Newswise — Under our feet lies a key resource for environmental health and human wellbeing. Every day, we walk across the substrate that provides global food security, the habitat for one quarter of the world’s biodiversity, and a carbon sink with huge storage potential. For this critical role, the United Nations declared this to be the “International Year of Soils.”

But none of these benefits would be possible without carbon-transforming microbes, fungi and decaying debris. This organic matter enriches the soil and can either drive the storage of carbon into the ground or release carbon into the atmosphere. Increasingly, human activities and climate conditions are disrupting this underground ecosystem, depleting this non-renewable resource. Yet scientists at EMSL are developing new methods to understand these dynamics, leading to insights and tools that could lessen our environmental impact and create more sustainable approaches to land management.

Traditionally, soil has been studied by bulk analyses to determine percentages of essential elements, such as carbon, or quantify various components of soil – the clay, silt, detritus and so on. Some techniques, such as thermal degradation, also get at molecular-level composition of functional groups.

“But there hasn’t been enough information to write a chemical formula,” says Nancy Hess, lead for the Terrestrial Ecosystem & Subsurface Science Theme at EMSL. “In every other branch of chemistry, the ability to write the relationship between reactants and products is something we take for granted. That’s been entirely missing in the characterization of soil organic matter.”

Without that level of detail, it’s impossible to make accurate models that can show how soil chemistry might change with climate, alternative agricultural practices, or other ecosystem perturbations.

To address that big gap, EMSL researchers have been developing high-resolution spectrometric techniques that can measure the mass–in parts per million accuracy–of thousands of organic molecules that exist in as little as a thimbleful of soil. When combined with information from other techniques such as nuclear magnetic resonance, infrared or fluorescence spectroscopy, even more information about these molecules can be teased out.

“These new methods are revolutionary,” says Hess. “They allow us to characterize soil in terms of molecular composition and in a spatially resolved way. That’s important because soils are incredibly heterogeneous.”

The Nitty GrittyOne of the scientists spearheading many of these new spectrometry efforts is Malak Tfaily, a postdoc at EMSL. She’s working with numerous researchers at other institutions (EMSL users) to understand how soil organic matter (SOM) behaves under altered environmental conditions.

“Right now, there are not many studies that talk about the actual composition of SOM,” says Tfaily. Without that knowledge, it’s difficult to know how climate change could affect these crucial soil elements.

Tfaily also worked with statistical approaches to help scientists correlate organic matter data with genomics. In this way, soil microbial transformations of elements like carbon can be linked to genetic information about the microbial community. Then, scientists can decipher not only the chemical reactions taking place, but also discern which microbes might be responsible for those reactions and the metabolic pathways involved.

For Hess, this innovative approach is helping her investigate the surprising results of a 17-year “reciprocal experiment” on soil transplants from Rattlesnake Mountain, a treeless sub-alpine ridge just a few miles from EMSL. There, to mimic environmental changes in climate warming, core samples from the bottom of the mountain were placed at the cooler and wetter 3,500-foot summit. In turn, the upper soil samples were replanted near the warmer and drier base. Then researchers looked for microbial genomic changes that might reflect adaptations in structure and function, and any resulting changes in soil chemistry caused by this change in climate.

Although the work is still in its early stages, researchers have already examined about 200 different soil samples and identified 300,000 different organic molecules. Generating a list of that size has never been done before, says Hess. They can assign chemical formulas to about 70 percent of those molecules. But it’s still just a list.

In this study, the microbes that relocated up to the summit didn’t adapt to the cooler temperature zone as expected. Hess wants to relate that long list of molecules to genomic data from the microbial community and information about enzymes the microbes are making.

“We’re really looking for evidence of activity,” Hess says. “That’s very different from the traditional approach of soil characterization where someone might take a sieve and separate the soil into fractions based on particle size.”

The Deep FreezerAnother study benefitting from EMSL’s mass spectrometry expertise is a study on permafrost supported by the DOE Joint Genome Institute (JGI)-EMSL Collaborative Science Initiative. Tfaily is one of 18 mass spectrometry experts at EMSL working on user projects.

Understanding carbon cycling in this frozen territory is critical, says Virginia Rich, a molecular microbial ecologist, from the University of Arizona who is leading this study. Permafrost is a big “freezer” that currently stores about twice as much carbon as the atmosphere. As the freezer thaws from climate change, that carbon will become available to microbes.

“So, it’s a big open question: How much of that frozen carbon will be released? We also want to know if that carbon will be respired as CO2 or as methane, which is 32 times more potent as a greenhouse gas over a 100-year time frame. This dynamic controls whether thaw will create a positive feedback to climate change,” she says.

Rich works with a team of researchers at a permafrost site in the Arctic. With advanced monitoring equipment, her colleagues collected detailed field observations of methane isotopes and fluxes from the study site–more than have ever been published before. Combining those observations with soil samples, Rich and her colleagues can then ask: What’s in “the guts” of the peat that leads to those emissions? Further, with the proteomic data Rich anticipates getting at EMSL this summer, the researchers hope to determine what the microbes are actively expressing. With all those levels of data, scientists can follow the organic matter transformations occurring across the thawing gradient and trace how that may lead to CO2 or methane emissions.

In addition, new organic matter and new carbon will be generated when the permafrost thaws, due to plant growth. Then, it will be important to understand how much of the “old” carbon will be transformed by microbes, and where the “new” carbon ends up. Through partnering with Tfaily, Rich says they can “really get into the nitty-gritty,” assigning chemical formulas to organic molecules across the gradient and finding signatures of the old and new carbon.

Burning QuestionsBig thaws aren’t the only aspect of climate change causing soil carbon storage concerns. Historically, fire has been a dominant determinant of carbon cycles in terrestrial ecosystems, says Johannes Lehmann, a biogeochemist at Cornell University. Even though we’ve been suppressing fire globally, research in the last decade shows that soils around the world contain a surprisingly large amount of “char,” the blackened byproduct of burned biomass. In Australia, for example, the soil char carbon can range up to 99 percent of soil organic carbon, while five to 50 percent of char is found in U.S. Midwestern land.

“It’s an underappreciated but very important part of SOM,” Lehmann says. This pyrogenic organic matter contains carbon that can be sequestered in soil and can also boost soil health. Lehmann wants to know what drives the decomposition of char – the slower it breaks down, the longer carbon stays in the soil – and what that might mean for the retention of nutrients and other organic carbon in soil.

At EMSL, Lehmann has worked with its scientists and used instruments such as NMR and Fourier Transform Infrared Spectroscopy to analyze the distribution of char carbon at a fine scale. This is especially critical, he notes, because soil carbon is largely particulate and has critical surface interactions. His research reveals that profound surface effects occur when char is oxidized: In this form, char retains more nutrients per unit of carbon, and per unit of surface area, than other organic matter.

In addition, many studies show that char can increase soil microbial populations and change community composition in ways that aren’t explained by simple effects such as changes in acidity, nutrients or added energy. Probing this mechanism, Lehmann found that surface interactions between soil carbon and char carbon may be responsible for reducing mineralization of existing carbon. Understanding more about these surface interactions could then help predict whether soils will gain or lose carbon through the addition of char.

To refine a soil carbon model that incorporates these mechanisms of “priming,” Lehmann plans to return to EMSL for expertise with the nanoSIMS (nanoscale Secondary Ion Mass Spectrometry) and Laser Ablation-Accelerator Mass Spectrometry.

Root of the MatterPerhaps microbes themselves have been another underappreciated component of soil organic matter.

“We’ve progressed from older ways of looking at roots and how their carbon is transformed to soil organic matter,” says Mary Firestone, a professor of environmental science at the University of California in Berkeley. “It’s only really been understood, in the last 10-15 years, that root carbon is stabilized through the eye of a needle, and the eye of the needle is the microbes.”

With a joint DOE JGI-EMSL study, Firestone follows carbon from the roots of Avena fatua, a common Mediterranean grass, into microbes and then into stabilized material. She’s also looking at how the carbon supply by roots disperses into the surrounding decomposing community, where it then enables or facilitates that community’s capacity to degrade older soil organic matter.

Her work will improve understanding of how roots may alter the rates of decomposition.

“We have a poor handle on this,” says Firestone. “We know roots can have large impacts–that can be as important as climate change–but we have a really hard time predicting these effects because we don’t understand the mechanisms well enough.”

By parsing the molecular mechanisms through which roots impact the rates of decomposition, and understanding how roots impact the enzymes and proteins produced by the surrounding microbial community, Firestone hopes to better predict how soil carbon stabilization processes will respond to environmental change. While Firestone is characterizing the metagenome through JGI, the soil bacterial proteomics are being sorted out at EMSL.

Digging DeeperOne advantage for scientists who bring their soil samples to EMSL is the capability to run up to 500 samples.

“That’s more than other labs. In geochemistry, the first question anyone asks is about replication,” says Tfaily. “Even within the same site, there can be a lot of heterogeneity, so you need all those samples.”

Fortunately, Tfaily has also developed streamlined techniques for soil extraction that allow faster processing with solvents that don’t interfere with sample chemistry. The technique is also sequential, meaning smaller samples are needed for testing.

In a few months EMSL scientists will be able to work with an even higher resolution mass spectrometer.

“We’ll get better identifications and perhaps another 20 percent of what we can’t get now,” says Hess.

In addition to these advances, EMSL research scientist Amity Andersen is refining computer models that simulate interactions of protein and other biologically–sourced organic molecules with mineral surfaces–a factor that can affect the stabilization of soil carbon. With these models, Andersen says she’ll be ready to “tackle other user projects that need large-scale simulations to understand these systems.”

With these state-of-the-art tools, Hess says, “We’re really on forefront of enabling so many advances, not only to create more predictive models, but also to better design more sustainable land use practices to preserve soil.

EMSL is a national scientific user facility funded by the Department of Energy’s Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory in Richland, Wash.

Funding for the research mentioned in this article comes from:

DOE’s Office of Biological and Environmental Research (Tfaily and Rich) EMSL’s Intramural Program (Amity Andersen) USDA’s National Institute of Food and Agriculture’s Carbon Cycle Science (Lehmann) National Science Foundation (Lehmann) DOE’s Office of Biological and Environmental Research (Firestone) PNNL Laboratory-Directed Research and Development Signature Discovery Initiative (Hess)

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Newswise: Ground Control



Newswise: Ground Control

Credit: Scott Butner

Caption: Rattlesnake Mountain is a treeless ridge in Eastern Washington overlooking the Hanford Site. It’s the field location where Nancy Hess is investigating the results of a 17-year “reciprocal experiment” on soil transplants mimicking environmental changes in climate warming.

Newswise: Ground Control

Credit: Image provide by Kristen DeAngelis, assistant professor at University of Massachusetts Amherst.

Caption: For Mary Firestone’s project, Avena spp. roots with associated bacteria are stained with a fluorescent stain.

Newswise: Ground Control



Newswise: Ground Control

Credit: Image provide by Kristen DeAngelis, assistant professor at University of Massachusetts Amherst.

Caption: For Mary Firestone’s project, Avena spp. roots with associated bacteria are stained with a fluorescent stain.

Newswise: Ground Control

Credit: Image taken by Scott Butner

Caption: Rattlesnake Mountain is a treeless ridge in Eastern Washington overlooking the Hanford Site. It’s the field location where Nancy Hess is investigating the results of a 17-year “reciprocal experiment” on soil transplants mimicking environmental changes in climate warming.

Newswise: Ground Control

Credit: Image provided by Mary Firestone, professor at University of California, Berkeley.

Caption: Mary Firestone researches root carbon in Avena fatua, a common Mediterranean grass.

Newswise: Ground Control

Credit: Image provided by Mary Firestone, professor at University of California, Berkeley.

Caption: For Mary Firestone’s research, Avena spp. is grown in chambers designed to control carbon dioxide concentration and allow 13C labelling of plant carbon and root carbon supply to associated microbes.