Environmental Atlas

ENIGMA diversity — The microbial diversity captured in the groundwater wells at Oak Ridge Reservation (ORR) taken with our in-house transmission electron microscope (TEM). Image: P.J. Walian. Staff Scientist. Environmental Genomics and Systems Biology Division. Lawrence Berkeley National Lab; Berkeley, CA.

Lab-based ENIGMA researchers enrich, isolate and physiologically/genetically characterize the specific 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, we 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.

Valentine Trotter, Biologist, Project Scientist, ENIGMA, studies growth plates inside a Biosafety Cabinet at the Aquatic Park site, Lawrence Berkeley National Laboratory, Berkeley, California.

Relevant Publications

Huang Explores How Bacteria Store Carbon at 2024 BioEPIC Research SLAM - Congratulations to Joshua Jiaqi Huang, a UC Berkeley graduate student researcher in Biosciences senior faculty scientist Adam Arkin’s group, who represented ENIGMA and Biosciences at the 2024 BioEPIC Research SLAM. More →

Snapshot showcasing the dashboard of fast.genomics, a new tool which shows a search query protein and several proteins that are related to that protein or located in a similar place to the searched protein in the genomes of many species of bacteria and archaea.

fast.genomics: A Fast Comparative Genome Browser for Diverse Bacteria and Archaea - ENIGMA researchers have developed fast.genomics, a new tool which allows users to search for a protein and identify other proteins that share a common ancestor or are located in similar genomic regions. More →

Aerial photo displaying four square ponds of brown and green water.

Multi-disciplinary research develops a deeper understanding of subsurface microbiology - ENIGMA is organized into three aims that reflect the different research scales (i.e., field level to molecular level) required to build a comprehensive picture of subsurface microbiology at the Oak Ridge Reservation (ORR): Subsurface Observatory, Environmental Atlas, and Environmental Simulations. Several key research initiatives, described in this cross-aim overview, highlight this framework in action. More →

Genome Editing in Rhodanobacter denitrificans - ENIGMA researchers demonstrated the development and application of a markerless deletion mutagenesis system in nitrate-reducing bacterium Rhodanobacter denitrificans. This method marks a crucial step in advancing Rhodanobacter as a model denitrifying bacterium for the study of denitrification in groundwater ecosystems and diverse molecular mechanisms of low-pH resistance. More →

Two model phages characterized by new CRISPR based technology extensible to diverse phages - ENIGMA researchers demonstrated for the first time that they can, on a genome-wide scale, identify phage genes that are essential (or not) to infecting bacteria, and then replace non-essential DNA with distinctive barcode tags. Their method could unlock potent biotechnology applications. More →

Schematic diagram showing the process of inputting cells of synthetic community and environment isolates into an automated benchtop liquid handler to prepare them for high-throughput proteomic analysis.

Novel Protocol Leverages Automatic Liquid Transfer to Prepare Hundreds of Microbial Cell Cultures for Proteomic Analysis - ENIGMA researchers detailed a step-by-step protocol that consists of cell lysis in alkaline chemical buffer (NaOH/SDS) followed by protein precipitation with high-ionic strength acetone in 96-well format. This protocol, combined with previously established automated protein quantification and protein normalization protocols, provides a rapid, cost-effective method to prepare LC-MS proteomic samples from bacteria and non-filamentous fungi cell cultures. More →