U.S. Department of Energy Office of Biological and Environmental Research

BER Research Highlights

Scavenging in the Dirt: How Microbes Take Up Scarce Nutrients
Published: January 24, 2019
Posted: May 22, 2019

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.

Program Manager
Paul Bayer
Department of Energy, Office of Science, Biological and Environmental Research

Principal Investigator
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]

Topic Areas:

  • Research Area: Carbon Cycle, Nutrient Cycling
  • Research Area: DOE Environmental Molecular Sciences Laboratory (EMSL)
  • Research Area: Microbes and Communities

Division: SC-23 BER


BER supports basic research and scientific user facilities to advance DOE missions in energy and environment. More about BER

Recent Highlights

Aug 24, 2019
New Approach for Studying How Microbes Influence Their Environment
A diverse group of scientists suggests a common framework and targeting of known microbial processes [more...]

Aug 08, 2019
Nutrient-Hungry Peatland Microbes Reduce Carbon Loss Under Warmer Conditions
Enzyme production in peatlands reduces carbon lost to respiration under future high temperatures. [more...]

Aug 05, 2019
Amazon Forest Response to CO2 Fertilization Dependent on Plant Phosphorus Acquisition
AmazonFACE Model Intercomparison. The Science Plant growth is dependent on the availabi [more...]

Jul 29, 2019
A Slippery Slope: Soil Carbon Destabilization
Carbon gain or loss depends on the balance between competing biological, chemical, and physical reac [more...]

Jul 15, 2019
Field Evaluation of Gas Analyzers for Measuring Ecosystem Fluxes
How gas analyzer type and correction method impact measured fluxes. The Science A side- [more...]

List all highlights (possible long download time)