New Study on "Dark Matter" of Biology Fills in Major Holes in Tree of Life

Through the use of cutting-edge DNA technology, a group of researchers have been able to gain a revelatory glimpse into microbes deemed the "dark matter" of biology due to their pervasive yet practically invisible presence throughout the planet.

In doing so, the scientists, led by microbiologist Tanja Woyke of the U.S. Department of Energy's Joint Genome Institute (DOE JGI), have been able to fill in holes in the bacterial and archaeal tree of life for the first time ever.

"Instead of wandering through the starkness of space, this achievement is more like the 21st Century equivalent of Lewis and Clark's expedition to open the American West," said Eddy Rubin, DOE JGI Director. "This is really the next great frontier."

Specifically, the researchers targeted uncultivated microbial cells from nine habitats: Sakinaw Lake in British Columbia; the Etoliko Lagoon of western Greece; a sludge reactor in Mexico; the Gulf of Maine; off the north coast of Oahu, Hawaii, the Tropical Gyre in the south Atlantic; the East Pacific Rise; the Homestake Mine in South Dakota; and the Great Boiling Spring in Nevada.

From these samples, the team laser-sorted 9,000 cells, from which they were able to reassemble and identify 201 distinct genomes that could be aligned to 28 major yet previously uncharted branches of the tree of life.

"Microbes are the most abundant and diverse forms of life on Earth," Woyke said. "They occupy every conceivable environmental niche from the extreme depths of the oceans to the driest of deserts. However, our knowledge about their habits and potential benefits has been hindered by the fact that the vast majority of these have not yet been cultivated in the laboratory."

For this reason, Woyke explained, scientists have only recently become aware of their roles in a variety of ecosystems. However, through advanced technology, scientists are beginning to discover "unexpected metabolic features that extend our understanding of biology and challenge established boundaries between the domains of life."

Through the study, team happened upon a number of surprising discoveries that, they explain, can be categorized into three main areas.

The first included the discovery of unexpected metabolic features. For example, the scientists observed certain traits in archaea that previously only were seen in bacteria and vice-versa. One such trait involves an enzyme commonly used by bacteria for creating space within their protective cell wall, which is needed so the cell can, for instance, expand during cell division. Now, for the first time, a group of archaea was found encoding this enzyme, possibly, the authors hypothesize, to employ in attacking bacteria.

The second main area was the correct reassignment, or binning, of data of some 340 million DNA fragments from other habitats to the proper lineage. As a result, scientists everywhere have access to new insights into how organisms function in the context of a particular ecosystem as well as a more accurate understanding of the associations of newly discovered genes with resident life forms.

The third area of discovery was the resolution of relationships within and between microbial phyla - the taxonomic ranking between domain and class - that led the team to propose two new superphyla, which are highly stable associations between phyla.

Regarding the study overall, Woyke explained that she often felt as though she was employed in some form of family history research.

"It's a bit like looking at a family tree to figure out who your sisters and brothers are," Woyke said. "Here we did this for groups of organisms for which we solely have fragments of genetic information. We interpreted millions of these bits of genetic information like distant stars in the night sky, trying to align them into recognizable constellations. At first, we didn't know what they should look like, but we could estimate their relationship to each other, not spatially, but over evolutionary time."

Going forward, Woyke and her colleagues say they are pursuing a more accurate characterization of these relationships so they can better predict metabolic properties and other key traits that can be expressed by different groups of microbes.