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  • Review Article
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Microbial community genomics in the ocean

Nature Reviews Microbiology volume 3, pages 459–469 (2005)Cite this article

Key Points

  • Over the past 20 years, molecular approaches, such as ribosomal RNA gene-sequence comparisons, have revolutionized our understanding of microbial diversity and ecology. Similarly, advances in genome sequencing technologies are now beginning to have a major impact on microbial ecology and the environmental sciences, particularly ocean science.

  • Several whole genome sequences for marine microorganisms have been completed and many more marine bacterial, archaeal and protistan genome sequencing projects are underway.

  • In addition to 'simple' genome sequencing, new genomic approaches to analyse natural microbial assemblages have been, and continue to be, developed. These new approaches, which are referred to by various names, including environmental genomics and metagenomics (the subject of this Focus issue), focus on cultivation-independent genomic survey strategies, such as the construction of large-insert bacterial artificial chromosome and fosmid libraries for large DNA inserts and the use of whole-genome shotgun sequencing for small DNA inserts.

  • Three main case studies are discussed in detail: the discovery of bacterial proteorhodopsin using a phylogenetically anchored chromosome walking strategy; the shotgun sequence analysis of the microbial community in the Sargasso Sea; and the reconstruction of methane oxidation pathways in deep-sea archaea by shotgun sequencing of methanotroph-enriched fractions.

  • In the future, comparative community genomic approaches will hopefully begin to yield important, detailed information on microbial distribution, population structure and dynamics in various different environments.

Abstract

Marine microbial communities were among the first microbial communities to be studied using cultivation-independent genomic approaches. Ocean-going genomic studies are now providing a more comprehensive description of the organisms and processes that shape microbial community structure, function and dynamics in the sea. Through the lens of microbial community genomics, a more comprehensive view of uncultivated microbial species, gene and biochemical pathway distributions, and naturally occurring genomic variability is being brought into sharper focus. Besides providing new perspectives on oceanic microbial communities, these new studies are now poised to reveal the fundamental principles that drive microbial ecological and evolutionary processes.

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Figure 1: Microbial community DNA sequencing.
Figure 2: Burkholderia and Shewanella gene content in Sargasso Sea samples.
Figure 3: Environmental genomics of deep-sea archaeal methanotrophs.
Figure 4: Apparent taxonomic affiliation of protein-encoding genes from different depths in Monterey Bay.

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Acknowledgements

I am indebted to all my students and collaborators, past and present, for their dedication, inspiration and perspiration. Thanks to S. Hallam for providing Fig. 3 and to my oceanographic collaborators and colleagues, especially F. Chavez at the Monterey Bay Aquarium Research Institute and D. Karl at the University of Hawaii, for ongoing collaborative field efforts. The author's work is supported by the National Science Foundation, the Gordon and Betty Moore Foundation, and sequencing support from the Department of Energy (DoE) carried out at the DoE Joint Genome Institute.

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  1. Division of Biological Engineering and Department of Civil and Environmental Engineering, Room 48-427, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, 02139, Massachusetts, USA

    Edward F. DeLong

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DATABASES

Entrez

gi44893855

gi 44893849

Methanocaldococcus jannaschii

Shewanella oneidensis

Synechococcus sp.

FURTHER INFORMATION

Edward F. DeLong's homepage

DoE Joint Genome Institute

The Gordon and Betty Moore Foundation

NSF Microbial Sequencing Program FY 2005

The organism bins assembled from the Sargasso Sea WGS environmental sample dataset

Glossary

EUPHOTIC ZONE

The uppermost stratum of the water column that receives sufficient light for photosynthesis.

BENTHIC

Living in, or on the bottom of, a body of water.

SPECIES RICHNESS

The number of different species in a given habitat, biotope, community or assemblage.

SYMPATRIC

Populations, species or taxa occurring in the same geographical area.

SPECIES EVENNESS

The relative abundance of species in a given habitat, biotope, community or assemblage.

ALLOCHTHONOUS

Non-native. Found somewhere other than the place of origin.

CONTINENTAL MARGIN

Shallow submarine extension of the continents, generally tens of meters deep, that extends seaward to the continental slope and the deep ocean.

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DeLong, E. Microbial community genomics in the ocean. Nat Rev Microbiol 3, 459–469 (2005). https://doi.org/10.1038/nrmicro1158

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