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Support Sara Gushgari-Doyle Berkeley Lab SLAM finalist

Sara Gushgari-Doyle of the Chakraborty Lab was selected as a finalist in the Berkeley Lab “Early Career Scientist Research SLAM.” She was selected as one of 12 finalists from a field of 44 submissions to go head-to-head in a “3-minute-describe-your-work-in-layman-terms” challenge that Berkeley Lab has hosted for the past 3 years. Finalists receive coaching via “Making the Most of Your Presentation” workshop and a unique opportunity for one-on-one coaching from a globally renowned speaker, Jean-Luc Coumont of Principiae. Finalists will compete on September 17 at 3pm for a chance to win a $3,000 first prize! You can read more at

She shares her experience to encourage other team members to participate!

How did you initially hear about the SLAM?

I heard about SLAM in one of my postdoc orientation sessions.

When did you decide to submit an entry, and what did that entail?

I decided to enter when I first heard about the SLAM. I recorded a 3 minute video using the Zoom app on my computer (thanks to remote work due to COVID-19, I’m very well-versed in Zoom functions now). I wrote and recorded a 3 minute talk about my work in microbial isolation strategies informed by computational analysis, including motivation of why everyone should care about microbes in the first place!

What are you most excited for in this experience?

I am thrilled to get a chance to have one-on-one coaching with Jean-Luc. I have never gotten professional public speaking coaching – I think it will be a really worthwhile experience.

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

Small is mighty: adaptation of Patescibacteria to groundwater environment drives their genome simplicity

(Video taken from Research Square)


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 and carbon utilization as well as basic systems for DNA replication and translation essential for growth and reproduction. Meanwhile, they lack numerous nonessential functions related to motility, chemotaxis, outer membrane function, polysaccharide metabolism etc. They also lack CRISPR-mediated phage defense, considered the most important mechanism of bacterial immunity; while possessing alternative strategies for phage resistance. 

The Impact 

Groundwater microbial communities are responsible for large-scale subsurface biogeochemical cycling, influencing the chemical profiles of the world’s water.  Patescibacteria are found prevalent in groundwater, sediment, lake, and other aquifer environments. It has been observed that bacteria from this superphylum have extremely small genome sizes and cell sizes, and they lack the CRISPR virus defense system. However, there is little understanding of the mechanisms used by Patescibacteria to thrive in the nutrient-limited groundwater environment. Also, their fragility to environmental stresses (such as heavy metal contamination) was not known. This study, based on previous studies and results, further explored the adaptive mechanisms of Patescibacteria comprehensively by comparing genomic features and linking them to environmental factors. We also found that Patescibacteria have a reduced stress response to environmental perturbations which might be related to its vulnerability to heavy metal contamination observed in this study. Since terrestrial subsurface aquifers are the repository of one-third of the Earth’s fresh water and an important source of water for human consumption; groundwater pollution may alter groundwater microbial communities, impacting water health.  Thus, understanding the characterization of Patescibacteria is important to the conservation of the groundwater.  


Samples from a site exposed to radioactive contamination; targeting 93 contaminated and uncontaminated groundwater wells over time, showed that Patescibacteria superphyla is diverse and includes over 20 candidate phyla. Defined by ultra-small cell sizes, simplified membrane structures, and loss of genes, facilitating genome sizes three times smaller than other well-established bacterial phyla; retaining essential functions of simple metabolism and genetic information processing. Based on analysis of Patescibacteria, we propose that their adaptation to groundwater environments drives their unique genomic features.

Low nutrient concentration and diversity in groundwater requires Patescibacteria to increase absorption rate. Smaller cells have a higher ratio of surface area to volume, thus speeding up substance exchange rates across the cell membrane. Small cell size and reduced membrane structures, which could be potential phage receptors, allow Patescibacteria to escape from phage attachment.  Groundwater has low oxygen concentrations and no light for photosynthesis. Thus, Patescibacteria rely on anaerobic respiration which provides less energy than aerobic respiration, losing genes for light capture & repair of light damage. Functions with high energy requirements such as flagellar motility and secondary metabolisms are also missing. Stable physical conditions such as temperature and pH in groundwater reduce the need for adaptive responses to environmental perturbation. Indeed, Patescibacteria abundance was significantly reduced in highly contaminated groundwater compared to uncontaminated /moderately contaminated groundwater, indicating that reduced metabolic potential and stress response make Patescibacteria sensitive to contamination.


Tian, R; D. Ning, Z. He, P. Zhang, S.J. Spencer, S. Gao, W. Shi, L. Wu, Y. Zhang, Y. Yang, B. G. Adams, A.M. Rocha, B.L. Detienne, K.A. Lowe, D.C. Joyner, D.M. Klingeman, A.P. Arkin, M.W. Fields, T.C. Hazen, D.A. Stahl, E.J. Alm, J. Zhou (2020) Small is mighty: adaptation of Patescibacteria to groundwater environment drives their genome simplicity. Microbiome. ISME Journal [doi]:1186/s40168-020-00825-w

Selective carbon sources influence the end-products of microbial nitrate respiration



The world’s population relies on nitrogen fertilizer to maintain productive agricultural ecosystems. However, as a consequence of industrial fertilizer use the nitrogen cycle has become the most anthropogenically perturbed element cycle, and nitrogen contamination of surface waters and groundwater has serious consequences for public and environmental health. For example, nitrate in water supplies can cause methemaglobinemia, nitrate in coastal waters leads to eutrophication, and incomplete denitrification drives the accumulation of nitrous oxide, a potent greenhouse gas.

The nitrogen cycle is driven by microbial activity, but we lack a predictive understanding of how varying environmental conditions interact with microbial communities to influence the fate of nitrogen in the environment. This observation motivated recent work by ENIGMA researchers at Berkeley Lab. In a recent publication in the ISME Journal, the authors write, “Such a framework would enable better monitoring and management of microbial communities to mitigate environmental damage while maximizing the productivity of agricultural lands.” The ENIGMA team investigated how different carbon sources influence the end-products of microbial nitrate respiration, a critical juncture in the nitrogen and carbon cycles. The team’s approach leverages high-throughput DNA sequencing and laboratory automation capabilities at Berkeley Lab to combine genome-resolved metagenomics with high-throughput cultivation, colorimetric assays and amplicon sequencing of low complexity microbial communities. “We found that some carbon sources tend to favor nitrate reduction to ammonium which maintains nitrogen in soils, while other carbon sources favor denitrification which leads to loss of nitrogen as dinitrogen gas” says the lead author on the study, Hans Carlson.

The work adds nuance to a prevailing paradigm in the scientific literature: that higher concentrations of carbon will always favor nitrate reduction to ammonium.”Thermodynamic calculations predict that higher concentrations of carbon will favor nitrate reduction to ammonium. We cannot argue with thermodynamics” says Carlson, “however, the pathways  for utilization of specific carbon sources are unevenly distributed with different nitrate reduction pathways in different microbial genomes. Therefore, in some environments, a particular carbon source may be utilized only by microbes that reduce nitrate to produce dinitrogen. In these environments, no amount of carbon added will induce nitrate reduction to ammonium”

Carlson hopes to extend the team’s approach to more microbial processes and environments. “By linking microbial gene content with activity in low-complexity microbiomes in high-throughput, we will be able to better predict how complex, variable environmental parameters influence microbial element cycling.” Ultimately, this could have real benefits for how industrial ecosystems are managed, for instance, by identifying selective carbon amendments to stimulate nitrate reduction to dinitrogen to could enhance the removal of remove nitrogen from wastewater and contaminated groundwater or to stimulate ammonium accumulation in agricultural soils.


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

Precisely Quantifying Ecological Processes in Shaping Subsurface Communities

Precisely Quantifying Ecological Processes in Shaping Subsurface Communities

Daliang Ning

ENIGMA researchers at the 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 subsurface communities. The new index normalized stochasticity ratio (NST) showed high accuracy and precision (>0.9; >0.3 higher than previous approaches on average). When applied to a groundwater microbial community in response to organic carbon (vegetable oil) injection, NST demonstrated stochasticity increased after injection and decreased when the oil was consumed. By highlighting the caveats, this study also provides guidance for the appropriate use of null model-based approaches for examining community assembly processes.

Ning, D.; Y. Deng, J. M. Tiedje, J. Zhou (2019) A General Framework for Quantitatively Assessing Ecological Stochasticity. Proceedings of the National Academy of Sciences of the United States of America. 116 (34): 16892-16898 [doi]:1073/pnas.1904623116

ENIGMA’s Fangchao Song is Berkley Lab SLAM Finalist!


Fangchao Song represents ENIGMA and Biosciences in the 2019 SLAM

Fangchao Song represents ENIGMA & Biosciences in the 2019 SLAM. 09/18/2019 Berkeley Lab, California

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 Berkeley Lab is hosting for postdocs. 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. Finalists had a chance to win a $3,000 first prize! You can read more about the results

He shares his experience, to encourage other team members to participate!

How did you initially hear about the SLAM?

I heard about SLAM when the lab called for the participation on SLAM2018. I read the instructions and felt it is interesting. I submitted a video last year but did not get into the finalists. That made me start thinking about how to do it better.

When did you decide to submit an entry, and what did that entail?

As I started improving on how to do a short scientific talk after my previous attempt, Lauren’s great talk inspired me a lot. Thus I did not hesitate to submit a recording this time. There are two steps in this SLAM. First, people were encouraged to submit a 3-minutes talk to describe their research. The judges from different backgrounds in the Lab reviewed all the submissions and selected 12 submissions as the finalists. All the finalists were informed and prepared for 3-minutes on stage talk in the SLAM final as people saw.

What did you get out of the experience?

This was definitely an awesome experience. I learned a lot about public speaking and started to notice some of my habits of talking, gestures, and expressions. This is the first time I recorded and listened to myself talk. It was weird but really helpful with recognizing a few things I had not realized before. For example, I found that I frequently speak fast and slur some words. And that I always step back and forward during talking. In addition, the feeling of talking in front of hundreds of people is totally different from talking in front of a camera or mirror. The stage performance is more about the overall feeling I create but not exact words. It is a package of content, gesture, body movement, eye contact, speed, rhythm, etc. The preparation of SLAM forced me to think about everything in detail and also the overall feeling. Besides this, I made lots of friends and got my research exposed in the whole lab. All the finalists got together one day before the final performance to rehearse, we had a really good time, made jokes, and gave feedback and suggestions on others’ talks. We did not consider the SLAM as a competition but a party.

What would you do differently?

There are three things I am going to do differently for future talks. First, practice more. I feel I practiced the content well this time. But there is huge room for improvement on how to coordinate my gestures, movement, expression, eye contact together with my speaking, in particular, changing some habits. Second, smile. I was too serious when I was talking. I wrote “smile” on the top of my document during preparation, but it seemed like I forgot to do this. Third, slow down, and use different pacing in various parts of my talk based on content.

Sulfonate utilization by Desulfovibrio may expand ecological niches

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 Day, an undergraduate student, has published a genome announcement for a strain of Desulfovibrio, a sulfate-reducing bacterium (SRB), that grows by respiration of sulfonates. Genome comparisons have identified a candidate pathway and probes to explore the taxonomic distribution of this metabolism. Data from the earlier survey work showed that the SRB and sulfate were nearly mutually exclusive in the groundwater of the ORR prompting Leslie to determine if alternative sources of sulfate could possibly explain this result. A literature review pointed to sulfonates, ubiquitous in nature, as potential electron acceptors for SRB. As part of the Environmental Ark Campaign, she has shown that the sulfonate isethionate is used by a subset of SRB as a terminal electron acceptor and has identified the transporter and potential metabolic pathway for isethionate. The widespread distribution of sulfonates in the terrestrial environment may contribute to an understanding of the abundance of SRB in niches low in sulfate.

ENIGMA publication highlighted by DOE

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 to encourage early-career scientists to develop risky and interesting ideas that may contribute to our ongoing mission or changing direction by providing new data or tools. Here Ankita Kothari successfully managed a Discovery proposal from pitching the idea, developing the project to publication.  This work was recently showcased at the national level by DOE

Bacteria often contain mobile genetic elements called plasmids that are circular DNA molecules that confer advantageous traits to the host and are capable of being horizontally transferred between different microbes. Studying the entire plasmid content (plasmidome) of a site can thus provide insights into genes that provide a selective advantage to a bacterial community. To study the incidence, diversity, and distribution of plasmids in groundwater along with exploring their role in environmental stress adaptation, we came up with the idea of exploring the plasmidome of the Oak Ridge Field Research Site. This Discovery proposal was risky because the existing plasmidome studies were limited to environments with high cell density. In contrast, at ENIGMA we focused on a challenging Department of Energy site characterized by low cell density and fluctuating populations. We developed and optimized methods to work with this environment and were successful in identifying over 600 different plasmids including several large plasmids that showed enrichment in metal tolerance genes in addition to antibiotic- and virus-resistance genes. Collaborations within ENIGMA helped to provide resources for environmental sampling, groundwater metal composition analysis, and sequence data analysis via KBase. This project now contributes to the 1) ENSuRC campaign since it continues to identify novel mobile genetic elements and accidentally discovered novel viruses along with 2) environmental ark campaign where the plasmids are being used to develop genetic tools to modify novel bacteria.

ENIGMA teamwork is featured in Elements

Estelle Couradeau – 2018 ENIGMA Strategic Planning – Lawrence Berkeley National Laboratory on Tuesday, October 9, 2018 in Berkeley, Calif. 10/09/18

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

Couradeau E.; J. Sasse, D. Goudeau, N. Nath, R. Chakraborty, T.C. Hazen, B.. Bowen, R.R. Malmstrom, T.R. Northen (2019) Challenging our view of the active fraction of soil microbiomes using BONCAT-FACS-Seq. Nature Communication. [doi]:1038/s41467-019-10542-0

DuBSEQ functional characterization Nature Communications

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 confirm known functional genes and identify interesting genes of novel function.

Vivek K. Mutalik, Pavel S. Novichkov, Morgan N. Price, Trenton K. Owens, Sean Carim, Astrid Terry, Adam M. Deutschbauer, Adam P. Arkin

ENIGMA authors; Front row-Morgan N. Price, Pavel S. Novichkov, Vivek K. Mutalik, Astrid Terry, Sean Carim. Back row-Trenton K. Owens, Adam M. Deutschbauer, Adam P. Arkin — In Emeryville, California, 1/16/2019

Dual-barcoded shotgun expression library sequencing for high-throughput characterization of functional traits in bacteria

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: