Host-Associated Microbial Diversity and Microhabitat Differentiation in Depuration Biodeposits and Shell-Wash Particulates of the Bivalve Molluscs Ruditapes philippinarum and Paratapes undulatus

Filter-feeding bivalves can reshape particle-associated microbial communities, yet differences between depuration biodeposits and shell-associated particulates remain unclear. We compared Ruditapes philippinarum and Paratapes undulatus using a paired 2 × 2 design (host species × sample type) and PacBio full-length 16S rRNA gene sequencing. R. philippinarum-associated samples showed higher Shannon diversity than P. undulatus-associated samples, whereas Chao1 richness differences were not significant after multiple-comparison correction. Genus-level NMDS clearly separated the four groups (stress = 0.011). In repeated-measures PERMANOVA of ASV-level Bray–Curtis dissimilarities, host species accounted for 56.1% of the observed variation, sample type for 13.7%, and their interaction for 17.1%. However, none reached statistical significance under the constrained exact permutation scheme (p = 0.100, 0.0625, and 0.100, respectively). Multivariate dispersion differed among groups (p = 0.012), with the greatest dispersion in R. philippinarum depuration biodeposits. R. philippinarum-associated communities exhibited broader multi-genus assemblages, whereas P. undulatus depuration biodeposits contained prominent Fusibacter and Culicoidibacter, and its shell-wash particulates were dominated by Arcobacter. These findings provide a microbial community baseline to guide future investigations into extracellular polymeric substance (EPS) production and the mechanisms underlying bioflocculation in bivalve-associated particulate systems.