Microbial basis of Fusarium wilt suppression by Allium cultivation

Abstract

Crop rotation and intercropping with Allium plants suppresses Fusarium wilt in various crops. However, the mechanisms underlying this phenomenon have not been fully elucidated. This study was designed to assess the role of microorganisms inhabiting Allium rhizospheres and antifungal compounds produced by Allium roots in Fusarium wilt suppression by Allium cultivation. Suppression of cucumber Fusarium wilt and the pathogen multiplication by Allium (Welsh onion and/or onion)-cultivated soils were eliminated by heat treatment at 60 °C, whereas those by Welsh onion-root extract were lost at 40 °C. The addition of antibacterial antibiotics eliminated the suppressive effect of Welsh onion-cultivated soil on pathogen multiplication, suggesting the contribution of antagonistic gram-negative bacteria to the soil suppressiveness. The Illumina MiSeq sequencing of 16S rRNA gene amplicons revealed that genus Flavobacterium was the predominant group that preferentially accumulated in Allium rhizospheres. Flavobacterium species recovered from the rhizosphere soils of these Allium plants suppressed Fusarium wilt on cucumber seedlings. Furthermore, confocal laser scanning microscopy revealed that Flavobacterium isolates inhibited the multiplication of the pathogen in soil. Taken together, we infer that the accumulation of antagonistic Flavobacterium species plays a key role in Fusarium wilt suppression by Allium cultivation.

Omics approaches inAlliumresearch: Progress and way ahead

“…A reduction in disease was observed due to the reduction in secondary plasmodia of Plasmodiophora . A similar study conducted by Nishioka et al (2019) revealed that cucumber crop rotation and mixed cropping with Allium species ( A. cepa and A. fistulosum ) suppress the Fusarium wilt. 16S rRNA gene sequencing by using Illumina MiSeq revealed the dominant presence of the Flavobacterium genus.…”

“…16S rRNA gene sequencing by using Illumina MiSeq revealed the dominant presence of the Flavobacterium genus. The predominance of Flavobacterium inhibits the multiplication of pathogens in soil ( Nishioka et al, 2019 ). The metagenomics study of Chinese leek ( A. tuberosum ) by using high-throughput 16S rRNA gene Illumina sequencing revealed the predominance of Proteobacteria, Acidobacteria, Bacteroidetes, Cyanobacteria , and Planctomycetes microbial communities responsible for potential antifungal and nematicidal activities ( Huang, 2018 ).…”

Rhizosphere Community Selection Reveals Bacteria Associated With Reduced Root Disease

“…Moreover, some strains of Flavobacterium and Chryseobacterium produce antimicrobial compounds and stimulate plant immune systems and have been used as bioremediation agents [64]. Most recently, Nishioka et al [65] recovered Flavobacterium species from the rhizosphere soils of the Allium plants that suppressed Fusarium wilt on cucumber seedlings and demonstrated that the Flavobacterium isolates inhibited the multiplication of the pathogen in soil. Flavobacterium was also found to be one of the most abundant bacterial genera present in the soil of banana elds in which Fusarium wilt decline had occurred [66].…”

“…Furthermore, DESeq2 analysis found that some OTUs were differentially abundant in the rhizosphere soil between 'Good' (G) and 'Bad' (B) treatment in both cycle 2 and cycle 9. Interestingly, the 'Good' treatment in cycles 2 and 9 were highly enriched the antagonistic microbe OTU 19 belonged to genera Flavobacterium [65]. In addition, a group of plant growth-promoting (PGP) microbes, including Rhizobium, Pedobacter, and Variovorax, were highly abundant in the rhizosphere soil from 'Good' (G) treatment in cycle 9.…”

Rhizosphere community selection reveals bacteria associated with reduced root disease 

“…Moreover, some strains of Flavobacterium and Chryseobacterium produce antimicrobial compounds and stimulate plant immune systems and have been used as bioremediation agents [68]. Most recently, Nishioka et al [69] recovered Flavobacterium species from the rhizosphere soils of the Allium plants that suppressed Fusarium wilt on cucumber seedlings and demonstrated that the Flavobacterium isolates inhibited the multiplication of the pathogen in soil. Flavobacterium was also found to be one of the most abundant bacterial genera present in the soil of banana elds in which Fusarium wilt decline had occurred [70].…”