NorthenLab: Exometabolomics linking genomes with environments to understand how webs of microbes sustain biomes

EcoFAB enables imaging of an entire root system

Lauren Jabusch, Benjamin Bowen, and Trent Northen are authors on the paper “Microfabrication of a Chamber for High-Resolution, In Situ Imaging of the Whole Root for Plant–Microbe Interactions.” As mentioned before, specialized plant growth chambers offer promise as a way of investigating rhizosphere interactions. The Imaging EcoFAB, presented in this paper, was used to record the root structure and the position of fluorescently tagged bacteria through a clear chamber.  

Image: Time series images of Brachypodium distachyon growing in an imaging EcoFAB. The white bars in days 0-7 are 1mm and 5mm for days 10-21.

Unlike a regular EcoFAB, which consists of an open, oval chamber for media with a port for the plant, the imaging EcoFAB introduces the use of pillars between the top and bottom of the PDMS growth chamber. This keeps the roots closer to the glass surface and corrects for differences in distance from a microscope objective. Using this structure, researchers imaged the roots and a fluorescently tagged synthetic comunity to determine spatiotemporal patterns in plant growth and bacterial colonization. 

To learn more about EcoFABs and the experiment, check out the full paper