A single-cell genome chart of dark ocean prokaryoplankton

The “dark ocean”, defined as water column below the sunlight surface layer, contains 90% of the ocean’s volume and three quarters of the marine prokaryoplankton biomass, yet remains underexplored. Here, we report Global Ocean Reference Genome (GORG)-Dark – the first large collection of single amplified genomes (SAGs) of planktonic bacteria and archaea inhabiting this vast environment. GORG-Dark consists of 9,000 curated SAGs representing 43 phyla, 81 classes, and 234 orders of bacteria and archaea. These SAGs were produced using a randomized cell selection strategy from globally sourced samples spanning a latitudinal range from pole to pole, geographic locations from open oceans to inland seas, depth layers from upper mesopelagic to hadal (>10,000 meter), and oxygen regimes from fully oxygenated to anoxic. By leveraging the fine-resolution genome representation of GORG-Dark and the massive gene-level representation of ~800 dark and surface ocean metagenomes through fragment recruitment, we produced a robust map of prokaryoplankton spatial distribution. This revealed pronounced stratification by depth and limited geographic differences in the open, oxygenated ocean. We discovered a previously undescribed SAR11 lineage that is abundant in the deep ocean and predominantly found on particles. Metabolic potential analyses indicated widespread autotrophy and a substantially more diverse capacity for secondary metabolite synthesis as compared to surface ocean. Meanwhile, low-oxygen environments, such as the subphotic zones of the Baltic Sea and the Black Sea, had highly distinct prokaryoplankton, with an unexpected abundance of Patescibacteria and DPANN archaea that may have been underestimated in earlier studies. This study offers a broad overview of the coding potential of the dark ocean prokaryoplankton and an extensive resource for further data exploration.

Presentation Preference: Oral

Primary Presenter: Tianyi Chang, Xiamen University (chtianyii@gmail.com)

Authors:

Tianyi Chang, Bigelow Laboratory for Ocean Sciences  (chtianyii@gmail.com)

Maria Pachiadaki, Woods Hole Oceanographic Institution  (mpachiadaki@whoi.edu)

Gregory Gavelis, Bigelow Laboratory for Ocean Sciences  (ggavelis@bigelow.org)

Keir Macartney, Bigelow Laboratory for Ocean Sciences  (kmacartney@bigelow.org)

James La Clair, University of California San Diego  (jlaclair@ucsd.edu)

Alaina Weinheimer, Bigelow Laboratory for Ocean Sciences  (aweinheimer@bigelow.org)

Julia Brown, Bigelow Laboratory for Ocean Sciences  (julia@bigelow.org)

Michael Burkart, University of California San Diego  (mburkart@ucsd.edu)

Steven Hallam, The University of British Columbia  (shallam@mail.ubc.ca)

Osvaldo Ulloa, Universidad de Concepción  (oulloa@udec.cl)

Federico Baltar, University of Vienna  (federico.baltar@univie.ac.at)

Klaus Juergens, Leibniz Institute for Baltic Sea Research  (klaus.juergens@io-warnemuende.de)

Takuro Nunoura, Japan Agency for Marine-Earth Science and Technology  (takuron@jamstec.go.jp)

Eva Sintes, The Spanish Institute of Oceanography  (eva.sintes@ieo.csic.es)

Gerhard Herndl, University of Vienna  (gerhard.herndl@univie.ac.at)

Ramunas Stepanauskas, Bigelow Laboratory for Ocean Sciences  (rstepanauskas@bigelow.org)