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Researchers Develop a Microscope that can see Bacteria in Soil & Plants

Imaging biogeochemical interactions in complex microbial systems like the soil-root interface are critical for climate, agricultural, and environmental health research.

Shivam Dwivedi
Close view of Seedling
Close view of Seedling

Scientists at Lawrence Livermore National Laboratory (LLNL) have developed a micrometer-scale microscope to examine bacteria in soil and plants. Live imaging of microbes in soil would help scientists better understand how soil microbial activities occur on the micrometre scale, where microbial cells interact with minerals, organic materials, plant roots, and other microorganisms. Because the soil environment is varied and dynamic, these interactions can change dramatically within a small region and over short periods of time.

Imaging biogeochemical interactions in complex microbial systems like the soil-root interface is critical for climate, agricultural, and environmental health research. However, it is hampered by the three-dimensional (3D) collation of materials with a diverse range of optical properties.

Microaggregates (250 m) formed by microbial breakdown of soil organic matter are inhabited by various microbial communities, potentially leading to very different metabolisms and functions within the volume of soil collected for molecular, genomic, or physiochemical studies. In addition to microbial heterogeneity, microorganisms respond quickly to changes in subsurface temperature, moisture, food availability, signaling molecules, and other factors.

‘Muddy’ Trials

Researchers have improved their understanding of the spatial and temporal aspects of these processes by employing various imaging techniques. Nonetheless, the combined properties of soil and microbes, such as physical properties and length scales, continue to make screening and characterizing microbe-plant-soil interactions difficult over time.

In recent years, X-ray computed tomography and magnetic resonance imaging have made some of the most spectacular advances in soil imaging. These modes are well-known for their ability to image deep into the soil, providing an unparalleled understanding of plant and soil structure, as well as water flow. They're even used in real-time imaging.

These methods, however, are unable to photograph microorganisms such as individual hyphae and bacteria due to contrast or resolution limitations. The LLNL researchers used optical technologies, such as imaging with light in the ultraviolet, visible, and infrared spectrums, to see bacteria in soil and plants.

The researchers developed a label-free multiphoton nonlinear optics technique that employs multiple imaging modes to provide contrast and chemical data for soil microorganisms in roots and minerals.

Janghyuk Lee, LLNL's lead scientist, added that multiphoton microscopy has several advantages over single-photon approaches such as fluorescence imaging and Raman. The primary advantage is that it provides a high signal with a lower risk of sample destruction.

In comparison to confocal microscopy, the LLNL team's approach provides a powerful signal for common microbe, plant, and mineral imaging; high contrast, label-free chemical imaging that can target diagnostic biomolecules and minerals; powerful signals from specific minerals and some biomolecules; and higher information content, deeper penetration, less scattering, and less photodamage. The findings were published in the journal Environmental Science and Technology.

This technology was used by the researchers to examine symbiotic arbuscular mycorrhizal fungal structures inside unstained plant roots in 3D to a depth of 60 m. In a clay particle matrix, high-resolution imaging was possible at depths of up to 30 m and 15 m in complex soil preparation.

(Source: Optic Flux)

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