Soil molecular diversity spikes as microbes decompose plants

Globally, soils contain three times as much carbon as exists in the atmosphere and all plants, combined. Which means that understanding how soil microbes recycle organic materials - sometimes sending CO2 back into the atmosphere, sometimes mineralizing it for long-term storage - may be crucial for the fight against climate change. To that end, new Cornell research has uncovered that soil molecular diversity changes as microbes decompose dead plants, with molecular diversity growing for the first month, then plateauing and dropping thereafter. The insight is reported in a paper published Dec. 10 in Nature Communications.

"This is a hugely important question: can we lose less carbon from soil, or can we even increase our soil carbon stocks, which will help regulate CO2 in the atmosphere?" said Johannes Lehmann, senior author on the paper and Liberty Hyde Bailey Professor of soil and crop sciences in the College of Agriculture and Life Sciences. "Because soils contain so much organic carbon, even small, incremental changes can make a big, big difference in the atmosphere and therefore for climate change."

First author is Rachelle Davenport, Ph.D. '24, formerly a graduate student in Lehmann's lab and now an independent research consultant. In all, 11 co-authors come from seven institutions across six U.S. states and the Netherlands. Their work was supported by four public and private grants, including two from Cornell: a Schmittau-Novak Small Grant through the School of Integrative Plant Science, and a Graduate Research Grant from the Cornell Atkinson Center for Sustainability.

For decades, scientists believed that soil organic carbon accumulated because of recalcitrant plant materials. But in a groundbreaking and widely cited paper in Nature in 2011, Lehmann among several co-authors reported that this was not the case. Rather, soil organic carbon results from complex ecosystem interactions, including with soil microorganisms, molecules and minerals. The authors called for "a new generation of experiments" to uncover the mechanisms that lead soils to store or release carbon, and how those mechanisms might be recruited to combat climate change.

In 2020, Lehmann and co-authors proposed another revolutionary theory: that greater molecular diversity in soils may limit decomposition, and therefore lead to soils retaining more carbon. The idea is that with lower molecular diversity, soil microbes that decompose plant materials can specialize more easily, consume more, and then release more CO2. With higher diversity, it becomes harder for decomposers to quickly consume materials, giving minerals more of a chance to capture and store carbon long-term.

The current paper is the first to provide empirical evidence that plant decomposition does increase molecular diversity in soils, but only for a short period, with diversity peaking at 32 days.

"It's been a long time coming, since 2011, and has required a series of papers and experiments, but we now have some empirical evidence that plant decomposition does increase molecular diversity, if only for a short time," said Lehmann, who is also a Cornell Atkinson faculty fellow. "We still have much to learn, but this is one important piece of the bigger puzzle."

The paper is also the first to use "18O heavy water" - water in which the oxygen atom is labeled with the oxygen-18 isotope - to trace changes in soil molecular composition due to microbial activity, Davenport said. Heavy water is traditionally used by microbiologists, and soil scientists generally use labeled carbon or nitrogen to trace soil ecosystem dynamics.

"When you trace activity via carbon, you usually feed microbes glucose - straight sugar - so when you're feeding microbes sugar instead of letting them use their natural food sources, it affects their metabolism and then you're not really accurately measuring microbial activity and what they'd normally consume and produce," Davenport said. "I think that method was a major success."

Collaborators from the Environmental Molecular Sciences Laboratory in Richland, WA, were critical in developing this new method, she said.

Davenport received a Graduate Research Grant from Cornell Atkinson in 2022, which enabled her to hire an undergraduate student, Caleb Levitt '24, to work on the project. Levitt was instrumental in taking measurements of soil carbon dioxide emissions and monitoring the effects of decomposition on organic matter molecular diversity, Davenport said.

Next steps for the research involve expanding out to determine whether greater diversity among soil molecules, microorganisms and minerals lead to greater carbon storage in soils. And if so, developing strategies to support this diversity, such as through farm and forest management practices, Lehmann said.

In addition to two internal Cornell grants, funding for the research came from the U.S. National Institute for Food and Agriculture and the Pacific Northwest National Laboratory.

Krisy Gashler is a writer for the Cornell Atkinson Center for Sustainability.