Bivalve Gut Microbiome Responses to Sediment Characteristics and Anthropogenic Activities in Cerastoderma edule (Linnaeus, 1758)

Abstract

Abstract Estuaries are dynamic ecosystems influenced by fluctuating environmental conditions and sediment-associated contamination, which may affect host-associated microbiomes. This study investigated the gut microbiome of the bivalve Cerastoderma edule across three estuarine sites differing in anthropogenic pressure. Bacterial 16S rRNA and fungal ITS metabarcoding data were integrated with sediment physicochemical parameters to assess spatial and seasonal variation in gut microbial diversity and composition. Bacterial communities showed clear differences among sites and seasons, with stronger variation in areas characterized by higher organic matter and trace metal concentrations. Fungal communities also varied among samples, although their interpretation was limited by the high proportion of unassigned ITS taxa. Multivariate analyses indicated associations between gut microbial composition and sediment parameters, including organic matter, salinity, and trace metals such as mercury (Hg), zinc (Zn), and lead (Pb). Putative bacterial functional profiles were inferred from taxonomic data using FAPROTAX, suggesting potential involvement in nitrogen, sulfur, and carbon cycling, as well as organic compound degradation. Nevertheless, it is important to note that these functional predictions should be interpreted as indicators of potential metabolic capacity rather than direct evidence of activity. Ultimately, these findings demonstrate that the C. edule gut microbiome has strong potential as a complementary tool for the assessment of estuarine environmental conditions and host–environment interactions.