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Pathogens, Plant Phenology, and Microbial Competition Impact the Structure and Function of the Citrus Microbiome

Creative Commons 'BY' version 4.0 license

Pivotal advances in sequencing and bioinformatics revealed that extensive microbial communities inhabit terrestrial plants. Microbiota extend beyond the plant host genetics to provide vital traits and services, including microbiome-mediated disease resistance, nutrient acquisition, and tolerance to changing climates. The development of engineered microbial based plant therapies could help sustainably enhance plant health and improve yield. To gain insight on plant associated microbiomes and contribute to evolving agrosystem management strategies we focused on connecting microbial populations with plant disease outcomes, phenological stages, and community self-regulation.

Considering the urgent demand for novel treatments to combat citrus Huanglongbing (HLB) disease, which continues to devastate the global citrus industry, we directed our efforts on perennial tree crop hosts from the Citrus genus. Using empirical dataset produced through metabarcoding amplicon-based sequencing we concluded that disease status and phenological stage are significant driving factors of bacterial and fungal leaf and root communities.

We provide evidence that pathogens can induce plant dysbiosis followed by a microbiome-mediated immune response and that cyclical community assembly is governed by classic community ecological mechanisms: selection, dispersal, and speciation. Correlations between community structure and host phenotypes, suggest that microbiota functionally contribute to the rate of HLB symptom development and host phenological plasticity. Additionally, laboratory based gnotobiotic experimentation with a synthetic community indicated that competition influences microbial niche selection and the structure of the microbiome.

Furthermore, we have built avenues for discovering and delivering beneficial citrus associated microbiota. Specifically, we established a citrus microbial culture collection, a microbial active metabolite discovery pipeline, compared product delivery methods, and developed a microbiota-free citrus system in an ongoing effort to unravel host-microbiome and inter-microbiome interactions. These tools and our identification of beneficial microbial candidates encourage future research projects. Overall, this dissertation advances basic knowledge of plant microbiome assembly and symbiotic relationships between perennial plants and microbial communities.

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