New research helps untangle the role of soil microbes in the global carbon cycle

When soil microbes eat plant material, the digested food follows one of two routes. Either the microbe uses the food to build its own body, or it exhales its meal as carbon dioxide (CO).₂) in the atmosphere.

Now, for the first time, a Northwestern University-led research team has tracked the pathways of a mixture of plant waste as it moves through the metabolism of bacteria to contribute to CO2 emissions into the atmosphere.₂. The researchers discovered that microbes inhale three times as much CO₂ of lignin carbons (aromatic units without sugar) compared to cellulosic carbons (glucose sugar units), which both add structure and support to plant cell walls.

These findings help untangle the role of microbes in the soil carbon cycle – information that could help improve predictions of how soil carbon will influence climate change.

The study, “Disproportionate carbon dioxide efflux in bacterial metabolic pathways for different organic substrates leads to variable contribution to carbon use efficiency,” was published June 11 in the journal Environmental sciences and technology.

“The carbon stock stored in the soil is about ten times the amount of carbon in the atmosphere,” said Ludmilla Aristilde of Northwestern University, who led the study.

“What happens to this reservoir will have a huge impact on the planet. Because microbes can unlock this carbon and convert it into atmospheric CO₂There is great interest in understanding how they metabolize plant waste. As temperatures rise, more organic matter of different types will become available in the soil. This affects the amount of CO₂ that is emitted by microbial activities.”

An expert in the dynamics of organic compounds in environmental processes, Aristilde is an associate professor of civil and environmental engineering at Northwestern’s McCormick School of Engineering and a member of the Center for Synthetic Biology and the Paula M. Trienens Institute for Sustainability and Energy. Caroll Mendonca, a former Ph.D. candidate in Aristilde’s laboratory, is the first author of the paper. Employees from the University of Chicago were involved in the research.

‘Not all processes are created equal’

The new study builds on ongoing work in Aristilde’s laboratory to understand how soils store or release carbon. While previous researchers typically tracked how broken down compounds from plant material move individually through bacteria, Aristilde’s team instead used a mixture of these compounds to represent what bacteria are exposed to in the natural environment.

To then track how different plant derivatives moved through a bacterium’s metabolism, the researchers tagged individual carbon atoms with isotope labels.

“Isotope labeling allowed us to track carbon atoms specific to each compound type in the cell,” Aristilde said. “By following the carbon pathways, we were able to capture their pathways in metabolism. That’s important because not all pathways are created equal in terms of carbon dioxide production.”

For example, sugar carbons in cellulose traveled via glycolytic and pentose phosphate pathways. These pathways lead to metabolic reactions that convert digested matter into carbon atoms to make DNA and proteins, which build the microbe’s own biomass. But aromatic, non-sugar carbons from lignin traveled a different route: via the tricarboxylic acid cycle.

“The tricarboxylic acid cycle exists in all life forms,” Aristilde said. ‘It occurs in plants, microbes, animals and humans. Although this cycle also produces precursors for proteins, it includes several reactions that produce CO.₂. Most of the CO₂ inhaled through metabolism comes from this route.”

Expanding the findings

After monitoring the metabolism pathways, Aristilde and her team performed quantitative analyzes to determine the amount of CO₂ produced from different types of plant material. After consuming a mixture of plant material, microbes inhaled three times as much CO₂ of carbons derived from lignin compared to carbons derived from cellulose.

“Even though microbes consume these carbon atoms at the same time, the amount of CO₂ generated from each carbon type is disproportionate,” Aristilde said. That’s because the carbon is processed through two different metabolic pathways.

In the first experiments, Aristilde and her team used Pseudomonas putida, a common soil bacterium with a versatile metabolism. Curious whether their findings also applied to other bacteria, the researchers studied data from previous experiments in the scientific literature. They found the same relationship they discovered between plant material, metabolism and CO2₂ manifests itself in other soil bacteria.

“We propose a new metabolism-driven perspective to think about how different carbon structures accessible to soil microbes are processed,” Aristilde said. “That will be critical in helping us predict what will happen to the soil carbon cycle under a changing climate.”