Genomic Science Program
U.S. Department of Energy | Office of Science | Biological and Environmental Research Program

2024 Abstracts

EcoFAB 3.0: A Controlled Ecosystem for Bioenergy Crops


Kshitiz Gupta1,3* ([email protected], [email protected]), Yang Tian2,3, Aymerick Eudes2,3, Henrik V. Scheller2,3, Trent R. Northen2,3, Paul D. Adams2,3, Jay D. Keasling2,3


1Lawrence Livermore National Laboratory; 2Lawrence Berkeley National Laboratory; 3Joint BioEnergy Institute



The Joint BioEnergy Institute’s (JBEI) mission is to establish the scientific knowledge and new technologies in feedstock development, deconstruction and separation, and conversion needed to transform the maximum amount of carbon available in bioenergy crops into biofuels and bioproducts.


Plant-microbe interactions are critical to sustainable agriculture. Technologies are needed that enable studying these interactions under sterile and controlled laboratory conditions to decouple their complexities and identify molecular mechanisms. There are several existing systems such as EcoFABs, RootArray, RootChip, and Tracking Root Interaction System (TRIS). Typically each has advantages for studying different aspects of plant-microbe interactions. Researchers have demonstrated the repeatability of observations using these platforms. For example, EcoFAB 2.0 was recently used to study the effects of nitrogen starvation on root exudates by Novak et al. (2024) and Stanley et al. (2018) used RootChip to observe asymmetric root hair growth in response to an asymmetric phosphate perfusion. However, these platforms are designed for small model plants such as Brachypodium distachyon and Arabidopsis thaliana. This leaves a gap in translating findings from model plants to economically significant bioenergy crops such as sorghum.

In this work, researchers introduce a novel platform (EcoFAB 3.0) that is designed to study bioenergy plants such as sorghum for up to 4 weeks in a sterile and controlled environment. In addition to its larger size, EcoFAB 3.0 addresses many other limitations of previously used platforms. Its 2-step assembly makes it easy to set up and is highly user-friendly. Its root chamber is dark and allows the roots to grow more naturally by using a rhizotron-like window for imaging. The device has several multipurpose ports which can be used for exudate collection, ventilation and introducing various sensors for monitoring gaseous exchange, temperature, moisture, and other parameters. Excitingly, researchers have now found that EcoFAB 3.0 is able to recreate field and greenhouse observations made by Lin et al. (2022) showing that an engineered line of sorghum has higher accumulation of 4-hydroxybenzoic acid (4-HBA) and lower biomass in comparison to the wildtype.


Lin, C.-Y., et al. 2022. “Engineering Sorghum for Higher 4-Hydroxybenzoic Acid Content,” Metabolic Engineering Communications 15, e00207.

Novak, V., et al. 2024. “Reproducible Growth of Brachypodium in EcoFAB 2.0 Reveals that Nitrogen Form and Starvation Modulate Root Exudation,” Science Advances 10, eadg7888.

Stanley, C. E., et al. 2018. “Dual-Flow-RootChip Reveals Local Adaptations of Roots Towards Environmental Asymmetry at the Physiological and Genetic Levels,” New Phytologist 217, 1357–69.

Funding Information

This work was part of the DOE Joint BioEnergy Institute (http:// supported by the U.S. DOE, Office of Science, BER Program, through contract DE-AC02-05CH11231 between Lawrence Berkeley National Laboratory and the U.S. DOE.