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  • Review Article
  • Published:

Microbial structuring of marine ecosystems

Nature Reviews Microbiology volume 5, pages 782–791 (2007)Cite this article

An Erratum to this article was published on 01 December 2007

A Corrigendum to this article was published on 01 December 2007

Key Points

  • In this Review, Azam and Malfatti make a case for the need to elucidate in situ microbiology as a unifying basis for understanding and modelling the influence of microorganisms on marine ecosystems.

  • Bacteria dominate the ocean in abundance, diversity and metabolic activity. The uptake of organic matter by bacteria is a major carbon-flow pathway, and its variability can change the overall flux of carbon in the ocean and, therefore, globally.

  • Organic matter in seawater is present as transparent gels that are composed of colloids, mucus sheets and bundles. It is important to consider how microorganisms interact with organic matter that is present in this form. Growth rates of bacteria in the ocean are important, but estimates based on the bulk phase could be inaccurate. It is feasible that hot spots of nutrients allow bursts of fast growth in a boom-and-bust cycle.

  • Marine snow is an important component of the organic carbon in the ocean on which bacteria can reach high cell densities. Understanding the biochemical bases of the interactions of bacteria with marine snow will enable us to begin to link carbon storage and carbon biochemistry with gene expression in the bacteria that are present on these aggregates.

  • Microbial oceanography is a field that is caught between scales — microbial processes must be understood at the scale of the individual microorganism, but yet we want to understand the cumulative influence of microbial processes on how the ocean works as a biogeochemical system. We argue that understanding how bacteria interact with the ocean system at the nanometre to millimetre scales provides insights into biogeochemical processes of global significance.

Abstract

Despite the impressive advances that have been made in assessing the diversity of marine microorganisms, the mechanisms that underlie the participation of microorganisms in marine food webs and biogeochemical cycles are poorly understood. Here, we stress the need to examine the biochemical interactions of microorganisms with ocean systems at the nanometre to millimetre scale — a scale that is relevant to microbial activities. The local impact of microorganisms on biogeochemical cycles must then be scaled up to make useful predictions of how marine ecosystems in the whole ocean might respond to global change. This approach to microbial oceanography is not only helpful, but is in fact indispensable.

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Figure 1: Microbial structuring of a marine ecosystem.
Figure 2: The size range of organic matter and microbial interactions in the ocean.
Figure 3: Adaptive strategies of bacteria in the ocean.
Figure 4: Microbial cycling of carbon in marine snow.

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Acknowledgements

We thank T. Hollibaugh, G. Steward, D. Smith and J. Fuhrman for insightful comments on the manuscript. This work was supported by the Gordon and Betty Moore Foundation and grants to F.A. from the National Science Foundation.

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  1. Scripps Institution of Oceanography, University of California, San Diego, La Jolla, 92093, California, USA

    Farooq Azam & Francesca Malfatti

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Correspondence to Farooq Azam.

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DATABASES

Entrez Genome Project

Candidatus Pelagibacter ubique

Emiliania huxleyi

Pavlova lutheri

Pseudoalteromonas haloplanktis

Shewanella putrefaciens

TM1040

Glossary

Primary production

The original source of organic material in an ecosystem that is due to carbon dioxide fixation by photosynthetic bacteria, plants or algae, or chemosynthetic microorganisms.

Heterotrophic

The acquisition of carbon and metabolic energy by the consumption of living or dead organic matter.

Autotrophic

An organism that synthesizes organic carbon from the fixation of inorganic carbon, for example, by photo- or chemosynthesis.

Pelagic

Relating to or occurring in the oceanic water column.

Oligotrophic

An aquatic environment that has low levels of nutrients and primary production (for example, high mountain lakes or the open ocean).

Eutrophic

A marine or lake environment with a high nutrient concentration and high levels of primary production.

Phytoplankton

Composed of microscopic plants and photosynthetic cyanobacteria. These are the main primary producers in marine food webs, ranging in size from 1 μm to approximately 100 μm.

Chemotaxis

The sensing by bacteria of chemical gradients, and movement up or down a gradient towards or away from a chemical source.

Dimethyl sulphide

(DMS). A sulphur-containing organic chemical compound that is a breakdown product of dimethylsulphoniopropionate (DMSP). It is also produced by the metabolism of methanethiol by marine bacteria that are associated with phytoplankton.

Marine snow

Composed of organic aggregates more than 0.5 mm in diameter. These macroscopic particles are enriched in organic matter and are inhabited by a rich and diverse community of phytoplankton, protozoans and bacteria.

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Azam, F., Malfatti, F. Microbial structuring of marine ecosystems. Nat Rev Microbiol 5, 782–791 (2007). https://doi.org/10.1038/nrmicro1747

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