Seeking to Better Understand the Carbon Cycle

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A reconstructed X-ray computed tomography image that reflects soil core structures.Photo courtesy of PNNL-EMSL

A reconstructed X-ray computed tomography image reflects soil core structures. The gray image on the left is of the core, and brown image on the right is reconstructed pore space distribution.

Microbes are among the smallest organisms on Earth, but they could be goliaths in how carbon is stored, recycled and reused in the biosphere. Researchers are studying various microbial communities to better understand the role they play in carbon dioxide levels in the atmosphere.

"The impact of global climate change on our society could be huge," says Stephen Callister, Pacific Northwest National Laboratory (PNNL) senior research scientist. "We need to understand as much about the biology involved in global climate change as possible to gives us more predictive and management capabilities."

Part of the mission of the Department of Energy's Office of Biological and Environmental Research (BER) addresses global challenges and advances the understanding of the Earth's biogeochemical systems. BER is especially interested in carbon dioxide's role in global climate change.

EMSL, or the Environmental Molecular Sciences Laboratory, is a DOE national scientific user facility at PNNL that supports BER's mission by offering research capabilities to scientists studying the relationship between microorganisms and CO2.

Existing global climate models do not fully explain the impact of CO2 on the environment, but ongoing research will improve the precision of these models, according to Nancy Hess, EMSL chief scientist.

"Because the carbon cycling research at EMSL is at the molecular level, it allows us to develop a mechanistic understanding of the processes that will help reduce the uncertainties in global climate models," she says.

Scientists at EMSL are identifying the processes that govern the release of CO2 back into the atmosphere. One research project is studying microbial communities in soil and their role in the carbon cycle. A second study explores the function of aquatic photosynthetic microbes in carbon processing. The findings from these studies will help improve the accuracy of climate models and increase our fundamental knowledge of biological systems.

The Good Earth

Chongxuan Liu, a PNNL geochemistry scientist, oversees the terrestrial study at EMSL. The project investigates microbial activities in soils to develop pore-scale models to simulate biogeochemical reactions and processes at the microscopic level.

Liu uses X-ray computed tomography to look at the microscopic physical structures of soil samples. X-ray tomography offers resolution up to 10 microns and allows non-destructive measurements of soil cores.

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An X-ray computed tomography image used to generate porous media structure for virtual soil core.Photo courtesy of PNNL-EMSL

An X-ray computed tomography image used to generate porous media structure for virtual soil core and a numerical simulation using Chinook supercomputer. In this false-colored image, green represents pores and the combination of pore and organic matter, yellow represents mixture of pores and fine-grained materials, and pink are the solid grains.

EMSL's Chinook supercomputer uses digitized X-ray tomography images to create a numerical simulation platform called a "virtual soil model." The research team adds additional data to the model, including microbial functions, organic carbon and moisture content, as well as processes to describe the carbon cycle and moisture migration. The model allows the researchers to numerically simulate the rates of bio-degradation of organic carbons and to calculate fluxes of carbon dioxide at the pore scale.

The pore-scale model research is part of a much larger PNNL project studying soil microbial communities and biogeochemical processes in the carbon cycle and Earth System Models. The models are computational, numerical, dynamical and biogeophysical representations of the Earth system and its components.

"The project is just beginning," says Liu. "Our overall goal is to determine how these biogeochemical carbon reactions at the pore scale manifest at the macroscopic scale."

Vanessa Bailey, a PNNL microbiology scientist, is the principal investigator on the EMSL study. Part of the project will compare data from the virtual soil model with findings from field and lab measurements on how CO2 is produced at the macroscopic scale to help calculate the CO2 flux.

"We're developing a fundamental understanding of the biogeochemical processes controlling carbon turnover and cycling," says Bailey. "We're studying them from the pore scale to the macro-level to determine whether these processes are adequately represented in models."

As the larger PNNL project progresses, the team anticipates using additional EMSL capabilities, including scanning electron microscopes, transmission electron microscopes and nuclear magnetic resonance instruments.

Looking for Answers

EMSL's 2013 user meeting to be held Aug. 6 and 7 addresses research in the rhizosphere, the narrow region of soil directly influenced by roots and soil microorganisms. The meeting explores how rhizosphere research can enhance climate models. Laboratory staff will present how EMSL's state-of-the-art capabilities can enable rhizosphere research. The meeting is open to current users and non-users interested in the topic.

The Department's Office of Science is the single largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information about the labs mentioned, please visit EMSL and PNNL .

John Nicksich is a communications specialist for EMSL, at PNNL