{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,9]],"date-time":"2026-03-09T15:10:52Z","timestamp":1773069052617,"version":"3.50.1"},"reference-count":54,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T00:00:00Z","timestamp":1753833600000},"content-version":"vor","delay-in-days":210,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"UK Natural Environment Research Council through its AtlantiS programme","award":["NE\/Y005589\/1"],"award-info":[{"award-number":["NE\/Y005589\/1"]}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["NSF-OCE-1737409 to J.A.F"],"award-info":[{"award-number":["NSF-OCE-1737409 to J.A.F"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000893","name":"Simons Foundation","doi-asserted-by":"publisher","award":["CBIOMES-549943 to J.A.F"],"award-info":[{"award-number":["CBIOMES-549943 to J.A.F"]}],"id":[{"id":"10.13039\/100000893","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,1,17]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>High-throughput sequencing has provided unprecedented insights into microbial biodiversity in marine and other ecosystems. However, most sequencing-based studies report only relative (compositional) rather than absolute abundance, limiting their application in ecological modeling and biogeochemical analyses. Here, we present a metagenomic protocol incorporating genomic internal standards to quantify the absolute abundances of prokaryotes and eukaryotic phytoplankton, which together form the base of the marine food web, in unfractionated seawater. We applied this method to surface waters collected across 50\u00b0N to 40\u00b0S during the 29th Atlantic Meridional Transect. Using the single-copy recA gene, we estimated an average bacterial abundance of 1.0\u2009\u00d7\u2009109 haploid genome equivalents per liter. Leveraging a recent report that the psbO gene is typically single-copy in phytoplankton, we also quantified eukaryotic phytoplankton. Metagenomic estimates closely aligned with flow cytometry data for cyanobacteria (slope\u2009=\u20091.03, Pearson\u2019s r\u2009=\u20090.89) and eukaryotic phytoplankton (slope\u2009=\u20090.72, Pearson\u2019s r\u2009=\u20090.84). Compared to flow cytometry, taxonomic resolution for nano- and picoeukaryotes was greatly improved. Estimates for diatoms, dinoflagellates, and Trichodesmium were considerably higher than microscopy counts, likely reflecting microscopy undercounts and potential ploidy variation. These findings highlight the value of absolute quantification by metagenomics and offer a robust framework for quantitative assessments in microbial oceanography.<\/jats:p>","DOI":"10.1093\/ismeco\/ycaf131","type":"journal-article","created":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T11:53:53Z","timestamp":1753876433000},"source":"Crossref","is-referenced-by-count":2,"title":["Quantitative metagenomics for marine prokaryotes and photosynthetic eukaryotes"],"prefix":"10.1093","volume":"5","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5712-5440","authenticated-orcid":false,"given":"Qicheng","family":"Bei","sequence":"first","affiliation":[{"name":"Department of Biological Sciences, University of Southern California , Los Angeles, CA 90089 ,","place":["United States"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2496-9441","authenticated-orcid":false,"given":"Nathan L R","family":"Williams","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Southern California , Los Angeles, CA 90089 ,","place":["United States"]}]},{"given":"Laura E","family":"Furtado","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Southern California , Los Angeles, CA 90089 ,","place":["United States"]}]},{"given":"Daria Di","family":"Blasi","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Southern California , Los Angeles, CA 90089 ,","place":["United States"]}]},{"given":"Jelani","family":"Williams","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Southern California , Los Angeles, CA 90089 ,","place":["United States"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8612-4167","authenticated-orcid":false,"given":"Vanda","family":"Brotas","sequence":"additional","affiliation":[{"name":"Faculdade de Ci\u00eancias, Marine and Environmental Science Centre (MARE)\/Aquatic Research Network (ARNET), Universidade de Lisboa , 1749-016, Lisbon ,","place":["Portugal"]},{"name":"Plymouth Marine Laboratory, The Hoe , Plymouth, PL1 3DH ,","place":["United Kingdom"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3695-5151","authenticated-orcid":false,"given":"Glen","family":"Tarran","sequence":"additional","affiliation":[{"name":"Plymouth Marine Laboratory, The Hoe , Plymouth, PL1 3DH ,","place":["United Kingdom"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3070-3447","authenticated-orcid":false,"given":"Andrew P","family":"Rees","sequence":"additional","affiliation":[{"name":"Plymouth Marine Laboratory, The Hoe , Plymouth, PL1 3DH ,","place":["United Kingdom"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3835-6187","authenticated-orcid":false,"given":"Chris","family":"Bowler","sequence":"additional","affiliation":[{"name":"Institut de Biologie de l'\u00c9cole Normale Sup\u00e9rieure (IBENS), \u00c9cole Normale Sup\u00e9rieure, CNRS, INSERM , , 75005 Paris ,","place":["France"]},{"name":"PSL Universit\u00e9 , , 75005 Paris ,","place":["France"]},{"name":"Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022\/Tara GOSEE , 75016 Paris ,","place":["France"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2361-1985","authenticated-orcid":false,"given":"Jed A","family":"Fuhrman","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Southern California , Los Angeles, CA 90089 ,","place":["United States"]}]}],"member":"286","published-online":{"date-parts":[[2025,7,30]]},"reference":[{"key":"2025082608170457400_ref1","doi-asserted-by":"publisher","first-page":"200","DOI":"10.1126\/science.281.5374.200","article-title":"Biogeochemical controls and feedbacks on ocean primary production","volume":"281","author":"Falkowski","year":"1998","journal-title":"Science."},{"key":"2025082608170457400_ref2","doi-asserted-by":"publisher","first-page":"1257594","DOI":"10.1126\/science.1257594","article-title":"Rethinking 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