Evolutionary Genomics Guides Scalable Coral Probiotics for Climate Resilience

Coral reefs sustain nearly 30% of marine biodiversity ¹ and provide ecosystem services valued at $2.7 trillion USD annually ² , yet face catastrophic collapse under climate change ³ , with 70-90% projected for extinction by 2050 even if the 1.5°C Paris target is met ⁴ . While microbial probiotics could enhance resilience, scalability is limited by transient colonization and uncertain long-term efficacy ^5–9 . Here, we introduce an evolutionary genomics framework to select next-generation probiotics targeting bacteria undergoing irreversible transitions to host dependency. Through laboratory proof-of-principle, we show the coral-sourced Ruegeria MC10, identified by genomic signatures of host adaptation (insertion sequence proliferation and pseudogenization of essential metabolic genes), increases thermal tolerance thresholds by 1°C in model cnidarians. Subsequent, real-world application of one-month nursery inoculations enabled Acropora pruinosa corals to retain MC10 for the monitored period (eight months) post-outplanting, including persistence through a natural bleaching event, with evidence for increased resilience. This work establishes lifestyle-oriented probiotic selection as a scalable solution for microbial-driven reef restoration. Critically, this framework addresses poor probiotic colonization and limited scalability, which pose universal limitations across conservation and aquaculture that hinder microbial-based interventions ^10–13 . By merging evolutionary biology with conservation science, we provide a generalizable blueprint applicable to diverse threatened wildlife.