The Core Bacterial Microbiome of Banana (Musa spp.)

Abstract

Background
Bananas (Musa spp.) are a globally significant crop and are severely afflicted by diseases for which there are no effective chemical controls. Banana microbiomes may provide novel solutions to these constraints but are difficult to manage due to their high diversity and variability between locations. Hence ‘common core’ taxa, which are a subset of the microbiome that frequent all, or most, individuals of a host species, represent logical targets for the development of microbiome management approaches.
Results
To identify the common core bacterial microbiome of banana, we first performed a pot experiment to characterise the effects of two factors that are likely to differ between farms (viz. edaphic conditions and host genotype) on bacterial diversity in bulk soil and seven plant compartments. As diversity was found to differ between plant compartments and soils, but not genotypes, we identified populations that were frequent across most plants irrespective of the soil in which they were grown. Shortlisted ‘candidates’ were then refined according to whether they were also frequent in a survey of 52 field-grown Musa spp. This led to the selection of 36 ‘common core’ bacteria, that represented 65–95% of the dominant taxa in field-grown plants and were identified as highly interconnected ‘hubs’ using networks – a characteristic shown to be indicative of microbes that influence host fitness in studies of other plants. Lastly, by comparing the sequences of our core taxa with those reported in 22 previous studies, we demonstrated that they are closely related to banana-associated bacteria observed on five other continents.
Conclusions
Our study provides a robust list of common core bacterial taxa for Musa spp. Further research may now focus on how changes in the frequencies and activities of these most persistent taxa influence host fitness. Notably, for several of our core taxa highly similar populations have already been isolated in previous studies and may be amenable to such experimentation. This contribution should help to accelerate the development of effective Musa spp. microbiome management practices.