The mCAFEs project is a proposed 10-year Department of Energy (DOE) Science Focus Area(SFA) project with the goal of developing foundational tools and molecular ecosystems biologybased   understanding   required   to   predict,   manipulate,   and   design   rhizosphere   microbialcommunities. The project has two primary research foci: i) Tool Development and ii) ToolEnabled Systems Biology in Rhizosphere Microbial Communities

 

i) Tool Development:As part of our tool development we are attempting to pioneer microbial communityediting tools for dissecting the function of genes, pathways, and microbes within complexcommunities. This includes technologies for detection of transformation efficiency, DNA delivery,targeted CRISPR-Cas based editing, and microbial ablation. While this represents a significantchallenge, microorganisms do not naturally grow as isolates, and the development of genetictechnologies   to   manipulate   microbes   in   the   context   of   their   natural   communities   will   betransformative for understanding microbial community dynamics.We   are   also   developing   a   fabricated   ecosystem   (EcoFAB).   The   EcoFAB  is   astandardized   and   reproducible   analysis   platform   for   both   synthetic   consortia   and   naturalmicrobiomes in simulated and natural environments under controlled conditions. The system isparticularly suited for the study of rhizosphere microbiology as it accommodates plant growth,and allows live cell imaging.

 

ii) Tool Enabled Systems Biology:In this part of the project the tools such as EcoFABs and community editing techniquesare combined with a pipeline of large-scale phenotyping, genetics, and metabolomics to greatlyimprove our understanding of the gene functions of rhizosphere microbes. Using combinationsof rhizosphere isolates as well as naturally enriched communities, we are applying full spectrumomics’  technologies   (metagenomics,   transcriptomics,   and   proteomics)   to   characterize   theactivities and interactions of microbial assemblages.