Identifying novel biocontrol agents from New Zealand kiwifruit orchards

Martinez Perez, Javier (2022) Identifying novel biocontrol agents from New Zealand kiwifruit orchards. Doctoral thesis, University of East Anglia.

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Pseudomonas syringae pv. actinidae (Psa) biovar 3 is a major threat to New Zealand’s kiwifruit industry. With more than 90% of the production area infected, cumulative losses amount to well over NZ$1 billion since 2010. The most effective and commonly used treatments for Psa infection are copper compounds and bactericides. However, following the identification of Psa variants resistant to these treatments their long-term efficacy might be in danger. Therefore, there is an urgent need for effective and environmentally friendly treatment options against Psa.

By examining how the naturally-occurring population of kiwifruit-associated Pseudomonas strains respond to Psa infection, we aimed to discover and characterise novel anti-Psa treatments. In vitro characterisation of over 1,000 strains helped identify phenotypic traits associated with Psa-inhibition, such hydrogen cyanide, siderophore and protease production, and suppression of Gram-positive pathogens such as Streptomyces scabies. This characterisation also identified an extremely high correlation between copper and streptomycin resistance. Further analysis determined that genes previously published as essential for copper and streptomycin resistance were missing from most copper and streptomycin resistant strains. Whole genome sequencing and transposon mutagenesis identified phylogenetic clustering among copper and streptomycin resistant strains and several potential novel copper resistant genes.

Thirty-three Pseudomonas strains were identified that strongly suppressed Psa in vitro. In planta biocontrol experiments with these Psa-inhibitory Pseudomonas highlighted four biocontrol candidates that reduced Psa infection in model plants by almost 99%. Further work on kiwifruit vines under greenhouse conditions showed three biocontrol candidates were able to provide effective protection against Psa, with G59 performing as well as a commercially available biopesticide. Finally, whole genome sequencing, transposon mutagenesis and automated genome mining helped to unlock the soil Pseudomonas biosynthetic potential. We identified and started to characterise Cluster XX, a novel biosynthetic gene cluster (BGC), alongside genes predicted to contribute to other novel biosynthetic gene clusters.

Item Type: Thesis (Doctoral)
Faculty \ School: Faculty of Science > School of Biological Sciences
Depositing User: Chris White
Date Deposited: 04 Apr 2023 14:14
Last Modified: 05 Apr 2023 13:13

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