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

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.

Trichoderma and its role in biological control of plant fungal and nematode disease

“… (A–F) Schematic diagram of the mechanism of action of Trichoderma in plant fungal disease control ( Martínez-Medina et al, 2013 ; Lamdan et al, 2015 ; Morán-Diez et al, 2020 ; Manzar et al, 2022 ; Tamizi et al, 2022 ). …”

“… Manganiello et al (2018) found that the volatile secondary metabolites secreted by T. viride TG050 609 can cause the mycelium of P. nicotianae to grow irregularly, break, or even dissolve, proving that T. viride has an antibiosis effect on P. nicotianae . In addition, most Trichoderma strains can produce antimicrobial substances such as pentaibols, which can inhibit a variety of plant pathogenic fungi and can also cooperate with cell wall-degrading enzymes on pathogenic fungi to effectively inhibit their growth ( Debode et al, 2018 ; Mayo-Prieto et al, 2019 ; Kovács et al, 2021 ; Martínez-Salgado et al, 2021 ; Tamizi et al, 2022 ). Some studies have shown that some Trichoderma spp.…”

“…In recent years, research on the genome, transcriptome, proteome, and metabolome of Trichoderma has developed rapidly ( Zhang Y. et al, 2022 ). Genome and EST sequencing, and microarray and microarray based expression profiling have become important tools for exploring Trichoderma genes and studying the mechanism of action ( Tamizi et al, 2022 ). In genomics research, a cDNA library of T. harzianum EST has been constructed, and multiple new genes have been identified ( Ferreira Filho et al, 2020 ).…”

Trichoderma – genomes and genomics as treasure troves for research towards biology, biotechnology and agriculture

“…fungi controlling E. mallotivora identified, potential secondary metabolite pathways underpinning the antimicrobial properties of three antagonistic strains delineated (Tamizi et al, 2022) UKM-M-UW RA6…”

A newly isolated Trichoderma Parareesei N4-3 exhibiting a biocontrol potential for banana fusarium wilt by Hyperparasitism

“…In addition, Trichoderma has been shown to stimulate systemic induced resistance in host plants ( Mukherjee et al., 2013 ; Sood et al., 2020 ). Although a large number of studies on Trichoderma have been reported ( Tomah et al., 2020 ; Díaz-Gutiérrez et al., 2021 ; Tamizi et al., 2022 ), the inhibitory mechanism of different Trichoderma on pathogens still needs to be elucidated. Therefore, it is necessary to isolate Trichoderma strains with high antagonistic activity and characterize their antagonistic mechanism.…”