About This Project

Soil fungi and plant roots are important biological networks that can be difficult to observe with visible-light imaging. This project will use hyperspectral microscopy to characterize spectra of fungal hyphae and plant roots on aggregate surfaces and test whether they can be distinguished from the surrounding soil. We will identify useful wavelengths for separating these materials and generate a pilot open spectral dataset for soil biological imaging.

Ask the Scientists

What is the context of this research?

Hyperspectral imaging measures light reflectance across many wavelengths, making it possible to distinguish materials that look similar to the eye but reflect light differently across the spectrum. Although widely used aboveground to assess vegetation, spectral data remain limited for fungal and root networks belowground.

These networks respond to soil conditions and disturbance, making them useful indicators of soil health, but they are difficult to monitor. Soil aggregates expose surfaces where hyphae and fine roots can be observed within soil environments. However, fungal hyphae are only a few microns wide and can resemble roots or organic matter in visible-light images. Hyperspectral microscopy can isolate materials at the pixel scale to minimize spectral mixing and build reference spectra for individual structures.

What is the significance of this project?

Spectral reference data for fungal hyphae, plant roots, soil organic matter, and minerals on natural soil surfaces remain limited. Prior work has used hyperspectral imaging to distinguish roots from soil, but primarily in controlled rhizobox or laboratory settings rather than on field-collected soil surfaces. Without reference spectra from natural soil environments, we cannot evaluate whether imaging-based approaches can reliably distinguish biological structures in soil.

This project will identify which wavelengths, if any, carry the most useful information for separating these materials. These results could determine whether cheaper broadband, multispectral, or filtered RGB systems can substitute for full hyperspectral imaging and could provide endmember spectra to inform spectral unmixing at larger pixel scales. The resulting open spectral dataset would complement existing soil spectral libraries, which focus on bulk soil properties rather than microscale biological structures.

What are the goals of the project?

This project will test whether fungal hyphae, plant roots, mineral soil, and soil organic material can be distinguished by how they reflect light. I will collect 6 aggregates from existing field sites and prepare 9 targeted regions, 3 replicates per material class (i.e., hyphae, roots, soil), on each aggregate. These regions will be scanned using reflected-light hyperspectral microscopy at the UCSB Center for Polymers and Organic Solids Optical Characterization Facility.

I will compare spectra among these material classes to test whether they are spectrally separable and evaluate limitations including surface roughness, shadows, and mixed pixels. Region identity will be supported by optical microscopy to link spectra to confirmed surface materials. By the end of the project, I will produce a pilot open spectral dataset, identify the wavelengths most useful for separating biological and non-biological soil surface materials, and prepare spectra and metadata for sharing.