Metagenomic analysis of bacterial flora in rhizospheres of Allium plants and suppressive activity of Pseudomonas isolates against Fusarium wilt of cucumber

Abstract: Mixed cropping and rotation cropping with Allium plants have been used as effective method to control Fusarium wilt of cucurbits and banana. It has been believed that rhizobacteria of Allium plants might suppress Fusarium wilt. In this study, rhizosphere bacterial flora of Allium plants (Welsh onion, Chinese chive, onion, garlic) and non-Allium plants (cucumber, tomato) were cyclopaedically analyzed by next generation sequencing. Results showed that predominant rhizobacteria of Allium plants belong to four genera: Pseudomonas, Burkholderia, Flavobacterium and Chryseobacterium, whereas predominant rhizobacteria of non-Allium plants belong to genus Streptomyces. Pseudomonas spp., one of the predominant rhizobacteria of Allium plants, were isolated from every plant rhizosphere and were assessed for in vitro and in planta antagonism against F. oxysporum f. sp. cucumerinum (described as FOC). Results showed that the percentages of Pseudomonas isolates inhibitory to FOC in Allium rhizospheres were higher than non-Allium rhizospheres. Similarly, in in planta assay the percentages of the isolates suppressive to Fusarium wilt of cucumber in Welsh onion and onion rhizospheres were higher than non-Allium rhizospheres. These findings indicate that alleviation of Fusarium wilt in mixed rotating cropping systems is partly due to Pseudomonas spp. accumulated in the rhizospheres of Allium plants.