Microbes have many connections to humans. Gut microbes have a major influence on our health. For example, when we eat fruits, vegetables, chocolate, or red wine, gut microbes break down larger compounds in these foods, giving our bodies access to beneficial compounds in the foods, like polyphenols. Scientists have also been investigating bacteria in the soil microbiome. They are linked to humans too, through agriculture and the environment, for example. It's been thought that soil microbes wouldn't be able to utilize polyphenols in certain cases, and because of that, they were suggested to have the potential to act as carbon sinks that could absorb excess carbon from the environment. But new work has suggested polyphenols are actually food sources for soil microbes too.
There is a hypothesis called the enzyme latch theory, which suggests that if oxygen isn't easily available, microbes in places like peatlands or wetlands will not metabolize polyphenols; by adding polyphenols to it, peatland might become a carbon-trapping sink.
"We know that polyphenols are really sticky, and so people thought that, by being in the soil, not only they themselves wouldn't be broken down, but they'd stick to other carbons and enzymes in the soil and prevent further breakdown of everything else. So, if you had an already broken-down system like a degraded wetland, you could go in and add wood chips to the system, flood it again, and lock up all the carbon," explained Colorado State University (CSU) graduate student Bridget McGivern.
Study leader Kelly Wrighton, associate professor in the College of Agricultural Sciences' Department of Soil and Crop Sciences at CSU has thought for a while that there were serious problems with the enzyme latch theory in soils because we know the humans gut is free of oxygen, but microbes metabolize polyphenols there.
"The breakdown of polyphenols has to happen in the gut for us to access those antioxidants, and to appreciate chocolate and red wine and all their benefits," said Wrighton. "But then we would go into this other ecosystem, which had a totally different paradigm of how these compounds behaved. We couldn't rationalize that."
Wrighton knew it was possible there was something else at work causing polyphenols and microbes to act differently in soil. Her team created experiments to observe what might be happening. The findings were reported in Nature Communications.
In this work, the researchers monitored soil samples in the laboratory with metaproteomic tools, identifying which genes the microbes in the soil samples were expressing and what proteins they generated. They also used analytical chemistry techniques to identify the metabolites and small molecules that were present.
"It was just this chemical maze, tracking these compounds," Wrighton said.
The researchers showed that under oxygen-free conditions, soil microbes actually do break polyphenols down, and probably release carbon dioxide in the process; it doesn't look like they would be good facilitators of carbon sinks. That still has to be shown in the field, however. The researchers are already planning to do this work in Sweden, and have a new grant and a team of collaborators.
McGivern is strengthening the computational tools that will be used first, however.
"My next project is basically building a polyphenol module to insert into an existing annotation infrastructure in our lab so that if anybody goes in and annotates their genome, they'll start to see polyphenol metabolisms," McGivern said.