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Microbial oceanography: paradigms, processes and promise

Key Points

  • Microorganisms are the dominant organisms in the sea, both in terms of mass and ecological importance.

  • Most marine microorganisms have not yet been brought into pure cultures in the laboratory, so detailed information about their ecological roles is incomplete.

  • New molecular tools, including gene-based approaches, are beginning to provide data on the diversity and metabolic processes of novel microorganisms that are not yet in culture.

  • The new discipline of microbial oceanography endeavours to observe and understand microbial life in the sea well enough to make accurate ecological predictions of, for example, the impact of climate variations on microbial processes in the sea.

  • Research in microbial oceanography requires an interdisciplinary approach that includes: understanding the physical and chemical habitat properties; making observations over a broad range of time and space scales; designing and implementing hypothesis-testing field experiments; and integrating data into ecosystem-based models. These interdisciplinary interactions must be between scientists who have not traditionally worked together.

  • We are at a unique point in time — one that is characterized by important challenges and great opportunities. New training programmes to prepare the next generation of microbial oceanographers will be essential for continued progress in this important discipline.


Life on Earth most likely originated as microorganisms in the sea. Over the past 3.5 billion years, microorganisms have shaped and defined Earth's biosphere and have created conditions that have allowed the evolution of macroorganisms and complex biological communities, including human societies. Recent advances in technology have highlighted the vast and previously unknown genetic information that is contained in extant marine microorganisms, from new protein families to novel metabolic processes. Now there is a unique opportunity, using recent advances in molecular ecology, metagenomics, remote sensing of microorganisms and ecological modelling, to achieve a comprehensive understanding of marine microorganisms and their susceptibility to environmental variability and climate change. Contemporary microbial oceanography is truly a sea of opportunity and excitement.

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Figure 1: Solar energy flux and capture in the sea.
Figure 2: Oxygen concentrations and dynamics at the HOT Station ALOHA (22.75°N, 158°W).
Figure 3: Effects of nutrient perturbations on open-ocean ecosystems.
Figure 4: The relationships between inorganic phosphorus and dissolved organic phosphorus.


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I thank the HOT and C-MORE program scientists and staff for their important contributions, and the National Science Foundation, the Agouron Institute and the Gordon and Betty Moore Foundation for generous financial support of my research and training endeavors.

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Able to fix inorganic carbon using energy from light.


Able to acquire metabolic energy by the consumption of particulate or dissolved organic matter.


Small (2–20 m) prokaryotic or eukaryotic organisms that are dependent on organic matter.


Bacteria that inhabit the water column of lakes and oceans, either freely suspended or attached to particles.


Having low levels of nutrient and algal photosynthetic production (for example, the open ocean).

Radiative forcing

The difference between the incoming radiation energy and the outgoing radiation energy in a given climate system.


Derived from land or terrestrial ecosystems.


Water-column portion of marine and fresh-water habitats.

Euphotic zone

Upper realms of the oceans (or lakes) that are penetrated by sufficient amounts of light for photosynthetic organisms to grow.

Primary production

Process during which carbon dioxide is incorporated into organic matter by bacteria and algae, using any of a variety of energy sources.


Organisms that are part autotrophic and part heterotrophic, such as carnivorous plants.


The acquisition of metabolic energy from the fixation of inorganic carbon, for example, by photo- or chemosynthesis.


Organisms that are suspended in the water column that are less than 2 mm in size.

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Karl, D. Microbial oceanography: paradigms, processes and promise. Nat Rev Microbiol 5, 759–769 (2007).

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