Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Potential of indigenous crop microbiomes for sustainable agriculture


The intimate interactions of indigenous crops with their associated microbiomes during long-term co-evolution strengthen the capacity and flexibility of crops to cope with biotic and abiotic stresses. This represents a promising untapped field for searching novel tools to sustainably increase crop productivity. However, the current capability of harnessing the power of indigenous crop microbiomes for sustainable crop production is limited due to low efficiency of separating the targeted functional microbes. Here, we highlight the potential benefits and existing challenges of utilizing indigenous crop microbiomes to reduce agrochemical inputs and increase crop resistance to biotic and abiotic stresses. We propose a framework using Raman-spectroscopy-based single-cell-sorting technology combined with a synthetic community approach to design and optimize a functionally reliable ‘beneficial biome’ under controlled conditions. This framework will offer opportunities for sustainable agriculture and provide a new direction for future studies.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Fig. 1: Current ecological models used to analyse the relative importance of different community assembly processes.
Fig. 2: Potential impacts of domestication on plant phenotype and plant microbiome diversity.
Fig. 3: Functional single-cell framework based on Raman–SIP to design a beneficial SynComs to improve plant nitrogen fixation.


  1. 1.

    Savci, S. An agricultural pollutant: chemical fertilizer. Int. J. Environ. Sci. Dev. 3, 77–80 (2012).

    CAS  Google Scholar 

  2. 2.

    Guo, J. H. et al. Significant acidification in major Chinese croplands. Science 327, 1008–1010 (2010).

    ADS  CAS  PubMed  Google Scholar 

  3. 3.

    Raza, S. et al. Dramatic loss of inorganic carbon by nitrogen‐induced soil acidification in Chinese croplands. Glob. Change Biol. 26, 3738–3751 (2020).

    ADS  Google Scholar 

  4. 4.

    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).

    ADS  CAS  PubMed  Google Scholar 

  5. 5.

    Cordovez, V., Dini-Andreote, F., Carrion, V. J. & Raaijmakers, J. M. Ecology and evolution of plant microbiomes. Annu. Rev. Microbiol. 73, 69–88 (2019).

    CAS  PubMed  Google Scholar 

  6. 6.

    Duran, P. et al. Microbial interkingdom interactions in roots promote Arabidopsis survival. Cell 175, 973–983.e914 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  7. 7.

    Dini-Andreote, F. & Raaijmakers, J. M. Embracing community ecology in plant microbiome research. Trends Plant Sci. 23, 467–469 (2018).

    CAS  PubMed  Google Scholar 

  8. 8.

    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).

    ADS  CAS  PubMed  Google Scholar 

  9. 9.

    Hubbard, C. J. et al. The effect of rhizosphere microbes outweighs host plant genetics in reducing insect herbivory. Mol. Ecol. 28, 1801–1811 (2019).

    CAS  PubMed  Google Scholar 

  10. 10.

    Oldroyd, G. E. D. & Leyser, O. A plant’s diet, surviving in a variable nutrient environment. Science 368, eaba0196 (2020).

    CAS  PubMed  Google Scholar 

  11. 11.

    Tedersoo, L., Bahram, M. & Zobel, M. How mycorrhizal associations drive plant population and community biology. Science 367, eaba1223 (2020).

    CAS  PubMed  Google Scholar 

  12. 12.

    Martín‐Robles, N. et al. Impacts of domestication on the arbuscular mycorrhizal symbiosis of 27 crop species. New Phytol. 218, 322–334 (2018).

    PubMed  Google Scholar 

  13. 13.

    Genre, A., Lanfranco, L., Perotto, S. & Bonfante, P. Unique and common traits in mycorrhizal symbioses. Nat. Rev. Microbiol. 18, 649–660 (2020).

    CAS  PubMed  Google Scholar 

  14. 14.

    Liu, X. et al. Partitioning of soil phosphorus among arbuscular and ectomycorrhizal trees in tropical and subtropical forests. Ecol. Lett. 21, 713–723 (2018).

    PubMed  Google Scholar 

  15. 15.

    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).

    CAS  Google Scholar 

  16. 16.

    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).

    CAS  Google Scholar 

  17. 17.

    Sprent, J. I. Evolving ideas of legume evolution and diversity: a taxonomic perspective on the occurrence of nodulation. New Phytol. 174, 11–25 (2007).

    CAS  PubMed  Google Scholar 

  18. 18.

    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).

    ADS  CAS  PubMed  Google Scholar 

  19. 19.

    Young, N. D. et al. The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature 480, 520–524 (2011).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  20. 20.

    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).

    PubMed  Google Scholar 

  21. 21.

    Smil, V. Nitrogen in crop production: an account of global flows. Glob. Biogeochem. Cycles 13, 647–662 (1999).

    ADS  CAS  Google Scholar 

  22. 22.

    O’Hara, G. W. The role of nitrogen fixation in crop production. J. Crop Prod. 1, 115–138 (1998).

    Google Scholar 

  23. 23.

    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).

    CAS  PubMed  Google Scholar 

  24. 24.

    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).

    PubMed  Google Scholar 

  25. 25.

    Fisher, R. F. & Long, S. R. Rhizobium–plant signal exchange. Nature 357, 655–660 (1992).

    ADS  CAS  PubMed  Google Scholar 

  26. 26.

    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).

    CAS  PubMed  Google Scholar 

  27. 27.

    Ferguson, B. J. et al. Legume nodulation: the host controls the party. Plant Cell Environ. 42, 41–51 (2019).

    CAS  PubMed  Google Scholar 

  28. 28.

    Remans, R. et al. Effect of RhizobiumAzospirillum 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).

    CAS  Google Scholar 

  29. 29.

    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 

  30. 30.

    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).

    CAS  PubMed  PubMed Central  Google Scholar 

  31. 31.

    Saharan, B. S. & Nehra, V. Plant growth promoting rhizobacteria: a critical review. Life Sci. Med. Res. 21, 30 (2011).

    Google Scholar 

  32. 32.

    Cheng, Y. T., Zhang, L. & He, S. Y. Plant–microbe interactions facing environmental challenge. Cell Host Microbe 26, 183–192 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  33. 33.

    Dini-Andreote, F. Endophytes: the second layer of plant defense. Trends Plant Sci. 25, 319–322 (2020).

    CAS  PubMed  Google Scholar 

  34. 34.

    Carrión, V. J. et al. Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome. Science 366, 606–612 (2019).

    ADS  PubMed  Google Scholar 

  35. 35.

    Sieber, M. et al. Neutrality in the metaorganism. PLoS Biol. 17, e3000298 (2019).

    PubMed  PubMed Central  Google Scholar 

  36. 36.

    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).

    CAS  PubMed  Google Scholar 

  37. 37.

    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).

    CAS  PubMed  Google Scholar 

  38. 38.

    Sloan, W. T. et al. Quantifying the roles of immigration and chance in shaping prokaryote community structure. Environ. Microbiol. 8, 732–740 (2006).

    PubMed  Google Scholar 

  39. 39.

    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).

    CAS  PubMed  Google Scholar 

  40. 40.

    Carlström, C. I. et al. Synthetic microbiota reveal priority effects and keystone strains in the Arabidopsis phyllosphere. Nat. Ecol. Evol. 3, 1445–1454 (2019).

    PubMed  PubMed Central  Google Scholar 

  41. 41.

    Purugganan, M. D. & Fuller, D. Q. The nature of selection during plant domestication. Nature 457, 843–848 (2009).

    ADS  CAS  PubMed  Google Scholar 

  42. 42.

    Chen, Y. H., Gols, R. & Benrey, B. Crop domestication and its impact on naturally selected trophic interactions. Annu. Rev. Entomol. 60, 35–58 (2015).

    CAS  PubMed  Google Scholar 

  43. 43.

    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).

    CAS  Google Scholar 

  44. 44.

    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).

    CAS  PubMed  Google Scholar 

  45. 45.

    Perez-Jaramillo, J. E., Carrion, V. J., de Hollander, M. & Raaijmakers, J. M. The wild side of plant microbiomes. Microbiome 6, 143 (2018).

    PubMed  PubMed Central  Google Scholar 

  46. 46.

    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).

    CAS  Google Scholar 

  47. 47.

    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).

    CAS  PubMed  Google Scholar 

  48. 48.

    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).

    CAS  PubMed  Google Scholar 

  49. 49.

    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).

    PubMed  PubMed Central  Google Scholar 

  50. 50.

    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).

    PubMed  PubMed Central  Google Scholar 

  51. 51.

    Coleman‐Derr, D. et al. Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species. New Phytol. 209, 798–811 (2016).

    PubMed  Google Scholar 

  52. 52.

    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).

    PubMed  Google Scholar 

  53. 53.

    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).

    CAS  PubMed  Google Scholar 

  54. 54.

    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).

    PubMed  Google Scholar 

  55. 55.

    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).

  56. 56.

    Stenberg, J. A., Heil, M., Åhman, I. & Björkman, C. Optimizing crops for biocontrol of pests and disease. Trends Plant Sci. 20, 698–712 (2015).

    CAS  PubMed  Google Scholar 

  57. 57.

    Heil, M. & Baldwin, I. T. Fitness costs of induced resistance: emerging experimental support for a slippery concept. Trends Plant Sci. 7, 61–67 (2002).

    CAS  PubMed  Google Scholar 

  58. 58.

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

    CAS  PubMed  Google Scholar 

  59. 59.

    Schulz-Bohm, K. et al. Calling from distance: attraction of soil bacteria by plant root volatiles. ISME J. 12, 1252–1262 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  60. 60.

    Ehlers, B. K. et al. Plant secondary compounds in soil and their role in belowground species interactions. Trends Ecol. Evol. 35, 716–730 (2020).

    PubMed  Google Scholar 

  61. 61.

    Preece, C. & Penuelas, J. A return to the wild: root exudates and food security. Trends Plant Sci. 25, 14–21 (2020).

    CAS  PubMed  Google Scholar 

  62. 62.

    Rasmann, S. et al. Recruitment of entomopathogenic nematodes by insect-damaged maize roots. Nature 434, 732–737 (2005).

    ADS  CAS  PubMed  Google Scholar 

  63. 63.

    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).

    PubMed  PubMed Central  Google Scholar 

  64. 64.

    Lebeis, S. L. et al. Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa. Science 349, 860–864 (2015).

    ADS  CAS  PubMed  Google Scholar 

  65. 65.

    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).

    CAS  PubMed  Google Scholar 

  66. 66.

    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).

    CAS  PubMed  Google Scholar 

  67. 67.

    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).

    CAS  PubMed  PubMed Central  Google Scholar 

  68. 68.

    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).

    CAS  PubMed  Google Scholar 

  69. 69.

    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).

    CAS  PubMed  Google Scholar 

  70. 70.

    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).

    CAS  PubMed  Google Scholar 

  71. 71.

    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).

    CAS  PubMed  Google Scholar 

  72. 72.

    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).

    CAS  PubMed  Google Scholar 

  73. 73.

    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).

    CAS  Google Scholar 

  74. 74.

    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).

    CAS  Google Scholar 

  75. 75.

    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 

  76. 76.

    Uma, C., Sivagurunathan, P. & Sangeetha, D. Performance of bradyrhizobial isolates under drought conditions. Int. J. Curr. Microbiol. App. Sci. 2, 228–232 (2013).

    Google Scholar 

  77. 77.

    Tank, N. & Saraf, M. Salinity-resistant plant growth promoting rhizobacteria ameliorates sodium chloride stress on tomato plants. J. Plant Interact. 5, 51–58 (2010).

    CAS  Google Scholar 

  78. 78.

    Tahir, H. A. et al. Plant growth promotion by volatile organic compounds produced by Bacillus subtilis SYST2. Front. Microbiol. 8, 171 (2017).

    PubMed  PubMed Central  Google Scholar 

  79. 79.

    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).

    CAS  Google Scholar 

  80. 80.

    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 

  81. 81.

    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).

    CAS  PubMed  PubMed Central  Google Scholar 

  82. 82.

    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).

    CAS  Google Scholar 

  83. 83.

    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).

    CAS  PubMed  Google Scholar 

  84. 84.

    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).

    CAS  Google Scholar 

  85. 85.

    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).

    CAS  PubMed  Google Scholar 

  86. 86.

    Kwak, M.-J. et al. Rhizosphere microbiome structure alters to enable wilt resistance in tomato. Nat. Biotechnol. 36, 1100–1109 (2018).

    CAS  Google Scholar 

  87. 87.

    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).

    CAS  PubMed  Google Scholar 

  88. 88.

    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).

    ADS  PubMed  PubMed Central  Google Scholar 

  89. 89.

    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 

  90. 90.

    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).

    CAS  Google Scholar 

  91. 91.

    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).

    PubMed  PubMed Central  Google Scholar 

  92. 92.

    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).

    PubMed  Google Scholar 

  93. 93.

    Bhatti, A. A., Haq, S. & Bhat, R. A. Actinomycetes benefaction role in soil and plant health. Microb. Pathog. 111, 458–467 (2017).

    CAS  PubMed  Google Scholar 

  94. 94.

    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 

  95. 95.

    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).

    CAS  Google Scholar 

  96. 96.

    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 

  97. 97.

    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).

    CAS  Google Scholar 

  98. 98.

    Meeds, J. A. et al. Phosphorus deficiencies invoke optimal allocation of exoenzymes by ectomycorrhizas. ISME J. (2021).

Download references


This work was supported by the Australian Research Council (FT190100383 and DE210100271).

Author information




All authors contributed intellectual input and assistance to this work. The original concepts were conceived by J.-Z.H., Q.-L.C., H.-W.H. and Y.-G.Z. Q.-L.C. and J.-Z.H. wrote the first draft, with subsequent input during revision from H.-W.H., Z.-Y.H., L.C. and Y.-G.Z. All the figures are original from Q.-L.C.

Corresponding authors

Correspondence to Hang-Wei Hu or Ji-Zheng He.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Peer review information Nature Food thanks Josep Penuelas, Zhong Wei, Andrea Genre and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Chen, QL., Hu, HW., He, ZY. et al. Potential of indigenous crop microbiomes for sustainable agriculture. Nat Food 2, 233–240 (2021).

Download citation


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing