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Genomic Science Program

Systems Biology for Energy and the Environment

Department of Energy Office of Science. Click to visit main DOE SC site.

Genomic Science Program

Pilot Project: Lawrence Berkeley National Laboratory (LBNL)

m-CAFÉs: Microbial Community Analysis and Functional Evaluation in Soils

m-CAFÉs is a collaborative, coordinated and integrated, mission-driven project to interrogate the function of soil and rhizosphere microbiomes with critical implications for carbon cycling and sequestration, nutrient availability, and plant productivity in natural and managed ecosystems. The project will develop precisely controlled ecosystem fabrications (EcoFABs) that will enable recapitulation, observation, and manipulation of environments. The EcoFABs will reflect key functional attributes of plant-microbe interactions within soil, focusing on progressively increasing complexity of the system to mimic physical constraints in the soil environment (e.g. soil texture).

In concert with the development of EcoFABs, this research will pioneer the development of microbial community editing techniques for bacteria and fungi, using CRISPR-Cas and RNA interference (RNAi) respectively. Taking advantage of the simulated environments of EcoFABs, the genomes of single microorganisms within complex communities will be edited with repurposed Cas nucleases to lethally target chromosomal sequences in bacteria and using RNAi to silence genes in fungi. By manipulating EcoFAB complexity it will be possible to assess how different soil conditions affect the efficacy of editing/silencing mechanisms and the efficiency of delivery systems (e.g. phages, plasmids, or dsRNA).

Together, this new platforms will provide the fundamental genetic basis of the formation and functional importance of microbial metabolic interaction networks in the rhizosphere and soil environments. The results of these studies will be transformative for our understanding of environmental microbiology, with applications to DOE missions in energy and environment.

Laboratory Research Manager/Principal Investigator: N. Louise Glass

Co-Investigators: Eoin Brodie1, Adam Deutschbauer1, Peter Nico1, Trent Northen1, Rodolphe Barrangou2, Jill Banfield3, Mary Firestone3, Jennifer Doudna3, and Anup Singh4

Participating Institutions:
1Lawrence Berkeley National Laboratory (LBNL), 2North Carolina State University, 3University of California, Berkeley, and 4Sandia National Laboratory (SNL)

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