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Papayas and fungi, a biocontrol dream team!

During my second year of my PhD in the Alberti group, I had the pleasure to be awarded the Jim Brewster scholarship from the University of Warwick. This award is given every year for a PhD student in their 2nd year of research for their work on crop improvement. So, let’s dive into my research for a few minutes and talk about Papayas and biocontrol!

Erwinia mallotivora, as many members of the genus, is a plant pathogen which causes papaya dieback disease, the most important cause of yield loss in Malaysia and other East Asian countries. The disease can be spread via both biotic and abiotic factors such as insects of rainfall. Symptoms include water-soaked lesions on stems and leaves, spots on leaves, opening the plant for further infections and eventually death of the affected plant.

Thank you to Noriha Mat Amin for the pictures!

Biocontrol is the most promising strategy to mitigate this disease as others such as crop management, chemical treatment or the use of resistant plants are either not manageable or not available. My project focuses on three strains of Trichoderma koningiopsis which have been isolated and identified as being active against E. mallotivora. My aim is to characterise specialised metabolites from those three Trichoderma strains showing bioactivity against E. mallotivora.

3 strains of Trichoderma koningiospsis (from left to right RA3a, RA5, RA6)

So far, results show that crude extracts of all three strains have antibacterial activity with one showing additional antifungal activity. Citric acid was identified as one of the antibacterial compounds active against Gram negative bacteria and E. mallotivora specifically. Other antimicrobial compounds have been isolated using different cultivation strategies (carbon sources, solid/liquid cultivation methods, epigenetic manipulation) and their structures are being elucidated using NMR spectroscopy.

In addition, the genomes of the three Trichoderma strains have been sequenced and natural product biosynthetic gene clusters (BGC) have been identified through AntiSMASH. Clusters of interest have been selected for their unusual structures and will be targeted for knock-outs. A transformation method for the environmental strains of T. koningiopsis is being developed and CRISPR/Cas9 knockouts will be created to investigate the BGCs producing the antimicrobial compounds. Recently, mutants expressing a fluorescence maker attached to the Cas9 protein were obtained.

Now my work will focus on applying the CRIPSR-Cas9 method developed here to study the BGC that my strains carry and study their potential for producing new antimicrobials. I will also be looking for differential gene expression of my strains when cultivated in different conditions where the antimicrobial compounds produced differ.

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