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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Nature Portfolio
2025-07-01
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| Series: | Scientific Data |
| Online Access: | https://doi.org/10.1038/s41597-025-05423-9 |
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| author | 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 |
| author_facet | 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 |
| author_sort | Jesse McNichol |
| collection | DOAJ |
| 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. |
| format | Article |
| id | doaj-art-e08b4abbdadc4de1b756f8e69b955846 |
| institution | Kabale University |
| issn | 2052-4463 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Data |
| spelling | doaj-art-e08b4abbdadc4de1b756f8e69b9558462025-08-20T04:01:26ZengNature PortfolioScientific Data2052-44632025-07-0112111610.1038/s41597-025-05423-9Characterizing organisms from three domains of life with universal primers from throughout the global oceanJesse McNichol0Nathan L. R. Williams1Yubin Raut2Craig Carlson3Elisa R. Halewood4Kendra Turk-Kubo5Jonathan P. Zehr6Andrew P. Rees7Glen Tarran8Mary R. Gradoville9Matthias Wietz10Christina Bienhold11Katja Metfies12Sinhué Torres-Valdés13Thomas Mock14Sarah Lena Eggers15Wade Jeffrey16Joseph Moss17Paul Berube18Steven Biller19Levente Bodrossy20Jodie Van De Kamp21Mark Brown22Swan L. S. Sow23E. Virginia Armbrust24Jed Fuhrman25Department of Biological Sciences–Marine and Environmental Biology, University of Southern CaliforniaDepartment of Biological Sciences–Marine and Environmental Biology, University of Southern CaliforniaDepartment of Biological Sciences–Marine and Environmental Biology, University of Southern CaliforniaEcology, Evolution, and Marine Biology, University of CaliforniaEcology, Evolution, and Marine Biology, University of CaliforniaOcean Sciences Department, University of California Santa CruzOcean Sciences Department, University of California Santa CruzPlymouth Marine LaboratoryPlymouth Marine LaboratoryColumbia River Inter-Tribal Fish CommissionAlfred Wegener Institute Helmholtz Centre for Polar and Marine ResearchAlfred Wegener Institute Helmholtz Centre for Polar and Marine ResearchAlfred Wegener Institute Helmholtz Centre for Polar and Marine ResearchAlfred Wegener Institute Helmholtz Centre for Polar and Marine ResearchSchool of Environmental Sciences, University of East AngliaAlfred Wegener Institute Helmholtz Centre for Polar and Marine ResearchCenter for Environmental Diagnostics and Bioremediation, University of West FloridaCenter for Environmental Diagnostics and Bioremediation, University of West FloridaDepartment of Civil and Environmental Engineering, Massachusetts Institute of TechnologyDepartment of Biological Sciences, Wellesley CollegeCSIRO EnvironmentCSIRO EnvironmentIndependent ResearcherCSIRO EnvironmentSchool of Oceanography, University of WashingtonDepartment of Biological Sciences–Marine and Environmental Biology, University of Southern CaliforniaAbstract 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.https://doi.org/10.1038/s41597-025-05423-9 |
| spellingShingle | 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 Characterizing organisms from three domains of life with universal primers from throughout the global ocean Scientific Data |
| title | Characterizing organisms from three domains of life with universal primers from throughout the global ocean |
| title_full | Characterizing organisms from three domains of life with universal primers from throughout the global ocean |
| title_fullStr | Characterizing organisms from three domains of life with universal primers from throughout the global ocean |
| title_full_unstemmed | Characterizing organisms from three domains of life with universal primers from throughout the global ocean |
| title_short | Characterizing organisms from three domains of life with universal primers from throughout the global ocean |
| title_sort | characterizing organisms from three domains of life with universal primers from throughout the global ocean |
| url | https://doi.org/10.1038/s41597-025-05423-9 |
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