Berkeley Lab

2018 Publications

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  1. De León, K.B.; G.M. Zane, V.V. Trotter, G.P. Krantz, A.P. Arkin, G.P. Butland, P.J. Walian, M.W. Fields, J.D. Wall (2018) Unintended laboratory-driven evolution reveals genetic requirements for biofilm formation by Desulfovibrio vulgaris Hildenborough. mBio. 8(5) [doi]:e01696-17.
  2. Flowers, J.; M. Richards, B. Meyer, N.S. Baliga, D.A. Stahl (2018) Constraint-Based Modeling Captures the Metabolic Versatility of Desulfovibrio vulgaris. Environmental Microbiology and Environmental Microbiology Reports. [doi]:10.1111/1758-2229.12619
  3. Franco, L; S. Steinbeisser, G. Zane, J.D. Wall, and M.W. Fields (2018) Cr(VI) reduction and physiological toxicity are impacted by resource ratio in Desulfovibrio vulgaris. Applied Microbiology and Biotechnology. [doi]:10.1007/s00253-017-8724-4
  4. Garber, M.E.; L. Rajeev, A.E. Kazakov, J. Trinh, D. Masuno, M.G. Thompson,N. Kaplan, J. Luk, P.S. Novichkov and A. Mukhopadhyay (2018) Multiple signaling systems target a core set of transition metal homeostasis genes using similar binding motifs. Molecular Microbiol.[doi]:10.1111/mmi.13909.
  5. He Z, Zhang P, Wu L, Rocha AM, Tu Q, Shi Z, Wu B, Qin Y, Wang J, Yan Q, Curtis D, Ning D, van Nostrand JD, Wu L, Yang Y, Elias DA, Watson DB, Adams MWW, Fields MW, Alm EJ, Hazen TC, Adams PD, Arkin AP, Zhou J (2018) Groundwater microbial functional diversity predicts environmental contamination and ecosystem functioning. mBio 9 [doi]:10.1128/mBio.02435-17
  6. Jenkins, S.; T.L. Swenson, R. Lau, A.M. Rocha, A. Aaring, T.C. Hazen, R. Chakraborty, T.R. Northen (2018) Construction of soil defined media using quantitative metabolomics analysis of soil metabolites. Frontiers in Microbiology. [doi]: 10.3389/fmicb.2017.02618
  7. Liu, H.; A.M. Deutschbauer (2018) Rapidly moving new bacteria to model-organism status. Current Opinion in Biotechnology. [doi]1016/j.copbio.2017.12.006
  8. Liu,H. ; Price, R.J. Waters, J. Ray, H.K. Carlson, J.S. Lamson, R. Chakraborty, A.P. Arkin, A.M. Deutschbauer (2018) Magic pools: parallel assessment of transposon delivery vectors in bacteria. Msystems.
  9. Paradis, C.J.; .R. Dixon, L.M. Lui, A.P. Arkin, J.C. Parker, J.D. Istok, E. Perfect, L.D. McKay, T.C. Hazen (2018) Improved method for estimating reaction rates during push-pull tests. Ground Water. [doi]:10.1111/gwat.12770
  10. Price, M Grant M Zane, Jennifer V Kuehl, Ryan A Melnyk, Judy D Wall, Adam M Deutschbauer, Adam P Arkin (2018) Filling Gaps in Bacterial Amino Acid Biosynthesis Pathways with High-throughput Genetics. PLoS Genetics 14(1) [doi]:10.1371/journal.pgen.1007147.
  11. Price, M.N.; K.M. Wetmore, R.J. Waters, M. Callaghan, J. Ray, H. Liu, J.V. Kuehl, R.A. Melnyk, J.S. Lamson, Y. Suh, H.K. Carlson, Z. Esquivel, H. Sadeeshkumar, R. Chakraborty, G.M. Zane, B.E. Rubin, J.D. Wall, A. Visel, J. Bristow, M.J. Blow, A.P. Arkin, A.M. Deutschbauer (2018) Mutant Phenotypes for Thousands of Bacterial Genes of Unknown Function. Nature. doi:10.1038/s41586-018-0124-0
  12. Zeng, L.; E. Wooton, D.A. Stahl, P.J. Walian (2018) Identification and Characterization of the Major Porin of Desulfovibrio vulgaris Hildenborough. Journal of Bacteriology. [doi]:10.1128/JB.00286-17
  13. Zhou, A.; R. Lau, R. Baran, J. Ma, F. von Netzer, W. Shi, D. Gorman-Lewis, M. L. Kempher, Z. He, Y. Qin, Z. Shi, G. M. Zane, L. Wu, B. P. Bowen, T. R. Northen, K. L. Hillesland, D. A. Stahl, J. D. Wall, A. P. Arkin, and J. Zhou (2018) Key metabolites and mechanistic changes for salt tolerance in an experimentally evolved sulfate-reducing bacterium, Desulfovibrio vulgaris. mBio. [doi]: 10.1128/mBio.01780-17

Submitted/In Review Manuscripts

  1. Carlson, H. K.; M. N. Price, M. Callaghan, A. Aaring, R. Chakraborty, H. Liu, A.P. Arkin, A. M. Deutschbauer (2018) Defining the toxicity limits on a microorganism’s range in a metal-contaminated aquifer. Revision
  2. Christensen, GA; JW Moon, AM. Veach, JJ. Mosher, AM. Wymore, JD. van Nostrand, J. Zhou, T. C. Hazen, AP Arkin, DA. Elias (2018) Use of in-field bioreactors demonstrate groundwater filtration influences planktonic bacterial community assembly, but not biofilm composition. Public Library of Science ONE. Accepted
  3. Erbilgin O; O. Rübel, KB. Louie, M. Trinh, M. DeRaad, T. Wildish, D. Udwary, C. Hoover, S. Deutsch, T. Northen*, B.P. Bowen (2018) MAGI: Metabolite, annotation, and gene integration to efficiently link metabolomics data to (meta)genome sequencing. Revision
  4. Franco, S. Steinbeisser, and M.W. Fields (2018) Chromium reduction under nutrient limiting conditions by the sulfate reducing bacterium Desulfovibrio vulgaris. Applied and Environmental Microbiology. Accepted
  5. Kempher, M.L; A.S. Burns, P.S. Novichkov, K.S. Bender. (2018) Characterization Of A Dual Functioning Small RNA/Riboswitch In Desulfovibrio Vulgaris Hildenborough. Nucleic Acids Research. Submitted
  6. Kosina, S.M.; A. Greiner (NERSC), R.K. Lau, S. Jenkins, R. Baran,, Bowen, P.; T,R. Northen (2018) Web of Microbes: an online exometabolomics database and visualization tool for microbial metabolic interactions. BioMed Central: Microbiology. Submitted
  7. Paraids, C.J.; J. Moon, D. A. Elias, L. D. McKay, T. C. Hazen (2018) In situ decay of polyfluorinated benzoic acids under anaerobic conditions. Journal of Contaminant Hydrology. In review
  8. Vaccaro, B.J.; W.A. Lancaster, and M.W.W. Adams (2018) Molybdenum and Mineral Depletion in Aluminum and Iron Contaminated Environments: Effects on Eutrophication and the Nitrogen Cycle. International Society for Microbial Ecology. Submitted
  9. Vaccaro, B.J.; W.A. Lancaster, M.P. Thorgersen, G. Zane, K.M. Wetmore, A.E. Kazakov, F.L. Poole II, P.S. Novichkov, A.M. Deutschbauer, A.P. Arkin, J.D. Wall, and M.W.W. Adams (2018) Novel Metal Cation Resistance Systems from Mutant Fitness Analysis of Pseudomonas stutzeri strain RCH2. Applied and Environmental Microbiology. Submitted
  10. Wu,X.; L. Wu, Y. Liu, P. Zhang, Q. Li, J. Zhou, N.J. Hess, T.C. Hazen, W. Yang, R. Chakraborty (2018) Microbial succession and activity associated with carbon dynamics of natural organic matter in groundwater. Frontiers in Microbiology. Accepted
  11. Zelaya A; A. Parker, K. L. Bailey , P. Zhang, J. Van Nostrand, D.A. Elias, J. Zhou, M.W. Fields (2018) High temporal variability in bacterial populations and association networks of an undisturbed, pristine aquifer. ISME Journal. Submitted

Books/Book Chapters


Legacy and Synergistic External Research