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Functional and Systems Biology

How Belowground Aspects of Plant Neighbors Influence Each Other’s Microbiomes

Scientists show that plant root exudates play a key role in the makeup of their neighbors’ microbiomes, especially when competing.  

grass in laboratory

To investigate how plant neighbors affect each other belowground, scientists grew switchgrass with other common perennial prairie plants in a greenhouse and then submerged the former in a water-based solution (left) to collect root secretions, or exudates (close-up, right). (Photos courtesy of Michigan State University)

The Science 

Plant neighbors are widely known to affect each other’s interactions with other organisms, especially insects, but what goes on belowground isn’t so clear. In the soil, plants interact with their neighbors through roots and complex chemical signals, as well as with distinct groups of microbes like bacteria and fungi. Microbes that live near the plant root in the rhizosphere have many important roles, including helping plants grow and tolerate stress. A team of scientists has now determined that the composition of rhizosphere microbiomes is affected by neighboring plants of different species, especially when all the plants are competing strongly with each other for common resources.  

The Impact

This research shows that studies of isolated plants might not be able to accurately predict the diversity and activity of microbiomes in the natural environment where multiple plant species coexist. A multi-institutional team of scientists demonstrated that not only does the host plant affect the assembly of its rhizosphere microbes, but that neighboring plants of different species also play a role, through multiple—possibly cooccurring—mechanisms, including root secretions (exudates) and spillover of microbes when roots are overlapping. This work emphasizes the importance of using plant neighborhoods with diverse species to better understand what drives changes in a natural rhizosphere influenced by different plant types, and to improve how the interactions of ecologically beneficial microbes can be predicted and managed. 


A plant’s neighborhood can influence how it interacts with other organisms aboveground, but belowground effects are less understood. Because root exudates influence rhizosphere makeup, scientists have predicted that they also likely affect neighbor-induced changes in the plant rhizosphere. To test this, a multi-institutional team of scientists conducted a greenhouse experiment to study how the bacterial community of Panicum virgatum, or switchgrass, changed with other species of perennial prairie plant neighbors. They found that various neighbors altered both the exudates and the rhizosphere community of the focal switchgrass plant and that these changes were most significant when the neighbor was highly competitive (in this case, Rudbeckia hirta, or black-eyed Susan). Some of the mechanisms through which neighbors affected the focal plant’s rhizosphere composition include changes in root exudates during nitrogen limitation and microbe spillover from larger plants. It was also found that neighbor-induced changes in root exudates can have even stronger effects on soil nutrients than microbes. Altogether, this study shows that a plant’s neighbors affect its rhizosphere assembly, as well as nutrient cycling, and that root exudates may play a key role.  

A portion of this work was performed at the Environmental Molecular Sciences Laboratory (EMSL), a Department of Energy scientific user facility located in Richland, WA. 


Tayler Ulbrich, Michigan State University, 

Albert Rivas-Ubach, Environmental Molecular Sciences Laboratory, 

Sarah Evans, Michigan State University, 


Support for this work includes funding from the Department of Energy, Office of Science, Biological and Environmental Research program through the Great Lakes Bioenergy Research Center; the Microbially Mediated Perennial Rhizosphere Nitrogen Transformations project; the National Science Foundation (NSF) Long-term Ecological Research Program; and an NSF Field Stations and Marine Laboratories grant. Tayler Ulbrich was supported by an NSF Graduate Research Fellowship. 


T. Ulbrich, et al., “Plant root exudates and rhizosphere bacterial communities shift with neighbor context.” Soil Biology and Biochemistry 172, 108753 (2022). [DOI: 10.1016/j.soilbio.2022.108753]