Metagenomes of symbionts from the cephalothorax of juvenile shrimps Rimicaris exoculata and R. chacei, BICOSE3 cruise, 2023, BIOcean5D project
The cephalothoracic cavity of adult hydrothermal vent shrimps Rimicaris exoculata and Rimicaris chacei is colonized by dense and diverse communities of chemosynthetic symbionts. Although both shrimp species host similar symbiotic assemblages, they exhibit markedly different population densities, fine-scale distribution patterns, and feeding regimes, as well as differences in post-colonization morphological modifications leading to the adult stage. A previous study (Gueganton et al., 2024) revealed the presence of cephalothoracic symbiotic lineages as early as the first juvenile stages in both species, using metabarcoding, fluorescence in situ hybridization (FISH), and scanning electron microscopy (SEM). These analyses showed an overall diversity comparable to that observed in adults. However, tissue colonization appears to be a progressive process, increasing in density throughout juvenile development towards adulthood. A new study was therefore conducted using a metagenomic approach to more precisely characterize the structure and dynamics of the symbiotic communities in both species across juvenile stages, in order to determine whether the same metabolic or ecological functions are maintained throughout the establishment of the symbiosis. To this end, juvenile specimens of both R. exoculata and R. chacei were collected during the BICOSE3 cruise (2023) from two hydrothermal vent fields along the Mid-Atlantic Ridge (MAR)  TAG and Snake Pit  using the HOV Nautile. Triplicate samples were selected for each juvenile stage: A, B, and sub-adult C for R. exoculata, and A and B for R. chacei. Cephalothorax-associated DNA (branchiostegite plate + scaphognathite + exopodite) was extracted using the Macherey-Nagel NucleoMag DNA Microbiome kit, resulting in a total of 30 DNA extracts. Metagenomic sequencing was performed by Integragen on an Illumina NovaSeq X platform using short-read technology.