The soil microbiota associated with New Zealand’s kauri (Agathis australis) forests under threat from dieback disease : A thesis submitted in partial fulfilment of the requirements for the Degree of Doctor of Philosophy at Lincoln University

Abstract

Kauri (Agathis australis) is one of New Zealand’s most iconic native tree species, which are of cultural significance to Māori and function as an ecological foundation species. However, only around 1% of the original kauri forest remains as a consequence of logging and clearance for agriculture. These remnant, fragmented kauri forests are now under threat from the spread of dieback disease caused by the soil-borne oomycete pathogen Phytophthora agathidicida, and urgent action is needed to manage the spread of dieback and secure the long-term health of kauri forests. Soil microbiota are known to play a key role in supporting plant health and defending against soil-borne pathogens. Studying their response to disease outbreaks can guide the identification of disease suppressive microbial antagonists against pathogens such as P. agathidicida. In addition, investigating how disturbances impact the soil microbiota allows us to assess the indirect, secondary impacts of disturbances on forest ecosystems. Our knowledge on the microbial diversity of kauri forest soils and their responses to disturbances such as biological invasions is limited. The primary aim of this research was to characterise the taxonomic diversity of the kauri soil microbiota and their response to dieback, whilst screening members of the soil microbiota against P. agathidicida to test their potential to inhibit the pathogen. A secondary aim was to quantify differences in soil microbiota between kauri and adjacent pine (Pinus radiata) located at Waipoua Forest (Northland Region, New Zealand). The findings of this study revealed that the establishment of pine significantly altered soil microbial community composition compared to that of old growth kauri forests, which included the loss of microbial taxa linked to plant health. This highlights the impact of historical disturbance on the soil environment surrounding kauri forests, which may impact their susceptibility to invading plant pathogens. Significant differences were found in the diversity and composition of soil microbial communities associated with asymptomatic kauri compared to symptomatic kauri. Several microbial genera which have previously been reported to antagonise Phytophthora pathogens, such as Penicillium, Trichoderma and Pseudomonas, were found in higher abundance in asymptomatic kauri soils. These results may assist in the discovery of microbial taxa which enhance soil disease suppression. A supplementary kauri seedling infection study using soils from Waipoua Forest(Northland Region, New Zealand) identified that soil bacterial communities responded strongly to seedling infection. Using in vitro screenings, microbial strains belonging to the genera Burkholderia, Paraburkholderia, Pseudomonas and Penicillium that significantly inhibited the mycelial growth of P. agathidicida were identified. Their modes of inhibition, particularly for the Burkholderia strains, appear to be by the production of volatile and diffusible organic compounds. This PhD thesis is the first study to have fully characterised the fungal and bacterial communities of old growth kauri soils using high throughput sequencing techniques. By doing so, this research has 1) assessed the impacts of forestry disturbance on the characteristics of the kauri soil microbiota 2) guided the identification of microbial taxa associated with potentially disease suppressive soils 3) highlighted the secondary impacts of dieback disease on the functional properties of the soil microbiota and 4) identified candidate microbial antagonists against P. agathidicida.