Response to Edaphoclimatic Conditions and Crop Management of the Bacterial Microbiome of Musa acuminata Rhizosphere Profiled by 16S rRNA Gene Amplicon Sequencing

Torre-González, Francisco J. De la; Fernández-Castillo, Elisa; Azaharez-Llorente, Dailen; Lara, J. A. F. de; Avendaño, Enrique; Castañeda, Alexis; Gómez, Sergio Romero; Gaxiola, José Alfredo Samaniego; Asaff-Torres, Alí; Verdín, Jorge

doi:10.1128/mra.01437-20

Cited by 1 publication

(1 citation statement)

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“…3). This is in broad agreement with other studies that have identified Musa spp.-associated bacteria using methods that target the 'whole' domain, albeit these tend to have either focussed exclusively on bulk soil [54][55][56][57], or characterised single plant compartments, such as the pseudostem [58], endorhizosphere [59,60], shoot tips [50], or ectorhizosphere [61]. In contrast, comparisons of bacterial diversity between multiple banana plant compartments tend to have focussed on specific lineages, such as the Gammaproteobacteria [24,62,63],…”

Section: Musa Spp Are Associated With Diverse Bacterial Communitiessupporting

confidence: 86%

The core bacterial microbiome of banana (Musa spp.)

Birt

Pattison

Skarshewski

et al. 2022

Environmental Microbiome

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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. Here, 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. From this experiment, we created shortlisted core ‘candidates’ that were then refined using a survey of 52 field-grown Musa spp. We confirmed the importance of the core through network analysis and by comparing the sequences of our core taxa with those reported in 22 previous studies. Results Diversity was found to differ between plant compartments and soils, but not genotypes. Therefore, we identified populations that were frequent across most plants irrespective of the soil in which they were grown. 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 network analysis – a characteristic shown to be indicative of microbes that influence host fitness in studies of other plants. Lastly, we demonstrated that the core taxa 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.

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