While chemosymbiosis offers deep-sea bathymodioline mussels a critical metabolic advantage, this dependence makes them vulnerable when removed from their native environment, and their early post-recovery dynamics remain poorly resolved. We maintained adult Gigantidas haimaensis collected from the Haima cold seep at atmospheric pressure and sampled gill tissues at 0, 3 and 9 h after collection. Coupled 16S rRNA amplicon sequencing and RNA-Seq were used to follow changes in the gill microbiota, host transcription and descriptive temporal covariation. Methyloprofundus remained the dominant bacterial genus throughout the experiment, whereas Ca. Vesicomyosocius, the SUP05 cluster, and operational taxonomic units (OTUs) assigned to Vibrio and Pseudoalteromonas had higher relative abundances at 9 h in the descriptive analysis and exhibited positive temporal covariation. RNA-Seq showed a stronger transcriptional shift at 3 h than at 9 h. Stress-related genes, including HSP70, HSP105, Toll-like receptors, fibrinogen-related proteins, dual oxidase, thioredoxin-system genes, ferritin, taurine transporter and sulfide:quinone oxidoreductase, changed markedly, while energy-consuming ribosome biogenesis was suppressed to conserve energy under combined physical and nutritional stressors. The temporal patterns of Ca. Vesicomyosocius and other low-abundance bacterial signals coincided with broad host stress and immune and metabolic transcriptional changes; gene-level microbiome-transcriptome associations were exploratory and did not survive false-discovery-rate (FDR) correction. These results document rapid short-term transcriptional and microbiome changes after recovery, while their causal drivers and consequences require controlled validation.
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