Members of Gammaproteobacteria as indicator species of healthy banana plants on Fusarium wilt-infested fields in Central America

Martina Köberl,Miguel Dita,Gabriele Berg,Alfonso Martinuz,Charles Staver

doi:10.1038/srep45318

Abstract

Culminating in the 1950’s, bananas, the world’s most extensive perennial monoculture, suffered one of the most devastating disease epidemics in history. In Latin America and the Caribbean, Fusarium wilt (FW) caused by the soil-borne fungus Fusarium oxysporum f. sp. cubense (FOC), forced the abandonment of the Gros Michel-based export banana industry. Comparative microbiome analyses performed between healthy and diseased Gros Michel plants on FW-infested farms in Nicaragua and Costa Rica revealed significant shifts in the gammaproteobacterial microbiome. Although we found substantial differences in the banana microbiome between both countries and a higher impact of FOC on farms in Costa Rica than in Nicaragua, the composition especially in the endophytic microhabitats was similar and the general microbiome response to FW followed similar rules. Gammaproteobacterial diversity and community members were identified as potential health indicators. Healthy plants revealed an increase in potentially plant-beneficial Pseudomonas and Stenotrophomonas, while diseased plants showed a preferential occurrence of Enterobacteriaceae known for their plant-degrading capacity. Significantly higher microbial rhizosphere diversity found in healthy plants could be indicative of pathogen suppression events preventing or minimizing disease expression. This first study examining banana microbiome shifts caused by FW under natural field conditions opens new perspectives for its biological control.

Highlights

The use of resistant varieties is the only known option for producing bananas on FOC-infested soils
We showed that AFS lead to shifts within the gammaproteobacterial microbiome of banana plants cultivated in Central America[9,17]
A barcoded 16S rRNA gene amplicon sequencing approach based on Illumina MiSeq sequencing of the gammaproteobacterial microbiota associated to the rhizosphere, endorhiza, pseudostem and leaves of healthy and FOC-infected banana plants grown in Nicaragua and Costa Rica yielded in 4,473,541 gammaproteobacterial quality sequences with a read length ≥200 nucleotides, between 4,822 and 111,332 quality reads per sample

Summary

Introduction

The use of resistant varieties is the only known option for producing bananas on FOC-infested soils. Integrated disease management strategies are needed aiming both to reduce the impact of the disease on susceptible varieties and increase the durability of resistant varieties. In this scenario, banana and soil microbiota are hypothesized to play an important role[13,14] as already shown in other agricultural systems[15,16]. Little is known about the plant and soil microbiome profiles and potential relationships to FW infestation in banana, we hypothesize a substantial response of Gammaproteobacteria. We show for the first time how FOC infection affects the banana plant microbiome under natural field conditions

Methods

Results

Conclusion