S. L. et al. Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa. Science 349, 860–864 (2015).
Google Scholar
Vorholt, J. A., Vogel, C., Carlstrom, C. I. & Muller, D. B. Establishing causality: opportunities of synthetic communities for plant microbiome research. Cell Host Microbe 22, 142–155 (2017).
Google Scholar
Zhang, J. et al. NRT1.1B is associated with root microbiota composition and nitrogen use in field-grown rice. Nat. Biotechnol. 37, 676–684 (2019).
Google Scholar
Hatzenpichler, R., Krukenberg, V., Spietz, R. L. & Jay, Z. J. Next-generation physiology approaches to study microbiome function at single cell level. Nat. Rev. Microbiol. 18, 241–256 (2020).
Google Scholar
Cui, L., Zhang, D., Yang, K., Zhang, X. & Zhu, Y. G. Perspective on surface-enhanced Raman spectroscopic investigation of microbial world. Anal. Chem. 91, 15345–15354 (2019).
Google Scholar
Wang, Y., Huang, W. E., Cui, L. & Wagner, M. Single cell stable isotope probing in microbiology using Raman microspectroscopy. Curr. Opin. Biotechnol. 41, 34–42 (2016).
Google Scholar
Cui, L. et al. Functional single-cell approach to probing nitrogen-fixing bacteria in soil communities by resonance Raman spectroscopy with 15N2 labeling. Anal. Chem. 90, 5082–5089 (2018).
Google Scholar
Yang, K. et al. Rapid antibiotic susceptibility testing of pathogenic bacteria using heavy-water-labeled single-cell Raman spectroscopy in clinical samples. Anal. Chem. 91, 6296–6303 (2019).
Google Scholar
Li, H. Z. et al. D2O-isotope-labeling approach to probing phosphate-solubilizing bacteria in complex soil communities by single-cell Raman spectroscopy. Anal. Chem. 91, 2239–2246 (2019).
Google Scholar
Moutia, J.-F. Y., Saumtally, S., Spaepen, S. & Vanderleyden, J. Plant growth promotion by Azospirillum sp. in sugarcane is influenced by genotype and drought stress. Plant Soil 337, 233–242 (2010).
Google Scholar
Bashan, Y. & De-Bashan, L. E. How the plant growth-promoting bacterium Azospirillum promotes plant growth—a critical assessment. Adv. Agron. 108, 77–136 (2010).
Google Scholar
Figueiredo, M. V. B., Burity, H. A., Martínez, C. R. & Chanway, C. P. Alleviation of drought stress in the common bean (Phaseolus vulgaris L.) by co-inoculation with Paenibacillus polymyxa and Rhizobium tropici. Appl. Soil Ecol. 40, 182–188 (2008).
Google Scholar
Uma, C., Sivagurunathan, P. & Sangeetha, D. Performance of bradyrhizobial isolates under drought conditions. Int. J. Curr. Microbiol. App. Sci. 2, 228–232 (2013).
Tank, N. & Saraf, M. Salinity-resistant plant growth promoting rhizobacteria ameliorates sodium chloride stress on tomato plants. J. Plant Interact. 5, 51–58 (2010).
Google Scholar
Tahir, H. A. et al. Plant growth promotion by volatile organic compounds produced by Bacillus subtilis SYST2. Front. Microbiol. 8, 171 (2017).
Google Scholar
Vardharajula, S., Zulfikar Ali, S., Grover, M., Reddy, G. & Bandi, V. Drought-tolerant plant growth promoting Bacillus spp.: effect on growth, osmolytes, and antioxidant status of maize under drought stress. J. Plant Interact. 6, 1–14 (2011).
Google Scholar
Santoyo, G., Orozco-Mosqueda, M. D. C. & Govindappa, M. Mechanisms of biocontrol and plant growth-promoting activity in soil bacterial species of Bacillus and Pseudomonas: a review. Biocontrol Sci. Technol. 22, 855–872 (2012).
Google Scholar
Leclere, V. et al. Mycosubtilin overproduction by Bacillus subtilis BBG100 enhances the organism’s antagonistic and biocontrol activities. Appl. Environ. Microbiol. 71, 4577–4584 (2005).
Google Scholar
Hu, J. et al. Probiotic Pseudomonas communities enhance plant growth and nutrient assimilation via diversity-mediated ecosystem functioning. Soil Biol. Biochem. 113, 122–129 (2017).
Google Scholar
Kohler, J., Hernández, J. A., Caravaca, F. & Roldán, A. Plant-growth-promoting rhizobacteria and arbuscular mycorrhizal fungi modify alleviation biochemical mechanisms in water-stressed plants. Funct. Plant Biol. 35, 141–151 (2008).
Google Scholar
Nassar, A. H., El-Tarabily, K. A. & Sivasithamparam, K. Growth promotion of bean (Phaseolus vulgaris L.) by a polyamine-producing isolate of Streptomyces griseoluteus. Plant Growth Reg. 40, 97–106 (2003).
Google Scholar
Gopalakrishnan, S. et al. Evaluation of Streptomyces strains isolated from herbal vermicompost for their plant growth-promotion traits in rice. Microbiol. Res. 169, 40–48 (2014).
Google Scholar
Kwak, M.-J. et al. Rhizosphere microbiome structure alters to enable wilt resistance in tomato. Nat. Biotechnol. 36, 1100–1109 (2018).
Google Scholar
Sang, M. K. & Kim, K. D. The volatile‐producing Flavobacterium johnsoniae strain GSE09 shows biocontrol activity against Phytophthora capsici in pepper. J. Appl. Microbiol. 113, 383–398 (2012).
Google Scholar
Naznin, H. A. et al. Systemic resistance induced by volatile organic compounds emitted by plant growth-promoting fungi in Arabidopsis thaliana. PLoS ONE 9, e86882 (2014).
Google Scholar
Kiss, L., Russell, J. C., Szentiványi, O., Xu, X. & Jeffries, P. Biology and biocontrol potential of Ampelomyces mycoparasites, natural antagonists of powdery mildew fungi. Biocontrol Sci. Technol. 14, 635–651 (2004).
Google Scholar
Lee, S., Yap, M., Behringer, G., Hung, R. & Bennett, J. W. Volatile organic compounds emitted by Trichoderma species mediate plant growth. Fungal Biol. Biotechnol. 3, 1–14 (2016).
Google Scholar
Zhang, S., Gan, Y. & Xu, B. Application of plant-growth-promoting fungi Trichoderma longibrachiatum t6 enhances tolerance of wheat to salt stress through improvement of antioxidative defense system and gene expression. Front. Plant Sci. 7, 1405 (2016).
Google Scholar
van der Meij, A., Worsley, S. F., Hutchings, M. I. & van Wezel, G. P. Chemical ecology of antibiotic production by Actinomycetes. FEMS Microbiol. Rev. 41, 392–416 (2017).
Google Scholar
Bhatti, A. A., Haq, S. & Bhat, R. A. Actinomycetes benefaction role in soil and plant health. Microb. Pathog. 111, 458–467 (2017).
Google Scholar
Chaurasia, A. et al. Actinomycetes: an unexplored microorganisms for plant growth promotion and biocontrol in vegetable crops. World J. Microbiol. Biotechnol. 34, 1–16 (2018).
Google Scholar
Ercoli, L., Schüßler, A., Arduini, I. & Pellegrino, E. Strong increase of durum wheat iron and zinc content by field-inoculation with arbuscular mycorrhizal fungi at different soil nitrogen availabilities. Plant Soil 419, 153–167 (2017).
Google Scholar
Xu, L. et al. Arbuscular mycorrhiza enhances drought tolerance of tomato plants by regulating the 14-3-3 genes in the ABA signaling pathway. Appl. Soil Ecol. 125, 213–221 (2018).
Google Scholar
Ghorchiani, M., Etesami, H. & Alikhani, H. A. Improvement of growth and yield of maize under water stress by co-inoculating an arbuscular mycorrhizal fungus and a plant growth promoting rhizobacterium together with phosphate fertilizers. Agric. Ecosyst. Environ. 258, 59–70 (2018).
Google Scholar
Meeds, J. A. et al. Phosphorus deficiencies invoke optimal allocation of exoenzymes by ectomycorrhizas. ISME J. https://doi.org/10.1038/s41396-020-00864-z (2021).
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