Investigating companion plant-associated microbial communities for antagonistic activity towards Phytophthora agathidicida
Authors:   , Summers Monica 
Published: July 2024

<p><strong>Plant-associated microbes are known influencers of plant health, enhancing growth and increasing tolerance to stressors. Another key role that they play in plant health is disease suppression through inhibiting and out-competing pathogens and/or boosting plant defences. One way to help recruit these beneficial microbes is through companion planting. Strong biocontrol microbes can associate with companion plants, favourably altering the microbial composition of the environment to aid in disease suppression. Altogether, this makes companion plants and their associated microbes excellent choices for the exploration of environmentally friendly and sustainable disease control treatments.</strong></p><p>Phytophthora agathidicida, the causal agent of kauri dieback, is threatening kauri, one of New Zealand’s important native species. P. agathidicida has been rapidly spreading through kauri forests, leading to the death of numerous kauri. However, treating it is challenging due to specialised spores for infection, spread, and survival. With limited treatments currently available and disease rapidly spreading, there is an urgent need for the discovery of new treatments.</p><p>The overall aim of this thesis was to explore companion plant-associated microbial communities for their potential to inhibit P. agathidicida. Many native plants are well known in mātauranga Māori (Māori knowledge) for their use in rongoā (traditional medicine) or their importance in forest health. Here, the microbial communities of plants identified by mātauranga Māori knowledge holders were explored to identify potential antagonists of P. agathidicida.</p><p>In Chapter Two, the identity and mechanism of inhibition of an unknown bacterium isolated from kūmerahou flowers were investigated. The bacterium was identified as a new strain of Pseudomonas fluorescens, and it was shown that it inhibited P. agathidicida through volatile compounds. These volatile compounds were subsequently identified, and three of these compounds, 1-undecene, 3-methyl-1-butanol, and undecanal, were confirmed to inhibit P. agathidicida mycelial growth. One of these compounds, undecanal, was also shown to further inhibit other life cycle stages important in survival and spread. In Chapters Three and Four, microbial communities associated with karamū and māpou plants in a companion planting field trial in Waipoua Forest were explored. Amplicon sequencing of the 16S rRNA and ITS regions of soil and leaf samples revealed that karamū and māpou established different microbial communities, especially in their leaves. Furthermore, these microbial communities contained members with potential for plant growth promotion and biocontrol. Further screening of the bacteria associated with these plants found that many bacterial isolates associated with both karamū and māpou were capable of inhibiting P. agathidicida mycelial growth. Two characteristic types of inhibition were seen: long-range, where P. agathidicida was inhibited far away from the bacteria, and short-range, where P. agathidicida was only inhibited when near the bacteria due to differences in the diffusibility of active compounds through agar. Six bacteria that were phenotypically distinct and that inhibited P. agathidicida through the different modes were further explored. These bacteria were identified as different species belonging to the Pseudomonas, Pantoea and Curtobacterium genera that inhibited P. agathidicida mycelia through their diffusible compounds. Full genome assembly and annotation also revealed several biosynthetic gene clusters and carbohydrate-degrading enzymes that could be involved in the inhibition of P. agathidicida.</p><p>Altogether, this thesis has shown that potential companion plants, selected through mātauranga Māori, have distinct microbial communities, and contain multiple bacterial members that strongly inhibit P. agathidicida, supporting the continued exploration of companion plants and their microbes for bio-sustainable disease control.</p>