A new study is underscoring the importance of studying microbes in their natural setting, rather than relying solely on laboratory research. Researchers found that a set of corn root bacteria behaved completely differently when grown on the plant rather than in a lab, with thousands of proteins changing when placed in their natural habitat.
“Historically we’ve been reliant on in-vitro experiments and experiments in the lab, and they’re still very powerful,” said Anna Garrell, first author of a paper on the work and a postdoctoral researcher at North Carolina State University. “But I think this is a good reminder that what you find in the lab is not necessarily what’s going to be happening in the real environment.”
For the study, researchers grew seven corn root bacteria both in a lab setting (in vitro) and on the plant (in planta) to measure the differences in their behavior. While all the bacteria acted differently on the plant, the specifics varied from species to species.
“The biggest surprise we found was that all these bacteria interacted with the plant very differently,” said Garrell. “Some, when they got to the root, became more motile and seemed to upregulate functions that would help them move and swim. Others did the exact opposite, where they would attach to the root and become much more stationary. Not all bacteria are made the same, nor do they interact with the plant the same.”
Microbes on the plant showed a range of behaviors, from activating various secretion systems to solubilizing phosphate to consuming different sugars. The sheer magnitude of the behavior shift was notable, said principal investigator Manuel Kleiner, an associate professor of plant and microbial biology at NC State.
“Comparing the microbe growing on the plant to outside of the plant, the most mind-blowing thing was that these microbes completely changed their programming,” Kleiner said. “It’s not just ten or so genes, it’s thousands that completely shift as soon as they start interacting with the plant.”
The seven bacteria used in the study come from what is known as a defined community, a group of microbes with specific known parts that scientists can rely on as stable test subjects. These microbes were chosen because they colonize consistently, have known genomes and are known to come from corn roots, making them reliable for testing on the plant and in the lab.
“This research will help scientists improve our understanding of how those microbes react to their host plants,” Garrell said. “Further research can build off this work by studying how multiple microbes interact and influence each other when on their host plant, and how they work together to colonize plants. This will be important for developing real products to use in sustainable agriculture”
The paper, “Differential proteomics of bacteria grown in vitro and in planta reveals functions used during growth on maize roots,” is published in mSystems. This work was funded by the USDA National Institute of Food and Agriculture under awards 2021-67013-34537 and 2022-67013-36672, the Novo Nordisk Foundation InROOT project (NNF19SA0059362) and the National Science Foundation (IOS-2120593 and IOS-2421771). Co-authors include John Cheadle, Nathan Crook and Gaurav Pal, NC State University; Alecia Septer, University of North Carolina at Chapel Hill; Maggie Wagner, University of Kansas; and Ashley Beck, Carroll College and NC State University.
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