In situ evidence of tiered adaptations buffering a chemosynthetic clam holobiont against environmental sulfide fluctuations.

Deep-sea holobionts adapt to extreme environmental fluctuations, but the molecular mechanisms underlying resilience remain poorly understood. We investigated the vesicomyid clam Archivesica marissinica and its sulfur-oxidizing symbionts during sulfide shortage via in situ transplant experiments at the Haima cold seep. Transplanting clams to sulfide-depleted conditions (moderate at HM-3 and severe at HM-2) revealed distinct response patterns of host-symbiont interaction. Symbionts may mitigate sulfide loss by shifting from sulfide oxidation to thiosulfate oxidation, supported by thiosulfate generated through host sulfide detoxification pathways. Notably, symbiont abundance remained stable under moderate sulfide shortage (HM-3), accompanied by down-regulation of host endosomal maturation and fusion with lysosomes, potentially limiting symbiont turnover. Conversely, severe sulfide shortage (HM-2) was associated with up-regulation of lysosomal pathways and lower symbiont abundance. These results demonstrate tiered molecular adaptations-metabolic flexibility and shifts in symbiont dynamics-enabling holobiont resilience to spatially heterogeneous sulfide availability in deep-sea seeps, supporting ecosystem stability.