Phylogeny of Fusarium oxysporum f. sp. cubense strains and microbiome associated with banana cultivars

Abstract

Fusarium wilt (FWB), also known as Panama Disease, is the most important disease of banana. This disease is caused by Fusarium oxysporum (Foc), a fungus that occurs in three races based on host susceptibility. Race 1 (Foc R1) causes disease in banana cultivars such as Gros Michel (Group AAA) and Maçã (Seda, AAB); Race 2 (Foc R2) affects banana cultivars such as Bluggoe (ABB group), while race 4 (Foc 4) affects all cultivars, including Cavendish-type cultivars (AAA group), resistent to race 1 and 2. The use of resistant cultivars is considered as the only effective measure to control the disease. The aims of this study were (i.) to characterize Foc isolates obtained from the rhizosphere and roots of different cultivars by means of molecular phylogeny analysis and pathogenicity tests in differentiating cultivars; (ii.) to perform a comparative analysis of the bacterial microbiome of the rhizosphere and endorhizosphere of cultivars with different levels of resistance; (iii.) to clarify whether the observed microbial profiles present differences, which could be indicative of tolerance or resistance to the disease. Isolations of Foc were carried out in the rhizosphere and roots of the plants, obtaining nine isolates of the Fusarium oxysporum morphotype, which were submitted to molecular phylogenetic analysis using the EF-1α gene region. Two phylogenetic species, Fusarium callistephi and F. triseptatum, were identified. Representative isolates of both species induced symptoms when inoculated in the cultivars Grande Naine and traditional Maçã, resistant and susceptíbel respectively, thus representing race 1. For microbiome analysis, metagenomic DNA was obtained from the endosphere, rhizosphere and bulk soil samples of 4 cultivars with different levels of resistance to Foc, for amplification of the 16S rDNA region. An average of 12,000 operational taxonomic units (OTU's) were generated. The main groups identified were Proteobacteria (50.4%), Actinobacteria (20.3%), and Firmicutes (7.9%). Cultivars harbor distinct communities in each niche, showing differentiated microbial communities. In the rhizosphere, the genera Burkholderia and Klebsiella predominated, while in the endosphere the genera Mucilaginibacter, Sphingomonas, Fluviicola, Variovorax, Niastella and Ralstonia were found. This study supports the hypothesis that the microbiome may represent a supplementary source of plant defense mechanisms. Although obtained from a restricted collection, the results made it possible to identify two phylogenetic species and possible biological control agents. This result contributes to knowledge about Foc diversity in Brazil and to the development of diagnostic and control tools.