Berkeley Lab

2018 Publications

Jump to: Books/Book Chapters

  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. International Society for Microbial Ecology Journal. [doi]:10.1038/s41396-018-0328-1
  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. PLoS One. 13(3):e0194663 [doi]:10.1371/journal.pone.0194663 {PMID}:29558522; PMCID: PMC5860781
  3. 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)e01696-[doi]:10.1128/mBio.01696-17 {PMID}:29042504; PMCID: PMC5646257
  4. Duncombe TA, De Raad M, Bowen BP, Singh AK, Northen TR (2018) Insulator Nanostructure Desorption Ionization Mass Spectrometry. Analytical Chemistry. [doi]:10.1021/acs.analchem.8b01989
  5. 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
  6. 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
  7. 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 Microbiology. [doi]:10.1111/mmi.13909
  8. Ge, X., Vaccaro, B.J., Thorgersen, M.P., Poole, F.L., Majumder E.L., Zane, G.M., De Leon K., Lancaster A.L., Moon J., Lowe, K.A., Paradis C.J., Joyner D.C., von Netzer F., Stahl D.A., Adams P.D., Arkin A.P., Wall J.D., Hazen T.C., Adams M.W. (2018) Iron- and Aluminum-Induced Depletion of Molybdenum in Acidic Environments Impedes the Nitrogen Cycle. Environmental Microbiology. [doi]:10.1111/1462-2920.14435
  9. 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 pii: e02435-17. {PMID}:29463661
  10. 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
  11. Justice NB, Sczesnak A, Hazen TC, Arkin AP. Environmental Selection, Dispersal, and Organism Interactions Shape Community Assembly in High-Throughput Enrichment Culturing. (2018) Appl Environ Microbiol. 83(20). pii: e01253-17. [doi]: 10.1128/AEM.01253-17. {PMID}: 28778896; PMCID: PMC5626985.
  12. Kosina, S.M.; A. Greiner (NERSC), R.K. Lau, S. Jenkins, R. Baran,, Bowen, B.P.; T,R. Northen (2018) Web of Microbes: an online exometabolomics database and visualization tool for microbial metabolic interactions. BioMed Central: Microbiology. 18:115 [doi]:10.1186/s12866-018-1256-y
  13. Liu, H.; A.M. Deutschbauer (2018) Rapidly moving new bacteria to model-organism status. Current Opinion in Biotechnology. [doi]10.1016/j.copbio.2017.12.006
  14. Liu,H. ; M. 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. [doi]: 10.1128/mSystems.00143-17
  15. Otwell A.E.; A.L. García de Lomana, S.M. Gibbons, M.V. Orellana, Nitin S. Baliga (2018) Systems biology approaches towards predictive microbial ecology. Environmental Microbiology. [ doi]: 10.1111/1462-2920.14378
  16. 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
  17. Paradis, 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. [doi]: 10.1016/j.jconhyd.2018.08.009
  18. 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)
  19. 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. 557(7706):503-509. [doi]: 10.1038/s41586-018-0124-0
  20. Rajeev, L.; M.E. Garber, G. M. Zane, M.N. Price, I. Dubchak, J.D. Wall, P.S. Novichkov, A. Mukhopadhyay, A.E. Kazakov (2018) A new family of transcriptional regulators of tungstoenzymes and molybdate/tungstate transport. Environmental Microbiology. [doi]:10.1111/1462-2920.14500
  21. Smith H.J.; A.J. Zelaya, K.B. De León, R. Chakraborty, D.A. Elias, T.C. Hazen, A.P. Arkin, A.B. Cunningham, M.W. Fields (2018) Impact of hydrologic boundaries on microbial planktonic and biofilm communities in shallow terrestrial subsurface environments. FEMS Microbiology Ecology.  [doi]:10.1093/femsec/fiy191
  22. Wu,X.; L. Wu, Y. Liu, P. Zhang, Q. Li, J. Zhou, N.J. Hess, T.C. Hazen, W. Yang, R. Chakraborty (2018) Microbial interactions with dissolved organic matter drive carbon dynamics and community succession. Frontiers in Microbiology [doi]:10.3389/fmicb.2018.01234
  23. 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
  24. 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

  25. Books/Book Chapters

  26. De Raad M, Northen TR, Bowen BP (2018) Analysis and interpretation of mass spectrometry imaging datasets. Book chapter in CAC Vol 82: Data Analysis for Omic Sciences: Methods and Applications [doi]:10.1016/bs.coac.2018.06.006
  27. Hazen, T.C. (2018) Cometabolic Bioremediation. Consequences of Microbial Interactions with Hydrocarbons, Oils, and Lipids: Biodegradation and Bioremediation, Handbook of Hydrocarbon and Lipid Microbiology. Springer International Publishing AG, part of Springer Nature 2018. R. Steffan (ed.) [doi]: 10.1007/978-3-319-44535-9_5-1
  28. Hazen, T.C. (2018) In Situ: Groundwater Bioremediation. Consequences of Microbial Interactions with Hydrocarbons, Oils, and Lipids: Biodegradation and Bioremediation, Handbook of Hydrocarbon and Lipid Microbiology. Springer International Publishing AG, part of Springer Nature. R. Steffan (ed) .) [doi]: 10.1007/978-3-319-44535-9_5-1