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Annual Review of Earth and Planetary Sciences

Volume 53, 2025

Microbial Ecology to Ocean Carbon Cycling: From Genomes to Numerical Models

  • Naomi M. Levine1,2,3, Harriet Alexander4, Erin M. Bertrand5, Victoria J. Coles6, Stephanie Dutkiewicz7, Suzana G. Leles1 and Emily J. Zakem8
  • 1Department of Biological Sciences, University of Southern California, Los Angeles, California, USA; email: [email protected] 2Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California, USA 3Department of Earth Sciences, University of Southern California, Los Angeles, California, USA 4Biology Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA 5Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada 6Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, Maryland, USA 7Center for Sustainability Science and Strategy and Department of Earth, Atmospheric, and Planetary Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA 8Department of Global Ecology, Carnegie Institution for Science, Stanford, California, USA
  • Vol. 53:595-624 (Volume publication date May 2025)
  • First published as a Review in Advance on February 21, 2025
  • Copyright © 2025 by the author(s).
    This work is licensed under a Creative Commons Attribution 4.0 International License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. See credit lines of images or other third-party material in this article for license information.

Abstract

The oceans contain large reservoirs of inorganic and organic carbon and play a critical role in both global carbon cycling and climate. Most of the biogeochemical transformations in the oceans are driven by marine microbes. Thus, molecular processes occurring at the scale of single cells govern global geochemical dynamics, posing a challenge of scales. Understanding the processes controlling ocean carbon cycling from the cellular to the global scale requires the integration of multiple disciplines including microbiology, ecology, biogeochemistry, and computational fields such as numerical models and bioinformatics. A shared language and foundational knowledge will facilitate these interactions. This review provides the state of knowledge on the role marine microbes play in large-scale ocean carbon cycling through the lens of observational oceanography and biogeochemical models. We conclude by outlining ways in which the field can bridge the gap between -omics datasets and ocean models to understand ocean carbon cycling across scales.

  • ▪  -Omic approaches are providing increasingly quantitative insight into the biogeochemical functions of marine microbial ecosystems.
  • ▪  Numerical models provide a tool for studying global carbon cycling by scaling from the microscale to the global scale.
  • ▪  The integration of -omics and numerical modeling generates new understanding of how microbial metabolisms and community dynamics set nutrient fluxes in the ocean.

Keyword(s): -omics, biogeochemical models, carbon cycle, marine microbes, microbial ecology
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Microbial Ecology to Ocean Carbon Cycling: From Genomes to Numerical Models
Annual Review of Earth and Planetary Sciences 53, 595 (2025); https://doi.org/10.1146/annurev-earth-040523-020630
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