Metagenomic Insights of the Root Colonizing Microbiome Associated with Symptomatic and Non-Symptomatic Bananas in Fusarium Wilt Infected Fields

Abstract

Plants tissues are colonized by diverse communities of microorganisms called endophytes. They are key determinants of plant production and health, for example by facilitating nutrient exchanges or limiting disease development. Endophytic communities of banana plants have not been studied until very recently, and their potential role in disease development has not been explored so far. Roots from symptomatic and non-symptomatic banana plants were sampled from fields infected by Fusarium oxysporum f.sp. cubense race 1. The goal was to compare the endophytic microbiota between symptomatic and non-symptomatic plants through high throughput sequencing of 16s rDNA and shotgun metagenome sequencing. The results revealed that the endophytic root microbiome in bananas is dominated by Proteobacteria and Bacteroidetes followed to a lesser extent by Actinobacteria. The development of disease greatly impacted the endophytic microbial communities. For example, Flavobacteriales abundance was correlated with symptom development.

The Banana Root Endophytome: Differences between Mother Plants and Suckers and Evaluation of Selected Bacteria to Control Fusarium oxysporum f.sp. cubense

“…According to high-throughput sequencing results, and at the bacteria phylum level, the banana root endosphere was dominated by Proteobacteria (in agreement with the composition of the culturable bacterial collection generated) and Bacteroidetes , and to a lesser extent by Actinobacteria . This result agrees with that from Kaushal and co-workers [ 31 ], who recently studied the microbiome associated with FWB symptomatic and non-symptomatic bananas, and also with results from other authors [ 75 , 77 , 78 ]. In contrast, another work [ 37 ] mostly identified representatives of the phylum Actinobacteria among the endophytic bacteria present in banana plants.…”

“…The banana-associated belowground microbiome from Fusarium wilt symptomatic and asymptomatic plants has previously been studied by culturable and non-culturable methods [ 1 , 2 , 29 , 31 , 32 , 37 , 75 , 76 ]. The present study is the first one to perform an in-depth comparative characterization of the root endophytic microbial communities of banana when plants are in two different phenological stages: mother plants (at fruiting stage, unripe) and suckers (juvenile stage).…”

“…It is accepted that the plant-associated microbiome, usually an important source of BCA, is crucial for the host’s health, development, and productivity [ 26 ]. In this framework, the banana belowground microbiome is hypothesized to play essential roles, as it has already been studied in different agricultural pathosystems [ 27 , 28 ], including the banana– Foc interaction [ 1 , 2 , 29 , 30 , 31 , 32 ]. Thus, in-depth analyses of the structure, composition, dynamics, and functionality of the root-associated microbiome are useful to improve disease control approaches.…”

“…as potential health indicators that can be used as BCA against FWB [ 1 , 29 ]. Root-associated microbiomes in symptomatic and non-symptomatic banana plants were also investigated with the aim to unravel the responses and functions of the endophytic community during Foc infection in Tanzania [ 31 , 32 ]. Proboningrum and co-authors [ 38 ] demonstrated that the co-inoculation of two Bacillus strains (one rhizospheric and another endophytic) was effective to control FWB and to promote banana growth.…”

Phospholipid signaling pathway in Capsicum chinense suspension cells as a key response to consortium infection

“…The roots of plants establish a relationship with the microorganisms present in the rhizosphere. These interactions can involve either beneficial or pathogenic microorganisms [ 24 , 25 ]. Both types of interactions trigger a complex response that determine the success of pathogenic proliferation and development in the plant.…”