Engineering Coral Resilience: Functional Testing of Probiotic Bacterial Isolates in Aiptasia Under Thermal Stress

Coral reefs are rapidly declining under local and global stressors, raising urgent questions about how to enhance their resilience. Because corals depend strongly on their associated microbiomes, targeted bacterial interventions are emerging as potential solutions to support coral resilience and safeguard reef ecosystems. Yet, the mechanisms by which beneficial bacteria increase host stress tolerance, particularly heat tolerance, remain poorly understood.

In my thesis, I use the sea anemone Aiptasia as a coral model to bridge this gap. In Chapter I, I establish standardized acute heat stress assays using the Coral Bleaching Automated Stress System (CBASS) for reproducible testing of bacterial impacts on Aiptasia host thermal tolerance. In Chapter II, I generate isolate libraries from two Aiptasia strains (F003 and H2) and develop a novel pre-screening framework, including a newly developed physiological metric, the Behavioral Phenotype Score (BPS), to resolve isolate-specific effects on host stress responses. Building on this, using CBASS, I identify beneficial isolates that enhance host thermal tolerance by up to 1.4 °C, with some bacterial candidates acting across host anemone genotypes as potential universal probiotics. Finally, Chapter III presents the first genome assembly of Aiptasia strain F003, contributing a valuable resource to the model system for future genomic analyses of host-bacteria interactions.

Together, my work establishes experimental tools as well as microbial and genomic resources and identifies beneficial bacterial isolates from within the Aiptasia host microbiome. Collectively, my thesis lays the groundwork for the functional mechanistic exploration of probiotic host-bacteria interactions necessary to refine microbiome-based strategies that support reef conservation.