Characterizing organisms from three domains of life with universal primers from throughout the global ocean

Characterizing organisms from three domains of life with universal primers from throughout the global ocean

Abstract We introduce the Global rRNA Universal Metabarcoding Plankton database (GRUMP), which consists of 1194 samples that were collected from 2003–2020 and cover extensive latitudinal and longitudinal transects, as well as depth profiles in all major ocean basins. DNA from unfractionated (>0.2...

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Main Authors: Jesse McNichol, Nathan L. R. Williams, Yubin Raut, Craig Carlson, Elisa R. Halewood, Kendra Turk-Kubo, Jonathan P. Zehr, Andrew P. Rees, Glen Tarran, Mary R. Gradoville, Matthias Wietz, Christina Bienhold, Katja Metfies, Sinhué Torres-Valdés, Thomas Mock, Sarah Lena Eggers, Wade Jeffrey, Joseph Moss, Paul Berube, Steven Biller, Levente Bodrossy, Jodie Van De Kamp, Mark Brown, Swan L. S. Sow, E. Virginia Armbrust, Jed Fuhrman
Format: Article
Language:English
Published: Nature Portfolio 2025-07-01
Series:Scientific Data
Online Access:https://doi.org/10.1038/s41597-025-05423-9
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Summary:Abstract We introduce the Global rRNA Universal Metabarcoding Plankton database (GRUMP), which consists of 1194 samples that were collected from 2003–2020 and cover extensive latitudinal and longitudinal transects, as well as depth profiles in all major ocean basins. DNA from unfractionated (>0.2 µm) seawater samples was amplified using the 515Y/926 R universal three-domain rRNA gene primers, simultaneously quantifying the relative abundance of amplicon sequencing variants (ASVs) from bacteria, archaea, eukaryotic nuclear 18S, and eukaryotic plastid 16S. Thus, the ratio between taxa in one sample is directly comparable to the ratio in any other GRUMP sample, regardless of gene copy number differences. This obviates a problem in prior global studies that used size-fractionation and different rRNA gene primers for bacteria, archaea, and eukaryotes, precluding comparisons across size fractions or domains. On average, bacteria contributed 71%, eukaryotes 19%, and archaea 8% to rRNA gene abundance, though eukaryotes contributed 32% at latitudes >40°. GRUMP is publicly available on the Simons Collaborative Marine Atlas Project (CMAP), promoting the global comparison of marine microbial dynamics.
ISSN:2052-4463

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