Berkeley Lab

ENIGMA Researchers Uncover Factors in Microbial Community Collapse

Serdar Turkarslan, a Senior Research Scientist at the Institute for Systems Biology in Seattle, Washington; along with a team of researchers has developed a framework to quantify microbial community resilience in the face of environmental changes. This framework will be invaluable for observing the behavior of microbial communities under simulations of current and projected environmental conditions. Their […]

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Temporal Dynamics of In-Field Bioreactor Populations Reflect the Groundwater System and Respond Predictably to Perturbation

  A collaboration of researchers at Johns Hopkins University, Colorado State University, The University of Tennessee, The Lawrence Berkley National Laboratory, The Massachusetts Institute of Technology, The University of Oklahoma and the University of Georgia, Oak Ridge National Laboratory researchers in the Bioscience Division for the ENIGMA have released an article in Environmental Science and Technology. They have […]

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Predicting metabolic properties using dynamic substrate preference

Exometabolomic profiling was used to examine the time-varying substrate depletion from a mixture of 19 amino acids and glucose by two Pseudomonads and one Bacillus FRC isolates. ENIGMA researchers at Lawrence Berkeley National Lab examined if the first substrates depleted resulted in maximal growth rate, or related to growth medium or biomass composition and found […]

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Are free-living bacteria optimized by natural selection?

Free-living bacteria are usually thought to have large effective population sizes, and so tiny selective differences can drive their evolution. However, because recombination is infrequent, “background selection” against slightly deleterious alleles should reduce the effective population size (Ne) by orders of magnitude. For example, for a well-mixed population with 1012 individuals and a typical level […]

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Comparative metagenomics reveals impact of contaminants on groundwater microbiomes

Significant portions of natural groundwater reserves have been contaminated due to anthropogenic activities that result from by-products of industry, agricultural runoff, and human/animal waste. The contamination at the Department of Energy’s (DOE) Oak Ridge Integrated Field Research Challenge (OR-IFRC) includes radionuclides (e.g., uranium and technetium), nitrate, sulfide, and volatile organic compounds due to nuclear weapon […]

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Bacterial Communities As Precise Biosensors Of Environmental Damage

ENIGMA scientists show that DNA from natural bacterial communities can be used as a quantitative biosensor to accurately distinguish unpolluted sites from those contaminated with uranium, nitrate or oil. Bacterial communities yield a predictable response to environmental constraints. Bacterial systems can be used forensically to report the occurrence of environmental perturbations. Bacterial systems have the […]

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Desulfovibrio – Methanococcus Co-Evolution

Krona Website →

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DBC: Distribution-Based Clustering

Inferring operational taxonomic units (OTUs) by combining phylogenetic and ecological information.

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SLIME: Supervised Learning in Microbial Ecology

Machine learning tools for the analysis of 16S rRNA and shotgun metagenomics datasets.

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