Metabarcoding of Cell-Free rRNA from Surface and Deep Seawater in Muroto

Metabarcoding of Cell-Free rRNA from Surface and Deep Seawater in Muroto aimed to investigate the ecology of microeukaryotes in the deep ocean. Seawater samples were collected seasonally between September 2023 and April 2024 from both surface (0.5 m) and mesopelagic (320 m) layers at a coastal station in Muroto, Kochi, Japan. Specifically, six samples were used for cell-free size 18S rRNA metabarcoding, six for the corresponding cell-particle size 18S rRNA metabarcoding, and six for the corresponding cell-particle size 18S rDNA metabarcoding. Here, we provide the raw sequencing data. The sequencing reads were processed to generate amplicon sequence variants (ASVs). This dataset provides insights into extracellular rRNA dynamics and particle-associated microeukaryotic diversity in marine environments.