Intricate chemosymbiosis in a widespread shallow-water thyasirid clam

Chemosynthetic symbioses between animals and bacteria are common in marine ecosystems, but the symbioses in shallow-water thyasirid clams inhabiting suboxic sediments remain understudied despite their widespread occurrence. Here, we report that the shallow-water thyasirid clam <i>Thyasira tokunagai</i>, dominant in Yellow Sea sediments, harbors sulfur-oxidizing <i>Sedimenticola</i> symbionts in pouch-like structures on the gill; the symbionts exhibit highly consistent genomic content and functionality across the region. Two phylotypes of symbionts are present, differing by a single base in the 16<i>S</i> rRNA gene while sharing key functional genes with minimal differences. Spatial metabarcoding analyses of gills showed that individuals also vary in the level of spatial heterogeneity concerning the two phylotypes. These symbionts exhibit active Calvin cycle gene expressions and close-knit host-symbiont metabolic integration. Furthermore, we estimated the capacity of dissolved inorganic carbon assimilation in the live holobiont by radiocarbon tracing (29.3 ± 8.7 nmol C·clam^-1·day^-1). Our findings provide the basis for understanding chemosymbiosis in thyasirid clams, highlight the potential of <i>T. tokunagai</i> as a model for studying symbiosis, and underscore the ecological significance of shallow-water chemosymbioses overall.