Nand, S. | bioRxiv Science

bioRxiv2025

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

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.

genomics↗

bioRxiv2024

Combinatorial characterization of bacterial taxa-driven differences in the microbiome of oyster reefs

Oyster reefs are invaluable ecosystems that provide a wide array of critical ecosystem services, including water filtration, coastal protection, and habitat provision for various marine species. However, these essential habitats face escalating threats from climate change and anthropogenic stressors. To combat these challenges, numerous oyster restoration initiatives have been undertaken, representing a global effort to preserve and restore these vital ecosystems. A significant, yet poorly understood, component of oyster reefs is the microbial communities. These communities account for a substantial proportion of marine reefs and are pivotal in driving key biogeochemical processes. Particularly, the environmental microbiome plays a crucial role in supporting the health and resilience of oyster populations. In our study, we sought to shed light on the microbiome within oyster reef ecosystems by characterizing the abundance, and diversity of microorganisms in the soil, biofilm, and oysters in 4 sites using a combinatorial approach to identify differentially abundant microbes by sample type and by sampling location. Our investigation revealed distinct microbial taxa in oysters, sediment and biofilm. The maximum Shannon Index indicated a slightly increased diversity in Herons Head (5.47), followed by Brickyard park (5.35), Dunphy Park (5.17) and Point Pinole (4.85). This is likely to be driven by significantly higher oyster mortality observed at Point Pinole during routine monitoring and restoration efforts. Interestingly Ruminococcus, Streptococcus, Staphylococcus, Prevotella, Porphyromonas, Parvimonas, Neisseria, Lactococcus, Haemophilus, Fusobacterium, Dorea, Clostridium, Campylobacter, Bacteroides, and Akkermansia were positively associated with the biofilm. Yet we have limited understanding of their beneficial and/or detrimental implications to oyster growth and survival. By unraveling the intricate relationships in microbial composition across an oyster reef, our study contributes to advancing the knowledge needed to support effective oyster reef conservation and restoration efforts.

microbiology↗