Mapping the pathobiome and rhizosphere microbiome in Cajanus cajan-Fusarium interaction across agroclimatic zones and crop varieties

Abstract

Purpose

In soil, several factors, like environment and pathogens, can modulate the rhizospheric microbial communities, thereby impacting the overall fitness of host. A pathobiome includes members of the microbiome that interact with the host and pathogen to favor the infection process.

Methods and results

In this study, the microbial diversity was assessed in Fusarium-infested and control soil collected from the rhizosphere of two Cajanus cajan varieties grown in two agroclimatic zones. The core bacterial community included Steroidobacter, Pseudomonas, and Acidibacter, while Mortierella, Actinomortierella, and Naganishia were the abundant fungal genera. A disruption in the rhizospheric microbiome was delineated upon exposure to Fusarium udum, and a pathobiome uniquely associated with Fusarium wilt was identified. The members of the pathobiome included some common core bacterial and fungal members like Acidibacter and Actinomortierella, respectively. However, some bacterial genera, including Brevundimonas, Calenema, Delftia, and fungal genera, Aplosporella, Cristinia, Kwoniella, were unique to the infected samples. The correlation analysis between Fusarium and other common genera also pointed out the negative association of Bacillus with Fusarium. Hence, a culture bank of Bacillus strains was generated with isolates exhibiting strong antagonism against F. udum in vitro and in vivo.

Conclusions

The current study identified the core rhizosphere microbiome associated with pigeonpea, irrespective of the genotype and agroclimatic zone. In addition, several bacterial and fungal genera involved in the manifestation of infection through positive interactions with the fungal pathogen were identified, constituting the pathobiome associated with F. udum.