Abiotic and biotic factors structuring the microbiomes of conifers in the family Pinaceae

The overall aim of my dissertation was to determine the abiotic and biotic factors that structure the foliar bacterial communities in conifers in the family Pinaceae. In plants, microbial communities can benefit their host organism by acting as an extension of their phenotype and responding rapidly to environmental fluctuations. Long-lived species of plants, such as conifers, can survive in harsh and nutrient limited environments. This is a result of adaptations in the plant genome, but their microbial communities can also assist, especially in the face of a changing environment, as the plant microbiome has been found to protect against biotic and abiotic stress and help acquire limiting nutrients. However, the factors that drive the variation in the conifer microbiome at micro- and macroscales are not well studied, limiting our understanding of how the microbiome may contribute to host health and stress resilience. Previous work on foliar microbial communities of adult conifers have identified a core microbiome that is consistently dominated by the potentially nitrogen-fixing family Acetobacteraceae across sites, host species and time. However, previous sampling was too limited to identify the main drivers of variation in the foliar conifer microbiome. To address this knowledge gap, I used 16S rRNA sequencing to look at effects of abiotic and biotic factors on bacterial community structure. First, I investigated the effect of host age, tissue type (root vs shoot), and experimental heating and watering on microbial community structure. I found that host age was a strong driver of microbial community structure. Seedling shoots hosted a different core microbiome, dominated by the family Oxalobacteraceae, compared to adult tree foliage. Shoot and root communities of seedlings were significantly different, but with extensive overlap in taxa present. Experimental watering restructured microbial communities in seedlings, with enrichment of antifungal strains, potentially showing recruitment of endophytes to protect against fungi under increased soil moisture. These results suggest differences in community assembly and ecological function across conifer life stages. Second, I explored the effects of land mass age (nutrient availability) and host species in a coastal ecosystem on microbial diversity and structure. I found that foliar bacterial communities were structured by both land mass age and host species. The core microbiome of Acetobacteraceae was found in all samples showing a consistent relationship regardless of nutrient availability. Third, I examined the effects of needle age and longevity, plant compartment, host species and geographic location on the bacterial communities of four Pinus species across 15 sites. I found that needle age significantly structured the bacterial communities, but that it explained less of the variation among samples than did host species, plant compartment and geographic location. Needle age was a stronger driver of endosphere communities than phyllosphere communities, with the strongest effect in the endosphere of Pinus longaeva which can retain its needles for up to 45 years, suggesting that both accumulation of taxa over time and host selection shapes the needle endophyte community. Finally, I investigated the effect of site, host species and plant compartment across the native range of Pinus flexilis. I found site to be the strongest driver of bacterial communities in both plant compartments. However, the influence of site was not due to geographic distance of trees, suggesting that foliar microbial communities are not dispersal limited. The occurrence of identical sequence variants across large geographic distances, along with sequence identity between our sequence variants and taxa previously identified in air, dust, and rain suggests that the foliar microbiome of conifers is transmitted through the atmosphere. Thus, rather than geographic location, environmental heterogeneity and varying abiotic factors across sites appear to be the strongest drivers of variation in the foliar microbiome. Time and dispersal history (immigration) are also likely contributors to the differences observed across sites. Host species explained a small amount of variation in the bacterial communities, although the effect was dependent on plant compartment. There was extensive overlap in bacterial communities between plant compartments suggesting a possible colonization route from the needle surface to the endosphere