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

Abstract

Oyster reefs and beds provide crucial ecosystem services, including water filtration, coastal protection, and habitat provision for marine species. However, these habitats face significant threats from climate change and anthropogenic stressors. To address these challenges, numerous oyster restoration initiatives have been undertaken globally. Intertidal microbial communities, comprising diverse bacteria, archaea, and unicellular eukaryotes, drive key biogeochemical processes, but remain poorly understood in ecosystems targeted for oyster restoration. We investigated the microbiome associated with the Olympia oyster (Ostrea lurida), a key restoration target in the western USA, by characterizing microbial abundance and diversity in sediment, oyster-associated biofilm, and oysters at four sites in San Francisco Bay. Our findings revealed distinct microbial assemblages in oysters and sediment compared to biofilm. Diversity, measured by the Shannon index, was highest at Heron’s Head (5.47), followed by Brickyard Park (5.35), Dunphy Park (5.17), and Point Pinole (4.85). Notably, microbes Ruminococcus, Streptococcus, Staphylococcus, Prevotella, Porphyromonas, Parvimonas, Neisseria, Lactococcus, Haemophilus, Fusobacterium, Dorea, Clostridium, Campylobacter, Bacteroides, and Akkermansia were positively associated with biofilm collected from hard surfaces where oysters were attached at most sites. Potential implications of these microbial associations for oyster growth, survival, and interactions with environmental factors remain largely unexplored. Future research is warranted on culturing specific microbes to assess their functions and investigating environmental and ecological drivers of microbial diversity to determine relationships indicative of oyster health and potential for enhancing oyster recruitment.