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Functional and Systems Biology

State-of-the-Art Imaging of Microbial–Mineral Associations in Soil

EMSL’s advanced instrumentation shows us the nitty gritty of organic matter–mineral interactions

researcher holds gold patterned sample on a silicon wafer.

Materials scientist Shuttha Shutthanandan holds a gold patterned sample on a silicon wafer. He’ll transfer it to the helium ion microscope, or HIM, which improves on older techniques that researchers used to image materials. The instrument’s high-resolution (0.35 nm) and outstanding depth of field (microns) for imaging uncoated organic and biological material makes it especially suitable for biological and environmental research. (Photo by Andrea Starr | Pacific Northwest National Laboratory)

What’s the key to understanding crop production, water storage, and even climate change?

It’s in the soil.

Soil organic matter, or SOM, holds the answers to numerous scientific challenges. SOM, composed of both living microbial and dead plant material, helps soil store and provide essential nutrients as well as decompose soil minerals.

With this multifaceted, vital role in Earth’s processes, it’s important for researchers to study and understand SOM. By applying advanced microscopy available at the Environmental Molecular Sciences Laboratory (EMSL), scientists can examine mineral-associated organic matter and microbial–mineral interactions, with implications for how nutrients are processed and recycled in soil.

EMSL, a Department of Energy Office of Science user facility at Pacific Northwest National Laboratory, offers more than 200 instruments that are available to researchers across the world who submit a research proposal through an open call and are provided funding through a competitive peer-review process. Among them are microscopes designed for imaging organic matter–mineral interactions. These include cryogenic transmission electron and helium ion microscopes.

These resources for imaging SOM as well as overall organic matter–mineral interactions will be highlighted at a free EMSL LEARN webinar at 12 p.m. PDT on March 22, 2023. Featured speakers will include EMSL senior scientist Scott Lea , EMSL Earth scientist Alice Dohnalkova, and EMSL user Rebecca Lybrand of the University of California, Davis.

Cryogenic transmission electron microscopy

Researchers use transmission electron microscopy, or TEM, for precise imaging of both biological and mineral materials at a sub-micron scale. The interactions between organic matter and minerals are prime examples.

Using TEM, researchers can characterize a wide variety of microbial–mineral interactions on a scale of tens of microns, scaled down to sub-nanometer resolution. This insight helps the scientific community understand how certain changes occur in the environment.

“TEM can provide high-resolution imaging of soil organic carbon, including microbes, fungi, residual plant litter, necromass, and other components of soil organic matter,” Dohnalkova said. “These can be clearly distinguished from the soil minerals, and using analytical methods coupled to the TEM, we can get a clear idea on the structural, chemical, and crystallographic nature of the complex mineral–SOM associations.”

Researcher sits in front of computer screen
Alice Dohnalkova works with EMSL users to apply cryo-TEM to organic matter and mineral interaction research. (Photo by Andrea Starr | Pacific Northwest National Laboratory)

Helium ion microscopy

With helium ion microscopy, or HIM, the surface of a material becomes larger than life. The system’s high resolution, depth of field, and contrast make it ideal for imaging uncoated organic and biological material. HIM uses helium ions to investigate samples with a smaller, more focused probe.

“For high-resolution, surface-sensitive imaging of organic matter–mineral interactions, the HIM would be the microscope of choice to help provide insight into processes occurring at fine scales,” Lea said.

HIM also has an unprecedented ability to map specific micro-environments surrounding microbial cells. Part of these environments are pores, which the instrument can reveal at a scale of a few nanometers. A clear picture of a sample’s pore architecture reveals pathways or networks between organic matter and mineral interactions.

images from helium ion microscope
Image of a gold on carbon test sample using a SEM (left) and a HIM (right). Note the difference in the depth of field in the image on the right. The surface details are more visible with the HIM. (Images provided by Shuttha Shutthanandan)

Examination of mineral weathering and biomineralization are also possible using a HIM. Mineral weathering tells us how microorganisms broke down minerals to which they are bound. Using HIM, researchers can see surface details that aren’t visible using other instruments such as scanning electron microscopes (SEMs).

images from scanning electron microscope and helium ion microscope
A comparison of the surface detail shown under a scanning electron microscope versus a HIM. (Images provided by Shuttha Shutthanandan)

In recent work, researchers were studying bone tissue engineering—another example of organic matter–mineral interactions—to understand what occurs at the earliest stages of biomineralization.

Shuttha Shutthanandan prepares to load a sample into the HIM.
Shuttha Shutthanandan prepares to load a sample into the HIM. (Photo by Andrea Starr | Pacific Northwest National Laboratory)

Visit EMSL’s website to learn more about available instruments and resources as well as proposal call opportunities. Register to attend the March 22 EMSL LEARN webinar to hear presentations about these resources and to pose questions to the panel.