mCAFE: Microbial community analysis and functional evaluation in soils
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.
Learn more about the project at https://mcafes.lbl.gov/