Senior Scientist DOE Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, California
In recent years we have begun to appreciate the importance of the root microbiome for plant health and the enormous potential for harnessing the microbiome to sustainably increase crop yield to meet projected demands. Unfortunately, the extreme complexity of the root microbiome is a significant hurdle to gaining the detailed knowledge of plant-microbiome interactions necessary to optimize microbiome composition or create interventions that reliably increase yield. Fabricated ecosystems (EcoFABs, https://eco-fab.org/) are an experimental system that allows researchers to reproducibly create simplified ecosystems that enable the experiments necessary to understand plant-microbiome interactions at a molecular level. These small devices consist of a chamber that allows a plant to be grown under sterile conditions in a small volume of solid or liquid media. Sampling ports allow for the non-destructive sampling or replacement of liquid media to facilitate metabolomic analyses and the addition of known microbes. The bottom of the chamber is a microscope coverslip which enables non-destructive imaging. We conducted a ring trial with five labs on three continents to demonstrate the reproducibility of microbiome formation on the model grass Brachypodium distachyon after inoculation with 16 or 17-member synthetic microbial communities. Interestingly, we observed that a single bacterial strain reproducibly altered the entire microbiome. In addition, we have developed a robotic platform, EcoBOT, to increase the throughout and reproducibility of the system. The DOE joint Genome Institute has recently added EcoFAB devices to the suite of capabilities offered to the scientific community through its Community Science Program.