Variation in Soil Microbiomes Associated With Kauri Trees Threatened by Dieback Disease

Abstract

Forest ecosystems are increasingly threatened by climate change, land-use pressures, and emerging pathogens, highlighting the need to understand how different ecosystem components mediate and respond to such disturbances. Soil microbial communities are central to nutrient cycling, plant growth, and disease suppression, yet their interactions with soil-borne pathogens in natural forest systems remain poorly understood. This thesis addresses this gap using Agathis australis (kauri), a foundation tree species endemic to New Zealand currently threatened by the soil-borne oomycete Phytophthora agathidicida (causal agent of kauri dieback), as a case study. The work investigated how pathogen presence, tree health, spatial location, and edaphic gradients relate to forest soil microbial community composition and functional potential.

Soils were collected around the basal trunk of 96 kauri trees comprising healthy, declining, and dead canopy states across three sites and six plots in the Waitākere Ranges, Auckland, New Zealand. By combining amplicon sequencing, shotgun metagenomics, loop-mediated isothermal amplification (LAMP), and measurements of soil physicochemical properties, this framework provided a comprehensive view of the soil microbiome across tree health and environmental gradients.

Results showed that soil microbial communities were strongly structured by spatial and edaphic variation. Soil carbon, nitrogen, C:N ratios, pH, and moisture consistently emerged as dominant drivers of both bacterial and fungal communities. Pathogen presence, confirmed by LAMP, and tree health status were only weakly related. Nevertheless, specific bacterial and fungal taxa were significantly more abundant in pathogen-detected soils, including taxa previously linked with disease suppression. Soils beneath declining trees contained significantly greater abundance of taxa associated with later stages of litter decomposition, suggesting links between canopy decline, litter accumulation, and microbial community structure. While bacterial communities were relatively stable across all health states, fungal communities were more strongly related to tree decline. Functional profiles derived from shotgun metagenomics revealed that broad metabolic capacities were conserved across health states, consistent with functional redundancy. However, fine-scale shifts in some gene families and pathways indicated that microbial communities could reorganise their functions under changing conditions, with possible implications for decomposition and nutrient cycling.

This work demonstrates the complementarity and value of combining multiple molecular approaches to assess different components of the microbial community. It also suggests that soil microbial communities in kauri forests are influenced by strong environmental and spatial filtering, with pathogen and host decline potentially contributing secondary, but small, influences. By providing one of the first comprehensive metagenomic baselines for kauri soil microbial communities under threat of dieback, this thesis contributes to understanding how pathogen presence, tree health decline, and microbial communities interact in a natural forest system. Together, these insights advance ecological understanding of how a biotic disturbance shapes soil microbiomes in natural forest ecosystems and informs long-term monitoring and future research on kauri dieback. Building our understanding of the long-term consequences of forest decline due to death of kauri, and by extension, other foundation tree species worldwide, will depend on recognising the resilience and sensitivity of soil microbial communities within their complex environmental contexts.