Native Olympia Oysters in San Francisco Bay: Microbiome and Antimicrobial Resistance Derived Insights Into Restoration

Abstract

Restoration of Olympia oyster (Ostrea lurida) reefs can deliver ecological and public-health co-benefits. Characterization of the microbiome can provide valuable insights towards reef health but remains underused especially in San Francisco Bay. To overcome this gap, we applied shotgun metagenomics to oyster tissue, water, sediment, and biofilm collected from five San Francisco Bay sites (Loch Lomond, Point San Quentin, Brickyard Park, China Camp, Dunphy Park; Nov 2023) to profile community structure, Vibrio diversity, and antimicrobial-resistance (AMR) potential. Evaluating beta-diversity based on Bray-Curtis dissimilarities, we saw strong clustering by sample type (PERMANOVA R2 = 0.645, p = 0.001) and no significant clustering by location (R2 = 0.068, p = 0.937). Alpha diversity (Shannon) differed by matrix (Kruskal-Wallis p = 0.000416), with sediment and water highest and oyster tissues lowest. Vibrio taxa occurred at low relative abundance across matrices but were slightly enriched in biofilms and tissues; several Vibrio phages were also detected, consistent with potential (but unconfirmed) top-down control. Resistome profiling revealed a long-tailed distribution dominated by the tetracycline efflux pump tet(C) (70,049 reads) and APH(3)-Ia (4,498 reads), alongside multidrug efflux components (acrAB/-D, mdtABC/H/F/P, mdfA, MexF/MexW). Biofilms were AMR hotspots, while oyster tissues uniquely harbored Vibrio cholerae varG (Subclass B1 {beta}-lactamase). Collectively, our results indicate that matrix, not geography, structures reef microbiomes, that Vibrio is present but scarce, and that biofilms concentrate AMR potential. We propose a microbiome-integrated monitoring approach that stratifies by matrix, prioritizes biofilm resistome tracking, and targets Vibrio surveillance in oysters to align restoration performance with ecosystem-health safeguards.