Berkeley Lab

Environmental Microbiology

Environmental MicrobiologyResearchers in ENIGMA’s Field Microbiology component work with microbial communities in the environment to investigate how biological structure and function relate to critical biochemical conditions/changes, such as the immobilization of toxic metals and the flow of carbon and nitrogen. The goal is to identify key microbial populations and determine the community events and mechanisms of these populations that impact and control environmental activities of interest, ultimately predicting how perturbations of the environment may affect community structure. From these results, models will be developed using various bioinformatic tools (e.g., AdaptML, random matrix theory, multivariate statistics) that can be applied to microbial populations overlaid with geochemical parameters and engineering controls.

Current efforts include optimizing omics protocols for environmental samples, and designing efficient field sampling studies that maximize the geochemical diversity of study sites, and enhance the associations between microbial communities and key geochemical features. To this end, researchers in ENIGMA’s Field Microbiology component have developed a Monte Carlo search algorithm to optimize site selection for geochemical diversity. A search is now underway for 100 wells where metagenomic analyses can be performed in cooperation with a relevant existing program at Oak Ridge National Laboratory.

Field Microbiology Team

  • Fields Matthew
    Fields, Matthew
    Deputy Director Environmental Microbiology matthew.fields@erc.montana.edu (406) 994-7340
  • Chakraborty Romy
    Chakraborty, Romy
    Principle Investigator rchakraborty@lbl.gov (510) 486-4091
  • Hazen Terry
    Hazen, Terry
    Director, Environmental Microbiology tchazen@utk.edu (707) 631-6763
  • Elias Dwayne, PHD
    Elias, Dwayne
    Principal Investigator eliasda@ornl.gov (865) 574-0956
  • Zhou Jizhong Joe
    Zhou, Jizhong (Joe)
    Principal Investigator jzhou@ou.edu (405) 325-6073
  • Pseudomonasstutzeri_RCH2_Chakraborty
    Complete genome sequence of Pseudomonas stutzeri...
    Dr Chakraborty and a team of ENIGMA researchers have published the...
  • Bioreactors_Elias2
    Temporal Dynamics of In-Field Bioreactor Populations...
    Researchers at Johns Hopkins University, Colorado State University, The University of...
  • Predicting-metabolic-properties-using-dynamic-substrate-preference (1)
    Predicting metabolic properties using dynamic substrate...
    Exometabolomic profiling was used to examine the time-varying substrate depletion from...
  • UraniumBindingComplex_Pelosinus_Adams
    Uranium binding complex a potential tool...
    Widespread uranium contamination from industrial sources poses hazards to human health...
  • Biosensor_RochaHazen1
    Rapid Detection of Microbial Cell Abundance...
    ENIGMA post doctoral fellow developed the application of ACEK-enhanced capacitive sensing technology...
  • DigitalDropletDisplacementAmplification_Singh
    Digital Droplet Multiple Displacement Amplification
    Digital Droplet Multiple Displacement Amplification (ddMDA) for whole genome sequencing of...
  • Preferential-oxidation-of-microbial-mediated-reduced-sulfur-by-nitrate-limits-the-in-situ-mobility-of-uranium
    Preferential oxidation of microbial-mediated reduced sulfur...
    Reoxidation and mobilization of previously reduced and immobilized uranium by dissolved-phase...
  • Comparisons of phylogenetic groups
    Comparative metagenomics reveals impact of contaminants...
    Significant portions of natural groundwater reserves have been contaminated due to...
  • 2015_RochaPoster
    Andrea Rocha is featured in DOE’s...
    Andrea Rocha is featured in DOE’s online Women @ Energy Series...
  • Methanosarcina Nature Acetate
    Potential Role of Acetyl-CoA Synthetase (acs)...
    Elliott P. Barnhart1,2,3, Marcella A. McClure1, Kiki Johnson1, Sean Cleveland1, Kristopher...
  • CoExtraction_DNA_PLFA_Soil_Hazen
    Differences in diversity between extraction techniques
    ENIGMA researchers at University of Tennessee Knoxville examined differences in diversity...
  • Smith_Rocha1
    Bacterial Communities As Precise Biosensors Of...
    ENIGMA scientists show that DNA from natural bacterial communities can be...