Talking with plants
UW research is digging into the microbiome of native Wyoming plants, investigating how plants and their immediate microscopic neighbors influence one another.
Ph.D. candidates at the University of Wyoming are studying how plants communicate with their microbial neighbors and how those plants and microbes influence each other. This research could have several important impacts on the agricultural sector, and for land restoration, ecosystem health and general scientific knowledge.
Plants, just like humans, live among a multitude of microbes. And just as the microbes in a human body play a key role in that body’s functions, the microbes in the soil around a plant influence and are influenced by that plant. To understand that influence, UW doctoral candidate Ali Ceretto is looking at what are known as “plant exudates.”
“The field of sampling plant exudates — the chemicals plants give off — is very complicated”, she said. Ceretto’s research is looking at “top-down feedback,” or what the plant is doing to the microbes.
While plants provide a complex habitat for microbes both below and aboveground, Ceretto’s research is focused on the microbes that colonize the rhizosphere, the narrow region surrounding plant roots, and the plant-root secretions that occur there.
Plants photosynthesize more or less at specific times of day, and how much photosynthesis a plant does is linked with how many chemicals they excrete from their roots. Based on factors such as location, that circadian rhythm differs, and some plants will have a 14-hour cycle while others have a 24-hour cycle.
Other graduates have noticed that the microorganisms in the soil around the plant roots will change throughout the course of a single day based on the plant’s circadian rhythm.
“So, what I did was take this project into the field, where I grew the plants outside rather than in a stable growth chamber,” Ceretto said. “If it’s not outside, then it’s not biologically relevant in terms of what it means in real life.”
Boechera stricta, a plant native to Wyoming, is being investigated for this project. Commonly known as Drummonds rockcress, Boechera stricta is a species of plant in the mustard family and can be found naturally across much of North America and Canada.
The species is popular among researchers.
“We have genetically sequenced this plant a lot, other people have used it for similar environmental studies and it's very closely related to the “white mouse” equivalent of plant studies,” Ceretto said.
Boechera stricta falls within the same family as the organism Arabidopsis thaliana, the first plant to have its genome sequenced. Arabidopsis thaliana is considered a model organism, the “white mouse” of plant research, according to Ceretto. Boechera stricta, however, is native to Wyoming and much of North America, making its traits of uniformity and predictability useful for localizing and applying scientific research.
“I’m looking at if the microbes I sampled in the soil around the plant roots are able to metabolize the chemicals coming from the plant,” Ceretto said. “Which would have a direct impact on the microbial community.”
How the microbial community around plant roots behaves can affect the health of the plant, the flowering time of the plant, whether a plant can survive in an environment and more, she said.
“When I’m sampling I do it at a very specific time, so regarding the circadian rhythm of plants, they will give off different chemicals based on whether they are in the light or the dark,” Ceretto said.
Through a process called chlorophyll fluorescence, scientists can measure photosynthesis activity inside of plant leaves.
“I determined that in the dark pre-dawn and in the early afternoon — at around 2:00 p.m. — is when this plant’s rate of photosynthesis is most different,” Ceretto said. “So, if I’m trying to find out what the microbes are doing, if I look at those two time points, that should technically be when the microbial community around the plant’s roots are the most different from one another.”
Ceretto is trying to determine if the changes in the microbial community around the plant roots are associated with the different chemicals released by the plant throughout its circadian rhythm.
“What we are doing is essentially a confirmation of methods, we are trying to prove that what we are detecting in the soil is actually coming from the plant,” she said.
Ceretto is partnering with postdoctoral members at the UW Basile Lab who are trying to utilize chemical principles to better explain a variety of environmental questions.
“We have been working really hard in proving that the methods that we’re creating actually work, which has required us to do a lot of backtracking to prove that what we’re seeing is real,” Ceretto said.
She has also been working with Dave Williams, a UW professor of botany and ecology, to develop methods using stable isotopes. Isotopes are atoms with a specific number of neutrons. So a carbon atom with the traditional six neutrons is one isotope (C-12), while a carbon atom with eight neutrons would be a different isotope (C-14). “Stable” isotopes are the ones with staying power — atoms that don’t shed their extra neutrons as quickly as possible.
Because stable isotopes stick around, and because different quantities of them are found in different places, they are helpful in several fields of research and investigation. For example, the oxygen isotopes in human remains can sometimes tell researchers where ancient peoples lived.
Ceretto tags the plant leaves with a stable isotope that will show up in anything that originates in the plant, proving that the chemicals they are seeing in the plant exudates are actually coming from the plant.
During this process, they will brush the leaves of a plant with a fertilizer containing an isotopic molecule while covering the soil in plastic to ensure that none of the fertilizer drips off the leaves onto the soil. If later this isotope is found in the soil, it means the isotopic atoms were absorbed into the plant leaves, traveled through the plant, and were broken down into other byproducts now found in the soil.
“If I find it (the isotope) later, that means that the isotope I put on the leaves is in the soil, so what I’m detecting must have come from the plant,” Ceretto said. “This will prove that what I’m finding is coming from the place I say it’s coming from. It would be like sending food coloring through a hose.”
Ultimately, Ceretto is looking into how plants grow where they do and determining if that is affected by microorganisms. Ceretto said this research may be useful for land management and restoration.
“There have been some studies that have shown that integrating disturbed soil with specific microbes from undisturbed lands can help reintroduce native plants,” she said. “We don’t know why this happens, but we know microbes interact with plants in positive and negative ways.”
This research might also be important for replacing certain chemical-synthetic technologies such as fertilizers and pesticides, which can have negative effects on the environment. Agricultural techniques involving microorganisms are “much better from an ecological perspective, compared to spraying pesticides on crops,” Ceretto said.
UW’s Program in Ecology is a transdisciplinary doctoral program that provides advanced, integrated training in the science of ecology. The research is funded through a massive grant to study microbial ecology that comes to UW from the National Science Foundation by way of the university’s EPSCoR program. That grant also funds the Science Journalism Internship Program, which has funded several journalists who have worked or are working for the Laramie Reporter, including the author of this story.
This story is supported by a grant through Wyoming’s Established Program to Stimulate Competitive Research (EPSCoR) and the National Science Foundation.