Scavenging in the Dirt: How Microbes Take Up Scarce Nutrients

Study identifies siderophores from soil samples, building fundamental understanding of how microbes obtain scarce nutrients from their environment.

The Science

Important compounds called siderophores help bacteria and fungi scavenge essential nutrients like iron from the soil. But how the microbes release and use these compounds remains murky. Few siderophores have been identified in nature. Now scientists have not only identified four major classes of siderophores from chalky soils for the first time, but they have also uncovered the strategies microbes use to gather iron when nutrients are scarce.

The Impact

Soil has a diverse microbial ecosystem that includes many metabolic processes and products that remain to be discovered. Building a fundamental understanding of how enzymes, metabolites, and microbes interact in soil is key to predicting how these interactions shift in response to changing environmental conditions. This understanding could help farmers improve soils and increase crop yields.


Researchers at Oregon State University teamed with colleagues at Pacific Northwest National Laboratory and EMSL to study bacteria in chalky soils that are traditionally low in biosoluble iron. They wanted to evaluate the diversity of siderophores in nature and find a better way to detect these compounds. Using EMSL’s ultra-high-resolution Fourier transform ion cyclotron resonance mass spectrometry at 21 Tesla, the scientists quickly and confidently detected and identified thousands of molecular features. They then employed two varying approaches to structurally characterize compounds that belong to four major siderophore classes. Their efforts helped identify the best method for studying these compounds and highlighted the diversity of siderophores produced by co-existing soil microbes. Each of these four classes possesses different chemical characteristics and ways of taking up nutrients. These differences likely contribute to fierce competition for iron within these chalky soils, shedding light on how microbes scavenge nutrients in other soils.

Principal Investigator(s)

Rene Boiteau
Oregon State University


This work was supported by the U.S. Department of Energy’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.


Boiteau, R.M., S.J. Fansler, Y. Farris, J.B. Shaw, D.W. Koppenaal, L. Pasa-Tolic, and J.K. Jansson. “Siderophore profiling of co-habitating soil bacteria by ultra-high resolution mass spectrometry.” Metallomics 11,166-175 (2019). [DOI: 10.1039/C8MT00252E].