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Updated: Sep 17, 2026

An Aquatic Microbial Metaproteomics Workflow: From Cells to Tryptic Peptides Suitable for Tandem Mass Spectrometry-based Analysis
Published on: September 15, 2015
Single-cell-resolved genome atlas of prokaryoplankton inhabiting the ocean's interior
Tianyi Chang1, Maria G Pachiadaki2, Gregory S Gavelis3
1Bigelow Laboratory for Ocean Sciences, East Boothbay, ME 04544, USA; Helmholtz Institute for Functional Marine Biodiversity, 26129 Oldenburg, Germany.
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.
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