Shallow-water Mussels (<i>Mytilus galloprovincialis</i>) Adapt to Deep-Sea Environment Through Transcriptomic and Metagenomic Insights

Recent studies have unveiled the deep sea as a rich biosphere, populated by species descended from shallow-water ancestors post-mass extinctions. Research on genomic evolution and microbial symbiosis has shed light on how these species thrive in extreme deep-sea conditions. However, early adaptation stages, particularly the roles of conserved genes and symbiotic microbes, remain inadequately understood. This study examined transcriptomic and microbiome changes in shallow-water mussels Mytilus galloprovincialis exposed to deep-sea conditions at the Site-F cold seep in the South China Sea. Results reveal complex gene expression adjustments in stress response, immune defense, homeostasis, and energy metabolism pathways during adaptation. After 10 days of deep-sea exposure, shallow-water mussels and their microbial communities closely resembled those of native deep-sea mussels, demonstrating host and microbiome convergence in response to adaptive shifts. Notably, methanotrophic bacteria, key symbionts in native deep-sea mussels, emerged as a dominant group in the exposed mussels. Host genes involved in immune recognition and endocytosis correlated significantly with the abundance of these bacteria. Overall, our analyses provide insights into adaptive transcriptional regulation and microbiome dynamics of mussels in deep-sea environments, highlighting the roles of conserved genes and microbial community shifts in adapting to extreme environments.近年来的研究揭示，深海是一个物种丰富的生物圈，其栖息物种均为大灭绝事件后由浅海祖先演化而来的类群。针对基因组演化与微生物共生的研究，已阐明这些物种如何在极端深海环境中存活繁衍。然而，对于其早期适应阶段，尤其是保守基因与共生微生物所发挥的作用，目前仍缺乏充分的认知。本研究以浅海贻贝（Mytilus galloprovincialis）为研究对象，将其暴露于南海F位点冷泉的深海环境中，分析其转录组与微生物组的变化特征。研究结果显示，在适应过程中，贻贝在应激响应、免疫防御、稳态维持以及能量代谢通路中出现了复杂的基因表达调控变化。经10天深海暴露后，实验用浅海贻贝及其微生物群落，与本土深海贻贝及其菌群已高度相似，这表明宿主与微生物组在适应性转变过程中出现了趋同响应。值得注意的是，作为本土深海贻贝关键共生体的甲烷氧化细菌，在暴露实验的贻贝中成为了优势类群。宿主中参与免疫识别与胞吞作用的基因，与这类细菌的丰度呈现显著相关性。综上，本研究解析了贻贝在深海环境中的适应性转录调控与微生物组动态变化，阐明了保守基因与微生物群落转变在物种适应极端环境过程中的关键作用。