FISH, a new tool for in situ preservation of RNA in tissues of deep-sea mobile fauna

Abstract

Accessing the metabolic functioning of deep-sea animals in situ remains a technological challenge as the recovery time of samples is incompatible with the short lifespan of such molecules as mRNAs. Tools able to preserve RNA in situ exist, but they are incompatible with the study of mobile fauna. Here, we describe a new sampling tool, named FISH (fixer in situ of homogenized substrates), implemented on a submersible and equipped with a number of new specific features to collect and preserve in situ tissue of mobile fauna. Connected to the suction pump of a submersible, the FISH sampler incorporates a sampling bowl to which two bottles of a preservative reagent are attached, a suction hose, and a support containing a motor connected to the sampling bowl by a magnetic coupling system. We used the deep-sea hydrothermal shrimp Rimicaris exoculata from the Mid-Atlantic Ridge as a model to test the suitability of our new tool. The FISH sampler was compared to two other sampling methods, which use a metatranscriptomic approach targeting microbial communities associated with cephalothorax symbionts. RNA quality, gene assignment, and taxonomic and gene function diversity showed differences between in situ and on-board preservation of tissues. Of the alternative sampling methods tested, the suction sampler was clearly not suitable for RNA-based studies, while pressurized recovery showed results closer to the sample quality obtained with FISH sampling. The FISH sampler has therefore demonstrated to be a cost-effective and reliable tool to efficiently preserve RNA recovered from deep-sea environments.