In This Article Expand or collapse the "in this article" section Microbial Oceanography

  • Introduction
  • The Ocean as a Habitat for Microorganisms
  • Microbial Ecology at Sea
  • Organic Matter Cycling and the Microbial Loop
  • Who’s New in the Sea of Microbes?
  • Genomics-Informed Taxonomic Diversity
  • Genomics-Informed Metabolic Function
  • Major Cycles: Nitrogen
  • Major Cycles: Phosphorus and Elemental Stoichiometry
  • Plankton Growth and Metabolism in the Epipelagic Zone
  • Particle Sizes, Composition, and Dynamics in the Epipelagic Zone
  • Biological Carbon Pump
  • Subeuphotic Zone Processes
  • Modeling and Predicting Marine Microbes and Their Processes
  • Microbial Dynamics in Time and Space: Selected Case Studies
  • Sea Microbes and Climate Change

Ecology Microbial Oceanography
David M. Karl, Matthew J. Church
  • LAST REVIEWED: 26 October 2023
  • LAST MODIFIED: 26 October 2023
  • DOI: 10.1093/obo/9780199830060-0248


The research mission of this relatively new subdiscipline is anchored at the intersections of oceanography, marine microbiology, and ecology. While the specific disciplinary boundaries are not well defined, the core foci are biogeochemistry, especially element cycles, the microbial loop, and controls on microbial population distributions and dynamics in time and space. This current bibliography is restricted to pelagic ecosystems, those seaward of the continental shelves and above the seafloor. Future microbial oceanography themed bibliographies could focus on benthic habitats (from littoral habitats to the abyss), microbial life in extreme environments (e.g., oxygen minimum zones, hydrothermal and seep habitats, life in polar seas), or other relevant topics, but the pelagic ocean is the largest biome on Earth, so our stated focus is well justified. A central challenge of microbial oceanography is to conduct comprehensive field campaigns to track the physical and chemical variables that define specific marine biomes and to understand how these habitat characteristics influence in situ microbial processes. The key physical processes, ranging in scale from molecular diffusion to global ocean circulation to ocean-atmosphere-climate interactions, cannot be reproduced in a laboratory setting. The target populations in microbial oceanography include bacteria, archaea, protists, microalgae, and small (<150 μm) metazoans, as well as their viruses. Symbiosis, including parasitism and mutualism, syntrophy, and other direct and indirect cell-to-cell interactions are important phenomena in the sea, but they are also difficult to reproduce in a shore-based laboratory setting. Consequently, access to the sea and the ability to conduct at-sea experiments is vital for research success in the discipline of microbial oceanography. Finally, a major challenge in microbial oceanography is the training of the next generation of practitioners and leaders. Because the research foci are transdisciplinary, the formal training should also be at the intersections of oceanography, marine microbiology, and ecology, but few academic degree programs are designed for this purpose. Like many emergent scientific disciplines, microbial oceanography is rapidly evolving, so we have endeavored to select several “classic” publications to provide an intellectual foundation of knowledge rather than rely solely on “last week’s” discovery papers. The hope is that this annotated bibliography will serve as a useful starting point to identify key concepts in the discipline and will help to educate and to inspire those interested in pursuing a career in this important and timely discipline.

The Ocean as a Habitat for Microorganisms

The ocean is a complex four-dimensional fluid environment that varies on a broad range of time and space scales. The discipline of microbial oceanography is as much about the physical and chemical dynamics of oceanic habitats as it is about the distribution and dynamics of its microbial inhabitants. Sverdrup, et al. 1942 is one of the first publications to consolidate extant information on the ocean as a habitat. Stommel 1963 and Mann and Lazier 2006 further explore the coupled biological-physical processes with implications to the study of marine microorganisms, and McCarthy, et al. 2002 summarizes emergent findings and new directions in the study of biological-physical interactions in the sea. Using satellite-based global observations, Longhurst 2007 presents a novel biogeographic classification scheme for pelagic ecosystems, further linking physical processes to phytoplankton ecology, and Kavanaugh, et al. 2014 provides an extended analysis of satellite-based ecosystem structure and function. Falkowski, et al. 2008 takes these concepts a large step further by discussing the evolution of Earth’s biogeochemical cycles, including energy transformations and microbial redox reactions. All energy flow in the open sea can be traced back to sunlight, so a thorough understanding of behavior of light is central to microbial oceanography (Kirk 2011). Karl and Proctor 2007 reviews important waypoints in the development of microbial oceanography as a discipline, and Munn 2020 consolidates key concepts in microbial ecology into a useful textbook. This collection of primary research articles, comprehensive reviews, and monographs will serve as a comprehensive introduction to the ocean as a habitat for microorganisms.

  • Falkowski, P. G., T. Fenchel, and E. F. DeLong. 2008. The microbial engines that drive Earth’s biogeochemical cycles. Science 320:1034–1039.

    DOI: 10.1126/science.1153213

    Enzymes catalyzing global biogeochemical cycles have arisen through billions of years of co-evolution among interacting and diverse microorganism communities. This review highlights modes of energy acquisition and material cycling associated with microbial redox reactions that drive cycles of carbon, nitrogen, phosphorus, hydrogen, and sulfur.

  • Karl, D. M., and L. M. Proctor. 2007. Foundations of microbial oceanography. Oceanography 20:16–27.

    DOI: 10.5670/oceanog.2007.44

    This introduction to a special issue, A Sea of Microbes, traces the historical developments and major benchmarks in the emergence of microbial oceanography as a unique scientific discipline.

  • Kavanaugh, M. T., B. Hales, M. Saraceno, Y. H. Spitz, A. E. White, and R. M. Letelier. 2014. Hierarchical and dynamic seascapes: A quantitative framework for scaling pelagic biogeochemistry and ecology. Progress in Oceanography 120:291–304.

    DOI: 10.1016/j.pocean.2013.10.013

    A novel quantitative, objective framework that can be used to identify coherent marine biomes and associated processes is based on satellite-derived observations. Conceptually similar to the analysis in Longhurst 2007, the current seascape analysis explores ecosystem functions (e.g., net primary production, biophysical forcing of carbon dioxide exchange) and the temporal dynamics in eight North Pacific Ocean biomes.

  • Kirk, J. T. O. 2011. Light and photosynthesis in aquatic ecosystems. 3d ed. New York: Cambridge Univ. Press.

    Light is life . . . all energy flow in open ocean ecosystems begins with light energy capture via photosynthesis. This comprehensive monograph explains the behavior of light in the ocean. In Part 1, the author reviews the physics of electromagnetic radiation from light adsorption and scattering processes to underwater light detection methods. In Part 2, the author presents a detailed account of light capture by aquatic plants and controls on aquatic photosynthesis.

  • Longhurst, A. R. 2007. Ecological geography of the sea. 2d ed. Burlington, MA: Academic Press.

    This unique monograph proposes a biogeographic classification scheme for pelagic ecosystems worldwide based on the availability of new data sets from sensors carried on Earth-orbiting satellites (e.g., sea surface temperature, sea surface elevation, and chlorophyll). Analysis provides a rigorous framework that links physical oceanographic processes to phytoplankton ecology.

  • Mann, K. H., and J. R. N. Lazier. 2006. Dynamics of marine ecosystems: Biological-physical interactions in the oceans. 3d ed. Malden, MA: Blackwell.

    This comprehensive monograph introduces the reader to many key biological-physical interactions in the sea. The text is organized around a hierarchy of spatial scales ranging from millimeters to thousands of kilometers, and beyond, each with important consequences for the survival of microorganisms and their predators.

  • McCarthy, J. J., A. R. Robinson, and B. J. Rothschild. 2002. Introduction – Biological-physical interactions in the sea: emergent findings and new directions. In The Sea. Vol. 12. Edited by A. R. Robinson, J. J. McCarthy, and B. J. Rothschild, 1–17. New York: John Wiley & Sons.

    This lead-in chapter sets the stage for a special volume that reviews progress on understanding the interactive dynamics of physical processes that influence biogeochemical cycles and communities of organisms in the sea, including microbes. The volume emphasizes the interdisciplinary nature of biological-physical interactions and the imperative to study microbial processes at multiple scales of time and space.

  • Munn, C. B. 2020. Marine microbiology: Ecology & applications. 3d ed. Boca Raton, FL: CRC Press.

    This textbook covers introductory materials on the microbial inhabitants of the world’s oceans, approaches to field sampling and laboratory-based analyses, principles of cellular metabolism and growth, microbial loop processes, and nutrient cycles. An excellent starting point for advanced undergraduate and graduate students who wish to enter the field of microbial oceanography.

  • Stommel, H. 1963. Varieties of oceanographic experience. Science 139:572–576.

    DOI: 10.1126/science.139.3555.572

    An important paper that explores the interaction of space and time among oceanographic physical processes, from large-scale circulation to tides to transient dynamics at the mesoscale to scales of turbulence. Stresses the importance of quantifying the spatiotemporal spectra of ocean phenomena to improve the planning and design of oceanographic expeditions and experiments.

  • Sverdrup, H. U., M. W. Johnson, and R. H. Fleming. 1942. The oceans, their physics, chemistry, and general biology. New York: Prentice-Hall.

    This magnum opus is an encyclopedia of information about the ocean including, but not limited to, the physical properties of seawater, the sea as a habitat, major water masses and currents, and phytoplankton in relation to physical-chemical properties of the environment. While this treatise was published eighty years ago, it still contains foundational information of relevance to investigations of microbial oceanography.

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