Universal Metabarcodes (16S & 18S) from FRAM STRAIT

This metabarcoding dataset is derived from PCR amplification of marine plankton-derived DNA that was collected from Remote Access Samplers in the West Spitsbergen Current, central Fram Strait, and East Greenland Current within the FRAM / HAUSGARTEN Observatory (Soltwedel et al., 2016). Metabarcoding reads were generated using a single primer set that simultaneously amplifies both 16S and 18S genes, though users should note that specific bioinformatic procedures are required to recover and analyze 18S sequences (see: https://github.com/jcmcnch/eASV-pipeline-for-515Y-926R).This dataset is part of a larger collaborative project called GRUMP (Global rRNA Universal Metabarcoding of Plankton) which has produced metabarcoding data from worldwide cruises from the same universal primer set (Parada et al., 2016, doi:10.1111/1462-2920.13023) on unfractionated samples (> 0.2 um). This primer set perfectly matches the rRNA of most surface ocean organisms, including eukaryotic and metazoan 18S (McNichol et al., 2021, doi:10.1128/msystems. 00565-21). As a result, the sequences here represent a full-community profile of each water sample with the same denominator and the same primer set (Yeh et al., 2021, doi:10.1111/1462-2920.15553).Notes for data users:Only limited environmental covariate data has been uploaded with the raw sequences. More data will be made available at the locations specified below.Final, processed data (16S + 18S relative abundances with taxonomic annotations) will be provided through the Simons Foundation CMAP (Collaborative Marine Atlas Project; https://simonscmap.com/) alongside environmental covariates. If you do not wish to reanalyze these data, we suggest using this data product.Bioinformatic intermediates, and scripts are stored at OSF in a single umbrella repository (https://osf.io/57dpa/). This is a useful place for those who might wish to analyze only a subset of our data (e.g. 18S or 16S only) or who wish to understand the bioinformatic processing in greater detail.Additional updates (e.g. linking additional environmental covariates to metabarcoding data) will be provided at our github page (https://github.com/jcmcnch/Global-rRNA-Univeral-Metabarcoding-of-Plankton). This is a good place to check for the latest updates to the GRUMP project.Specific notes for this dataset:This dataset contains relative abundance and taxonomic information for planktonic organisms in whole seawater, collected via Remote Access Samplers on seafloor moorings operated within the FRAM/HAUSGARTEN Observatory (Soltwedel et al., 2016), covering the West Spitsbergen Current, central Fram Strait, and East Greenland Current/Marginal Ice Zone from July 2016 - August 2017 in programmed intervals (weekly to monthly). 700 mL filtered onto 0.2 um Sterivex cartridges, and stored at -20C until DNA extraction with PowerWater kit (QIAGEN, Germany). 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 ((Bolyen et al., 2019; Callahan 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).PCR amplification and sequencing:5' master mix (product 2200400/2200410) was used for DNA amplification with the 515Y (5'-GTGYCAGCMGCCGCGGTAA) and 926R (5'-CCGYCAATTYMTTTRAGTTT) primers with Illumina adapters and barcodes pre-ligated (as noted here: dx.doi.org/10.17504/protocols.io.vb7e2rn). Sequencing was done at Tufts University Medical School using HiSeq Rapid Run technology (2x250 bp).