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.