Factors affecting the diversity and assembly of arbuscular mycorrhizal fungi : A thesis submitted in partial fulfilment of the requirements for the Degree of Doctor of Philosophy at Lincoln University

Abstract

Global shifts in land use and climate are disrupting plant-soil ecosystems worldwide, threatening biodiversity, productivity and sustainability. A growing body of research highlights the importance of belowground biota in maintaining ecosystem services despite these pressures. Arbuscular mycorrhizal fungi (AMF) are symbionts that form an intricate and intimate relationship with plant roots, making them a key component of these plant-soil ecosystems. AMF are crucial to both aboveground and belowground processes and may play a key role in ecosystem resilience due to their ability to adapt to changing environmental conditions. However, the factors that shape AMF community diversity, particularly in the context of land use and climate change, remains a key knowledge gap. It is also unclear whether these symbiotic fungi respond to environmental drivers in the same way as the broader fungal community. Understanding of these factors, and whether AMF differ in their response from other fungi, would inform management practices to support resilient soil ecosystems. This thesis investigated how AMF and fungal communities differ across an annual monocropping system, a perennial orchard and indigenous forest | ngāhere, over two years in Aotearoa | New Zealand. It also explores the effect of inoculation with whole soil on AMF community assembly and the responses of both plants and AMF to warming. The first objective (Chapter Two) characterised the AMF and total fungal community in plant roots and bulk soil from three different land uses and evaluated associations with soil nutrient status. AMF and fungal biomass were both lower in managed systems than in unmanaged ngāhere. Community structure for both groups differed between land uses, indicating the effect of plant host or land management. Among the measured soil chemical properties, the carbon-to-nitrogen ratio was most strongly associated with AMF biomass, while labile carbon was most strongly associated with total fungal biomass. Objective two (Chapter Three) explored the seasonal dynamics of the communities characterised in Objective one, by assessing trends in diversity across all three land uses over two years. While total fungal biomass remained stable, AMF biomass showed consistent seasonal fluctuations in both managed and unmanaged systems. This suggests that for AMF, plant host physiology (with an annual cycle) exerts a stronger influence on biomass than management. Seasonal effect on both fungal and AMF community structure was minimal and specific to kiwifruit orchards, a managed land use with continuous plant cover. Predictable shifts in fungal taxa were not seen in any land use, suggesting a level of stability despite changes in abiotic conditions. The combination of fatty acid analysis and next-generation Illumina sequencing in Objectives one and two allowed for the quantification of biomass and taxonomic profiling of root- and soil-associated communities, providing a more comprehensive picture of diversity than either method alone. This is the first field study in Aotearoa to apply these complementary techniques to assess AMF diversity and to compare AMF patterns with those of the broader fungal community. By incorporating plant species of both economic and cultural importance, this research offers valuable insights for agricultural sustainability and conservation. This thesis makes a significant contribution to the limited knowledge of AMF in Aotearoa, being the first to characterise the community in kiwifruit orchards and maize fields, the first to compare diversity across multiple land uses, and the first to assess seasonal trends. Using native AMF communities from the soils in Objectives one and two, Objective three (Chapter Four) considered the role that AMF inoculation with whole soil has on the assembly of the AMF community and on plant responses to warming. The results of this experiment reinforced the importance of host plant identity, with each plant species forming a distinct AMF community from the same soil inoculum. In contrast to plants, the response of the AMF community to warming was not evident, indicating a degree of stability in the face of environmental change. By modelling a predicted regional temperature increase specific to Aotearoa, this objective offered a rare, locally relevant perspective on AMF–plant interactions in the context of climate change. By integrating field observations with experimental findings, this doctoral research provides a comprehensive picture of the factors shaping AMF community diversity in Aotearoa | New Zealand. Over two years of sampling, complementary techniques revealed the effects of both land use and seasonality on AMF diversity and compared these patterns to those of broader fungal communities. Land use (which is inextricably tied to certain plant species) influenced both communities, while seasonal trends were observed only in AMF. While the influence of plant host identity on AMF communities is well-documented globally, this study provides the first experimental evidence in Aotearoa that different plant species assemble distinct AMF communities. Overall, these findings deepen our understanding of AMF ecology and highlight the complexity of leveraging AMF-plant symbioses for sustainable land management.