News Articles Archives

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

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 Domingo and Scripps Research Institute team has […]

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. In this study, we tested the effects of C:NO3− ratio and substrate concentration on pathway selection between ammonification and denitrification in the dual-pathway organism Intrasporangium calvum C5. We challenge the paradigm that C:NO3− ratio controls pathway selection based on a simple principle: ratios do not account for substrate concentrations, which can impose resource limitation for C or NO3−

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 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 https://doi.org/10.1038/s41467-018-08177-8

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 Ridge Research Field Site in Tennessee, highly collaborative work between ENIGMA and JGI generates data from sediment to use high-throughput genetics to discover a novel catabolic pathway as the first of many. Diverse bacteria use oxidative pathways to consume deoxyribonate (a waste product of metabolism).

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 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.

https://www.ce.washington.edu/news/article/2019-01-03/david-stahls-discovery-honored-seattle-aquarium

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 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.”

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 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 https://today.lbl.gov/2018/09/05/finalists-selected-to-compete-in-sept-20-postdoc-research-slam/
May “Microbial war and peace” win!

Link to the original invitation to participate: https://today.lbl.gov/2018/05/17/postdocs-and-early-career-scientists-can-win-cash-prizes-at-lab-research-slam/