DNA Sequencing Led Researchers to Discover "Microbial Dark Matter"

Scientists have gotten pretty good at sequencing genomes: We've gotten complete sequences of humans, Neanderthals, all sorts of endangered species, and even pathogens such as malaria. But when it comes to the massively diverse world of bacteria, researchers have only scratched the surface.

A recent project by the Department of Energy's Joint Genome Institute has taken a huge leap forward. The team, whose research was published in Nature, sequenced the genomes of 201 bacterial species and archaeal cells.

Those species were sampled from nine environments diverse and extreme enough, like hydrothermal vents, that researchers could reasonably expect to hold unique species. And that's what they found. None of the 201 species had ever been sequenced before. As the authors write, "our single-cell genome data set provides an 11% greater coverage of known phylogenetic diversity than currently available genomes."

"This is what we call 'microbial dark matter,'" Tanja Woyke, a researcher at the DOE's Lawrence Berkeley National Laboratory, said. "They are branches in the tree of life that have no representatives."

Researchers discovered relationships between bacterial species that they never would have known existed without genetic data, and based on those findings, suggest forming a pair of new superphyla combining previously-known phyla of bacteria and archaea. The researchers suggest Patescibacteria, or "bare bacteria," for the former, and DPANN for the latter.

Figuring out the genetic code of microbes is important because it can help scientists cultivate them in labs. There are untold numbers of unidentified bacteria that could lead to new drug discoveries and advances in biofuel and genetic engineering.

"Only a few percent of all microbes that exist we can cultivate in the lab. We hope that now that we have some genomic insight, the scientific community will pick up on this data and people can try to do some specialized cultivation methodologies," she said. "It's useful to have this genomic data, but we're hoping it can lead to scientists doing new experimentation on them."

One of the reasons we have such a poor knowledge of microbial genomes is because isolating single cells can be difficult. If you've been following the news, you know that bacteria can live just about anywhere: In clouds, under a mile of ice, in volcanoes, and that sort of thing. Woyke says that taking an environmental sample and trying to isolate the DNA from a single bacterial cell is something that scientists are still struggling with.

"Isolating a single cell sounds easy, but it's not easy," she said. "Everything has to be extremely clean, there's often problems with free DNA floating in a sample."

They've turned to metagenomics, where they will sequence the entire genome of an environmental sample, which could include dozens of species of bacteria. They then go back and try to piece it together. This can tell scientists what exists in a certain environment, but it makes it difficult to create an entire genome. But with a technique known as binning, researchers can sometimes separate out individual organisms.

Sequencing as a whole, Woyke says, is "becoming more of a commodity," but annotating and creating a library of genomes is still an intensive task that can take a long time and cost a lot of money. Her lab is going to continue trying to sequence the genomes of bacteria in hopes that some of them can become useful to humans.

"We can't say 'OK, we did one today, we're going to be able to do 1,000 tomorrow,'" she says. "We're still only at the bottom of the hill, but it's exciting because there's still a lot of dark matter to process."