The Ancient Memories of Microbes (And How They Could Heal Forests After Fire)

Jul 20, 2018

Field Technician Zach Swainson holds up the gravity core filled with 300 years of lake sediment.
Credit Melodie Edwards

In the last few years, researchers have discovered the earth is literally filled with microbes, those little single-celled critters we sometimes call germs. They’ve even been found living as deep as the earth’s core. And they say these microbes could help us gain access to thousands of years of knowledge. Now scientists at the University of Wyoming want to use those layers of ancient history to help us recover from wildfires as the climate warms up.

University of Wyoming Geology Researcher John Calder pumps up his rafts and sets out across an alpine lake in the Snowy Range, elevation nearly 11,000 feet. He says at the bottom of this high lake are undisturbed layers of living bacteria. Out on the water, his students Caleb Fackrell and Zach Swainson use a depth sounder to find the deepest spot in the lake.

“We get the deepest because that’s where the most sediment per year will fall and accumulate on the bottom of the lake,” says Calder, giving them a greater slice of history to look for microbes in.

Once they find that deep spot, they lower down a large clear tube called a gravity core. It has a plug on the top that Calder says works kind of like your thumb over the top of a straw to hold liquids inside the tube.

“We can drop it slowly down to the bottom and it’ll pick up like a foot of mud or so,” says Calder.

Swainson squirms out on his belly across the raft to pull the tube out while Fackrell mans the rope. I ask Fackrell how he’ll know when the tube reaches the bottom.

“The rope slackens,” he says. Then, “I just felt it snap.”

“So now we’re pulling up,” Calder says. “There’s a little bit of suction.”

A lot of suction. Swainson groans under the strain of bringing it back to the surface. It’s like hauling in a huge trout, and they’re just as happy with it.

“Keep it straight up!” Fackrell yells. “Keep it straight up. We got a mother!”

“Oh my gosh!” Swainson says when he sees the tube he’s finally brought into the raft.

“This is a lot of mud!” agrees Calder.

Thirty centimeters worth, to be exact. In lower elevation lakes, they might only get one centimeter. Calder says every centimeter represents more than ten years of time. That means they’ve just pulled up 300 years of sediment.

And by studying this mud they can understand how microbes got buried in the earth in the first place. Calder says when plants, or even a burnt log from a fire, fall in the water, it all drifts down to the bottom, carrying microbes with it. That matter turns to muck, but the microbes go on living, just very, very slowly.

“Their ancestors are there and it looks like the same community that was on the surface hang out below and they slowly reproduce in really inhospitable conditions.”

Calder says there’s a lot of microbes in the world, about half as much by weight as there is biomass on earth. And the diversity of these critters is vast--in the trillions, each playing roles in the environment.

Each tiny vial contains the DNA of microbes from around Wyoming. Botany Researcher Joshua Harrison expects to fill many freezers full.
Credit Melodie Edwards

Calder says, ever since DNA sequencing came along, it’s been a golden age in microbe research. People are quickly learning how important microbes are in the human body. But they haven't quite caught on to how important they are in nature. Calder says if you really dig that kind of work, Wyoming’s the place to be.

“Wyoming’s good because we don’t have many people,” he says. “We have so few people that we’ve got landscapes that have been relatively untouched.”

They’re untouched but also wide-ranging, from high mountains to low deserts, from hot springs to archaeology sites. And thanks to a $20-million grant by the National Science Foundation, UW is now sending out an army of scientists to take samples around the state. 

The crew puts the tube of lake mud on dry ice and takes it to a lab at UW where a new robot will process all the samples. Botany researcher Joshua Harrison is one of the robot’s handlers.

“The first step in the process is to do the DNA extraction,” says Harrison. “Basically, what that entails is breaking up the cells and getting the DNA in solution.

He punches some buttons and the machine comes to life. Harrison says this machine will help speed up the process of cataloging the huge array of microbes that have already started pouring in from all over the state.

UW Geology and Geophysics Professor Bryan Shuman says the robot will help them literally squeeze a lot of data out of these microbes, and fast.

“It does feel like this brand-new arena where we know this is important, but we don’t know who’s out there and what they do.”

So new, in fact, that it’s not entirely clear how they’ll apply all this science. But one goal is to create products with these microbes to help people deal with a warming climate that has played a role in more wildfires. 

Shuman says the idea isn’t as farfetched as you might think. In fact, he says, the microbe industry started in Wyoming.

“Some of the microbes that were found in hot springs in Yellowstone actually led to a major revolution in genetic studies,” he says, “which is kind of surprising, but has launched a whole biotech industry.”

The microbiology industry is worth billions of dollars these days. People use them in pharmaceuticals, to make clothes, to ferment foods. Shuman says UW researchers are also testing to see whether certain microbes could be used to eat up oil spilled in sensitive landscapes. Some of those microbes we dredged up from the alpine lake might have practical applications too.

“Do they tell us it was warmer or dryer, do we learn something about the conditions that made it more likely to have burned?” he asks. “Also, maybe we learn something about how microbes play an important role in reforesting areas after they burned.

Who knows, some microbes might find charcoal delicious. If released onto a burned landscape, they might make the soil fertile again for plants and trees to flourish.

Out at the lake, Researcher John Calder says, as the climate warms, more fires are expected to ravage the West.

“We’re racing against the clock to understand future climate change,” he says, “and we’re racing to understand the past in hopes to better be prepared.”

The key to getting prepared, Calder says, may be hiding in remote lakes under layers of mud thousands of years old.