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2021 ASM Award for Environmental Research






Hazen TerryTerry Hazen, Ph.D. receives 2021 ASM Award for Environmental Research
Recognizes an outstanding scientist with distinguished research achievements that have improved our understanding of microbes in the environment, including aquatic, terrestrial and atmospheric settings. For more information

David Stahl Honored by Seattle Aquarium

Stahl-David_thumbnailWe 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 2012; now he is also a local Seattle celebrity! His discovery, that ammonia-oxidizing archaea (AOA) microorganisms are the dominant nitrifiers in most natural systems, was honored by a plaque at the Seattle  Aquarium. His team was first to isolate AOA microorganisms from a water sample taken from a fish tank at the Seattle Aquarium.

Jizhong Zhou Honored with 2019 ASM Award for Environmental Research

zhou-jizhong-joeJizhong Zhou, Ph.D. (The University of Oklahoma in the Department
of Microbiology and Plant Biology)
american academy of microbiology

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 environment, including aquatic, terrestrial, and atmospheric settings.

His work with ENIGMA is multi-disciplinary, using integrative experimental and computational approaches, taking advantage of his broad background in microbial genomics, molecular biology,

molecular evolution, microbiology, ecology, mathematics, and bioinformatics.

“The American Academy of Microbiology is the honorific leadership group within the ASM, the world’s oldest and largest life science organization. The mission of the Academy is to recognize scientists for outstanding contributions to microbiology and provide microbiological expertise in the service of science and the public.”

Read more about the awards:


ENIGMA’s Lauren Lui is Berkley Lab SLAM Finalist!

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 support Lauren!
The SLAM will be streamed live so remote team members can show their support.

This is the “3-minute-describe-your-work-in-layman-terms” challenge that Berkeley Lab is hosting for postdocs.

She recorded & submitted a video “Microbial War and Peace” which was selected from a competitive field of 32 entries.

Finalists receive coaching via “Making the Most of Your Presentation” workshop, a unique opportunity to get one-on-one feedback from a globally renowned speaker, Jean-luc Doumont of Principiae.
Lauren will participate in the in-person competition next month for a chance to win $3,000 first prize!

You can read more here
May “Microbial war and peace” win!

Link to the original invitation to participate:

ENIGMA’s Romy Chakraborty honored at “Women @ the Lab”

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 this award by multiple people and teams, acknowledging her excellence in science, her leadership in her division as Ecology Department Chair for Earth and Environmental Sciences Area, and her service to the lab community as WSEC Empowerment Subcommittee Chair.

For excellence in science; leadership as Ecology Department Chair in EESA; service to the lab community as WSEC Empowerment Subcommittee Chair

Mike Adams wins 2018 DuPont Industrial Biosciences Award in Applied and Environmental Microbiology

Adams-Mike_portraitENIGMA 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 environments, such as ultra-hot geothermal vents, for practical applications including the generation of biofuels with a reduced carbon footprint. The award will be presented this summer at ASM’s ­annual meeting in Atlanta. The DuPont Industrial Biosciences Award, given annually since 1977, recognizes distinguished achievement in research and development in applied (nonclinical) and environmental microbiology. Past recipients include members of the National Academy of Sciences and the Howard Hughes Medical Institute as well as MacArthur Fellows. DuPont Biosciences is a worldwide organization with focus areas in bioactives, biomaterials, and biorefineries.  To read more

Leslie Day ENIGMA undergrad Honorable mention for poster Mizzou Life Sciences Week 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 Ecological, Evolutionary, and Developmental Biology.  In the 100 Well Survey of the Oak Ridge Reservation done by ENIGMA, sulfate-reducing bacteria and sulfate are nearly mutually exclusive in the groundwater. To predict the presence and metabolism of sulfate-reducing bacteria as part of the Environmental Ark Campaign, we must understand what oxidized sulfur compounds are available and can be utilized by sulfate-reducing bacteria. Leslie is characterizing sulfonates, ubiquitous in nature, as potential electron acceptors for sulfate-reducing bacteria.  She has shown that many sulfate reducers can utilize the sulfonate isethionate as a terminal electron acceptor and has identified the transporter and potential pathway for isethionate utilization. She is currently writing the manuscript for the work described in this poster for publication in a peer-reviewed journal.  Leslie has been working in the Wall lab as part of ENIGMA since Fall 2014 and upon graduation plans to enter a Ph.D. program to pursue her interest in environmentally-relevant anaerobes.

Poster Title: Sulfonate Utilization by Desulfovibrio vulgaris Hildenborough
Authors: Leslie A. Day, Kara B. De Leon, Judy D. Wall

Erica Majumder wins best overall poster at the International Symposium on Microbial Sulfur Metabolismw

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 microbes, the interaction of some microbes with metals, and can inhibit other metabolisms such as nitrate reduction. This project developed tools to be able to assay sulfur-containing metabolites and to begin to tease out their functions in microbial community interactions.

Authors: Erica L.-W. Majumder, Tao Huan, Erica M. Forsberg, Chavi Domingo, Gary Siuzdak, Judy D. Wall
Affiliations: 1-Mizzou, 2- Scripps

A strategy to determine all sulfur-containing metabolites from global untargeted metabolomics experiments has been employed to study the total metabolome and the sulfur-ome of model Sulfate-Reducing Bacterium (SRB) Desulfovibrio vulgaris Hildenborough (DvH). Total metabolite populations were measured from DvH samples at different growth stages, on different amounts of sulfate, with competing sulfur sources, spent media, and on medium simulating the groundwater at Oak Ridge Field Research Center. The metabolome and sulfur-ome of a nitrate-reducing bacterium, a different sulfate-reducing bacterium, and E. coli were also measured using the same treatment. Using a new script we developed, the sulfur-containing metabolites were identified from the data sets. SRB was found to produce more and distinct sulfur-containing metabolites than non-sulfur respiring bacteria. For DvH, the growth stage, sulfur source, and sulfate concentration impacted the sulfur-ome. The biosynthesis or assimilation of these sulfur-containing metabolites was further queried with stable isotope experiments by replacing sulfate with 34 SO4 2-. DvH was found to assimilate sulfur from sulfate into certain sulfur-containing metabolites. Overall, this work indicates that the population of sulfur-containing metabolites is larger than expected, assimilative pathways are happening in dissimilatory SRB, and in addition to hydrogen sulfide, excreted sulfur-containing metabolites could be playing a role in the various environments of SRB. We have developed a new way to study sulfur metabolites in systems, which is desirable because of their reactivity and chemical properties for field and medical applications.

Relevance to ENIGMA mission 
  • Sulfur is an essential element in all kingdoms of life and the sulfur cycle is a primary driver of carbon cycling in the subsurface.
  • Many sulfur-containing metabolites are unknown or uncharacterized due to challenging chemistry.
  • Sulfur-containing molecules have increased activity/function compared to their small percent of cellular elemental composition.
  • We hypothesized that in addition to essential S-metabolites, organisms using sulfur for respiration would have a different set S-metabolites than non-sulfur respiring microbes.
  • We found that sulfur-species respiring bacteria and other respiratory-mode bacteria all had about 200 sulfur-containing metabolites using global untargeted metabolomics coupled with a new script we developed for identifying sulfur-containing metabolites.
  • We found that sulfate-reducing bacteria assimilate the sulfate sulfur and can use thiosulfate to make cysteine using stable-isotope label sulfate.
  • We also found evidence of sulfur-containing metabolites regulating protein translation and other metabolic functions.
  • Sulfur-containing metabolites in the spent medium indicate how sulfur (and carbon) may be moving between organisms or how the redox state of the environment is regulated.

Dual Barcoded Shotgun Expression Library Sequencing (Dub-seq) wins R&D100 Award

Mutalik_VivekENIGMA’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 research

Dub-seq technology is based on creating a genomic fragment library in association with dual barcodes on broad-host vectors.  DNA (from any source) is sheared and cloned between dual barcodes. Then, the cloned genomic fragment is identified and associated with unique DNA barcode upfront and is done only once for each library. Once this step of associating barcodes to genomic fragment is performed, only one of the barcodes is used as a proxy for clonal isolate in the following experiments. This standardization enables researchers to assay the same library across diverse conditions with minimal cost per genome-wide assay. A simple analytic approach aids in connecting fragment score and gene score to gene function.

This technology fills a critical gap in elucidating gene-function in a very high-throughput assay set up and saves time, labor, and money as compared to state-of-the-art methods. Dub-seq technology is applicable in the discovery of novel enzymes/biocatalysts for biofuel production, improving and tolerance traits for toxic biochemicals, ensemble functional assessment of microbial communities, plant growth-promoting factors, bioremediation routes, novel green chemistries and biotechnologies in improving energy and environment missions. The technology is also extendable in diverse health and agriculture associated biotechnologies.

For more information associated with the award:

2017 R&D 100 Winner


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

andrea rocha featured top 50 women Latinas IT magazineENIGMA 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 is a post-doctoral fellow in the Biosciences Division at Oak Ridge National Laboratory. Rocha anchors the field sampling efforts at the Oak Ridge Field site in radioactively contaminated areas as well as background sites. As part of the ENIGMA [Ecosystems and Networks Integrated with Genes and Molecular Assemblies], a multi-institutional collaborative project, Rocha is trying to determine subsurface keystone bacteria species differences in gradients of pH, nitrate, uranium, and conductivity to enable modeling of microbial community resiliency. During her academic and research career, Rocha has received numerous honors and awards. These include the Facilis 2014 workshop travel award, American Society of Microbiology (ASM) minority travel award, Delores Auzzune Fellowship, Carl Storm Underrepresented Minority Fellowship, GEM fellowship, Successful Latino Student Award, Alfred P. Sloan fellowship, Florida-Georgia Louis Stokes Alliance for Minority Participation, Bridge to Doctorate Fellowship, and Hall-Bonner Fellowship.

A person performing technological functions, who has designed, developed, managed, or assisted in the development of a product, service, system, or intellectual property that is a substantial achievement in the field. The overall impact of technological achievement is the prime consideration, regardless of title or degrees earned. The committee sees a nominee that offers broad impact and high value to society as a whole.

Women recognized at this event include Special Recognition honorees, Promotion of Education Awardees as well as the women featured in the issues of Women of Color magazine and Hispanic Engineer magazine.  Some of the attendees include the Department of Defense officials, military service chiefs, political leaders, corporate executives and many others who promote workforce diversity and inclusion.

Through our participation in WOC STEM development programs, we hope to engage young people, build relationships, and influence STEM as a career choice for young people. Andrea serves as a role model for other postdocs and we are pleased to support her efforts in science.


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



Physical Biosciences ENIGMA Annual Retreat at the UC EBB – group photo, discussions, a poster session – August 11, 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.

David Stahl selected as EMSL Chief Scientist


Stahl-David_thumbnailDavid 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 theme research areas, reach out and raise awareness of EMSL to the BER PI community, and provide additional biology expertise.

David brings an international reputation in studying the application of molecular microbial ecology to environmental engineering. He’s received funding from DOE’s Office of Biological and Environmental Research and is a member of BER’s Advisory Committee. In 2012, he was elected to the National Academy of Engineering.
Before joining the UW in 2000, David held positions at the University of Illinois at Urbana-Champaign and at Northwestern University. He received his bachelors’ degree in Microbiology from the UW and his masters and Ph.D. in Microbiology from the University of Illinois.
David will spend one week each month at EMSL and then work remotely the remainder of each month from the UW’s Seattle campus.
Stahl, D.A. – Chief Scientist for the EMSL user program. Environmental Molecular Sciences Laboratory, PNNL. Richland, WA.