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Microbial Community and Functional Gene Profiling of Kauri Soil

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Thesis(11.23 MB)

Date

2024

Authors

Supervisor

Bugler, Donnabella Lacap
Padamsee, Mahajabeen
Lee, Kevin

Item type

Thesis

Degree name

Doctor of Philosophy

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Publisher

Auckland University of Technology

Abstract

Kauri (Agathis australis) is a significant native tree in Aotearoa New Zealand that holds cultural importance to Māori. The species plays a crucial role in maintaining ecological balance in kauri forests. Due to the intensified agriculture and timber industry many years ago, only about 1% of the original kauri forest remains today. This is now under threat from a soil-borne Oomycete pathogen known as Phytophthora agathidicida, that causes dieback disease in kauri. The immediate action to manage the spread of dieback disease and preserve the enduring health of kauri forests is paramount. Soil microbiota plays a crucial role in promoting plant health and preventing soil-borne diseases. The understanding of the microbial communities and diversity in kauri soils, such as in natural forests and anthropogenic settings, is limited. There is also sparse knowledge on possible microbial antagonists that can suppress plant diseases caused by pathogens like P. agathidicida. The main objective of this study was to characterise the microbial community structure in kauri soil, describe the functional potentials, and correlate these to the presence of the pathogen to the soil microbiome. Significant differences (p-values < 0.05) were found in soil microbial communities' diversity and species richness between soil from dieback symptomatic kauri trees and non-symptomatic kauri trees. Non-symptomatic kauri soils had a higher abundance of microbial genera such as Penicillium, Trichoderma, Aspergillus, Streptomyces and Pseudomonas, which have been reported to suppress growth of Phytophthora pathogens. These results may assist in the discovery of microbial taxa which enhance soil disease suppression. The findings indicated notable variances in the signal intensities of carbon cycling genes and microbial defence genes in natural versus planted kauri soil (p values < 0.05). Specifically, the carbon degradation genes were significantly more abundant in the natural kauri soil, which can be attributed to the accumulation of litter in the forest. Furthermore, a range of genes involved in the nitrogen and phosphorus cycle processes, as well as genes that promote plant growth were identified. Notably, crucial genes, including PhID, which are linked to microbial defence and production of antimicrobial compounds capable of suppressing the growth of several Phytophthora species were also observed. Through the in vitro screenings of fungal isolates, five different endophytes were identified to demonstrate varying levels of P. agathidicida growth inhibition in dual culture experiments. Coprinellus micaceus and Ilyonectria mors-panacis have shown to effectively inhibit the growth of P. agathidicida while also suppressing its zoospore formation. Further research needs to be conducted to understand the mechanism of inhibition and possible metabolite production of these isolates. It is worth considering these endophytes as potential biocontrol agents for plant pathogens, such as P. agathidicida in kauri.

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http://hdl.handle.net/10292/18333

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