Culturomic recovery of the banana core microbiome creates a biobank for functional microbiome engineering
Persistent core microbiome members are attractive targets for microbiome engineering because they are more likely than transient taxa to colonise hosts consistently across environments. However, most crop core microbiomes remain defined only by sequence data, limiting mechanistic understanding and practical deployment. Here, we used targeted high-throughput culturomics to recover the previously defined Australian banana (Musa spp.) core bacteriome from field-grown plants. Across five isolation experiments, we obtained cultured representatives of 24 of the 36 core bacterial taxa, corresponding to 66.7% of the banana core microbiome. Recovered isolates captured much of the persistent and quantitatively dominant fraction of the banana core microbiome, including many of the most prevalent and abundant core taxa across plant compartments. We established a biobank of verified core isolates and sequenced representative genomes, which revealed broad potential for plant-beneficial functions including nutrient acquisition, phytohormone modulation, and antagonism of plant pathogens. Several representative isolates inhibited Fusarium oxysporum f. sp. cubense (Foc) in vitro, and two significantly reduced Foc-induced rhizome necrosis in planta. Our study converts a sequence-defined crop core microbiome into a cultured and genomically characterised resource, providing a foundation for functional interrogation and the development of microbiome-based approaches to improve banana performance and resilience.
Persistent core microbiome members are attractive targets for microbiome engineering because they are more likely than transient taxa to colonise hosts consistently across environments. However, most crop core microbiomes remain defined only by sequence data, limiting mechanistic understanding and practical deployment. Here, we used targeted high-throughput culturomics to recover the previously defined Australian banana (Musa spp.) core bacteriome from field-grown plants. Across five isolation experiments, we obtained cultured representatives of 24 of the 36 core bacterial taxa, corresponding to 66.7% of the banana core microbiome. Recovered isolates captured much of the persistent and quantitatively dominant fraction of the banana core microbiome, including many of the most prevalent and abundant core taxa across plant compartments. We established a biobank of verified core isolates and sequenced representative genomes, which revealed broad potential for plant-beneficial functions including nutrient acquisition, phytohormone modulation, and antagonism of plant pathogens. Several representative isolates inhibited Fusarium oxysporum f. sp. cubense (Foc) in vitro, and two significantly reduced Foc-induced rhizome necrosis in planta. Our study converts a sequence-defined crop core microbiome into a cultured and genomically characterised resource, providing a foundation for functional interrogation and the development of microbiome-based approaches to improve banana performance and resilience.