Unexpected Complexity: A 3D Look into Plant Root Relationships with Nitrogen-Fixing Bacteria

Scientists develop a molecular map of metabolic products of bacteria in root nodules to aid sustainable agriculture.

The Science

By taking nitrogen out of the air and turning it into plant nutrients, some bacteria help plants like beans, peas, and clovers thrive. However, a recent study shows that the traditional view of this symbiotic relationship doesn’t capture the entire picture. Scientists resolved a 3D map of the metabolic products of bacteria found in plant root nodules. This spatial perspective could help unravel the overall complexity of these highly interdependent organisms.

The Impact

As bacteria found in plant root nodules interact with legumes like soybeans, the nodules grow on the plants’ roots. In these nodules, bacteria convert atmospheric nitrogen into molecules that the plants need to grow. Understanding the metabolic processes occurring within these nodules is essential for developing more sustainable agricultural practices for food crops used all over the world.


Previous studies led scientists to believe the distribution of bacterially derived metabolic byproducts within the nodules was uniform. Scientists from the Environmental Molecular Sciences Laboratory (EMSL), a U.S. Department of Energy Office of Science user facility, joined with colleagues at the University of Missouri and George Washington University to dig deep into the metabolic structure of soybean root nodules. They used one of EMSL’s high-field Fourier transform ion cyclotron resonance mass spectrometers to visualize the array of metabolites within the nodules. Of the approximately 140 regulating substances identified, some were located together in distinct anatomical compartments. A few, however, were more unevenly distributed throughout the middle of the nodule, where the bacteria reside. This discovery points to a previously unrecognized biochemical complexity in the nodules that is key for symbiotic plant-microbe interactions. Armed with this understanding, scientists can suggest ways to optimize crop production and sustainability.

Principal Investigator(s)

Christopher Anderton
Environmental Molecular Sciences Laboratory


This work was supported by the U.S. Department of Energy’s (DOE’s) Office of Science, Office of Biological and Environmental Research, including support of the Environmental Molecular Sciences Laboratory (EMSL), a DOE Office of Science user facility; the DOE Mickey Leland Energy Fellowship; University of Missouri’s Gus. T. Ridgel Fellowship; George Washington Carver Fellowship; and the National Science Foundation Plant Genome Program.


Velickovic, D., B. J. Agtuca, S. A. Stopka, A. Vertes, D. W. Koppenaal, L. Paša-Tolic, G. Stacey, and C. R. Anderton. “Observed metabolic asymmetry within soybean root nodules reflects unexpected complexity in rhizobacteria-legume metabolite exchange.” The ISME Journal 12, 2335 (2018). [DOI:10.1038/s41396-018-0188-8]