The use of fabricated ecosystems (EcoFABs) and standardized microbial communities can facilitate advancements in microbiome science by providing analysis of plant-microbe-soil interactions at user-defined levels of automation, standardization, and reproducibility. The TEAMs project, led by Lawrence Berkeley National Laboratory, is evaluating three different ways of disseminating fabricated ecosystems (EcoFABs) to users. These include (1) an automated, high-throughput system (left image), which provides the highest level of standardization and reproducibility, (2) EcoFAB “kits” that balance standardization with flexibility (middle), and (3) a Web Portal (right) that empowers the larger community to create their own EcoFABs. The standardized protocols used in these experiments make the resulting samples (plant tissues, root exudates, soils, and microbiota) compatible for analysis at DOE user facilities such as EMSL and JGI, which generate standardized data to populate the NMDC microbiome database. These data can then be analyzed in DOE’s KBase, a software and data science platform designed to predict and design biological function. [Courtesy LBNL]
Soil and plant microbiomes play vital roles in ecosystems, yet the lack of standardized and reproducible experimental systems to study these roles represents a major challenge for microbiome science. Fabricated ecosystems (EcoFABs) are sterile devices with tremendous potential to advance a mechanistic understanding of soil and plant microbiomes by providing unique control and measurement capabilities for simplified microbial communities. The Trial Ecosystems for the Advancement of Microbiome Science (TEAMS) project is creating, validating, and disseminating EcoFAB technologies, complete with standardized model microbial communities tailored to the needs of various U.S. Department of Energy (DOE) stakeholders, including users of DOE resources and facilities such as the Environmental Molecular Sciences Laboratory (EMSL), Joint Genome Institute (JGI), Systems Biology Knowledgebase (KBase), and National Microbiome Data Collaborative (NMDC). EcoFAB technology is distributed as kits validated through multilaboratory reproducibility studies and as online resources that guide users through EcoFAB construction and use. In addition, TEAMS is developing a powerful new robotic system (EcoBOT) that enables completely automated plant-microbe-soil EcoFAB experiments conducted according to detailed specifications. EcoBOT provides precise environmental control of plant growth within sterile environments, introduction and sampling of microbes for systems biology analysis, and multimodal imaging of the rhizosphere and the plant. The high level of control and reproducibility enabled by this system will provide powerful datasets that can be incorporated into NMDC, used with KBase modeling approaches, and leveraged to develop new machine-learning algorithms. Together, these standardized and reproducible experimental capabilities will help advance mechanistic microbiome science.