Biological 'Dark Matter': Scientists Reveal Infrastructure of Life

The final frontier may not just be in space exploration; it could be far closer to home. Scientists are beginning to look at the "dark matter" of biological sciences by studying the infrastructure of life that has profound influences on the natural cycles on Earth. They've employed next generation DNA sequencing of genomes isolated from single cells in order to systematically bring to light to and fill in uncharted branches in the bacterial and archaeal tree of life.

The latest effort to record microbial dark matter targeted nine diverse habitats that play home to uncultivated microbial cells. It included locations that range from British Columbia to Hawaii to Greece. After collecting samples from these areas, the researchers laser-sorted 9,000 cells and then reassembled and identified 201 distinct genomes. These genomes were then aligned to 28 major previously uncharted branches of the tree of life.

"Instead of wondering through the starkness of space, this achievement is more like the 21^st Century equivalent of Lewis and Clark's expedition to open the American West," said Eddy Rubin, U.S. Department of Energy Join Genome Institute Director, in a news release. "This is a powerful example of how the DOE JGI pioneers discovery, in that we can take a high throughout approach to isolating and characterizing single genomes from complex environmental samples of millions of cells, to provide a profound leap of understanding the microbial evolution on our planet. This is really the next great frontier."

That isn't the only thing that the researchers found, though. They discovered unexpected metabolic features and certain traits in Archaea that previously only were seen in Bacteria. In addition, the researchers managed to correctly reassign data of about 340 billion DNA fragments from other habitats to the proper lineage. This provided insights into how organisms function in the context of a particular ecosystem as well as a much improved and more accurate understanding of the associations of newly discovered genes with resident life forms.

In addition to these findings, the research also resolved the relationships within and between microbial phyla, the taxonomic ranking between domain and class. In fact, the scientists proposed two new superphyla, which are highly stable associations between phyla.

"Our single-cell genomes gave us a glimpse into the evolutionary relationships between uncultivated organisms--insights that extend beyond the single locus resolution of the 16S rRNA tree and are essential for studying bacterial and archaeal diversity and evolution," said Tanja Woyke, DOE JGI Microbial Program Head, in a news release. "It's a bit like looking at a family tree to figure out who your sisters and brothers are. Here we did this for groups of organisms for which we solely have fragments of genetic information."

The findings are huge when it comes to addressing the information knowledge gap in the tree of life. It could reveal new insights into the evolution of these organisms which could, in turn, help future research.

The findings are published in the journal Nature.