Dark ocean chemoautotrophy and other tales from tiny organisms with big impact

The microbial inhabitants of the dak ocean comprise one of the largest biota on Earth. They mediate all major biogeochemical cycles, and control the “dark end” of ocean’s biological pump. Yet, little is known about the key chemoautotrophic taxa in the aphotic realm. To address this challenge, we employed single cell genomics technology to generate 10,000 partial genomes of planktonic Bacteria and Archaea from all major water masses and the oxygen-depleted seas, Baltic and Black. Two thousand additional genomes were generated from the oxygen-deficient water columns of the Eastern Tropical North and South Pacific. Around a quarter of the recovered genomes are affiliated to Nitrosopumilaceae, and have the potential to fix inorganic carbon through the modified 3-Hydroxyproponate/4-Hydroxybutyrate cycle, confirming the established paradigm that archaeal ammonia oxidizers are the most abundant chemolithotrophs in the ocean. We also detected potential sulfur oxidizing lineages, encoding the genes of the CO₂ fixation Calvin-Benson-Bassham cycle, the majority of which belong to Gammaproteobacterial, followed by the SAR324. Nitrite Oxidizing Bacteria using the reductive tricarboxylic acid cycle to fix carbon, are also abundant and ubiquitous. The oxygen-depleted water columns also contain diverse chemoautotrophic lineages using the reductive acetyl-CoA pathway. Genomes affiliated to lineages that are not known to fix inorganic carbon (e.g. Patescibacteria, Nanoarchaeota and Marinisomatota) were also found, but their role in dark CO₂ fixation requires further investigation.

Presentation Preference: Oral

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

Authors:

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

Rayna Hamilton, Woods Hole Oceanographic Institution  (rayna.hamilton@whoi.edu)

Tianyi Chang, Bigelow Laboratory for Ocean Sciences  (tchang@bigelow.org)

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

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

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

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

Julia Anstett, University of British Columbia  (glinosju@mail.ubc.ca)

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

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

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

Takuro Nunoura, JAMSTEC  (takuron@jamstec.go.jp)

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

Eva Sintes, Instituto Espanol de Oceanografia  (eva.sintes@ieo.csic.es)

Osvaldo Ulloa, University of Conception  (oulloa@udec.cl)

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

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

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