DNA Sequencing Gives Insights into Expanding Nutrient Oceanic Dead Zones

The Science

Oceanic “dead zones” characterized by deficits of oxygen and resulting deficits of many forms of multicellular life are expanding, possibly due to global climate change. To better understand this phenomenon, DOE’s Joint Genome Institute (JGI) has sequenced samples from Saanich Inlet in British Columbia. Metagenomic sequencing (where the composite DNA from an isolated community is sequenced rather than DNA from individual microbes) was carried out. Complete sets of genes coding for a photosynthetic mechanism were found in these composite samples, as expected. However, an extensive set of sulfur-oxidation and nitrogen reducing genes consistent with an anaerobic (no oxygen) life style also was present. The results also suggest that expanding microbial populations in low-oxygen ocean regions similar to the type found here may play a role in CO2 sequestration. They may also prove useful as microbe-based monitoring systems for biological responses to changes in ocean dead zones. The research was led by David Walsh and Steven Hallam of the University of British Columbia, working with the JGI’s Susannah Tringe, and is published in the October 23, 2009, issue of Science.


This study presents metagenomic analyses of a ubiquitous, abundant, and uncultivated bacterium in oceanic dead zones. Similar bacteria, related to chemoautotrophic gill symbionts of deep-sea clams and mussels, play a role in sulfide detoxification in African shelf waters. Reconstruction of the carbon and energy metabolism of this enigmatic lineage revealed a metabolic repertoire mediating carbon sequestration, sulfur-detoxification, and biological nitrogen loss in oxygen-deficient oceanic waters.

BER Program Manager

Ramana Madupu

U.S. Department of Energy, Biological and Environmental Research (SC-33)
Biological Systems Science Division
[email protected]


Walsh, D. A., E. Zaikova, C. G. Howes, Y. C. Song, J. J. Wright, S. G. Tringe, P. D. Tortell, and S. J. Hallam. 2009. “Metagenome of a Versatile Chemolitho-Autotroph from Expanding Oceanic Dead Zones,” Science 326, 578–82. DOI:10.1126/science.1175309.