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UW–Madison assistant professor of soil science Thea Whitman stands next to an isotopic gas analyzer in her lab in Hiram Smith Annex on the UW–Madison campus. Photo by Michael P. King
UW–Madison assistant professor of soil science Thea Whitman stands next to an isotopic gas analyzer in her lab in Hiram Smith Annex on the UW–Madison campus. Photo by Michael P. King

In a small utility room in UW–Madison’s Animal Science Building, the world’s smallest and most precise forest fire is burning. The fuel today: 100 grams of white pine. The chips sit inside a steel tube enclosed in an oven-sized electrical furnace. In a few short hours, this woody mix of organic molecules will be pyrolyzed, reduced almost entirely to an essential grid of carbon. You’d call it charcoal, but assistant professor of soil science Thea Whitman calls it pyrogenic organic matter, or biochar.

Burning wood is sometimes pleasantly chaotic and sometimes a terrifying force of nature, but for this fire, Whitman and first-year Ph.D. student Nayela Zeba seek absolute control. Biochar may have a big role to play in understanding — and even combatting — climate change. But not without control.

The furnace, dubbed the Charcoalator, was custom-built by Whitman’s colleague and former labmate, Akio Enders, who drove through a February snowstorm to deliver it from Cornell University. Argon flows steadily through the chamber, the neutral gas crowding out any oxygen that would tip combustion out of control. A digital thermal controller raises the temperature by 5 degrees Celsius per minute until it reaches the desired temperature — usually between 300 and 600 degrees (572 and 1,112 degrees Fahrenheit) — then holds it for three hours. Water cooling halts the charring process and prevents spontaneous combustion when opening the chamber.

Every soil scientist knows the challenge of keeping things clean. In her primary lab, Whitman has a “very clean room” and a “pretty clean room.” The Charcoalator, however, is inescapably dirty; by design, it’s housed in a different building altogether. The grinding and sifting of char has only been happening for a few weeks, but already a fine black dust lingers. Zeba has resigned herself to an all-black wardrobe — only the face mask and lab coat are white — for the days she bakes the biochar.

While fire has a homogenizing impact on biological materials, not paying enough attention to the differences has led to some inconsistency in the way that we study and talk about biochar. The Charcoalator — and the techniques being refined by Zeba — are designed to bring some rigor to Whitman’s work in the field. “If you look at these chars under a scanning electron microscope, it looks like plant cell structure; you can still see the microstructure inside of a plant,” says Whitman. “Which means that different biomass will give it different properties. By being really consistent about the way we produce it, we can be more scientific.”

Ph.D. student Nayela Zeba places a stirring paddle in the Charcoalator, which is loaded with eastern white pine biomass ready to be pyrolized. Photo by Michael P. King
Ph.D. student Nayela Zeba places a stirring paddle in the Charcoalator, which is loaded with eastern white pine biomass ready to be pyrolized. Photo by Michael P. King

Escalating fire seasons and a growing interest in producing energy from agricultural biomass have spurred soil scientists and climate change advocates to look more closely at the role of carbon in soil. It’s the very basis of life on Earth. It’s a critical component of some of the most important greenhouse gases. There is twice as much carbon stored in soil as there is in the atmosphere. And yet we’re still not entirely clear on the myriad ways that carbon moves through and influences Earth’s biogeochemistry. How is it that carbon in a corn stalk will be returned to the organic mix of the soil inside of a year while it can remain stable in biochar for centuries? Can we use this to benefit agriculture and to fight climate change?

These very big questions have some very small answers: microbes. “How is [the char] being perceived by the microbes?” asks Zeba. “How are they metabolizing it? What microbes are doing it? Because it’s something very odd that you wouldn’t expect, but microbes can do everything.”

Just a Handful

“There are more microbes in a handful of soil than there are people on Earth,” says Whitman. “That’s one of my favorite go-to facts.”

She situates her lab’s work at the nexus of soil biogeochemistry, microbial ecology, and global environmental change, but Whitman came late to both soils and microbiology. As an undergraduate at Queens University in Kingston, Ontario, she focused on biology and the environment. Not until her final year did she take a soils class.

Soils integrated her interests in climate change and carbon, so she looked into the field for grad school. Not long after that, she saw “that microbes were basically controlling everything that I was interested in, and I realized I should probably engage with them.”

As both a teacher and an investigator, Whitman’s exploration of microbes begins with picturing the soil environment. With billions of organisms per tablespoon, it’s easy to imagine the soil as an unbroken panoply of life. Yet zoom in, and you’ll find a crazy-quilt universe. There are massive sand grains and tiny grains of clay. Bacteria themselves vary in size by several orders of magnitude. Moisture clings to some particles, while other areas are parched. Bacteria and fungi may teem around a leaf particle while millimeters away there is so little food and moisture that the bacteria have formed dormant spores that may not awaken for decades.

“Think about how dynamic the water environment is in soil,” Whitman says. Soil can be dry as any desert; then a simple, soaking rain flips the switch. “Bacteria in the soil are still effectively aquatic organisms, living in films of water. I think it’s kind of an extreme environment. I’m not the first person to make that argument.”

Their ability to adapt to a range of extreme environments gives bacteria a gee-whiz, trivia-question level of fame, and over the course of 3.7 billion years, they’ve leveraged that talent into an almost absurd level of diversity. No food? Scavenge energy from heat, light, or even sulfur. No oxygen? Go anaerobic. No water? Go dormant. Adapting to these extremes, over billions of years, bacteria have “discovered” some of the most important chemistry on the planet. Some of our most significant discoveries — from antibiotics to the nitrogen cycle that fuels agriculture — are microbial innovations. As masters of adaptation, bacteria are the most abundant organisms in soil, with a rich and necessary complement of fungi, viruses, archaea, and single-cell protists. Worms, mites, springtails, and all manner of insects are the giants that round out the census.

By one estimate, soils contain a quarter of the world’s biodiversity. Just picture it: 9 billion organisms, from perhaps 10,000 species, existing together in a single tablespoon. And yet, according to some theorists, it’s possible that most of these bacteria are only really perceiving organisms that are 20 micrometers away. “Soils are among the most diverse environments with the most different types of organisms,” says Whitman. “The question is: Why?”

This custom-built, automatically controlled growth chamber is being used to grow plants with a carbon-13 enriched atmosphere. The plants will be pyrolyzed in the Charcoalator and used in soil incubations, where the team will determine which microbes consume the charred organic matter.
This custom-built, automatically controlled growth chamber is being used to grow plants with a carbon-13 enriched atmosphere. The plants will be pyrolyzed in the Charcoalator and used in soil incubations, where the team will determine which microbes consume the charred organic matter. Photo by Michael P. King

One of her favorite exam questions asks students to write the autobiography of a microbe. The same essential question governs her lab’s work. “How do we better understand soil microhabitats effectively?” she asks. “Coming back to that is really essential for us as scientists — understanding and asking good questions about that environment. If you don’t reality-check yourself every so often, you can easily go off on paths that don’t necessarily make sense.”

From Compost to Biochar

Growing up in a scientific family in rural Nova Scotia, Whitman was the composter. “That was one of my chores at home,” she says. When her municipality began providing compost pickup while she was in high school, it fit with her emerging ideas about the human quest for sustainability. And when her graduate education turned toward soils, her initial plan was to try to calculate the global carbon impact of composting versus not composting.

Instead, Whitman discovered the burgeoning field of biochar. Dark, carbon-rich soils in the Amazon had been observed and cataloged over the last 150 years, but it wasn’t until the latter part of the 20th century that scientists began to understand that these uncharacteristically rich soils had been deliberately created by prehistoric peoples. Unlike the contemporary “slash-and-burn” agriculture often blamed for destroying rainforests, these people had used “char-and-burn” methods instead. By accident or by design, they lit controlled fires that produced relatively more char and less ash and then worked the charred organic matter back into the ground.

In 2008 Whitman joined the lab of Cornell University’s Johannes Lehmann, who had helped uncover the origin of this “terra preta,” or dark earth. His lab, broadly interested in nutrient cycling in soil, was exploring the potential of biochar for contemporary agriculture.

Soil is a carbon storehouse, but it’s also a major carbon producer. Under the right conditions, soil microbes can take apart almost any organic thing inside of a year, releasing that carbon as carbon dioxide or methane.

That cycle changes when organic matter is burned under the conditions mimicked by the Charcoalator: oxygen deprived, between 300 and 600 degrees Celsius. Most organic molecules are vaporized away, leaving a lattice of almost pure carbon.

So take corn stover — the rough-hewn leavings of a harvested cornfield — and plow it back into the soil. Inside of a year, it will be almost completely decomposed, the carbon cycle complete. But char that carbon properly, and it lasts significantly longer. “It’s not sequestered permanently,” explains Whitman. “But you’re talking decades, hundreds of years, thousands of years in residence times.”

In other words, pre-Columbian subsistence farming offers our carbon-challenged economy the precious commodity of time, a buffer — compounded yearly — in which to store our dangerous carbon surplus.

In the best-case biofuel scenario, biochar production would be a triple play. First, it could produce energy from the initial process. Second, as a soil amendment, it would sequester soil carbon and improve soil quality. Last, by preventing anaerobic decomposition, it could prevent the even more threatening emissions of methane and nitrous oxide — greenhouse gases many times more powerful than carbon dioxide.

Thea Whitman collects soil samples at a severely burned site in Canada’s Wood Buffalo National Park in June 2016. The samples were later analyzed to characterize the area’s soil and microbial communities. Photo by Ellen Whitman
Thea Whitman collects soil samples at a severely burned site in Canada’s Wood Buffalo National Park in June 2016. The samples were later analyzed to characterize the area’s soil and microbial communities. Photo by Ellen Whitman

“Biochar sits at the nexus of all these really interesting areas — some of our most pressing global issues,” says Whitman. Climate change, food security, biofuel and bioenergy systems, stabilizing carbon, deforestation, and even women’s issues because, in many cultures, the women gather the fuel and tend the cooking fires. “It’s really interesting, and it’s also certainly complex,” she says. “There are definitely systems in which biochar makes sense.” The goal right now is to continue to identify and better understand those systems.

Is it going to make sense in the high-input industrial agriculture of North America? Not necessarily. Transporting biomass and then biochar all over the landscape would probably negate the carbon benefit. But if the baseline scenario is simply letting that biomass rot in an anaerobic heap, then maybe it would make sense.

While earning her master’s degree, Whitman looked at low-tech cook stoves and did simple incubation studies measuring how quickly char decomposes compared to the original biomass. It’s not 100 percent stable in the first year. And sometimes the char appears to prime the soil’s metabolism, ramping up the carbon cycle. “If you’re adding biochar to soil to sequester carbon and it’s actually increasing decomposition rates of your existing soil carbon, that’s a problem,” she says.

She dug deeper, looking for nuances. Learning how and under what environmental conditions the char persists led to deeper questions. “Really understanding the mechanisms that are driving the carbon cycle is important for predicting in which systems you will see which effects and over what time scales.”

Microbes were clearly a huge part of this, but Whitman ran into a problem: Because carbon is such a fundamental biological building block, it was hard to delineate the biochar carbon from that already in the soil.

A burn site in Canada’s Wood Buffalo National Park where Thea and Ellen Whitman and their colleagues collected samples for analysis in June 2016. Photo by Thea Whitman
A burn site in Canada’s Wood Buffalo National Park where Thea and Ellen Whitman and their colleagues collected samples for analysis in June 2016. Photo by Thea Whitman

As she was banging her head against a wall of chemical equations, she hit upon some sleight of hand, a way to use carbon-13 isotopes to tag the carbon. Building on a technique that could delineate two sources, Whitman devised a way to separate three carbon sources — soil, char, and plants. “I think this works,” she recalls thinking as she hurried down the hall to whiteboard it for a colleague. “The idea is so simple, really, that it’s really just like three equations.”

Like its better-known radioactive cousin carbon-14, carbon-13 is a rare variant of the element that makes up less than 1 percent of natural carbon. The extra neutron allows it to be detected by sensitive equipment. By growing biomass in a carbon-13-enriched atmosphere, Whitman could char and then mix it with soil. A gas analyzer could then measure what portion of the respired carbon dioxide came from existing soil carbon and which came from char.

The more carbon-13 in the system, the more powerful the tool. For example, in higher proportions, the carbon-13 would get built into the bacterial DNA. If you extract the DNA using standard techniques and then put it into an ultracentrifuge — that’s 200,000 times the force of gravity for four days — the extra neutron makes the DNA physically heavier, and it sinks to the bottom.

“What’s cool is we can say conclusively this organism took up that carbon,” Whitman says. “There’s not really another way to say that.”

The knowledge doesn’t come cheaply. In June, the first jack pine seedling entered the lab’s new carbon-13 greenhouse. Whitman’s back-of-the-envelope calculation suggests that 100 liters of carbon-13, costing about $8,000, will produce only about 54 grams of jack pine destined for the Charcoalator.

Sibling Harmony

Thea is not the only Whitman daughter whose work is catching fire. Her younger sister, Ellen, is a Ph.D. candidate at the University of Alberta and a fire research assistant with the Canadian Forest Service. Interested in wildland fires and their interface with cities, Ellen began studying urban planning but eventually jumped into spatial analysis and the examination of things from an ecological angle.

“Being interested in science just had to do with growing up in our family,” says Ellen. Science fairs were a big deal, and when things got slow, their mom pulled out a microscope and pond water. “Thea knew early on that she was interested in the biological side of things,” adds Ellen. “She was mostly interested in climate change and carbon and the more global effects.”

Ellen’s and Thea’s worlds converged with a series of lightning strikes in the far north during the summer of 2014. That year, the Northwest Territories, following an extended drought, experienced what official reports designated “a truly exceptional fire season.” Nearly 400 fires burned a record 13,100 square miles. The fires dipped southward into Wood Buffalo National Park, which straddles the border between the Northwest Territories and Alberta.

Thea was generally aware of the big fire season, and then she learned that Ellen would be conducting extensive field research among the burns. “A lot of the questions that we’re asking in a biochar context can also be asked in a fire-affected ecosystem context,” she says. And the boreal forests of Canada are a massive account on Earth’s carbon ledger. With Ellen focused on questions at the square-kilometer level, what if Thea paired that with findings from the microscopic end of the spectrum?

Ellen ran the first field season, with Thea joining in 2016. Hitching rides on inactive fire choppers, they were able to access areas deep in the park. It’s not exceptionally hilly, though the karst landscape — barren, rocky, and porous — includes sinkholes. A UNESCO World Heritage site, it is home to a huge salt flat, the world’s largest inland river delta, and wild buffalo everywhere.

Most important, the boreal forest contains lots of spruce, jack pine, and aspen. It’s far enough north that the trees are not giants, but the region is rich in peat-forming wetlands. Overall the ecosystem stores immense amounts of carbon — an estimated two to three times as much carbon as stored by tropical forests.

As a fire-adapted ecosystem, fire is to be expected. But more intense fire seasons suggest both the possible impacts of climate change and a substantial enough release of carbon to fuel climate change.

It’s hard to imagine that a changing fire regime won’t shift ecosystem types. “An ecosystem that is adapted to a 100- or 150-year fire return interval is just not going to persist unchanged if that interval goes down to 20 years,” says Thea. It’s also important in terms of climate feedback cycles. “Understanding and predicting how fires will affect those carbon stocks is really important.”

Glass jars of soil are connected to an isotopic gas analyzer in Thea Whitman’s lab.
Glass jars of soil are connected to an isotopic gas analyzer in Thea Whitman’s lab. Photo by Michael P. King

A recent meta-analysis published in Nature looks at how changes in fire frequency affect soil carbon stocks. The authors predict that, overall, more frequent fires will decrease soil carbon stores. But different ecosystems behave differently, and the paper suggests that a moderately increased fire frequency might actually increase carbon storage in boreal forests.

Forest fires, of course, result in an immediate and major loss of carbon. But what remains is transformed into biochar, a relatively more stable form. Could there actually be a sweet spot where an increase in boreal forest fires would help our carbon balance? Whitman is skeptical. “Much more research needs to be done to be able to predict this conclusively.”

Analyzer ‘X’

For now, the challenge of climate change makes it easy to stay focused on the story of carbon. “There is no question that it is occurring; there is no question that the effects are going to be severe,” she says. “It’s a huge concern in my day-to-day life. It feels like one of the biggest, if not the biggest, challenge of our time.”

At least the quantum leaps happening in microbiology are helping delineate carbon-cycle challenges. Whitman is pairing the explosion in genetic decoding and related statistical techniques with her own bespoke tools.

In addition to the Charcoalator and her carbon-13 growth chamber, in the corner of her lab’s “very clean room” sits a curious pairing of a $50,000 isotopic gas analyzer and a collection of Mason jars. The jars and the analyzer are connected by a jumble of red tubing, valves, circuit boards, and the custom software of postdoc Timothy Berry. The still-unnamed system — Berry and Whitman agree that a generic acronym is unacceptable — will streamline the carbon-13 work. By incubating various soil types and microbial communities with the tagged carbon, they’ll be able to gather far more detailed data on biochar interactions.

It’s an exciting time to be a microbiologist, yet Whitman cautions that, amid the data deluge, we need to be modest about our limited ability as humans to pick out and think about stories. “In a paper, you interpret your data as a story,” she says. But recall those billions of microbial citizens in her proverbial handful of soil. “There’s also a million other narratives in there that we’re not pulling out,” she says. Even as we augment our analytical powers with artificial intelligence, there are still too many narratives. “I think we’re still going to be limited by the human brain.”