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ENIGMA scientific focus area (sfa)

Ecosystems and Networks Integrated with Genes and Molecular Assemblies

ENIGMA seeks to advance the increasingly high resolution mapping from molecules to microbes and leverage the discovery of mechanisms composing the subcellular, cellular, and intercellular networks of metabolite, protein, RNA and DNA molecules that drive macroscopic biogeochemical processes, integrating these into the larger framework of interacting microbial communities and ecosystems to address DOE goals. ENIGMA SFA Overview

By developing and applying high resolution and high throughput platforms of both ‘top down’ systems approaches (i.e. metagenomics, proteomics, metabolomics, etc) and ‘bottom up’ structural approaches (i.e. EM), we are rapidly advancing environmental microbes to model-organism status. Aided by critical consortium and field studies, the single-organism molecular data extend across increasingly complex microbial communities to determine how these networks transform environmental signals to behaviors and to link laboratory results to the measurements from field studies. The SFA enables these unique multiscale studies through the development of an increasingly sophisticated computational framework for storage, analysis, visualization and modeling of these data. The framework is designed to predict the key factors enabling microorganisms to survive, compete, and cooperate in DOE relevant environments while performing processes impacting remediation, carbon sequestration and bioenergy production. We develop new frameworks for collecting and quantitatively analyzing multi-scale information—from molecules to organisms, from cells to communities, and from communities to ecosystems in order to meet the challenges and opportunities of the DOE GTL mission.

Research in the ENIGMA Scientific Focus Area is funded by the U.S. Department of Energy Office of Biological and Environmental Research Division and managed within Lawrence Berkeley National Lab- Physical Biosciences Division (PBD).


Paul Adams (PBD) Laboratory Research Manager (510) 486-4225
Adam Arkin (PBD) Laboratory Research Manager (510) 486-4225
Joseph Graber DOE OBER Program Manager
Astrid Terry (PBD) Project Manager (510) 486-4928


  • Eric Alm(Massachusetts Institute of Technology)
  • Nitin Baliga (Institute for Systems Biology)
  • Adam Deutschbauer (PBD), Matthew Fields (Montana State University)
  • Terry Hazen (University of Tennessee), Trent Northen (Life Sciences Division)
  • Judy Wall (University of Missouri)