BioEPIC Science: ENIGMA
Ecosystems and Networks Integrated with Genes and Molecular Assemblies will be a key component at Berkeley Lab's new BioEPIC facility.
ENIGMA Strategic Planning meeting, 2019.
Established in 2009, the Ecosystems and Networks Integrated with Genes and Molecular Assemblies (ENIGMA) consortium is led by Berkeley Lab and includes investigators from 11 institutions. The goal of ENIGMA is to create a predictive model of the impacts of microbial communities on critical ecosystem processes.
ENIGMA researchers study subsurface microbiomes within the Bear Creek aquifer (pictured above) at the Oak Ridge Reservation (ORR) Field Research Center (FRC), a site with complex contaminants generated by research and production of nuclear materials. The FRC has well-mapped hydrology and geology and complex gradients of nutrients, stressors, and contaminants, making it an excellent site to study the reciprocal interactions of environmental factors on microbial ecology and activity. Contaminants at the site include nitrate, acidity, uranium, technetium, and volatile organic carbon species—the fate of which is influenced by the activity of subsurface microbial communities.
Outcrop showing typical bedrock layering of the ORR-FRC area. Contaminated groundwater wells colored by pH range at the ORR-FRC. The inset arrow shows the experimentally demonstrated molybdenum removal mechanism.
Across the site, a large number of active wells permit efficient groundwater sampling, and it is relatively cost-effective to drill new wells or retrieve depth-indexed sediment cores when the project requires it.
Pictured: Wellheads for sampling groundwater in the Bear Creek watershed at ORR-FRC. Wells are located in areas that span a contamination plume containing high concentrations of mixed metals that can impact the microbial community.
Field-based ENIGMA researchers sample sediment and groundwater to map the hydrology, geology, and chemical features of the area. At the same time, they are quantifying field processes and complex gradients of nutrients, stressors, and contaminants. The samples they collect are sent to the lab-based researchers who identify the microbes present in the subsurface communities. ENIGMA researchers want to discover and characterize the reciprocal interactions between shallow subsurface microbial communities and the geochemical and geophysical parameters of the FRC. With enough detail, they hope to model contaminant fate and microbial community dynamics.
Katie Walker, University of Tennessee Knoxville graduate student, deploys an Aquatroll remote telemetry device downwell at background site. Cone penetrometer testing (CPT) core sample. Erin Kelly and Andrew Putt, University of Tennessee Knoxville graduate students, process sediment samples from CPT drilling. Close-up of CPT core sediment.
Lucy Zeng, senior research associate, using transmission electron microscopy (TEM) to characterize isolates derived from the ORR-FRC. Collage of TEM images showing the microbial diversity captured in the groundwater wells at ORR-FRC.
Lab-based ENIGMA researchers enrich, isolate, and physiologically and genetically characterize the specific microbial taxa that are predicted to be the most important to the observed field processes. By characterizing genetic functions and linking genotype to phenotype in the laboratory, they can interpret field data mechanistically, leading to pointed hypotheses of the role of particular taxa, proteins, co-factors—and their interactions in creating systems behavior.
The Environmental Simulation and Modeling (EnvSim) campaign has strategically aligned efforts across ENIGMA to investigate ecologically important phenomena observed at the Oak Ridge FRC. Insights from simulations are then tested back at the FRC, demonstrating the “field-to-lab-to-field” iteration model employed across ENIGMA for investigating phenomena that emerge through the interrogation of complex interactions within a microbial community.
Custom fluidized bed reactors to study the population dynamics of FRC isolates as they partition between planktonic and attached phases of growth. Confocal image of sediment with stained cells shown in blue. Packed-bed reactors (PBRs) inoculated from field samples and incubated under field conditions. The PBRs consist of a packed-bed of sand particles that represent particle size distributions observed in field samples. Epifluorescent image of sectioned core material from a PBR. Microbial cells, in green, can be visualized on and between particles.
Together, the ENIGMA team aims to mechanistically understand how microbes are actively selected and transform the terrestrial subsurface. All these efforts are being integrated into predictive models with the goal to predict and control the fate of resources and contaminants in the environment.
More information about the ENIGMA SFA can be found at enigma.lbl.gov. The SFA is sponsored by the U.S. Department of Energy Biological and Environmental Research program.
