Bacterial community composition impacts the transformation of carbon in soils - Microorganisms have evolved various life-history strategies to survive fluctuating resource conditions in soils. However, it remains elusive how the life-history strategies of microorganisms influence their processing of organic carbon, which may affect microbial interactions and carbon cycling in soils. Here, ENIGMA researchers characterized the genomic traits, exometabolite profiles,… News Archive →
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. News Archive →
Mixed Nitrate and Metal Contamination Influences Operational Speciation of Toxic and Essential Elements - ENIGMA researchers compared the availability of elements in non-contaminated and acidic nitrate contaminated sediment and found that contamination impacted the bioavailability of essential elements. News Archive →
Environmental bacteria may have candidate genes for bioremediation - ENIGMA researchers identified important genes for improving Chromate resistance in genetically diverse bacteria through experimental evolution. News Archive →
To Study Competition and Cross-Feeding, Scientists Build Synthetic Microbiomes - A new study investigated complex interactions among four cross-feeding microorganisms in a synthetic community (SynCom) that converts cellulose to methane and carbon dioxide, paving the way toward a more predictive understanding of the impact of environmental perturbations on microbial interactions sustaining geochemically significant processes in natural systems. News Archive →
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… News Archive →
Decomposition Decreases Molecular Diversity and Ecosystem Similarity of Soil Organic Matter - ENIGMA researchers collaborated with the Lehmann Lab at Cornell University to find that microbial decomposition drives significant variability in the molecular richness and diversity of soil organic matter between soil horizons and ecosystems. News Archive →
Microbial Communities Vary Widely Underground, Even When Close - Study finds that geochemistry and hydrogeology can influence community type and function, even when those communities are only 10 cm apart. News Archive →
Metal Contamination Causes Metabolic Stress in Environmental Bacteria - ENIGMA researchers at Lawrence Berkeley National Laboratory and University of Georgia discovered that mixed metal waste common to industrial dumping sites causes a distinctive physiological response in bacteria that does not occur during single metal exposure. News Archive →
Multicopy suppressor screens reveal convergent evolution of single-gene lysis proteins - Using new barcoded screening technology, ENIGMA researchers uncovered genome-wide targets of diverse including single-stranded RNA-phages (ssRNA-phages)-derived protein antibiotics to efficiently identify the host mechanisms targeted in bacteriolysis. The novel approach could have significant applications for characterizing the hundreds of putative Sgl identified in genomic databases and recent studies. News Archive →
Examining adaptations of a dominant bacterial species at a contaminated subsurface site - Leveraging comparative genomics, community analysis, and geochemical data to understand adaptations that facilitate survival of a dominant community member in the contaminated Oak Ridge Reservation subsurface. News Archive →
ENIGMA researchers identify hundreds of new enzymes - Filling Gaps in Bacterial Metabolism with Computation and High-throughput Genetics: An analysis of genetic data from many different kinds of bacteria identified hundreds of new enzymes. News Archive →
The Contextual Ontology-based Repository Analysis Library (CORAL) facilitates FAIR ENIGMA datasets - Novichkov, PS*; Chandonia, J-M*; Arkin, AP. (2022) CORAL: A framework for rigorous self-validated data modeling and integrative, reproducible data analysis. GigaScience [DOI]:10.1093/gigascience/giac089 OSTI ID: 1888047 The Contextual Ontology-based Repository Analysis Library (CORAL) platform greatly facilitates adherence to the FAIR principles, including the especially difficult challenge of making… News Archive →
Using microcalorimetry and thermodynamic modeling to examine effects of thermal stress - Hunt KA, von Netzer F, Gorman-Lewis D, Stahl DA. (2022) Microbial maintenance energy quantified and modeled with microcalorimetry. Biotechnol Bioeng. 2022 Jun 9; [DOI]:10.1002/bit.28155. {PMID}: 35680566 OSTI:1874049 All known biology is driven by the partitioning of energy released from nutrient consumption, either into building new cells or maintaining… News Archive →
Discovering microbial adaptations to subsurface niches - Gushgari-Doyle, S; L.M. Lui, T.N. Nielsen, X. Wu, R.G. Malana, F.L. Poole II, M.W.W. Adams, A.P. Arkin, R. Chakraborty (2022) Genotype to ecotype in niche environments: Adaptation of Arthrobacter to carbon availability and environmental conditions. ISME Comm. [DOI]:10.1038/s43705-022-00113-8 OSTI:1860268 Different niche micro-environments can affect the structure and function… News Archive →
Whole genome sequence reveals molecular mechanisms underlying adaptation of Rhodanobacter strains to multiple stressors - The Genomic Features Underlying Adaptation of Rhodanobacter Strains to Stressful Conditions (denitrification processes, heavy metal resistance, and restriction-modification systems) present at ENIGMA Field Site ORR. Rhodanobacter species have been found dominant in the subsurface of Oak Ridge Reservation (ORR) site contaminated with acid, nitrate, metal radionuclides, and other… News Archive →
Sampling Down Well In Situ Microbial Colonization Conditions - LJ McKay*, HJ Smith*, E Barnhart, HD Schweitzer, RR Malmstrom, D Goudeau, MW Fields (2021) Activity-based, genome-resolved metagenomics uncovers key populations and pathways involved in subsurface conversions of coal to methane Nature ISME Journal [DOI]:10.1038/s41396-021-01139-x PMID: 34689183 Development of activity-based metagenomics, enabled the identification of translationally active microorganisms and… News Archive →
Uncovering metal tolerance mechanisms using ENIGMA tools and Analysis - Thorgersen, M.P., .; J. Xue, E.L.W. Majumder, V.V. Trotter, X. Ge, F.L. Poole II, T.K. Owens, L.M. Lui, T.N. Nielsen, A.P. Arkin, A.M. Deutschbauer, G. Siuzdak, and M.W.W. Adams Deciphering microbial metal toxicity responses using RB-TnSeq and activity-based metabolomics. Applied and Environmental Microbiology 87 (21), e01037-21 (2021).… News Archive →
Semi-Automated Complete Microbial Genome Assembly - Lui, Lauren M.; T.N. Nielsen, A.P. Arkin (2021) A method for achieving complete microbial genomes and better-quality bins from metagenomics data. PloS Computational Biology [DOI]:1371/journal.pcbi.1008972 OSTI:1788019 A Method for Achieving Complete Microbial Genomes and Improving Bins From Metagenomics Data Assembling complete microbial genomes from short read metagenomics data… News Archive →
Observing the Microbial Genome - Basics2Breakthroughs: Observing the microbial genome from Berkeley Lab on YouTube. ENIGMA Project Scientist Lauren Lui is profiled on LBL Basics2Breakthroughs, filmed for LBNL's 90th anniversary. She uses the latest bioinformatics technology to study microbes so we can learn how their genes shape the environment. Her ultimate goal is… News Archive →
Environmental exposure history is critical in groundwater contaminant attenuation - Paradis, CJ, JI Miller, J-W Moon, SJ Spencer, LM Lui, JD Van Nostrand, D Ning, AD Steen, LD McKay, AP Arkin, J Zhou, EJ Alm, TC Hazen Sustained Ability of a Natural Microbial Community to Remove Nitrate from Groundwater (2021) Groundwater [DOI]:10.1111/gwat.13132 OSTI:1807518 A consortium of ENIGMA researchers… News Archive →
A Simple, Cost-Effective, and Automation-Friendly Direct PCR Approach for Bacterial Community Analysis - November 22, 2021 Simple, cost-effective, and automation-friendly direct-PCR-based 16S rRNA sequencing method to study the dynamics, microbial interaction, and assembly of various microbial communities in a high-throughput format News Archive →
Automating Culturing Technology Aids In Scaling Bacterial Growth Experiments - An automated multiplexed turbidometric and data collection system for measuring growth kinetics of anaerobes dependent on gaseous substrates Hunt, KA; J Forbes, F Taub, N Elliott, J Hardwicke, R Petersen, N Stopnisek, DAC Beck, DA Stahl; Journal of Microbiological Methods, [DOI]:10.1016/j.mimet.2021.106294 For decades, the cloudiness (turbidity) of a… News Archive →
Fostering interest in science and engineering through community college outreach - Recently, ENIGMA Principal Investigator Romy Chakraborty hosted college student Mariam Alsaid; an intern who participated in the The Transfer-to-Excellence Research Experiences for Undergraduates (TTE REU)program. She worked with ENIGMA postdocs Mon Oo Yee, and Kristine Cabugao. Mariam shared her experience with the program in the following interview News Archive →
Host Bacteria Are Helped By Viral Genomes - Kothari, Ankita.; S. Roux, H. Zhang, A. Prieto, J-M Chandonia, S. Spencer, X. Wu, A M. Deutschbauer, A. P. Arkin, E J. Alm, R. Chakraborty, A Mukhopadhyay (2021) Ecogenomics of groundwater viruses suggests niche differentiation linked to specific environmental tolerance. mSystems [doi]:1128/mSystems.00537-21 {PMID}: 34184913 PMCID: PMC8269241 OSTI:1807913 Niche Specific Genes… News Archive →
Understanding how microbes adapt to stressful conditions - Adaptation to previous stressors influence which genes acquire mutations during experimental evolution M.L. Kempher, X. Tao, R. Song, B. Wu, D.A. Stahl, J.D. Wall, A.P. Arkin, A. Zhou, J. Zhou. “Effects of genetic and physiological divergence on the evolution of a sulfate-reducing bacterium under conditions of elevated temperature.”… News Archive →
Culturing of “Unculturable” Subsurface Microbes: Natural Organic Carbon Source Fuels the Growth of Diverse and Distinct Bacteria from Groundwater - June 8 2021. An effective cultivation and isolation strategy using natural complex carbon source recovers diverse and novel bacteria from the terrestrial subsurface. The Science.... Despite rapid technological advances in modern molecular tools for identification of key microbial taxa and critical metabolic processes in a given environment, a… News Archive →
Discovery Support Yields Phage Tailocin Insights - April 7, 2021-To ensure that the ENIGMA research program remains vibrant 10% of funding is set aside annually for a Discovery program. ENIGMA researchers may propose new, short-term, research projects that either explore a new research theme or develop a new technical capability. These proposals are reviewed internally… News Archive →
Microbial Nitrate Removal in a Highly Contaminated Environment is Limited by the Essential Metal Molybdenum - Apr 7, 2021-Molybdenum limitation in the Oak Ridge Reservation contaminated environment, caused by iron and aluminium precipitation, affects nitrate reduction by microorganisms. The Science...The Oak Ridge Reservation (ORR) in Tennessee is a uniquely acidic, high-nitrate- and high-metal-contaminated environment. Although nitrate can be removed by microbes living in this… News Archive →
An Integrated Conceptual Microbial Ecology Framework - March 24, 2021-AHolistic Modeling Framework Integrating Laboratory and Field Studies for Microbial Ecology. The Science Microbial communities serve critical roles in all ecosystems and have a profound impact on human health, environmental health, and industrial capabilities. As such, it is desirable to have robust, actionable directions for the intervention… News Archive →
Scientists Uncover Mechanistic Evidence on How Cooperation Evolves in Mutualistic Microbial Communities - February 21, 2021-Researchers map early adaptive events in evolution of mutualistic interactions with a broad range of applications for biotechnology, medicine and environment. Turkarslan, Serdar; N. Stopnisek, A.W Thompson, C.E Arens, J.J Valenzuela, J. Wilson, K.A Hunt, J. Hardwicke, S. Lim, Y.M Seah, Y. Fu, L. Wu, J-Z… News Archive →
Sulfur Metabolites Play Key System-Level Roles in Modulating Denitrification - JANUARY 2021 Using systems analysis to elucidate the roles that hydrogen sulfide and cysteine play in inhibiting the growth of a nitrate-reducing Otwell AE, Carr AV, Majumder ELW, Ruiz MK, Wilpiszeski RL, Hoang LT, Webb B, Turkarslan S, Gibbons SM, Elias DA, Stahl DA, Siuzdak G, Baliga NS.… News Archive →
New Tools Allow for Faster Mapping of Large Numbers of Phage Resistant Genes - Oct 13, 2020- Mutalik, V.K.; B.A. Adler, H.S. Rishi, D. Piya, C. Zhong, B. Koskella, E.M. Kutter, R. Calendar, P.S. Novichkov, M.N. Price, A.M. Deutschbauer, A.P. Arkin (2020) High-throughput mapping of the phage resistance landscape in E. coli. PLoS Biology [doi]:10.1371/journal.pbio.3000877 OSTI:1714384 Phage work supported by ENIGMA Discovery… News Archive →
How Much Microbial Community Composition Is Driven by Selection How Much by Chance - Nov 23, 2020-Life on our planet consists of many communities of plants, animals, and microbes. These communities are shaped by complex ecological processes. Those processes include natural selection, migration, and random shifts in births and deaths. Quantifying the relative importance of these processes is a major challenge in… News Archive →
Key function genes involved in nitrate tolerance are frequently mutated in experimentally evolved Desulfovibrio vulgaris - November 10, 2020-Nitrate tolerance mechanisms in D. vulgaris revealed by experimental evolution. Wu, B., Liu, F., Zhou, A. et al., “Experimental evolution reveals nitrate tolerance mechanisms in Desulfovibrio vulgaris.” ISME J 14, 2862-2876 (2020). [doi: 10.1038/s41396-020-00753-5] News Archive →
2021 ASM Award for Environmental Research Goes to Terry Hazen - August 28, 2020-Terry Hazen receives 2021 ASM Award for Environmental Research. This award recognizes an outstanding scientist with distinguished research achievements that have improved our understanding of microbes in the environment, including aquatic, terrestrial, and atmospheric settings. He will be presented the award at the joint virtual international… News Archive →
Small is Mighty: Adaptation of Patescibacteria to Groundwater Environment Drives Their Genome Simplicity - Aug 28, 2020-The Science...This new study, by ENIGMA researchers, examined the newly-defined superphylum Patescibacteria, finding that they have developed unique characteristics which help adapt themselves to nutrient-limited but stable conditions in groundwater. Characteristics include highly reduced genome sizes and ultra-small cell size with simplified metabolism pathways for energy… News Archive →
EISA-MRM: Quantitative MS Toward A $5 Metabolome - August 24, 2020-Xue J, Guijas C, Benton HP, Warth B, Siuzdak G (2020) METLIN MS2 molecular standards database: a broad chemical and biological resource. Nature Methods. 17(10) 953-954 [doi]: 10.1038/s41592-020-0942-5, PMID: 32839599 SCIENCE: A key ENIGMA Aim is linking field data to the phenotypic characterization of isolates, testing mechanistic hypothesis in the laboratory. EISA-MRM (Enhanced In-Source… News Archive →
Selective carbon sources influence the end-products of microbial nitrate respiration - July 21, 2020-Carlson, H.K.; L.M. Lui, M.N. Price, A.E. Kazakov, A.V. Carr, J.V. Kuehl, T.K. Owens, T. Nielsen, A.P. Arkin, A.M. Deutschbauer (2020) Selective carbon sources influence the end-products of microbial nitrate respiration. International Society for Microbial Ecology Journal. [doi]:10.1038/s41396-020-0666-7 The world's population relies on nitrogen fertilizer to… News Archive →
GapMind: Folate-independent Methionine Synthases - Jun 23, 2020-Diverse bacteria and archaea rely on unusual methionine synthases. The Science...Methionine is one of the amino acids that make up proteins, and the final step in methionine synthesis is the transfer of a methyl group. Usually, the methyl group is obtained from methyl folates, but some… News Archive →
Setting The Stage For Ongoing Geochemical/Geophysical Characterization of ENIGMA Field Site - May 12, 2020-Characterization of subsurface media from locations up- and down-gradient of a uranium-contaminated aquifer Moon, J.-W., Paradis, C.J., Joyner, D.C., von Netzer, F., Majumder, E.L.,Dixon, E.R., Podar, M., Ge, X., Walian, P.J., Smith, H.J., Wu, X., Zane, G.M., Walker, K.F., Thorgersen,M.P., Poole II, , F.L., Lui, L.M.,… News Archive →
Review of ENIGMA tools Proposes New Use for DAP-chip - April 5, 2020-Tools to map target genes of bacterial two-component system response regulators Rajeev L, Garber ME, Mukhopadhyay, A Environmental Microbiology Reports. 2020 doi.org/10.1111/1758-2229.12838 Microbial signaling and gene regulation is an important aspect of the ecology being studied by the ENIGMA project at the Oakridge Field Site. There… News Archive →
Assessing and Predicting Ability and Rate of Contaminant Immobilization by Bacteria - Franco, L.C.; S. Steinbeisser, G.M. Zane, J.D. Wall, and M.W. Fields. 2018. Cr(VI) reduction and physiological toxicity are impacted by resource ratio in Desulfovibrio vulgaris. Appl. Microbiol. Biotechnol. 102:2839-2850 [doi]:1007/s00253-017-8724-4 {PMID}:29429007 PMCID:PMC5847207 OSTI:1420176 The presented study shows that resource ratio at different temperature has profound impacts on Cr(VI) reduction… News Archive →
Characterizing Bacterial Diversity With Respect To Hydrochemistry - Zelaya, A.; A. Parker, K.L. Bailey, P. Zhang, J. Van Nostrand, D. Ning, D.A. Elias, J. Zhou, T.C Hazen, A.P Arkin and M.W. Fields (2019) High spatiotemporal variability of bacterial diversity over short time scales with unique hydrochemical associations within a shallow aquifer. Water Research. [doi]:1016/j.watres.2019.114917{PMID}:31387058 OSTI:1607016 Nov 5,… News Archive →
Precisely Quantifying Ecological Processes in Shaping Subsurface Communities - October 20, 2019–ENIGMA researchers at University of Oklahoma have developed a general framework for quantitatively assessing ecological stochasticity. This general framework provides an effective and robust tool to ecologists for quantifying ecological stochasticity. This allows ENIGMA to move towards a more precise quantitative understanding of ecological processes shaping… News Archive →
ENIGMA’s Fangchao Song is Berkley Lab SLAM Finalist! - October 18, 2019–Fanchao Song of Arkin Lab was selected to compete in Berkeley Lab "Early Career Scientist and Research SLAM." Here is his presentation from the SLAM "I am a Bubble Player," which was selected from a competitive field of 42 entries. This is the "3-minute-describe-your-work-in-layman-terms" challenge that… News Archive →
Dr Romy Chakraborty Wins Director’s Award for Outreach - https://recognition.lbl.gov/laureates/ 2019 Outreach: ROMY CHAKRABORTY, Citation: In recognition of Romy Chakraborty’s extensive service as a mentor for programs that engage underrepresented groups in science, and for her significant contribution to outreach that aims to increase diversity, equity, and inclusion in STEM fields. About the Director’s Awards The Director’s… News Archive →
Sulfonate utilization by Desulfovibrio may expand ecological niches - September 18, 2019–Day, L.A.; K.B. De León, M.L. Kempher, J. Zhou, J.D. Wall (2019) Complete Genome Sequence of Desulfovibrio desulfuricans IC1, a Sulfonate-Respiring Anaerobe. Microbiology Resource Announcements. [doi]: 1128/MRA.00456-19 As part of ongoing work related to the 100-Well Survey of the Oak Ridge Reservation (ORR) supported by ENIGMA, Leslie… News Archive →
Energy Restriction Impacts Growth Physiology in a Sulfate-Reducing Biofilm - Krantz, G.P.; K. Lucas, E.L.-W. Majumder, L.T Hoang, R. Avci, G. Siuzdak and M.W. Fields (2019) Bulk phase resource ratio alters carbon steel corrosion rates and endogenously produced extracellular electron transfer mediators in a sulfate-reducing biofilm. Biofouling. [doi]:10.1080/08927014.2019.1646731 {PMID}:31402749 The presented results demonstrate that energy restriction (EAL v.… News Archive →
Metal Resistant Bacteria Isolated from ORR Field Samples - Thorgersen, M.P.; X. Ge, F.L. Poole II, M.N. Price, A.P. Arkin and M.W.W. Adams (2019) Nitrate-Utilizing Microorganisms Resistant to Multiple Metals from the Heavily Contaminated Oak Ridge Reservation. Applied and Environmental Microbiology. [doi]:1128/AEM.00896-19{PMID}:31253673 PMCID:PMC6696972 OSTI:1650072 Multiple metal-resistant microorganisms were isolated from ORR environmental samples using contaminating environment relevant metal concentrations.… News Archive →
A New Generation of Functional Gene Array GeoChip 5.0 - Shi, Z.; H. Yin, J.D. Van Nostrand, J.W. Voordeckers, Q. Tu, Y. Deng, M. Yuan, A. Zhou, P. Zhang, N. Xiao, D. Ning, Z. He, L. Wu and J. Zhou (2019) Functional Gene Array-Based Ultrasensitive and Quantitative Detection of Microbial Populations in Complex Communities. International Society for Microbial… News Archive →
Plasmidome Retains Toxicity Tolerance ENIGMA publication highlighted by DOE - July 3, 2019–https://www.energy.gov/science/ber/articles/microbes-retain-toxicity-tolerance-after-they-escape-toxic-elements. * Kothari A, Wu Y-W, Charrier M, Rajeev L, Rocha AM, Paradis CJ, Hazen TC, Singer SW, Mukhopadhyay A. (2019) Large Circular Plasmids from Groundwater Plasmidomes Span Multiple Incompatibility Groups and Are Enriched in Multimetal Resistance Genes. mBio. [doi]:1128/mBio.02899-18 ENIGMA runs an internal proposal call… News Archive →
ENIGMA teamwork is featured in Elements - June 24, 2019–A highly collaborative Discovery project combines two techniques BONCAT+FACS, (Bioorthogonal Non-Canonical Amino Acid Tagging, and Fluorescent Activated Cell Sorting), to detect individual active microbes in soil from our Oak Ridge Field Research Site in Tennessee. To find out more https://newscenter.lbl.gov/2019/06/24/new-microbial-research-technique/ Couradeau E.; J. Sasse, D. Goudeau,… News Archive →
Adapting METLIN offers new metabolite identification opportunities - Domingo-Almenara, X.; J. R. Montenegro-Burke, C. Guijas, E. L.-W. Majumder, H. P. Benton and G. Siuzdak (2019) Autonomous METLIN-guided in-source fragmentation detection increases annotation confidence in untargeted metabolomics. ACS Analytical Chemistry. [doi]:1021/acs.analchem.8b03126 A clever adaptation of METLIN to turn an annotation problem into an identification advantage by Xavi… News Archive →
Challenging Carbon Nitrogen Ratios in a Dual-Pathway Actinobacterium - March 3, 2021-Vuono D.C., Read R.W., Hemp J., Sullivan B.W., Arnone, J.A., Neveux I., Blank R.R., Loney E., Miceli D., Winkler M-K.H., Chakraborty R., Stahl D.A., Grzymski J.J. 2019. Resource Concentration Modulates the Fate of Dissimilated Nitrogen in a Dual-Pathway Actinobacterium. Frontiers in Microbiology Vol 10, 3 [doi]:3389/fmicb.2019.00003{PMID}:30723459 PMCID:PMC6349771 OSTI:156058.… News Archive →
DuBSEQ functional characterization Nature Communications - January 18, 2019–ENIGMA researchers release DuBSEQ, a tool for broader use in microbial functional characterization and which allows for high throughput manipulation of specific strain libraries in Nature Communications. A multi-disciplinary team of bench scientists and computational scientists collaborated to generate the large data set and analyses that… News Archive →
Using High-Throughput Genetics to Discover a Novel Catabolic Pathway - January, 12 2019-Price, M. N.; J. Ray, A. T. Iavarone, H. K. Carlson, E. M. Ryan, R. R. Malmstrom, A. P. Arkin, A. M. Deutschbauer (2019) An Oxidative Pathway of Deoxyribose Catabolism. mSystems. [doi]:1128/mSystems.00297-18 As part of the Environmental Ark campaign to characterize bacteria found at our Oak… News Archive →
David Stahl Honored by Seattle Aquarium - January 8, 2019–We know David Stahl as a Principal Investigator in ENIGMA working in part on the microbial conversion of ammonia to nitrate, a major step in the global nitrogen cycle. Not only is he an internationally renowned microbial ecologist, elected to the National Academy of Engineering in… News Archive →
Jizhong Zhou Honored with 2019 ASM Award for Environmental Research - September 7, 2018–Jizhong Zhou, Ph.D. (The University of Oklahoma in the Department of Microbiology and Plant Biology) was honored with the 2019 American Society for Microbiology Award for Environmental Research, which recognizes an outstanding scientist with distinguished research achievements that have improved our understanding of microbes in the… News Archive → ENIGMA’s Lauren Lui is Berkley Lab SLAM Finalist! - September 5, 2018–Lauren Lui of Arkin Lab is a Finalist Selected to Compete in Berkeley Lab “Early Career Scientist and Research “SLAM” Date: Sept. 20, 2018 Time: 4 pm Location: Building 50 Auditorium NOTE: winners are chosen via in-person audience voting – so all local team should go… News Archive → ENIGMA’s Romy Chakraborty honored at “Women @ the Lab” - June 9, 2018–Romy Chakraborty is honored by Berkeley Lab sponsored by the Women Scientists and Engineers Council (WSEC) and the Diversity, Equity, and Inclusion Office. The program recognizes women at Berkeley Lab who demonstrate dedication, talent, STEM contributions, and commitment to the Lab’s mission. Romy was nominated for… News Archive →
Mike Adams wins 2018 DuPont Industrial Biosciences Award in Applied and Environmental Microbiology - June 8, 2018–ENIGMA Principal Investigator Mike Adams at the University of Georgia shares the 2018 DuPont Industrial Biosciences Award in Applied and Environmental Microbiology with Robert Kelly of North Carolina State University. They were recognized for their groundbreaking use and genetic manipulation of microorganisms that grow in extreme… News Archive →
ENIGMA Team Anchors Collaboration to Accelerate Experiment-based Gene Function Assignments - ENIGMA, May 16, 2018–As part of a large scale collaboration, a diverse team of scientists from ENIGMA — A Scientific Focus Area at Lawrence Berkeley National Laboratory (Berkeley Lab) — and other institutions lead by Adam Arkin (APA) as Technical Co-Manager, as well as researchers at the U.S.… News Archive →
Leslie Day ENIGMA undergrad Honorable mention for poster Mizzou Life Sciences Week 2018 - April 22, 2018–Leslie, a Senior in Biochemistry working in the laboratory of Judy Wall, received an honorable mention for her poster presentation titled “Sulfonate Utilization by Desulfovibrio vulgaris Hildenborough” at Mizzou Life Sciences Week 2018 in a competition among all presenting post-doctoral fellows, graduate students, and undergraduates in… News Archive →
Erica Majumder wins best overall poster at the International Symposium on Microbial Sulfur Metabolismw - April 18, 2018–ENIGMA postdoc Erica Majumder’s poster “Beyond Sulfide: The Sulfur-Metabolome of Sulfate-Reducing Bacteria” affirms ENIGMA’s contribution to the ability to sulfur sulfur metabolism on a molecular level. Sulfur-containing metabolites are key to the maintenance of the redox state of the environment, the cycling of essential nutrients between… News Archive →
Parts-Based Strategy Speeds Up Gene Function Annotation - ENIGMA, February 1, 2018–Hualan Liu an ENIGMA Researcher in Adam Deutschbauer‘s Lab at Lawrence Berkeley Lab announces a powerful genetic tool for gene function annotation, essential to advance our understanding of microbial biology and the impact of those genetic traits on their ecosystems. She says “We developed a… News Archive →
Most Free-Living Bacteria Likely Make All 20 Amino Acids - January 11, 2018–ENIGMA researchers at Lawrence Berkeley Lab and the University of Missouri systematically used high-throughput genetics to fill gaps in amino acid biosynthesis pathways. This explains how bacteria can grow on their own, in contrast to widespread speculation that bacteria cross-feed amino acids among community members. According… News Archive →
Rapidly Moving New Bacteria to Model Organism Status - ENIGMA, January 8, 2018–ENIGMA researchers describe our proposed workflow as a general guideline for studying new environmental microbes in a fast and comprehensive way. Liu, H.; A.M. Deutschbauer (2018) Rapidly moving new bacteria to model‐organism status. Current Opinion in Biotechnology. DOI: 10.1016/j.copbio.2017.12.006 Currently, there is a need to… News Archive →
Dual Barcoded Shotgun Expression Library Sequencing (Dub-seq) wins R&D100 Award - November 20, 2017–ENIGMA’s Vivek Mutalik, Adam Deutschbauer, Pavel Novichkov, and Adam Arkin win R&D100 Award for a tool developed under our “Discovery Program”; where high-risk projects are funded for a short duration to encourage high impact changes in science or technological capability that extend and enhance our ongoing… News Archive →
Key Cellular Components Persist in Bacteria Although Response to Salt Stress Changes - November 14, 2017–ENIGMA researchers at University of Oklahoma, Lawrence Berkeley Lab, University of Washington, and University of Missouri reveal that the accumulation and induction of key cellular components persist in bacteria for greater than 5000 generations. However, the physiological and transcriptional responses to high salinity are altered. The… News Archive →
New ENIGMA Study Finds Anaerobic Nitrate-Reducing Conditions Influence Metal Toxicity - ENIGMA, November 7, 2017–Prior observations of chromium (Cr[VI]) and uranium (U[VI]) toxicity under aerobic conditions, where metal toxicity was caused not only directly by the metal, but also indirectly due to redox reactions of the metal with oxygen and the resulting reactive oxygen species. ENIGMA researchers from University… News Archive →
Memory response and groundwater movement is relative to microbial communities and geochemistry - October 7, 2017–Hydraulic conductivity and effective porosity are requisite parameters for modeling specific discharge and average linear groundwater velocity. In situ characterization of both parameters is ideal, but such efforts are rarely performed in practice. In this study, both parameters were characterized in situ by utilizing single-well testing… News Archive →
PaperBLAST: A Text Mining Tool Find Publications About A Protein Or Its Homologs - July 31, 2017–ENIGMA researchers are excited to announce a new tool: PaperBLAST for text-mining to pull protein and homolog information from publications, which will make it much easier to interpret genomic data from a wide range of non-model organisms. Large-scale genome sequencing has identified millions of protein-coding genes… News Archive →
Rare environmental isolates found at ENIGMA field site - June 30, 2017–ENIGMA researcher Romy Chakraborty announced today that her team has successfully sequenced two Janthinobacterium lividum strains isolated from Oak Ridge Reservation background groundwater samples. These are the first representatives of Janthinobacterium available from a subsurface aquatic environment. To date, only a few environmental isolates of Janthinobacterium… News Archive →
Robustness of a model microbial community emerges from population structure among single cells of a clonal population - May 1, 2017–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 Wild type replicates begin to collapse after 3 transitions… News Archive →
ENIGMA Researchers Uncover Factors in Microbial Community Collapse - April 7, 2017–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… News Archive →
Complete genome sequence of Pseudomonas stutzeri strain RCH2 - February 8, 2017–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… News Archive →
Temporal Dynamics of In-Field Bioreactor Populations Reflect the Groundwater System and Respond Predictably to Perturbation - January 24, 2017–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… News Archive →
Predicting metabolic properties using dynamic substrate preference - January 23, 2017–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… News Archive →
Metabolizing Data in the Cloud - January 20, 2017–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,… News Archive →
Uranium binding complex a potential tool for environmental sequestration of uranium - December 3, 2016–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… News Archive →
Rapid Detection of Microbial Cell Abundance in Aquatic Systems - November 15, 2016–(A) Overview of approach. To provide proof of principle, capacitance measurements from laboratory-sourced batch culture and environmentally-sourced samples were obtained using silicon wafer-based capacitive sensor ENIGMA post-doctoral fellow developed the application of ACEK-enhanced capacitive sensing technology as a rapid screening tool for the detection and quantification… News Archive →
Digital Droplet Multiple Displacement Amplification - May 31, 2016–Fig. 1. The working principles of ddMDA. The ddMDA procedure partitions E.coli sample into millions of picoliter droplets(A) and amplification in each droplet occur independently from the other droplets(B). At ddMDA endpoint, each droplet contains a discrete hyper-branched MDA product(C). Scale bar =100µm. Fig. 2. Comparison… News Archive →
Nitrite Reduction Assay for Whole Pseudomonas Cells - May 20, 2016–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… News Archive →
Stable protein interactome of the model sulfate reducing bacterium Desulfovibrio vulgaris Hildenborough - April 20, 2016–The 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… News Archive →
Preferential oxidation of microbial-mediated reduced sulfur by nitrate limits the in situ mobility of uranium - April 2, 2016–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… News Archive → Post Doc Lauren Lui profiled by Berkeley Lab for her Public Service and contribution to Women in Science - March 15, 2016–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. https://diversity.lbl.gov/2016/03/14/berkeley-lab-celebrates-women-in-science-and-public-service/ Lauren Lui, an ENIGMA postdoctoral fellow in Adam Arkin’s Lab,… News Archive →
Benchmark properties for highly accurate bacterial protein interactions - February 20, 2016–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 News Archive →
Are free-living bacteria optimized by natural selection? - December 15, 2015–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… News Archive →
Comparative metagenomics reveals impact of contaminants on groundwater microbiomes - October 31, 2015–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,… News Archive →
Andrea Rocha featured in Top 50 Women “Latinas in Information Technology of Hispanic Engineer and IT” magazine - October 18, 2015–ENIGMA Post Doc Andrea Rocha one of the 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… News Archive →
Andrea Rocha is featured in DOE’s online Women @ Energy Series - October 6, 2015–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.Physical Biosciences ENIGMA Annual Retreat at the UC EBB - group photo, discussions, a poster session - August 11, 2015. http://www.energy.gov/diversity/listings/women-energy. News Archive →
Potential Role of Acetyl-CoA Synthetase (acs) and Malate Dehydrogenase (mae) in the Evolution of the Acetate Switch in Bacteria and Archaea - August 20, 2015–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… News Archive →
Differences in diversity between extraction techniques - August 1, 2015–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… News Archive →
Visiting STEM students gain insight to microbial metabolomics - May 27, 2015–CSUEB sponsored STEM Career Awareness Day, visiting high school students view an active demonstration of the mass spectrometry-based techniques used to understand microbial community metabolomics in the Northen Lab. In support of the Cal State University East Bay (CSUEB) sponsored STEM (Science Technology Engineering Maths) Career… News Archive →
Jizhong Joe Zhou Recipient of DOE’s Highest Scientific Honor- The Lawrence Award - May 21, 2015–ENIGMA’s Joe Jizhong Zhou, a professor at the 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… News Archive →
Bacterial Communities As Precise Biosensors Of Environmental Damage - May 11, 2015–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… News Archive →
ENIGMA researcher Michela Catena is a Fulbright Scholar this fall! - May 5, 2015–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… News Archive →
Trent Northen is “Science Guy”! - ENIGMA, February 20, 2015–ENIGMA’s Trent Northen is ‘Science Guy’ at Buena Vista Elementary in Walnut Creek CA for 3rd annual outreach to 22 classes of ~525 k-5 students. He uses a cart of science demos aimed at encouraging STEM careers and participation in the science fair (which he… News Archive →
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 News Archive →
New Community Leadership! Aindrila Mukhopadhyay - July 1, 2014–ENIGMA’s Aindrila Mukhopadhyay in ASM leadership role. Beginning July 1, 2014, Aindrila Mukhopadhyay of Lawrence Berkeley National Lab will be Chair-Elect of Division O (Fermentation and Biotechnology) of the American Society for Microbiology. Aindrila is honored by this appointment and looks forward to serving you and… News Archive →
Metallomics of Two Microorganisms Featured on Metallomics Blog - April 28, 2014–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. Metallomics Blog → Full Paper → Lancaster WA, Menon AL, Scott I, Poole FL, Vaccaro BJ, Thorgersen… News Archive →
Exploring the Role of CheA3 in Desulfovibrio vulgaris Hildenborough Motility Was One of the Most Viewed Frontiers in Microbiology Research Articles this March - April 21, 2014–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”. Frontiers Article → Full Paper → Ray J, Keller KL, Catena M, Juba TR, Zemla M, Rajeev L, Knierim B, Zane… News Archive →
Adam Arkin Recipient of DOE’s Highest Scientific Honor- The Lawrence Award - April 21, 2014–“Adam Arkin, director of Berkeley Lab’s Physical Biosciences Division (PBD) and a biologist who is recognized as a leading authority on the evolutionary design principles of cellular networks and populations and their application to systems and synthetic biology, has been named one of six recipients of… News Archive →
Andrea Rocha Featured Post Doc at ORAU - March 18, 2014–Since May 2012, Rocha has been a participant in the ORNL Postdoctoral Research Associates Program, administered by ORAU through the Oak Ridge Institute for Science and Education contract with the U.S. Department of Energy. The program advances scientific and technical training for doctorate-level scientists and engineers… News Archive → Environmental Microbiology Team Demonstrate the Importance and Dynamic Behavior of Stochastic Processes in Controlling the Succession of Microbial Communities - February 25, 2014–One of the ENIGMA goals is to map genotypes to phenotypes within an ecological context. 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. We show that… News Archive →
Montana State Team Overcomes Challenges, Proves That Microbes Swim to Hydrogen Gas - November 25, 2013–Knowledge of taxis (directed swimming) in the Archaea is currently expanding through the identification of novel receptors, effectors, and proteins involved in signal transduction to the flagellar motor. Although the ability for biological cells to sense and swim toward hydrogen gas has been hypothesized for many… News Archive →
Terry Hazen Inducted as AAAS Fellow - November 20, 2013–Please join me in congratulating our very own Terry Hazen on his election to the rank of AAAS Fellow by the American Association for the Advancement of Science Council for his “efforts on behalf of the advancement of science or its applications which are scientifically or… News Archive →
Publication Citation Report and Top Ten Highly Cited - June 14, 2013–Citation analysis performed June 13, 2013, at Web of Science on an available subset of publications (157/232). Please note these analytics are subject to change. Publications cited 157 Total number of times cited 2,168 Total number of times cited without self-citations 1,922 Citing articles 1,673 Citing… News Archive →
Indirect and Suboptimal Control of Gene Expression is Widespread in Bacteria - May 23, 2013–It is generally thought that bacteria regulate gene expression to adapt to changes in their environment. This implies that genes are expressed only when they are needed and are otherwise turned off to avoid producing proteins when they are not required or are toxic. A new… News Archive →
Metabolic Footprinting of Mutant Libraries to Map Metabolite Utilization to Genotype - February 28, 2013–The discrepancy between the pace of sequencing and functional characterization of genomes is a major challenge in understanding complex microbial metabolic processes and metabolic interactions in the environment. Here, we identified and validated genes related to the utilization of specific metabolites in bacteria by profiling metabolite… News Archive →
Zhou Wins OU Research Award - February 27, 2013–Joe Zhou wins the University of Oklahoma Vice President for Research Award for Outstanding Research Impact in 2012. Award Article → News Archive →
Genome Announcement of Pelosinus fermentans - February 27, 2013–Pelosinus fermentans JBW45 is an anaerobic, lactate-fermenting bacterium isolated from Cr(VI)-contaminated groundwater at the Hanford Nuclear Reservation 100-H site (Washington) that was collected after stimulation with a polylactate compound. The genome sequence of this organism will provide insight into the metabolic potential of a predominant population… News Archive →
Community Leadership! Steve Brown - February 27, 2013–ENIGMA’s Steve Brown in ASM leadership role. 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… News Archive →
Metallochaperones Regulate Intracellular Copper Levels - February 26, 2013–Copper (Cu) is an important enzyme co-factor that is also extremely toxic at high intracellular concentrations, making active efflux mechanisms essential for preventing Cu accumulation. Here, we have investigated the mechanistic role of metallochaperones in regulating Cu efflux. We have constructed a computational model of Cu… News Archive →
David Stahl Elected to National Academy of Engineering - February 7, 2013–Congratulations to ENIGMA’s David Stahl on this well-deserved and prestigious award! The ultimate goal of the ENIGMA SFA research is to generate a quantitative understanding of phenomena across these multiple scales so that scientists can predict and rationally alter the behavioral responses of microbes and their… News Archive →
Liquid Chromatography Quadrupole Time-of-Flight Mass Spectrometry Characterization of Metabolites Guided by the METLIN Database - February 1, 2013–Untargeted metabolomics provides a comprehensive platform for identifying metabolites whose levels are altered between two or more populations. 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… News Archive →
A Large-Scale Evaluation of Computational Protein Function Prediction - January 31, 2013–The discrepancy between the pace of sequencing and functional characterization of genomes is a major challenge in understanding complex microbial metabolic processes and metabolic interactions in the environment. Here, we identified and validated genes related to the utilization of specific metabolites in bacteria by profiling metabolite… News Archive →
ENIGMA Metabolic Footprinting Publication Recommended by Faculty of 1000 - January 31, 2013–The discrepancy between the pace of sequencing and functional characterization of genomes is a major challenge in understanding complex microbial metabolic processes and metabolic interactions in the environment. Here, we identified and validated genes related to the utilization of specific metabolites in bacteria by profiling metabolite… News Archive →
Metabolomics: Sifting Through Complex Samples - January 18, 2013-BlueMoleculeReview article of advances in Metabolomics about the team at Scripps Research Institute- Gary Siuzdak, Gary Patti and Ralph Tautenhahn et al. Biocompare Article → A view from above: cloud plots to visualize global metabolomic data. Patti G.J., Tautenhahn R., Rinehart, D, Cho, K.Shriver L., Manchester… News Archive →