Single Cell RNA-seq of deep-sea tube worm Paraescarpia echinospica

The deep-sea vestimentiferan tubeworms that rely on chemoautotrophic endosymbionts as sole carbon source have been one of the focus of symbiosis studies for decades. However, due to the complexity of the symbiotic tissue (a specialised organ called trophosome) and limitations in methodology, the detailed molecular mechanisms of interaction between the tubeworms and their endosymbionts have been challenging to elucidate. Our present study used an innovative approach for in situ single-cell fixation of deep-sea animals, specifically on the cold-seep vestimentiferan tubeworm Paraescarpia echinospica. By utilising single-cell RNA-seq and detailed characterisation of key genes/proteins/metabolites from both the tubeworm host and endosymbiont, our results revealed two distinct metabolic "micro-niches" maintained by the host trophosome. These micro-niches are each trophosome lobule's oxygenated periphery region and the hypoxic centre region. This surprising arrangement spontaneously divide the endosymbionts into two subpopulations, one conducting autotrophic carbon fixation and digested by the host for nutrients, and another conducting anaerobic denitrification to help the host remove ammonia waste.

以化能自养内共生体（chemoautotrophic endosymbionts）作为唯一碳源的深海管栖蠕虫（vestimentiferan tubeworms），数十年来一直是共生研究的核心焦点之一。然而，由于共生组织——一种被称为营养体（trophosome）的特化器官——的复杂性，以及研究方法的局限性，阐明管栖蠕虫与其内共生体之间相互作用的精细分子机制一直颇具挑战。本研究针对深海动物开发了一种创新的原位单细胞固定方法，并将其应用于冷泉（cold-seep）生境中的管栖蠕虫物种棘刺拟烟囱管虫（Paraescarpia echinospica）。通过整合单细胞RNA测序（single-cell RNA-seq）技术，并对宿主管栖蠕虫与内共生体的关键基因、蛋白质及代谢物开展细致表征，本研究结果揭示了宿主营养体所维持的两种截然不同的代谢微生态位。这两种微生态位分别对应每个营养体小叶的含氧外周区域与低氧中心区域。这种出人意料的空间排布将内共生体自发划分为两个亚群：一类进行自养碳固定，并被宿主消化以获取营养；另一类则通过厌氧反硝化作用协助宿主清除氨类废物。