Genome Sequencing and Analysis of Trichoderma (Hypocreaceae) Isolates Exhibiting Antagonistic Activity against the Papaya Dieback Pathogen, Erwinia mallotivora.

Amin-Asyraf Tamizi,Muhamad Afiq Akbar,Hamidun Bunawan,Richard T. Olumakaiye,Noriha Mat-Amin,Jack A. Weaver,Fabrizio Alberti,Sophie Jin

doi:10.3390/jof8030246

Abstract

Erwinia mallotivora, the causal agent of papaya dieback disease, is a devastating pathogen that has caused a tremendous decrease in Malaysian papaya export and affected papaya crops in neighbouring countries. A few studies on bacterial species capable of suppressing E. mallotivora have been reported, but the availability of antagonistic fungi remains unknown. In this study, mycelial suspensions from five rhizospheric Trichoderma isolates of Malaysian origin were found to exhibit notable antagonisms against E. mallotivora during co-cultivation. We further characterised three isolates, Trichoderma koningiopsis UKM-M-UW RA5, UKM-M-UW RA6, and UKM-M-UW RA3a, that showed significant growth inhibition zones on plate-based inhibition assays. A study of the genomes of the three strains through a combination of Oxford nanopore and Illumina sequencing technologies highlighted potential secondary metabolite pathways that might underpin their antimicrobial properties. Based on these findings, the fungal isolates are proven to be useful as potential biological control agents against E. mallotivora, and the genomic data opens possibilities to further explore the underlying molecular mechanisms behind their antimicrobial activity, with potential synthetic biology applications.

Highlights

Papaya dieback disease (PDD), or bacterial crown rot (BCR), is a bacterial-caused disease that has negatively affected papaya crops (Carica papaya L.) in Malaysia, reducing the national papaya export up to 70% [1]
Erwinia papayae was reported to be the causal agent of PDD [2], though later Mat Amin et al [3] molecularly validated the pathogen to have the closest match to E. mallotivora Goto strain DSM 4565 and this was further supported through genome sequencing [4]
We have discovered five Trichoderma isolates that showed antimicrobial activity against the E. mallotivora strain BT-MARDI, of which three were further characterised through genome sequencing to investigate the possible mechanisms behind their antimicrobial properties

Summary

Introduction

Papaya dieback disease (PDD), or bacterial crown rot (BCR), is a bacterial-caused disease that has negatively affected papaya crops (Carica papaya L.) in Malaysia, reducing the national papaya export up to 70% [1]. Erwinia papayae was reported to be the causal agent of PDD [2], though later Mat Amin et al [3] molecularly validated the pathogen to have the closest match to E. mallotivora Goto strain DSM 4565 and this was further supported through genome sequencing [4]. Water soak symptoms become prevalent on papaya petioles, leaves, and the apical stem, and the tree can succumb to the disease within one to two weeks [5–7]. E. mallotivora was reported to be affecting papaya in the Philippines and Indonesia, making this species a pathogen of concern that could affect the papaya industry in the entire Southeast Asia region [7,12]. A similar disease termed as papaya black rot has been recently detected in Japan and the pathogen was characterised to be from the genus Erwinia [13]

Methods

Results

Conclusion