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The importance of culturing bacterioplankton in the 'omics' age

Nature Reviews Microbiology volume 5, pages 820–826 (2007)Cite this article

Abstract

Progress in the culturing of microorganisms that are important to ocean ecology has recently accelerated, and technology has been a factor in these advances. However, rather than a single technological breakthrough, a combination of methods now enable microbiologists to screen large numbers of cultures and manipulate cells that are growing at the low biomass densities that are characteristic of those found in seawater. The value of ribosomal RNA databases has been reaffirmed, as they provide nucleic-acid probes for screening to identify important new species in culture. The new cultivation approaches have focused on specific targets that ecological studies suggest are significant for geochemical transformations, such as SAR11. Here, we review how to cultivate marine oligotrophs and why it is worth the effort.

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Figure 1: Integrated approaches in marine microbiology.
Figure 2: Phylogeny of selected marine bacteria.
Figure 3: Cultivation of oligotrophs.
Figure 4: Micrographs of important oligotrophic marine bacteria.

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Acknowledgements

This paper was supported by National Science Foundation grant DEB-0207085 and by a grant from the Gordon and Betty Moore Foundation.

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Authors and Affiliations

  1. Stephen Giovannoni and Ulrich Stingl are at the Department of Microbiology, Oregon State University, 220 Nash Hall, Corvallis, Oregon 97333, USA.,

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Correspondence to Stephen Giovannoni.

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Competing interests

Stephen Giovannoni and Oregon State University hold United States patent 6,951,714 (High Througput Microbial Culturing), which is licensed to Diversa Corporation. To the best of our knowledge this technology is not currently being applied commercially, and the statements made in our manuscript will not result in financial gain.

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DATABASES

Entrez Genome

Prochlorococcus marinus

Entrez Genome Project

Candidatus Pelagibacter ubique

Chlamydia trachomatis

HTCC2080

KT71

Nitrosopumilus maritimus SCM-1

Sphingopyxis alaskenis

Wolbachia pipientis

FURTHER INFORMATION

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Glossary

Bacterioplankton

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

Euphotic zone

A transitional region of the water column where light levels are low and labile organic matter is in even shorter supply than at the surface, but where macronutrients, such as iron, phosphorous and reduced forms of nitrogen, are readily available.

Heterotrophic

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

Oligotrophic

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

Pelagic

Relating to or occurring in the water column.

Tangential flow filtration

A technique that re-circulates the retentate (the part of a solution that does not cross the membrane) along a membrane surface that is only permeable to water and low-molecular-weight compounds.

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Giovannoni, S., Stingl, U. The importance of culturing bacterioplankton in the 'omics' age. Nat Rev Microbiol 5, 820–826 (2007). https://doi.org/10.1038/nrmicro1752

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