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]
Congratulations Sara Gushgari-Doyle Berkeley Lab SLAM 2nd place winner!
Aug 28, 2020-Two Percent https://slam.lbl.gov/2020-slam/2020-slam-finalists/sara-gushgari-doyle
ENIGMA’s Sara Gushgari-Doyle, of the Earth and Environmental Sciences Area, uses computational and big-data approaches to inform strategies for culturing rare and difficult-to-culture microorganisms. Watch Gushgari-Doyle’s SLAM presentation to find out more. She placed 2nd out of 12 Finalists.
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 World Microbe Forum
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 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.
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 Fragmentation/Annotation Multiple Reaction Monitoring):
This novel quantitative mass spectrometry technique allows the measurement of concentrations of the metabolites in ENIGMA samples using much cheaper instrumentation. These efforts characterizing key metabolites developing experimental quantitative methods to monitor the change of metabolome in bacteria are mission critical. The techniques will be used to design and test field-derived hypothesis in the laboratory.
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 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 methemoglobinemia, nitrate in coastal waters leads to eutrophication, and incomplete denitrification drives the accumulation of nitrous oxide, a potent greenhouse gas.
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 anaerobic microbes use vitamin B12-binding proteins instead. By analyzing the genomes of diverse bacteria and archaea, we identified four families of folate-independent methionine synthases. Three of these families co-occur with B12-binding proteins, which indicates their likely partners. The fourth family does not require vitamin B12; instead, it obtains methyl groups from an oxygen-dependent partner protein.
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., Adams, B.G., De León, K.B., Brewer, S.S., Williams, D.E., Lowe, K.A.,Rodriguez Jr., , M., Mehlhorn, T.L., Pfiffner, S.M., Chakraborty, R., Arkin, A.P., Wall, J.D., Fields, M.W.,Adams, M.W.W., Stahl, D.A., Elias, D.A., Hazen, T.C.
Chemosphere, https://doi.org/10.1016/j.chemosphere.2020.126951