Research Challenges Theory on Polyphenol’s Role in Carbon Sequestration

Peatlands represent the largest terrestrial carbon store in the world, accounting for one third of the globe’s carbon in soil. As a result, damaged peatlands can be a major source of greenhouse gas emissions, making these soils significant in fighting climate change.

A long-held theory, known as the enzyme latch model, claims that when peat soil is deprived of oxygen, enzyme-inhibiting compounds known as polyphenols reduce microbial activity and “latch” onto carbon-containing molecules in the soil. However, this mechanism has not been thoroughly studied in peatlands, or in any soils.

A multi-institutional team of researchers, led by Wrighton Lab at Colorado State University, tested the theory in a soil system and found chemical evidence that polyphenols can be broken down in soils absent of oxygen. The study, funded in part through the Facilities Integrating Collaborations for User Science proposal call, is the first to use high-resolution tools to study polyphenol metabolism in oxygen-deprived soils.

The research, published in a recent Nature Communications paper, represents a critical step in redefining the metabolic roles of soil microbiomes. The findings also demonstrate the importance of clarifying the interactions between soil microbiota and polyphenols to better understand their roles in soil carbon sequestration.

“The study opens the door for further study of polyphenol metabolism in the field and how it fits into natural carbon cycles,” said Bridget McGivern, a PhD student in the Wrighton Lab who led the research.

Researchers used microbiome technologies, including genome sequencing and high-resolution chemical techniques, at the Environmental Molecular Sciences Laboratory (EMSL) and Joint Genome Institute (JGI) to integrate data—establishing a library of microbial genomes, enzymes, and metabolites related to polyphenol metabolism to help grow knowledge in this area.

Putting polyphenols to the test 

Polyphenols are important, abundant plant metabolites with more than 10,000 different compounds. They enter soil systems through litter decay or are drained away from the soil. In the human gut, polyphenols are consumed through polyphenol-rich foods like wine, chocolate, and berries.

In this study, the researchers wanted to study microbially mediated polyphenol transformations in soils deprived of oxygen, known as anoxic soils, and determine how polyphenols affect the overall function of microbial communities.

“We saw this as an opportunity to use [the] Wrighton Lab’s strength in anaerobic microbiology and in high-resolution omics to see what the microbial community is doing,” McGivern said.

To do this, the team added a condensed tannin, which is a polyphenol substrate, to controlled anoxic wetland soil from the Old Woman Creek National Estuarine Research Reserve in Ohio. The wetland soils were chosen for this study because they contained polyphenols and are tractable with multi-omics methods, making them ideal for evaluating anaerobic polyphenol metabolism.

Researchers put the soil in jars and removed all the oxygen. Each sample was analyzed over a 20-day period using genome-resolved proteomes and metabolites made available by JGI and EMSL. The metagenome sequencing was done at JGI.

EMSL’s mass spectrometry and nuclear magnetic resonance capabilities allowed for molecular analyses of the soil microbiome. The use of these tools is significant to this research because they identify ecological and biochemical mechanisms underlying existing soil biogeochemical paradigms, McGivern said.

David Hoyt, a chemist with the Biomolecular Pathways team at EMSL, used nuclear magnetic resonance to identify and quantitate what was happening in the soil and compare it with other samples. Mary Lipton, a chemist with the Proteomics team and lead of the Biomolecular Pathways Integrated Research Platform, analyzed metaproteomes using mass spectrometry at EMSL.

Previously, polyphenol chemistry has not been well established, Hoyt said. Through this work, metabolite libraries are already expanding, paving the way for future work.

“This is where EMSL sits in the sweet spot of metaproteomics and metabolomics platforms,” said Hoyt. “We can really contribute to these underrepresented areas.”

Future polyphenol metabolism studies

Because this research was done in a laboratory, the next step will be putting insights to the test in the field, McGivern said.

She also plans to use this research to explore how this affects the human gut. Future work could compile a resource of known enzymes that break down polyphenols—something that is currently lacking in databases used to annotate genomes.