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Potential of indigenous crop microbiomes for sustainable agriculture

Abstract

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.

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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.

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Acknowledgements

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

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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.

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

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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.

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Chen, QL., Hu, HW., He, ZY. et al. Potential of indigenous crop microbiomes for sustainable agriculture. Nat Food 2, 233–240 (2021). https://doi.org/10.1038/s43016-021-00253-5

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