16S and 18S rRNA metabarcoding of water, rock and Rimicaris exoculata and chacei symbiont samples from TAG and Snake Pit vent fields, BICOSE2 oceanographic cruise (2018), French REMIMA deep-sea mining exploration contract.
During the reproductive period, Rimicaris exoculata thermal shrimp exhibit a marked spatial segregation along hydrothermal fluid emissions: dense aggregations composed predominantly of females with a few males occur close to vent fluid sources, while most males are found in a dispersed distribution at the periphery of vent fields. This raises questions as to whether the different habitats represent specific microbial niches, how environmental parameters or substrate type may influence these niches, and whether the spatial structuring of shrimps impacts the symbiotic communities within their different compartments, as assessed through a first metabarcoding-based approach. Samples were collected at two hydrothermal vent fields along the Mid-Atlantic Ridge (MAR), TAG and Snake Pit, during the BICOSE2 cruise (2018) using the HOV Nautile. Both dispersed Rimicaris exoculata males from peripheral areas and males and females from dense aggregations were sampled. DNA was extracted from symbiont-bearing tissues (cephalothorax, midgut tube, and foregut) using the NucleoSpin Soil kit (Macherey-Nagel), yielding 54 extracts. In addition, 9 DNA extracts from equivalent tissues of Rimicaris chacei collected at the Lucky Strike vent field (MoMAR 2020 cruise), together with four negative controls, were processed following the same protocol. All samples were subsequently amplified and sequenced with primers targeting the symbiont 16S rRNA gene. Samples from the shrimp habitat were collected : 2 samples from hydrothermal rock located near Rimicaris exoculata shrimp aggregates at the TAG site and 19 seawater samples from the vicinity of distinct habitats of Rimicaris exoculata and Rimicaris chacei both at the TAG and Snake Pit vent fields. DNA from both rock and water samples was extracted using the NucleoSpin Soil kit (Macherey-Nagel) and amplified in several replicates with different primers targeting bacterial 16S rRNA gene, archaeal 16S rRNA gene, and finally metazoan 18S rRNA gene. This resulted in 17 libraries of rock-associated communities and 144 water-associated communities including 9 negative control libraries. All samples were sequenced using the Illumina MiSeq platform (short-read technology) and performed by the Genotoul sequencing platform.