Berkeley Lab

Robustness of a model microbial community emerges from population structure among single cells of a clonal population

Robustness of a model microbial community emerges from population structure among single cells of a clonal population Thompson, A.W, Turkarslan S., Arens, C.E, López García de Lomana, A., Raman, A., Stahl, D.A., Baliga, N.S. Environmental Microbiology, 10.1111/1462-2920.13764  

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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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Complete genome sequence of Pseudomonas stutzeri strain RCH2

Dr Chakraborty and a team of ENIGMA researchers have published the complete genome sequence of P. stutzeri strain RCH2 using targeted enrichment to isolate the microbe from samples at Hanford 100 H area; where hexavalent Chromium [Cr(VI)] is a widespread contaminant found in soil, sediment, and ground water. The Pseudomonas strain RCH2 is now a model nitrate reducing organism […]

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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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Metabolizing Data in the Cloud

ENIGMA researchers at Scripps Research Institute have developed tools with available data to enable microbial and environmental research. ENIGMA’s XCMS Online systems biology data processing and the METLIN database represent a successful model of how community oriented cloud-computing can be implemented on a global scale. This free, cloud-based platform provides users with processing tools, data streaming, […]

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Uranium binding complex a potential tool for environmental sequestration of uranium

Widespread uranium contamination from industrial sources poses hazards to human health and the environment.  ENIGMA researchers from University of Georgia and Lawrence Berkeley National Lab identified a highly abundant uranium-binding complex (UBC) from Pelosinus sp. strain UFO1.  The complex makes up the primary protein component of the S-layer of strain UFO1 and binds 3.3 atoms of […]

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Rapid Detection of Microbial Cell Abundance in Aquatic Systems

ENIGMA post doctoral fellow developed the application of ACEK-enhanced capacitive sensing technology as a rapid screening tool for the detection and quantification of microbial abundance in aquatic environments, such as groundwater wells at our Oak Ridge field site. As a proof of principle, she applied the tool to samples from ORNL and the Great Australian Bight. […]

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Digital Droplet Multiple Displacement Amplification

  The ddMDA technique enabled significantly lower bias and non-specific amplification than conventional MDA thus achieving more uniform coverage of amplification over the entire genome This technique can be a powerful tool for genomic studies where DNA samples are limited such as single cells, microaggregates, and uncultured microbes from many different environments Digital Droplet Multiple […]

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Nitrite Reduction Assay for Whole Pseudomonas Cells

ENIGMA researchers  at University of Georgia developed and published a rapid high-throughput assay for whole cell nitrite reductase activity.  Such activity assays will be key for future ENIGMA endeavors to relate biological activities of individual microorganisms and their communities to the environment. A rapid high-throughput assay was constructed to measure whole cell nitrite reductase activity. […]

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Stable protein interactome of the model sulfate reducing bacterium Desulfovibrio vulgaris Hildenborough

First demonstration of a highly accurate, genome-wide method for detecting stable protein-protein interactions, without the requirement for genetic manipulation of the organism (prior tagless methodologies have false discovery rates of >85%). Combined with our study of protein complexes published in February 2016, which was based on affinity purification coupled with mass spectroscopy (AP-MS), this experiment […]

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Preferential oxidation of microbial-mediated reduced sulfur by nitrate limits the in situ mobility of uranium

Reoxidation and mobilization of previously reduced and immobilized uranium by dissolved-phase oxidants poses a significant challenge for remediating uranium-contaminated groundwater. Preferential oxidation of reduced sulfur-bearing species, as opposed to reduced uranium-bearing species, has been demonstrated to limit the mobility of uranium at the laboratory scale yet field-scale investigations are lacking. In this study, the mobility […]

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Post Doc Lauren Lui profiled by Berkeley Lab for her Public Service and contribution to Women in Science

During March- Women’s History Month, Berkeley Lab recognizes and celebrates the diverse and historic accomplishments of women by honoring those who have shaped America’s history and its future through their public service and government leadership. http://diversity.lbl.gov/2016/03/14/berkeley-lab-celebrates-women-in-science-and-public-service/ Lauren Lui, an ENIGMA post doctoral fellow in Adam Arkin’s Lab, was one of three women profiled by the […]

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Benchmark properties for highly accurate bacterial protein interactions

SUMMARY Numerous affinity purification – mass-spectrometry (AP-MS) and yeast two hybrid (Y2H) screens have each defined thousands of pairwise protein-protein interactions (PPIs), most between functionally unrelated proteins. The accuracy of these networks, however, is under debate. Here we present an AP-MS survey of the bacterium Desulfovibrio vulgaris together with a critical reanalysis of nine published […]

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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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Andrea Rocha featured in Top 50 Women “Latinas in Information Technology of Hispanic Engineer and IT” magazine

ENIGMA Post Doc Andrea Rocha one of top 50 women featured in the “Latinas in Information Technology of Hispanic Engineer and IT” magazine. She was honored for her contribution during the Women of Color (WOC) STEM Conference in Detroit on October 16, 2015. Andrea Rocha is a post-doctoral fellow in the Biosciences Division at Oak […]

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Andrea Rocha is featured in DOE’s online Women @ Energy Series

Andrea Rocha is featured in DOE’s online Women @ Energy Series in a formal announcement from Minorities in Energy Kickoff Year 2 event in Washington, D.C. http://www.energy.gov/diversity/listings/women-energy.

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David Stahl selected as EMSL Chief Scientist

David Stahl, an environmental microbiologist at the University of Washington, has been selected to serve as Chief Scientist for the EMSL user program. David will fill this position as a dual appointment and maintain his teaching and research at the UW. As Chief Scientist, he will lead efforts to build user communities in EMSL’s science […]

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Potential Role of Acetyl-CoA Synthetase (acs) and Malate Dehydrogenase (mae) in the Evolution of the Acetate Switch in Bacteria and Archaea

Elliott P. Barnhart1,2,3, Marcella A. McClure1, Kiki Johnson1, Sean Cleveland1, Kristopher A. Hunt2,4 & Matthew W. Fields1,2,5,6,7 1Department of Microbiology and Immunology, Montana State University, Bozeman, MT. 2Center for Biofilm Engineering, Montana State University, Bozeman, MT. 3US Geological Survey, Helena, MT. 4Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT. 5Energy Research Institute, […]

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Differences in diversity between extraction techniques

ENIGMA researchers at University of Tennessee Knoxville examined differences in diversity between extraction techniques. Lipid/DNA co-extraction from one sample is attractive in limiting biases associated with microbial community analysis from separate extractions. We sought to enhance established co-extraction methods and use high-throughput 16S rRNA sequencing to identify preferentially extracted taxa from co-extracted DNA. Co-extraction results […]

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Environmental Microbiology Faculty- Montana State University- 2601

The Department of Microbiology & Immunology at Montana State University-Bozeman (http://www.montana.edu/mbi) invites candidates with a PhD in Microbiology or related area to apply for a full-time, nine-month tenure-track position in Environmental Microbiology (Assistant/Associate/Full Professor) beginning January 2016. The successful candidate will have postdoctoral and/or Assistant Professor experience and will be responsible for developing/growing an extramurally […]

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Computational Biologist- ISB- 267266

Department: Baliga Lab Location: Seattle, WA The Baliga lab is seeking a motivated Computational Biologist to join a team of computational and experimental scientists to develop algorithms for integrating and analyzing large-scale biological data. The research scientist will pursue projects solving central problems in the analysis and modeling of integrated sets of data including genomics, […]

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Visiting STEM students gain insight to microbial metabolomics

The Northen lab hosted ~60 high school students as part of the STEM Career Awareness Day sponsored by CSUEB. Groups of students were given a brief introduction to microbial metabolomics.

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Jizhong Joe Zhou Recipient of DOE’s Highest Scientific Honor- The Lawrence Award

  ENIGMA’s Joe Jizhong Zhou, a Professor at University of Oklahoma  will receive the U.S Department of Energy’s highest scientific award from U.S. Energy Secretary Ernest Moniz in a ceremony in Washington, D.C., later this year. The prestigious 2014 Ernest Orlando Lawrence Award acknowledges outstanding contributions in the biological and environmental sciences supporting research and […]

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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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ENIGMA researcher Michela Catena is a Fulbright Scholar this fall!

ENIGMA student Michela Catena has been selected for a Fulbright Scholarship near Kochi, Kerala, India.  While in the Mukhopadhyay Lab, Michela worked with Desulfovibrio vulgaris on ENIGMA projects to better understand two-component signaling systems in bacteria. D. vulgaris has three chemotaxis systems, and she helped to characterize the CheA3 mutant using the Palleroni chamber assay […]

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Research Associate (LBNL)-80628

This position has been filled.

This Research Assistant(RA) position will be part of the ENIGMA scientific focus area, a collaborative effort to understand the environmental impact of microbial communities. The successful candidate will perform routine microbiological work supporting ongoing projects on isolating and characterizing environmental microbes from soil, sediment and groundwater.

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Lara Rajeev Stars in video demonstrating DNA-affinity-purified chip (DAP-chip) method to determine gene targets for bacterial two component regulatory systems

Rajeev, L., E. G. Luning and A. Mukhopadhyay (2014). DNA-affinity-purified chip (DAP-chip) method to determine gene targets for bacterial two component regulatory systems. Journal of Visualized Experiments (89). Epub 2014/08/01. doi:3791/51715. PMID:25079303 http://www.jove.com/video/51715/dna-affinity-purified-chip-dap-chip-method-to-determine-gene-targets#.VR3XCenZIek.google_plusone_share In vivo methods such as ChIP-chip are well-established techniques used to determine global gene targets for transcription factors. However, they are of […]

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Metallomics of Two Microorganisms Featured on Metallomics Blog

Metallomics of Two Microorganisms Relevant to Heavy Metal Bioremediation Reveal Fundamental Differences in Metal Assimilation and Utilization was selected as a Hot Article and featured on the Metallomics blog.

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Judy Wall Recognized With 2014 Faculty Achievement Award

These annual awards recognize a faculty member from every SEC university who demonstrates outstanding records of teaching, research and scholarship. SEC Faculty Achievement Award winners receive a $5,000 honorarium from the Southeastern Conference and become his or her university’s nominee for the SEC Professor of the Year Award.

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Exploring the Role of CheA3 in Desulfovibrio vulgaris Hildenborough Motility Was One of the Most Viewed Frontiers in Microbiology Research Articles this March

Our paper has been featured in the Frontiers top viewed microbiology research articles blog post, “Top 10 most viewed Microbiology research articles in March 2014”.

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Adam Arkin Recipient of DOE’s Highest Scientific Honor- The Lawrence Award

DOE’s E.O. Lawrence Awards were established by President Dwight Eisenhower in 1959, to honor Ernest Lawrence, the Nobel Prize-winning inventor of the cyclotron, the forerunner of today’s particle accelerators, and the founder and namesake of Berkeley Lab.

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Desulfovibrio – Methanococcus Co-Evolution

Krona Website →

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Barcoded Transposon Mutant Library

A D. vulgaris Hildenborough barcoded transposon mutant library →

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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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DOE Systems Biology Knowledgebase

DOE Systems Biology Knowledgebase Website →
ENIGMA data stored at KBase →

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Andrea Rocha Featured Post Doc at ORAU

Andrea Rocha holds a doctorate in engineering science from the University of South Florida and is part of a team of scientists across Oak Ridge National Laboratory (ORNL) and other academic and national labs who hope to advance the understanding of Earth’s most numerous life form—microorganisms—upon which all life forms rely.

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ENIGMA 100-Well Survey Data Site

ENIGMA Field Sample Info Site →

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Network Portal

Network Portal Website →
Desulfovibrio Netowrk Portal →

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Environmental Microbiology Team Demonstrate the Importance and Dynamic Behavior of Stochastic Processes in Controlling the Succession of Microbial Communities

In this study, a novel theoretical framework comprised of four different cases was developed for fluidic and non-fluidic ecosystems to conceptualize the relationships between stochasticity and ecological succession.

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Montana State Team Overcomes Challenges, Proves That Microbes Swim to Hydrogen Gas

Here we show that the average swimming velocity increases in the direction of a source of hydrogen gas for the methanogen, Methanococcus maripaludis using a capillary assay with anoxic gas-phase control and time-lapse microscopy.

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Terry Hazen Inducted as AAAS Fellow

The new AAAS Fellows, whose names will be published in the 29 November issue of Science, will be honored at the AAAS Fellows Forum on Saturday, 15 February during the AAAS Annual Meeting in Chicago, where they will receive a certificate and a blue and gold rosette as a symbol of their distinguished accomplishments.

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Judy Wall Awarded Curators’ Professorship in Biochemistry at University of Missouri

During the upcoming year the chancellor may recommend an outstanding faculty member for this honor. These are prestigious positions, and only outstanding scholars with established reputations will be considered for appointment.

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Publication Citation Report and Top Ten Highly Cited

Citation analysis performed June 13, 2013 at Web of Science on available subset of publications (157/232).  Please note these analytics are subject to change.

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MicrobesOnline

MicrobesOnline Website →

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Gaggle

Gaggle Website →

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GLAMM: Genome-Linked Application for Metabolic Maps

GLAMM Website →

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METLIN: Metabolite and Tandem MS Database

METLIN Website →

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RegPrecise

RegPrecise Website →

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SIFTER: Statistical Inference of Function Through Evolutionary Relationships

SIFTER Website →

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RegTransBase

RegTransBase Website →

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XCMS Online: Scripps Center for Metabolomics

XCMS Online →

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RegPredict

RegPredict Website →

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Adams, Mike

Principal Investigator
adams@bmb.uga.edu
(706) 540-1645

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Indirect and Suboptimal Control of Gene Expression is Widespread in Bacteria

A new study by Arkin and colleagues challenges this view of adaptive regulation of gene expression and shows that in bacteria grown in the laboratory, there is little correlation between when genes are important for fitness and when they are more highly expressed.

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Adams, Paul

SFA Laboratory Research Manager
pdadams@lbl.gov
(510) 486-4225

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Arkin, Adam

SFA Technical Co-Manager
Director, Laboratory Microbiology
aparkin@lbl.gov
(510) 643-5678

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Terry, Astrid

SFA Project Manager
ayterry@lbl.gov
(510) 486-4928

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Alm, Eric

Deputy Director, Computation
ejalm@mit.edu

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Wall, Judy

Deputy Director, Laboratory Microbiology
wallj@missouri.edu
(573) 882-8726

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Northen, Trent

Director, Biotechnology Development
trnorthen@lbl.gov
(510) 486-5240

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Hazen, Terry

Director, Environmental Microbiology
tchazen@utk.edu
(707) 631-6763

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Fields, Matthew

Deputy Director, Environmental Microbiology
matthew.fields@erc.montana.edu
(406) 994-7340

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Deutschbauer, Adam

Deputy Director, Biotechnology Development
amdeutschbauer@lbl.gov
(510) 643-5683

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Baliga, Nitin

Director, Computation
nbaliga@systemsbiology.org
(206) 732-1266

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Walian, Peter

Principal Investigator
pjwalian@lbl.gov
(510) 486-7469

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Stahl, David

Principal Investigator
dastahl@u.washington.edu
(206) 685-3464

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Siuzdak, Gary

Principal Investigator
siuzdak@scripps.edu
(858) 784-9415

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Singh, Anup

Principal Investigator
aksingh@sandia.gov
(925) 294-1260

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Mukhopadhyay, Aindrila

Principal Investigator
amukhopadhyay@lbl.gov
(510) 495-2628

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Elias, Dwayne

Principal Investigator
eliasda@ornl.gov
(865) 574-0956

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Dubchak, Inna

Principal Investigator
ildubchak@lbl.gov
(925) 296-5713

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Chandonia, John-Marc

Principal Investigator
jmchandonia@lbl.gov
(510) 292-9495

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Chakraborty, Romy

Principle Investigator
rchakraborty@lbl.gov
(510) 486-4091

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Butland, Gareth

Principal Investigator
gpbutland@lbl.gov
(510) 486-6905

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Brenner, Steven

Principal Investigator
sebrenner@lbl.gov
(510) 643-9131

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Bender, Kelly

Principal Investigator
bender@micro.siu.edu
(618) 453-2868

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Auer, Manfred

Principal Investigator
mauer@lbl.gov
(510) 486-7702

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Zhou, Jizhong (Joe)

Principal Investigator
jzhou@ou.edu
(405) 325-6073

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Functional Gene Array Design and Microarray Data

Website →

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Metabolic Footprinting of Mutant Libraries to Map Metabolite Utilization to Genotype

Here, we identified and validated genes related to the utilization of specific metabolites in bacteria by profiling metabolite utilization in libraries of mutant strains.

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Zhou Wins OU Research Award

Joe Zhou wins University of Oklahoma Vice President for Research Award for Outstanding Research Impact in 2012.

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Genome Announcement of Pelosinus fermentans

The genome sequence of this organism will provide insight into the metabolic potential of a predominant population during stimulation for metal-reducing conditions.

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Community Leadership! Steve Brown

Beginning July 1, 2013, Steven D. Brown of Oak Ridge National Lab will be Chair-Elect of Division O (Fermentation and Biotechnology) of the American Society for Microbiology. Steven is honored by this appointment and looks forward to serving you and ASM.

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Metallochaperones Regulate Intracellular Copper Levels

Here, we have investigated the mechanistic role of metallochaperones in regulating Cu efflux. We have constructed a computational model of Cu trafficking and efflux based on systems analysis of the Cu stress response of Halobacterium salinarum.

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David Stahl Elected to National Academy of Engineering

David Stahl, a University of Washington professor of civil and environmental engineering, has been elected to the National Academy of Engineering.

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Liquid Chromatography Quadrupole Time-of-Flight Mass Spectrometry Characterization of Metabolites Guided by the METLIN Database

By using liquid chromatography quadrupole time-of-flight mass spectrometry (LC-Q-TOF-MS), hundreds to thousands of peaks with a unique m/z ratio and retention time are routinely detected from most biological samples in an untargeted profiling experiment.

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A Large-Scale Evaluation of Computational Protein Function Prediction

Here we report the results from the first large-scale community-based critical assessment of protein function annotation (CAFA) experiment. Fifty-four methods representing the state of the art for protein function prediction were evaluated on a target set of 866 proteins from 11 organisms.

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ENIGMA Metabolic Footprinting Publication Recommended by Faculty of 1000

Here, we identified and validated genes related to the utilization of specific metabolites in bacteria by profiling metabolite utilization in libraries of mutant strains. Untargeted mass spectrometry based metabolomics was used to identify metabolites utilized by Escherichia coli and Shewanella oneidensis MR-1.

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Metabolomics: Sifting Through Complex Samples

Review article of advances in Metabolomics about the team at Scripps Research Institute- Gary Siuzdak, Gary Patti and Ralph Tautenhahn et al.

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OpenMSI: Open Mass Spectrometry Imaging

OpenMSI Website →

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