GO_SHIP_P16NS_2005_2006_515Y_926R

This dataset contains relative abundance and taxonomic information for planktonic organisms collected by filtering whole seawater (~1L P16S, ~2L P16N) collected at various depths onto 0.2 µm 25mm Supor filter filters during two latitudinal transects of the Pacific Ocean (P16S[http://bcodata.whoi.edu/CLIVAR_AEROSOL/CLIVAR_P16S_2005ado.pdf], P16N[http://bcodata.whoi.edu/CLIVAR_AEROSOL/CLIVAR_P16N_2006ado.pdf]) in 2005/2006. Samples were collected at sea by Elisa Halewood and Meredith Meyers (Carlson Lab, UCSB) as part of the GO-SHIP repeat hydrography program (then known as CLIVAR). Samples were stored as partially extracted lysates in sucrose lysis buffer at -80°C until analysis. DNA was isolated, purified, amplified, and sequenced by Jesse McNichol, Yubin Raut, & Bruce Yanpui Chan (Fuhrman Lab, USC) in 2020 and 2021.

Relative abundance information was generated by PCR amplification of extracted DNA using a universal primer pair that amplifies both 16S and 18S simultaneously (515Y/926R) and subsequent denoising to amplicon sequence variants (ASVs) using a custom analysis pipeline based on qiime2 and DADA2 (Callahan et al., 2016; Bolyen et al., 2016; https://github.com/jcmcnch/eASV-pipeline-for-515Y-926R). The final dataset contains merged abundance information from both 16S and 18S ASVs using the same denominator. Merging of 16S and 18S ASV tables was accomplished using a dataset-specific correction factor that adjusts for a known bias against longer 18S sequences during Illumina sequencing (Yeh et al., 2021). 

Organisms quantified range from small Bacteria and Archaea to protists (photosynthetic and non-photosynthetic) as well as larger planktonic organisms such as Arthropods, Salps, and Jellyfish. Please note that some organisms will be quantified more than once using this approach, such as eukaryotic algae for which we have ASV information from both chloroplast 16S and nuclear 18S.

This dataset also contains several environmental covariates, including nutrient and CTD data derived from publicly-accessible GO-SHIP records (CLIVAR and Carbon Hydrographic Data Office; https://cchdo.ucsd.edu/), DNA concentrations from extractions (a proxy for community biomass), community 18S fraction (a measure of whether the sample is prokaryote- or eukaryote-dominated), as well as manual assignments of whether a sample was from the euphotic or non-euphotic zone.

Raw reads are available on NCBI. Relevant scripts, bioinformatic intermediates, and output files are available on OSF and github as part of the Global rRNA Metabarcoding of Plankton (GRUMP) umbrella project. The github page (https://github.com/jcmcnch/Global-rRNA-Univeral-Metabarcoding-of-Plankton) contains links to all relevant underlying data, including processing steps used to link environmental covariates with sequencing data, as well as dataset-specific correction factors for merging 16S and 18S data.