Unveiling the specific microbiome of bivalves: insights into host microbial dynamics and pathogen interactions in a shared environment

Introduction The microbiome is crucial for the health and resilience of marine species; however, in most cases its complexity and host-specific dynamics remain poorly understood. Methods This study provides a multi-year and multi-seasonal analysis of eukaryotic and prokaryotic microbiomes in three ecologically important bivalves - mussels ( Mytilus galloprovincialis ), clams ( Ruditapes philippinarum ), and cockles ( Cerastoderma edule ) – coexisting within the same coastal ecosystem in the Rı́a of Vigo (NW Spain). Results High-throughput sequencing of the V9 region of 18S rRNA and the V4 region of 16S rRNA genes revealed distinct microbiomes for each bivalve species, demonstrating significant host specificity and a stable microbial composition across seasons. Prevalent eukaryotic parasites, including Mytilicola intestinalis in mussels and trematodes such as Bucephalus minimus in cockles, were identified. Perkinsus olseni and Marteilia cochilia , protozoans associated with bivalve mortality and ecosystem disruption under environmental stress, were also detected. Endozoicomonas and Vibrio dominated the prokaryotic communities of all the three bivalves; however, species-specific bacteriomes were observed due to the presence of other distinct taxa. A meta-analysis comparing bivalve and environmental microbiomes, revealed that despite the microbial diversity in the water column and sediment, each bivalve maintained its own stable and specific microbiome, exceeding the habitat effect. We identified Vibrio, Woeseia and Lutimonas as keystone genera that shape these microbiomes through both competitive and cooperative interactions. Functional predictions suggest that mutualistic relationships enhance host health through metabolic and defensive roles, including the biosynthesis of secondary metabolites. Conclusion These findings demonstrate that host identity is the primary determinant of bivalve microbiome composition, with different keystone taxa that could serve as biomarkers for ecosystem and health monitoring in Rı́a de Vigo.