The Quest to Kill the Superbug That Can Survive in Outer Space

After the tiny survivors returned from orbit, they showed greater resistance to antibiotics.

Technicians and engineers in cleanroom garb monitor the first drive test of NASA's Curiosity rover. (NASA / JPL-Caltech )

Highbay 1 at NASA’s Jet Propulsion Laboratory (JPL) is one of the most sterile cleanrooms on Earth. Not long from now, NASA’s next big Mars mission, the life-hunting Mars 2020 rover will have its parts attached here and so will the first probe sent to Europa. As long as un-crewed missions keep going to space, their Frankenstein bodies will be attached piece-by-piece in this room.

To sterilize the robots, the hardware is either baked, bathed in hydrogen peroxide steam, or wiped down with the same pure isopropyl alcohol used to clean open wounds. However, there’s one bacteria that has managed to survive in this extreme environment. SAFR-032 is a radiation-resistant bacterial spore found only in spacecraft cleanrooms. Indeed, it takes its very name from its peculiar habitat: SAFR stands for: Spacecraft Assembly Facility,( the R is for the medium in which it’s cultured.)

SAFR-032 has been found in all of NASA’s cleanrooms, from California all the way to Kennedy Space Center in Florida. Its spores have evolved a unique survival tactic where they can build up layers of cells to use as shields that in turn protect their DNA. Not unlike the way we slather ourselves with sunscreen before going outside to protect ourselves from U.V. radiation, endospores create a type of biological fortress until they’re able to find a safer situation and can reactivate their metabolism.

NASA is keen to keep these microbes off of its equipment. The agency’s Office of Planetary Protection is tasked with making sure we aren’t contaminating the entire solar system with earthly bacteria. Its guidelines limit how many viable microbes are allowed on a spacecraft before it’s even granted access to the launch pad. The office was created to make sure that NASA observes the Outer Space Treaty, a legal document drafted during the space race, and now recognized by 105 countries around the world. The treaty forbids space agencies from interfering with the integrity of other planetary bodies in the solar system. In other words, transporting viable microbes from Earth to places like Mars is off-limits.

Scientists whose missions need to comply with the law have been wondering whether space itself might kill off SAFR-032, and so they decided to send it there. The E-mist experiment (Exposing Microorganisms in the Stratosphere) was run out of NASA’s Ames Research Center in Silicon Valley by the microbiologist Dr. David J. Smith and his team. As its name suggests, it was designed to expose a large sample of SAFR-032, swiped from the Mars Odyssey orbiter before its launch to the stratosphere.

Smith’s team sent a balloon 32 kilometers above the Earth’s surface for eight hours, exposing pre-filled cartridges of dormant SAFR-032 samples, 40 million of them in total. In the stratosphere, conditions resemble the dangerous landscape of the Martian surface—it’s extremely dry and cold, and there’s less atmosphere to shield anything from getting blasted by cosmic radiation. The team was hoping to find out how many of the spores would re-activate after exposure to freezing temperatures, increased cosmic radiation, and U.V. radiation, something SAFR-032 is known to be especially resistant to. They were also watching to see how quickly the spores would deactivate.

“When we got the samples back to the lab a couple of weeks later we saw that there was almost a complete kill,” says Smith. “99.9 percent of the entire population was destroyed.” Smith didn’t expect them to survive the journey, so the outcome wasn’t too surprising to him.

SAFR-032 has been tested in the lab repeatedly over the years, and scientists know that UV radiation can kill it if it has enough exposure. But, Smith was surprised by just how fast they were killed. He exposed different pre-filled cartridges to the elements for two, four, six, and eight hours respectively, and after 500 minutes, almost all were irreparable.

“Our results predict that most terrestrial bacteria would be inactivated within the first [day] on Mars if contaminated spacecraft surfaces receive direct sunlight.” That seems like really good news for planetary protection, Smith explains. “Let the rovers sunbathe [and] help keep Mars pristine,” he said.

But, an almost complete kill of 99.9 percent is not a total kill. Out of the 40 million SAFR spores sent to space, 267 were able to reactivate upon their return, and while that’s not very much given the starting number, it’s what many of the remaining 267 had in common that has Smith confounded.

A large number of the surviving 267 spores showed evidence of a very common genetic change called a single nucleotide polymorphism, or a SNP (snip). A SNP is a kind of genetic do-si-do between base pairs when an A changes to a T and so on. It may not result in any change of gene expression, or it may serve to be a benefit, or even cause disease, they aren’t exactly sure. In 2008 a team out of JPL led by Kasthuri Venkateswaran went so far as to send samples of SAFR-032 to live outside of the International Space Station for 18 months. Unlike E-Mist, the ISS samples weren’t exposed at different intervals, and were run in unison with controlled simulations on the ground. Some of the ISS microbes were exposed to less sunlight, and they tended to survive in greater numbers.

But like Smith’s microbes, the samples that were subject to direct U.V. radiation were mostly killed. The few that managed to survive the vacuum of space for 18 months had undergone changes to the proteins associated with genetic expression. Their offspring also showed an even greater resistance to UV-C exposure, the most harmful category of U.V. radiation, than those in the control group on Earth. Nine years later, Venkat and the team are still trying to make sense of the data. “And what’s particularly interesting,” Smith says, “is that those that were alive from the ISS experiment also ended up showing a resistance to antibiotics.” The type of SNPs that changed the survivors from E-Mist were varied. Some experienced an A to a T swap, others a C to a T, and some of those were in cartridges that were exposed for different lengths of time to the sun. While both teams aren’t exactly sure what the genetic changes mean in either of the experiments, they suspect that they may be playing a role in their survival.

For planetary-protection purposes, resistant strains like SAFR-032 pose an interesting problem. Scientists are learning how to kill them, and direct sunlight seems to do the trick. But, on Mars in particular, there are dust storms that sweep up the fine rusty regolith, coating robotic rovers like powdered sugar on a pancake. Over time those layers build up, and while the gentle breeze that is sure to follow can clean the spacecraft, it’s not a guarantee that there won’t be a coating of dirt just thick enough to protect the bacteria from the Martian sunlight.

Inactive microorganisms like SAFR-032 have been found attached to dust as far back as 200 years ago. When Charles Darwin returned to England on the H.M.S Beagle he brought back with him a collection of dust that had settled on his ship while sailing off the coast of Africa. After looking through the microscope he made a note that there appeared to be dead microbes like fungus and bacteria mixed into the dust. Just 10 years ago scientists were able to experiment with some of those 200-year-old samples in a lab, and successfully brought them back to life. What Darwin thought were remains, was just an evolved temporary state of a very living thing.

Bacterial spores—like Darwin’s stowaways—are skilled at using material like particles of dust as life rafts to protect themselves, whether it’s on a ship sailing the open seas of the Atlantic or those sloughed onto the surface of Mars.

Perhaps the most complex issue in relying on direct sunlight to kill hitchhikers is that not all parts of a spacecraft will be exposed to sunlight. Bacteria don’t just conveniently survive on the surfaces of things, but they can work their way into wiring and tiny microscopic crevices in the aluminum-those well hidden and permanently shaded in the unreachable areas are the ones that Smith and the office of planetary protection are most concerned about.

Smith and his team plan on launching another experiment later this year where other spacecraft cleanroom microbes will travel alongside SAFR-032 to space. This time they plan on trying to better understand what these genetic swaps mean for the resistance function of these spores.

“If we’re sending viable biomass to Mars, we want to make sure we’re not going to hit a spot where terrestrial contaminants can start to propagate and take over the environment,” Smith says. Those spots on Mars with ice and any warmer regions are strictly off limits to human missions for that very reason, for now anyway.

Missions like the Europa Clipper, which is expected to fly through a plume on Jupiter’s icy moon sometime in the 2020s, will be more complicated. Because the mission will be looking for extraterrestrial life, it will be all the more important not to send along microbes from Earth.

Back in the cleanroom at JPL, there are several empty rectangular frames lining the walls some 50 feet above the medicinal white floor. Above those are circular mission patches, each representing a spacecraft that’s been built in Highbay 1 and launched to space.  From Voyager to Juno, these colorful badges are the only eye-catching thing about this austere room, with the exception of a spacecraft. Each empty rectangle waits for its own mission. Perhaps one will tell us if life exists elsewhere in the cosmos, so long as we can be certain that our extraterrestrial find isn’t a stowaway from our terrestrial world of wonders.