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Lab Microbiology

DvG20Research in the Lab Microbiology component of ENIGMA is closely coordinated with the Field Microbiology, Biotechnology and Computation components. The initial focus of this work is proof of principal on the biology and interactions of a small suite of bacteria identified relevant in microbial communities such as Desulfovibrio, Methanococcus maripaludis and Pelosinus. For example the sulfate-reducing bacterium Desulfovibrio is a rod-shaped anaerobic bacterium that has drawn keen interest for its potential use as a bioremediator for its ability to reduce important toxic metals from the environment.

In collaboration with the Field Microbiology component, Lab Microbiology researchers are characterizing key microbes and microbial communities that are directly enriched from metal-contaminated sites. They are prioritizing these systems for deep functional annotation based on physiological properties, interactions with other microorganisms, and potential biogeochemical activities. In concert with the Biotechnology component, Lab Microbiology researchers are elucidating the biology of DvH using the tools of metabolomics, proteomics, transcriptomics, high-resolution microscopy, and high-throughput mutagenesis/phenotyping. They plan to apply these techniques to other relevant microbes identified by the Field Microbiology team. Lab Microbiology researchers are working with the Computation component to construct predictive models of DvH metabolism and gene regulation. Independently, Lab Microbiology researchers are determining how information flows among microbes to assess the specificity, mutualism and antagonism among pairs and groups of microbes.

Lab Microbiology Team

  • Arkin, Adam
    Arkin, Adam
    SFA Technical Co-Manager Director, Laboratory Microbiology [email protected] (510) 643-5678
  • Adams-Mike_thumbnail
    Adams, Mike
    Principal Investigator [email protected] (706) 540-1645
  • enigma team members
    DuBSEQ functional characterization Nature Communications
    January 18, 2019–ENIGMA researchers release DuBSEQ, a tool for broader use...
  • annethompson
    Robustness of a model microbial community...
    May 1, 2017–Robustness of a model microbial community emerges from population...
  • DvH_MM_PopulationCurves_Turkarslan2
    ENIGMA Researchers Uncover Factors in Microbial...
    April 7, 2017–Serdar Turkarslan, a Senior Research Scientist at the Institute...
  • Metabolizing Data in the Cloud
    January 20, 2017–ENIGMA researchers at Scripps Research Institute have developed tools...
  • Biosensor_RochaHazen1
    Rapid Detection of Microbial Cell Abundance...
    November 15, 2016–(A) Overview of approach. To provide proof of principle,...
  • DigitalDropletDisplacementAmplification_Singh
    Digital Droplet Multiple Displacement Amplification
    May 31, 2016–Fig. 1. The working principles of ddMDA. The ddMDA...
  • NitrateReductaseActivity_ThorgersenAdams
    Nitrite Reduction Assay for Whole Pseudomonas...
    May 20, 2016–ENIGMA researchers at University of Georgia developed and published...
  • lauren-liu
    Post Doc Lauren Lui profiled by...
    March 15, 2016–During March- Women’s History Month, Berkeley Lab recognizes and...
  • BacterialNaturalSelectionSimulations_Arkin_Price2016
    Are free-living bacteria optimized by natural...
    December 15, 2015–Free-living bacteria are usually thought to have large effective...
  • Lara_Rajeev
    Lara Rajeev Stars in video demonstrating...
    Rajeev, L., E. G. Luning, and A. Mukhopadhyay (2014). DNA-affinity-purified chip...
  • American Society for Microbiology
    New Community Leadership! Aindrila Mukhopadhyay
    July 1, 2014–ENIGMA’s Aindrila Mukhopadhyay in ASM leadership role. Beginning July 1,...
  • Metallomics, Issue 5 2014_front cover
    Metallomics of Two Microorganisms Featured on...
    April 28, 2014–Metallomics of Two Microorganisms Relevant to Heavy Metal Bioremediation...
  • Mukhopadhyay-Aindrila_thumbnail
    Mukhopadhyay, Aindrila
    Principal Investigator [email protected] (510) 495-2628
  • Stahl, David
    Stahl, David
    Principal Investigator [email protected] (206) 685-3464