Temporal Dynamics and Molecular Functional Profiling of Poplar Root Fungal Communities

Abstract

Plants roots are host to diverse fungal communities that perform important functions for the plant host including nutrient acquisition, protection from abiotic stress, and deterrence of pathogens. Fungal communities found within roots are often a subset of the community found in the surrounding soil, suggesting a strong host filter that selects for unique species assemblages. This host filter operates through the production of plant defense compounds, transfer of molecular signals, and provisioning of carbon resources. Additionally, root fungal communities are structured by an environmental filter that selects for taxa with varying preferences for unique soil and climatic conditions. The complex interplay between host and environmental filtering generates variability in fungal community structure and function through space and time. Both host and environmental variation are also likely to affect the expression of molecular functions by members of the root fungal microbiome. However, It is still unknown how temporal variation in the plant host and environment interact to determine the structure and function of the root fungal microbiome. In this thesis, I present work that shows how temporal variation in the structure and function of the Populus root fungal microbiome is generated by plant development, seasonal dynamics, and sequential heat stresses. I apply a combination of microscopy, metabarcoding, metatranscriptomics, and plant physiology measurements to describe the community composition and whole community gene expression profiles of root fungal communities. I find that root fungal communities are dynamic during early growth, responding to plant developmental stage with predictable changes in community composition. Community composition was found to be generally resistant to seasonal changes, but fungal symbionts exhibited marked fluctuations in activity across seasons. Gene expression patterns demonstrated niche partitioning between fungal symbionts occupying the same root system and dynamism in expression of carbohydrate transfer and metabolism pathways consistent with versatility in carbon usage.