Scientists set up a microchip lab to study living trees

Plants interact with certain microbes, such as bacteria and fungi, in mutually beneficial ways that scientists are just beginning to fully understand. Researchers at the US Department of Energy’s (DOE) Argonne National Laboratory have come up with a way to study these interactions using a newly developed microfluidic device – a chip with tiny channels. This device could aid research aimed at discovering more effective ways to stimulate plant growth, create drought-resistant crops, restore the environment, and even increase the production of bioenergy feedstocks. Research paper published in the journal Frontiers in Plant Science.

The process of plant root-microbe interactions (RMI) is hidden under the soil. This prevents researchers from continuously observing the attachment of microbes and the exchange of nutrients without interruption and for a long time. To get around this problem, scientists traditionally analyzed the root environment by growing plants in pots, between glass sheets or agar bowls, and then observed the roots for physical changes and microbial interactions by sacrificing a sample. An agar dish is a Petri dish containing agar as a solid culture medium plus nutrients used to culture microorganisms.

However, the ideal way to monitor the relationship between plant roots and surrounding microorganisms in the rhizosphere – the nutrient-rich area of ​​soil surrounding a plant root – is to observe all interactions as they occur over extended periods of time and in high resolution. So researchers at the Argonne Biosciences Division, along with scientists at the Argonne Nanoscale Materials Center, a user facility of the US Department of Energy’s Science Office, developed an RMI chip: a tiny microfluidic device that allows a small amount of liquid to pass through microchannels or paths on a chip that is only a few squares in size. centimeters across.

“Channels are created using soft lithography, an approach to creating three-dimensional structures using soft materials,” explains Giorgi Babnigg, a bioinformatist and molecular biologist at Argonne who co-developed the device.



Babnigg and his colleagues used this technique to create a negative impression of their device. They then doused the mold with a plastic-like silicone, heated it to solidify, and then removed it from the mold. The researchers then punched holes in the material to form inlets and outlets, and finally fused it with a piece of microscope coverslip so they could observe what was going on inside the channels through the microscope. The result is a miniature laboratory for studying trees.

Microfluidic devices like those created by Babnigg and his team have long been used by researchers to study the interactions of roots and microbes, albeit exclusively in small, short-lived flowering plants. The new device is the first to be used on living woody plants.

The new development has already allowed researchers to determine whether symbiotic processes are observed, such as the absorption of nutrients by the plant root by microbes, or the release of materials such as phosphorus and plant hormones that control the movement of the root.

For several weeks, the researchers continuously observed how different types of microbes grow and interact with living roots through a microscope, and found that in the absence of external nutrients, microbes actually attach to the root surface and use root exudates to grow.

We visualized all these interactions while the plant was still alive. Our ability to do this with our device for several weeks is what sets this job apart.

Gyorgy Babnigg, bioinformatist and molecular biologist from Argonne, co-inventor of the device

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