Single-cell-resolved genome atlas of prokaryoplankton inhabiting the ocean's interior

Tianyi Chang; Maria G Pachiadaki; Gregory S Gavelis; Nicole J Poulton; Brian Thompson; Corianna Mascena; Keir Macartney; Julia M Brown; James J La Clair; Alaina R Weinheimer; Taichi Yokokawa; Paula Ruiz-Fernández; Julia Anstett; Paul M Berube; Steven J Biller; Beth N Orcutt; Federico Baltar; Michael D Burkart; Steven J Hallam; Klaus Jürgens; Osvaldo Ulloa; Takuro Nunoura; Eva Sintes; Gerhard J Herndl; Ramunas Stepanauskas

doi:10.1016/j.cell.2026.08.036

Single-cell-resolved genome atlas of prokaryoplankton inhabiting the ocean's interior

Tianyi Chang
, Maria G Pachiadaki
, Gregory S Gavelis
, Nicole J Poulton
, Brian Thompson
, Corianna Mascena
, Keir Macartney
, Julia M Brown
, James J La Clair
, Alaina R Weinheimer
, Taichi Yokokawa
, Paula Ruiz-Fernández
, Julia Anstett
, Paul M Berube
, Steven J Biller
, Beth N Orcutt
, Federico Baltar
, Michael D Burkart
, Steven J Hallam
, Klaus Jürgens

Osvaldo Ulloa, Takuro Nunoura, Eva Sintes, Gerhard J Herndl, Ramunas Stepanauskas

Functional and Evolutionary Ecology

Publications: Contribution to journal › Article › Peer Reviewed

Abstract

The ocean's aphotic interior harbors three-quarters of planktonic bacteria and archaea (prokaryoplankton), whose composition, ecology, and biotechnological potential remain poorly constrained. To address this knowledge gap, we created Global Oceans Reference Genomes (GORG)-Dark, a dataset of 9,698 genomes from individual prokaryoplankton cells sampled unselectively across a broad range of depths, geographic locations, and environmental conditions below the ocean's photic surface. Biogeographic analyses revealed prokaryoplankton vertical stratification extending to abyssal depths, the presence of particle-attached lineages of Pelagibacterales, and the previously overlooked abundance of Patescibacteria and Nanoarchaeota in the Baltic and Black Seas. We identified coding potential for chemolithoautotrophy, pharmacologically relevant secondary metabolisms, and a distinct type of proteorhodopsins in prokaryoplankton lineages prevalent throughout the aphotic ocean. This study offers a quantitative, global assessment of the composition and coding potential of microorganisms inhabiting the vast ocean's interior and contributes an extensive, single-cell-resolved dataset to microbial oceanography's cyberinfrastructure.

Original language	English
Journal	Cell
DOIs	https://doi.org/10.1016/j.cell.2026.08.036
Publication status	E-pub ahead of print - 15 Sept 2026

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 14 Life Below Water

Austrian Fields of Science 2012

106021 Marine biology

Access to Document

10.1016/j.cell.2026.08.036

Cite this

Chang, T., Pachiadaki, M. G., Gavelis, G. S., Poulton, N. J., Thompson, B., Mascena, C., Macartney, K., Brown, J. M., La Clair, J. J., Weinheimer, A. R., Yokokawa, T., Ruiz-Fernández, P., Anstett, J., Berube, P. M., Biller, S. J., Orcutt, B. N., Baltar, F., Burkart, M. D., Hallam, S. J., ... Stepanauskas, R. (2026). Single-cell-resolved genome atlas of prokaryoplankton inhabiting the ocean's interior. Cell. Advance online publication. https://doi.org/10.1016/j.cell.2026.08.036

@article{1907eae85f3a4ecd8279064cd0fa18c1,

title = "Single-cell-resolved genome atlas of prokaryoplankton inhabiting the ocean's interior",

abstract = "The ocean's aphotic interior harbors three-quarters of planktonic bacteria and archaea (prokaryoplankton), whose composition, ecology, and biotechnological potential remain poorly constrained. To address this knowledge gap, we created Global Oceans Reference Genomes (GORG)-Dark, a dataset of 9,698 genomes from individual prokaryoplankton cells sampled unselectively across a broad range of depths, geographic locations, and environmental conditions below the ocean's photic surface. Biogeographic analyses revealed prokaryoplankton vertical stratification extending to abyssal depths, the presence of particle-attached lineages of Pelagibacterales, and the previously overlooked abundance of Patescibacteria and Nanoarchaeota in the Baltic and Black Seas. We identified coding potential for chemolithoautotrophy, pharmacologically relevant secondary metabolisms, and a distinct type of proteorhodopsins in prokaryoplankton lineages prevalent throughout the aphotic ocean. This study offers a quantitative, global assessment of the composition and coding potential of microorganisms inhabiting the vast ocean's interior and contributes an extensive, single-cell-resolved dataset to microbial oceanography's cyberinfrastructure.",

author = "Tianyi Chang and Pachiadaki, \{Maria G\} and Gavelis, \{Gregory S\} and Poulton, \{Nicole J\} and Brian Thompson and Corianna Mascena and Keir Macartney and Brown, \{Julia M\} and \{La Clair\}, \{James J\} and Weinheimer, \{Alaina R\} and Taichi Yokokawa and Paula Ruiz-Fern{\'a}ndez and Julia Anstett and Berube, \{Paul M\} and Biller, \{Steven J\} and Orcutt, \{Beth N\} and Federico Baltar and Burkart, \{Michael D\} and Hallam, \{Steven J\} and Klaus J{\"u}rgens and Osvaldo Ulloa and Takuro Nunoura and Eva Sintes and Herndl, \{Gerhard J\} and Ramunas Stepanauskas",

year = "2026",

month = sep,

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doi = "10.1016/j.cell.2026.08.036",

language = "English",

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Chang, T, Pachiadaki, MG, Gavelis, GS, Poulton, NJ, Thompson, B, Mascena, C, Macartney, K, Brown, JM, La Clair, JJ, Weinheimer, AR, Yokokawa, T, Ruiz-Fernández, P, Anstett, J, Berube, PM, Biller, SJ, Orcutt, BN, Baltar, F, Burkart, MD, Hallam, SJ, Jürgens, K, Ulloa, O, Nunoura, T, Sintes, E, Herndl, GJ & Stepanauskas, R 2026, 'Single-cell-resolved genome atlas of prokaryoplankton inhabiting the ocean's interior', Cell. https://doi.org/10.1016/j.cell.2026.08.036

TY - JOUR

T1 - Single-cell-resolved genome atlas of prokaryoplankton inhabiting the ocean's interior

AU - Chang, Tianyi

AU - Pachiadaki, Maria G

AU - Gavelis, Gregory S

AU - Poulton, Nicole J

AU - Thompson, Brian

AU - Mascena, Corianna

AU - Macartney, Keir

AU - Brown, Julia M

AU - La Clair, James J

AU - Weinheimer, Alaina R

AU - Yokokawa, Taichi

AU - Ruiz-Fernández, Paula

AU - Anstett, Julia

AU - Berube, Paul M

AU - Biller, Steven J

AU - Orcutt, Beth N

AU - Baltar, Federico

AU - Burkart, Michael D

AU - Hallam, Steven J

AU - Jürgens, Klaus

AU - Ulloa, Osvaldo

AU - Nunoura, Takuro

AU - Sintes, Eva

AU - Herndl, Gerhard J

AU - Stepanauskas, Ramunas

PY - 2026/9/15

Y1 - 2026/9/15

N2 - The ocean's aphotic interior harbors three-quarters of planktonic bacteria and archaea (prokaryoplankton), whose composition, ecology, and biotechnological potential remain poorly constrained. To address this knowledge gap, we created Global Oceans Reference Genomes (GORG)-Dark, a dataset of 9,698 genomes from individual prokaryoplankton cells sampled unselectively across a broad range of depths, geographic locations, and environmental conditions below the ocean's photic surface. Biogeographic analyses revealed prokaryoplankton vertical stratification extending to abyssal depths, the presence of particle-attached lineages of Pelagibacterales, and the previously overlooked abundance of Patescibacteria and Nanoarchaeota in the Baltic and Black Seas. We identified coding potential for chemolithoautotrophy, pharmacologically relevant secondary metabolisms, and a distinct type of proteorhodopsins in prokaryoplankton lineages prevalent throughout the aphotic ocean. This study offers a quantitative, global assessment of the composition and coding potential of microorganisms inhabiting the vast ocean's interior and contributes an extensive, single-cell-resolved dataset to microbial oceanography's cyberinfrastructure.

AB - The ocean's aphotic interior harbors three-quarters of planktonic bacteria and archaea (prokaryoplankton), whose composition, ecology, and biotechnological potential remain poorly constrained. To address this knowledge gap, we created Global Oceans Reference Genomes (GORG)-Dark, a dataset of 9,698 genomes from individual prokaryoplankton cells sampled unselectively across a broad range of depths, geographic locations, and environmental conditions below the ocean's photic surface. Biogeographic analyses revealed prokaryoplankton vertical stratification extending to abyssal depths, the presence of particle-attached lineages of Pelagibacterales, and the previously overlooked abundance of Patescibacteria and Nanoarchaeota in the Baltic and Black Seas. We identified coding potential for chemolithoautotrophy, pharmacologically relevant secondary metabolisms, and a distinct type of proteorhodopsins in prokaryoplankton lineages prevalent throughout the aphotic ocean. This study offers a quantitative, global assessment of the composition and coding potential of microorganisms inhabiting the vast ocean's interior and contributes an extensive, single-cell-resolved dataset to microbial oceanography's cyberinfrastructure.

U2 - 10.1016/j.cell.2026.08.036

DO - 10.1016/j.cell.2026.08.036

M3 - Article

C2 - 42743927

SN - 0092-8674

JO - Cell

JF - Cell

ER -