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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