Microbial diversity by 16S and 18S RNA analysis during Atlantic Meridional Transect cruise AMT28 (JR18001) from September to October 2018.

This dataset contains microbial diversity by 16S and 18S RNA analysis of samples collected between September and October 2018 during cruise AMT28. Discrete CTD water samples were taken from surface and Deep Chlorophyll Maximum (DCM) depths and filtered through a 0.22 μm Sterivex filter by Cecilia Liszka in the cold constant temperature room. After filtration the Sterivex filter was sealed at both ends with Parafilm and stored frozen at -80°C. Ribosomal RNA (rRNA) was extracted according to the method described in the Direct-zol RNA MiniPrep (Zymo Research) - Samples were prepared by adding TRI Reagent. The prepared sample was then added to a Zymo-Spin IC Column, RNA in the sample binds to the column. The columns were then washed to remove impurities, ensuring that only RNA remained bound. Finally, the purified RNA was eluted from the column. Minor modifications were made to the published protocol which included using IC Columns from the MicroPrep kit instead of the MiniPrep, removal of the filter from the Sterivex case and additional centrifugation (30 s, 12000 rpm) at the end of the process. PCR was performed by specific primers: primers that flank the V4-V5 hypervariable region of bacterial 16S rRNAs (515F/907R) and primers that flank the V4 hypervariable region of eukaryotes 18S rRNAs (528F/706R) connecting with barcodes. To minimize effects of random sequencing errors, sequences that did not perfectly match the PCR primer at the beginning of a read were eliminated. Less than 0.01% of the reads were removed during the sequencing data filtration. Libraries was performed on a paired-end Illumina platform to generate 250bp paired-end raw reads. In order to study the microbial community composition in each sample, Operational Taxonomic Units (OTUs) were obtained by clustering with 97% identity on the Effective Tags of all samples, and then identified.