Discovery of prevalent Ciliophora, Discoba and Copepoda protists in deep sea water by in situ nucleotide extraction

Abstract

Abstract Deep-sea eukaryotic microorganisms play an important role in degradation of deep-sea organic matter and geochemical cycle of various elements. However, whether sampling methods can affect detection of eukaryotic microbial community under high hydrostatic pressure in deep ocean remains a question. In this study, we compared traditional water sampling method using a Niskin bottle, an in situ microbial filtration and fixation method (ISMIFF) and a multiple in situ nucleic acid collection method (MISNAC) to exhibit differences in the community structures in the samples collected at ~ 590-3,100 m depths in the South China Sea (SCS). The MISNAC samples were separated into lysed cells on filtration membranes in a chamber and subsequent precipitated DNA attached on silica resin columns connected to the chamber. The classification and biodiversity indices of 18S rDNA Illumina sequencing reads from V9 variation region showed that the diversity of samples collected by MISNAC DNA absorption columns was much higher than that of other samples. More importantly, the relative abundance of Ciliophora, Copepoda and Diplonemea in the MISNAC adsorption column samples was significantly higher than that in the others, while Retaria were dominant in the MISNAC membrane samples. This indicates that MISNAC columns might in situ collect more DNA for the naked protists, while Retaria with a carbonate shell were more likely retained on the membrane. We therefore report a group of dominant protists in deep-sea water column, which have been missed by previous sampling methods probably due to environmental changes that may damage the naked protist cells.