Hardy microbe’s DNA could be a time capsule for the ages

Information was encoded in the DNA of a strain of salt-tolerant Halobacterium salinarum.


Joe Davis is looking for the ultimate time capsule. He wants to preserve a record of humanity that could survive for eons, to be read by successors to Homo sapiens on Earth or by sapient extraterrestrials. He has now found the right medium, he thinks: the DNA of an odd microbe that lives in deposits of rock salt. He believes this archive—protected by salt and renewed by the microbe—could possibly survive for hundreds of millions of years.

It’s a visionary idea, owing as much to art as science. Davis, an artist affiliated with a Harvard University biology lab, bridges both worlds. His project took a step forward last week with a study posted on bioRxiv, a preprint repository. In the study, Davis and his colleagues show they can encode information in the DNA of Halobacterium salinarum (Hsal)—a hard-to-kill, salt-tolerant microbe that has, on average, 25 backup copies of each of its chromosomes.

Other researchers have explored the storage potential of DNA, which packs the equivalent of about 300 megabytes of data into the nucleus of a human cell. But Davis is combining that capacity with the resilience of an extraordinarily hardy organism. “If you want to keep data for a long, long time, the best way to do that may be to hold it inside cells and utilize the cellular machinery for DNA self-repair,” he says. “They can conveniently and economically reproduce themselves with little or no intervention.”

Jeff Nivala, a biological engineer at the University of Washington, Seattle, who studies halophiles and DNA storage, agrees. “For archival storage over millions of years, this might be a great application,” he says. “If all other life is destroyed on Earth, and this is the only thing left, maybe that information could propagate on its own.”

Davis has no formal training in biology, save for a single course at a Mississippi junior college in the 1960s. But he has a record of turning biology into performance art that sometimes leads back to science. In 1987, for an artistic venture called Microvenus, he encoded a depiction of the female form into the DNA of living Escherichia coli bacteria—a feat that is widely cited as the first experimental demonstration of DNA data storage.

Now, Davis is working with a tougher microbe than E. coli. Hsal can withstand desiccation, thermal extremes, prolonged vacuum, and intense radiation. Davis has even exposed it to ethylene oxide, a poisonous gas used to sterilize laboratory equipment, with no discernible effects. Hsal does have a kryptonite: Immersion in freshwater bursts its cells. But when entombed in briny pockets within salt crystals, Davis muses, Hsal could be “the thing that couldn’t die.”

For commercial DNA storage, in vitro techniques—encapsulating synthetic DNA in glass or stainless steel—are more advanced than in vivo approaches, says Emily Leproust, an organic chemist and CEO of Twist Bioscience. But living things could preserve DNA far longer, says Davis, who has revived hibernating Hsal cells from salt deposits hundreds of millions of years old. His collaborator, Harvard geneticist George Church, considers it “totally plausible” that the cells found deep within stable crystals survived all this time in a dormant state. The cells stop growing, and their DNA remains unchanged except for gradual degradation, he says. “But they can also replicate quickly when they need to,” he adds, repairing damage and generating lots of copies for researchers to work with. “So Hsal appears to be a good choice.”

Jocelyne DiRuggiero, a Johns Hopkins University biologist and Hsal expert, regards the plan as “a cool idea.” Besides enduring environmental stresses, she says, Hsal is good at removing reactive oxygen species that harm DNA. With minimal nutrients, an Hsal colony could hibernate in salt for hundreds of thousands of years or more, she says. The microbes would not grow or reproduce, she says, and would only use energy to make repairs and counteract threats, such as DNA damage from cosmic rays.

The first step in the new work was to encode data in Hsal’s DNA. Davis chose the coordinates for a 3D picture of a needle and egg—objects in a Russian folktale about a wizard who hid his soul in the tip of a needle concealed inside an egg. After Davis synthesized the DNA, Alexandre Bisson, a biologist at Brandeis University, attached it to a site in the Hsal genome that wouldn’t affect the microbe or produce anything in the cell. Bisson encouraged the modified halobacteria to replicate and sequenced their DNA to ensure the new code was unaltered.

To learn more about the microbes’ potential as time capsules, Bisson is studying how they behave in salt crystals, which “is largely a mystery.” Over the course of 10 years or more, he plans to compare Hsal strains encased in salt with “parent” or control strains kept in a freezer to see whether any mutations occur in the presumably more active salt strains. That data will help fill a void, though extrapolating it to millions of years “would be a stretch,” he says. Bisson also plans to use fluorescent proteins to find out whether the organisms stay trapped within the briny pockets that sustain them or if they move around.

Davis hasn’t lost sight of the project’s primary motivation. “What kind of legacy should humans leave behind as a species?” he asks. Davis doesn’t claim to know; he plans to gather input from scientists, historians, artists, poets, and philosophers. But he wants to safeguard more than just information. “I want to preserve the meaning,” he says.

source: sciencemag.org