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

McNichol, J; Williams, NLR; Raut, Y; Carlson, C; Halewood, ER; Turk-Kubo, K; Zehr, JP; Rees, AP; Tarran, G; Gradoville, MR; Wietz, M; Bienhold, C; Metfies, K; Torres-Valdés, S; Mock, T; Eggers, SL; Jeffrey, W; Moss, J; Berube, P; Biller, S; Bodrossy, L; Van De Kamp, J; Brown, M; Sow, SLS; Armbrust, EV; Fuhrman, J

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

McNichol, J Williams, NLR Raut, Y Carlson, C Halewood, ER Turk-Kubo, K Zehr, JP Rees, AP Tarran, G Gradoville, MR Wietz, M Bienhold, C Metfies, K Torres-Valdés, S Mock, T Eggers, SL Jeffrey, W Moss, J Berube, P Biller, S Bodrossy, L Van De Kamp, J Brown, M Sow, SLS Armbrust, EV Fuhrman, J

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Publisher:: Springer Nature
Publication Type:: Journal Article
Citation:: Sci Data, 2025, 12, (1), pp. 1078
Issue Date:: 2025-07-01

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Field	Value	Language
dc.contributor.author	McNichol, J
dc.contributor.author	Williams, NLR
dc.contributor.author	Raut, Y
dc.contributor.author	Carlson, C
dc.contributor.author	Halewood, ER
dc.contributor.author	Turk-Kubo, K
dc.contributor.author	Zehr, JP
dc.contributor.author	Rees, AP
dc.contributor.author	Tarran, G
dc.contributor.author	Gradoville, MR
dc.contributor.author	Wietz, M
dc.contributor.author	Bienhold, C
dc.contributor.author	Metfies, K
dc.contributor.author	Torres-Valdés, S
dc.contributor.author	Mock, T
dc.contributor.author	Eggers, SL
dc.contributor.author	Jeffrey, W
dc.contributor.author	Moss, J
dc.contributor.author	Berube, P
dc.contributor.author	Biller, S
dc.contributor.author	Bodrossy, L
dc.contributor.author	Van De Kamp, J
dc.contributor.author	Brown, M
dc.contributor.author	Sow, SLS
dc.contributor.author	Armbrust, EV
dc.contributor.author	Fuhrman, J
dc.date.accessioned	2025-07-19T07:10:30Z
dc.date.available	2025-06-17
dc.date.available	2025-07-19T07:10:30Z
dc.date.issued	2025-07-01
dc.identifier.citation	Sci Data, 2025, 12, (1), pp. 1078
dc.identifier.issn	2052-4463
dc.identifier.issn	2052-4463
dc.identifier.uri	http://hdl.handle.net/10453/188561
dc.description.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.
dc.format	Electronic
dc.language	eng
dc.publisher	Springer Nature
dc.relation.ispartof	Sci Data
dc.relation.isbasedon	10.1038/s41597-025-05423-9
dc.rights	info:eu-repo/semantics/openAccess
dc.subject.mesh	Archaea
dc.subject.mesh	Bacteria
dc.subject.mesh	Eukaryota
dc.subject.mesh	Seawater
dc.subject.mesh	Oceans and Seas
dc.subject.mesh	DNA Barcoding, Taxonomic
dc.subject.mesh	DNA Primers
dc.subject.mesh	Plankton
dc.subject.mesh	Plankton
dc.subject.mesh	Bacteria
dc.subject.mesh	Archaea
dc.subject.mesh	DNA Primers
dc.subject.mesh	Seawater
dc.subject.mesh	Oceans and Seas
dc.subject.mesh	Eukaryota
dc.subject.mesh	DNA Barcoding, Taxonomic
dc.subject.mesh	Archaea
dc.subject.mesh	Bacteria
dc.subject.mesh	Eukaryota
dc.subject.mesh	Seawater
dc.subject.mesh	Oceans and Seas
dc.subject.mesh	DNA Barcoding, Taxonomic
dc.subject.mesh	DNA Primers
dc.subject.mesh	Plankton
dc.title	Characterizing organisms from three domains of life with universal primers from throughout the global ocean.
dc.type	Journal Article
utslib.citation.volume	12
utslib.location.activity	England
pubs.organisational-group	University of Technology Sydney
pubs.organisational-group	University of Technology Sydney/Faculty of Science
utslib.copyright.status	open_access	*
dc.rights.license	This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0). To view a copy of this license, visit https://creativecommons.org/licenses/by/4.0/
dc.date.updated	2025-07-19T07:10:28Z
pubs.issue	1
pubs.publication-status	Published online
pubs.volume	12
utslib.citation.issue	1

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.

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http://hdl.handle.net/10453/188561