Dog Days and “Dark Matter”

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Crab Spa is a diffuse-flow hydrothermal vent site on the East Pacific Rise and one of the nine sampling sites.Photo courtesy of Stefan Sievert, Woods Hole Oceanographic Institution

Crab Spa is a diffuse-flow hydrothermal vent site on the East Pacific Rise and one of the nine sampling sites for this study.

During the deep dog days of summer, it's often difficult to find the energy to move, much less accomplish anything of consequence.

In contrast, microbes must muster the energy – it's kind of important to that whole staying alive thing – no matter how hot or humid their environments, whether deep in a mine or far under the ocean; on a Mediterranean lagoon or even inside a sludge reactor (the latter used for treating sewage and wastewater).

The ability of microbes to do just that – to find energy in all sorts of ugly environs – makes them of interest to researchers supported by the Department of Energy's (DOE's) Office of Science. That's especially true since comparatively few families of microbes are fully known (more about that below), and their ancient techniques of pulling energy from unlikely and inhospitable places might be applied to many modern needs.

Recently, an international collaboration of scientists led by DOE's Joint Genome Institute took a look at the vast world of previously undiscovered microbes. Specifically, the scientists used sophisticated new sequencing techniques to reveal entire new families of microbes, whose presence had been inferred but never revealed, biology's "dark matter."

To find that "microbial dark matter" researchers took samples from nine different habitats, including a hydrothermal vent in the Pacific, the Homestake Mine in South Dakota, the Etoliko Lagoon in Greece, and yes, a sludge reactor in Mexico. They sorted some 9,000 cells from those samples, from which they reassembled and read 201 new and distinct DNA sequences (genomes) from what turned out to be 29 previously unknown microbial families.

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Study first author Chris Rinke shows off the DOE JGI’s single-cell genomics capabilities during the annual Genomics of Energy & Environment Meeting.Photo courtesy of Roy Kaltschmidt, Berkeley Lab

Study first author Chris Rinke shows off the DOE JGI's single-cell genomics capabilities during the annual Genomics of Energy & Enviornment Meeting.

Those microbes – none of which had previously been grown in a laboratory – had a number of unexpected features. For instance, researchers found 'modern' cellular tools in bacteria previously regarded as ancient and vice versa (a bit like having a branch of the family in which the grandparents are addicted to Twitter and their grandkids can't get enough of bingo). Scientists found another microbial family which sees a common "Stop" translation signal and keeps on going. And they found bacteria using a wide range of sources for food and energy; some depending on oxygen (via cellular respiration), and others metabolizing hydrogen or utilizing sulfur. (For more detail, see the Nature paper:

There's no way to say what applications these discoveries might lead to. But the possibilities are myriad. As JGI noted, the families that make up microbial dark matter, "Can have profound influences on the most significant environmental processes, from plant growth and health to nutrient cycles in terrestrial and marine environments, the global carbon cycle and possibly even climate processes." They may be able to teach us a few things about gathering energy from unexpected places too.

Much has been discovered, but, as is so often the case in science, much more remains to be uncovered. There may be millions more microbial species just waiting to be found, each with its unique potential. That's the Office of Science at work: Illuminating dark matter, and energizing the dog days of summer.

The Department's Office of Science is the single largest supporter of basic research in the physical sciences in the United States and is working to address some of the most pressing challenges of our time. For more information please visit For more information about the Joint Genome Institute please go to

Charles Rousseaux is a Senior Writer in the Office of Science,