Shinkaia crosnieri is an invertebrate that inhabits an area around deep-sea hydrothermal vents in the Okinawa Trough in Japan by harboring episymbiotic microbes as the primary nutrition. To reveal physiology and phylogenetic composition of the active episymbiotic populations, metatranscriptomics is expected to be a powerful approach. However, this has been hindered by substantial perturbation (e.g., RNA degradation) during time-consuming retrieval from the deep sea. Here, we conducted direct metatranscriptomic analysis of S. crosnieri episymbionts by applying in situ RNA stabilization equipment. As expected, we obtained RNA expression profiles that were substantially different from those obtained by conventional metatranscriptomics (i.e., stabilization after retrieval). The episymbiotic community members were dominated by three orders, namely, Thiotrichales, Methylococcales, and Campylobacterales, and the Campylobacterales members were mostly dominated by the Sulfurovum genus. At a finer phylogenetic scale, the episymbiotic communities on different host individuals shared many species, indicating that the episymbionts on each host individual are not descendants of a few founder cells but are horizontally exchanged. Furthermore, our analysis revealed the key metabolisms of the community: two carbon fixation pathways, a formaldehyde assimilation pathway, and utilization of five electron donors (sulfide, thiosulfate, sulfur, methane, and ammonia) and two electron accepters (oxygen and nitrate/nitrite). Importantly, it was suggested that Thiotrichales episymbionts can utilize intercellular sulfur globules even when sulfur compounds are not usable, possibly also in a detached and free-living state.

中文翻译：

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原位 RNA 稳定的宏转录组学直接和全面揭示深海蹲龙虾的外共生微生物群落

Shinkaia crosnieri是一种无脊椎动物，栖息在日本冲绳海槽的深海热液喷口周围，以附生共生微生物为主要营养物质。为了揭示活跃的外共生群体的生理学和系统发育组成，宏转录组学有望成为一种强大的方法。然而，这受到了从深海耗时的回收过程中的大量扰动（例如，RNA 降解）的阻碍。在这里，我们通过原位应用对S. crosnieri 外共生体进行了直接宏转录组学分析RNA稳定设备。正如预期的那样，我们获得的 RNA 表达谱与通过传统宏转录组学（即检索后的稳定性）获得的那些谱显着不同。该episymbiotic社区成员是由三个数量级，即主导Thiotrichales，Methylococcales和Campylobacterales和Campylobacterales成员主要由主导Sulfurovum属。在更精细的系统发育尺度上，不同宿主个体上的外共生群落共享许多物种，表明每个宿主个体上的外共生体不是少数始祖细胞的后代，而是水平交换的。此外，我们的分析揭示了群落的关键代谢：两条碳固定途径、一条甲醛同化途径以及五种电子供体（硫化物、硫代硫酸盐、硫、甲烷和氨）和两种电子受体（氧和硝酸盐/亚硝酸盐）的利用）。重要的是，有人提出即使硫化合物不可用，也可能处于分离和自由生活状态时，Thiotrichales 外共生体也可以利用细胞间硫球。