Universal Metabarcodes (16S & 18S) from the GRADIENTS 2 Cruise (SCOPE-Gradients)

This metabarcoding dataset is derived from PCR amplification of marine plankton-derived DNA from the 2017 SCOPE-Gradients cruise, from DNA provided by the Zehr Lab. Samples were taken and extracted by Mary R. Gradoville, Brittany Stewart, and Esther Wing (Zehr lab). 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 collected by filtering whole seawater (0.7-4 L) collected at sea using the ships uncontaminated underway system (7 m) and the rosette sampler (15-125 m) and filtered onto 0.2um 25mm Supor membranes filter during the 2017 and 2019 SCOPE-Gradients cruises. Samples were collected at sea by Mary R. Gradoville, Brittany Stewart, and Esther Wing (Zehr lab). Details on 2017 sample collection and DNA extraction are provided in Gradoville et al. 2020; 2010 cruise samples were extracted using the same methodology. Samples were stored at -80C until analysis. DNA was isolated and purified by the Zehr lab using the extraction method described by (Gradoville et al., 2020). DNA was then amplified, and sequenced by Jesse McNichol, Yubin Raut, & Bruce Yanpui Chan (Fuhrman Lab, USC) in 2020 and 2021. This DNA was amplified and sequenced by Jesse McNichol, Yubin Raut, & Bruce Yanpui Chan (Fuhrman Lab, USC) in 2020 and 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).