Northwest scientists look to soil microbes to fuel space ambitions

Yuliya Farris buttons her lab coat as she strides over to a stack of about 10 white boxes at the front of the room. She hits the tops percussively with both hands.

“OK, this is me. First time touching it!” she calls over her shoulder to Marci Garcia, smiling.

Farris examines the stickers plastered on the outside: “Critical Space Item. Handle with Extreme Care.”

“Take one and just keep it,” Garcia tells her.

“Oh, I’m taking all of them,” Farris jokes back.

The boxes arrived at the Pacific Northwest National Laboratory earlier in the morning to much anticipation from these scientists.

The cargo inside — about a hundred test tubes of frozen soil — has made an incredible journey, from a Washington State University research field in Prosser to the national lab in Richland for preparation to Kennedy Space Center in Florida and all the way up to the International Space Station.

“That was a little emotional, just seeing all your hard work go up,” says Garcia, an earth scientist at PNNL. “But we’ve been planning for them to come back as soon as they went up.”

Now, the soil samples are back home in Washington.

Yet, the samples in these boxes contain much more than just soil. There’s millions of soil microbes, which the researchers believe are critical allies to have if we want to feed ourselves in space.

The experiment

More than 50 years have passed since a human walked on the moon. Now, the federal government has sights set on building a basecamp there. But if we’re going to have a successful long-term settlement somewhere other than Earth, we’re likely going to need to grow our own food — for nutrition and our psychological well-being.

The researchers at the Pacific Northwest National Laboratory have been working with NASA for years to figure out how the soil microbiome can contribute to this goal. The soil samples that just returned from space could offer some clues.

Scientists have been studying the impact of microgravity on microbes (though not specially soil microbes) for at least 50 years, often using simulated low-gravity conditions. A review article published in 2018 concluded that the results of that early research yielded mixed and incomplete results, in part because simulated spaceflight on Earth is no substitute for the real thing. NASA has been funding microbial research on the International Space Station for more than decade now.

“Our primary goal here is to understand how interactions between different microbial species change when they’re growing and cultured on the Earth versus when they’re growing and cultured in the International Space Station,” says PNNL microbiologist Ryan McClure.

To do this, they grew communities of soil microbes and added them to sterilized soil collected from Prosser. Half the samples were kept on the ground at Kennedy Space Station. But the other half went to the space station for more than three months, where they were exposed to the higher carbon dioxide and radiation levels found on the space station. The microbes also experienced very low gravity.

Both groups of samples were then frozen at different points to stop their activity, giving the scientists snapshots of how the microbial communities function and change over time on Earth and in space.

“We want to essentially pause the community at that point in time so that we can go through and look at it in a little bit more detail,” McClure says.

The soil samples are still frozen on dry ice when the team opens the boxes for the first time.

“I think they’re probably grouped by the week that they were [frozen]. So zero weeks, four weeks, eight weeks and 12 weeks,” says McClure as he pulls out the first group of soil tubes.

The samples have to be sorted and then dried before any of the analysis can begin.

Microbe power

So why all the fuss about soil microbes? Well, for the same reason we care about them on Earth.

“A lot of what the soil microbiome does here on Earth is really important,” McClure says.

Our soil is alive, teeming with microorganisms that make compost and add nutrients and make plants much happier, increasing crop yields.

“If we want to take those benefits of the soil microbiome that we have here on Earth and start to transfer them to other situations like the space station, an environment where growing plants might be really useful, we really need to understand the details of how these microbial species interact,” he says.

There are more microbes in a teaspoon of soil than there are people on the planet, and their interactions are incredibly complex.

“They call it community. It’s like humans: We all live and interact and share some resources with each other. It’s the same way on the microbial level,” says Farris, the biomedical scientist.

To get a clear picture of their interactions, the team had to simplify things. This meant going from thousands of microbe species to just eight kinds of bacteria that are known to work together.

“They all visually look different. They all smell different. And they all have … their own little key roles just even in acting as a community together,” Garcia says.

The soil microbes in these tubes interact with each other in a variety of ways. For example, some will break down a kind of carbon in the soil called chitin, and in turn produce by-products that other microbes need.

But a big question for these researchers is whether the microbes will be able to share those nutrients when there’s no gravity. McClure thinks the answer is yes.

“If two people are in a room and one of them wants to interact with the other by throwing a ball, under a condition of low gravity, that ball’s for sure going to get there. It’s just much easier to pass things to your partner,” he says.

A ball tossed in space will just keep going without gravity (or friction) to slow it down.

“And I’m wondering if that might be the same thing that we see with these microbial communities where nutrients and these chitin breakdown products … are easier to share,” he says.

The researchers won’t know this hypothesis is correct until they look more carefully at the samples.

The dirty work

In the lab, Garcia pulls a vial of space soil off a freeze-dryer called a lyophilizer, which releases a throaty groan in response.

“I love this smell,” she says, catching a whiff of the now-dry soil-microbe mixture. “It’s like a breath of fresh air.”

Once dry, the soil samples are ready for analysis, and the researchers are using several tools to understand what happened to the microbes in space.

“My next few weeks are going to be right here in this lab, pretty much at this bench,” she says, looking at the racks of tiny sample tubes she will be prepping to be tested.

The team will analyze DNA to figure out how the microbe populations change in space.

“It’s going to tell if they grew or not,” Farris says. “Or maybe they all died — who knows? But we’re hoping that did not happen.”

They look at RNA and proteins, which gives them clues about what the microbes were doing.

“A microbial species or a community could be identical between two sites or between two conditions. But that doesn’t really matter if the processes that are being expressed are very different,” McClure says.

The scientists also look at metabolites that show how the microbes are interacting with each other.

“It’s when you merge these four puzzle pieces together that you can get the best view of the complete community,” he says.

The research team will run all of these analyses this spring to see how the microbes fared on the International Space Station. And the data they collect will start to reveal the best mix of microbes we should be harnessing to grow food in space.

“One day, we will be traveling to other planets, to different stations, and we can grow food that will be tasting just like it’s growing on Earth,” Farris says. “It’s in some way far off, but… give it another 10, 20 years and it [won’t] be.”