Berkeley Lab

2017 Publications

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  1. Chakraborty, R; H. Woo, P. Dehal, R. Walker, M. Zemla, M. Auer, L.A. Goodwin, A. Kazakov, P. Novichkov, A.P. Arkin, and T.C. Hazen. (2017). Complete genome sequence of Pseudomonas stutzeri strain RCH2 isolated from a Hexavalent Chromium [Cr(VI)] contaminated site. Standards in Genomic Sciences, 12, 23. [doi]:1186/s40793-017-0233-7 {PMID}:28194258
  2. de Raad, M; T. de Rond, O. Rübel, J.D. Keasling, T.R. Northen, B.P. Bowen. (2017) OpenMSI Arrayed Analysis Toolkit: Analyzing spatially defined samples using mass spectrometry imaging. Analytical Chemistry. [doi]:1021/acs.analchem.6b05004
  3. Erbilgin, O.; B.P. Bowen, S. Jenkins, S.M. Kosina, R.K. Lau, T.R. Northen (2017) Dynamic substrate preferences and predicted metabolic properties of a simple microbial consortium. BMC Bioinformatics. [doi]:1186/s12859-017-1478-2 {PMID}:28114881
  4. Huan, T., E.M. Forsberg, D. Rinehart, C.H. Johnson, J. Ivanisevic, H.P. Benton, M. Fang, A. Aisporna, B. Hilmers, F.L. Poole, M.P. Thorgersen, M.W.W. Adams, G. Krantz, M.W. Fields, P.D. Robbins, L.J. Niedernhofer, T. Ideker, E.L. Majumder, J.D. Wall, N.J.W. Rattray, R. Goodacre, L.L. Lairson, and G. Siuzdak. (2017) Systems biology guided by XCMS Online metabolomics. Nat Meth. 14(5): p. 461-462. [doi]:1038/nmeth.4260
  5. Jenkins, S., T.L. Swenson, R. Lau, A. Rocha, A. Aaring, T.C. Hazen, R. Chakraborty, and T.R. Northen. (2017) Construction of soil defined media using quantitative exometabolomic analysis of soil metabolites. bioRxiv. [doi]: 1101/151282.
  6. King, A.J; S.P. Preheim, K.L. Bailey, M.S. Robeson II, T. Roy Chowdhury, B.R. Crable, R.A. Hurt Jr., T. Mehlhorn, K.A. Lowe, T.J. Phelps, A.V. Palumbo, C.C. Brandt, S.D. Brown, M. Podar, P. Zhang, W.A. Lancaster, F. Poole, D.B. Watson, M.W. Fields, J.M. Chandonia, E.J. Alm, J. Zhou, M.W.W. Adams, T.C. Hazen, A.P. Arkin, and D.A. Elias. (2017)  Temporal Dynamics of In-Field Bioreactor Populations Reflect the Groundwater System and Respond Predictably to Perturbation.  Environmental Science & Technology. 51 (5), pp 2879–2889 [doi]:1021/acs.est.6b04751 {PMID}:28112946
  7. Kothari, A. Y-W. Wu, M. Charrier, L. Rajeev, A.M. Rocha, T.C. Hazen, S.W. Singer, and A. Mukhopadhyay.(2017)  Plasmid DNA analysis of pristine groundwater microbial communities reveal extensive presence of metal resistance genes.  BioRxiv.
  8. Majumder, E.L-W; J.D. Wall. (2017). Uranium Bio-transformations: Chemical or Biological Processes? Open Journal of Inorganic Chemistry: Actinide Special Issue. [doi]:4236/ojic.2017.72003
  9. Price M. N.; and A. P. Arkin (2017) PaperBLAST: Text-mining papers for information about homologs. bioRxiv. [doi]:1101/133041
  10. Sagawa S, Price MN, Deutschbauer AM, Arkin AP (2017) Validating regulatory predictions from diverse bacteria with mutant fitness data. PLoS ONE 12(5): e0178258. [doi]:1371/journal.pone.0178258
  11. Thompson, A.W., S. Turkarslan, C.E. Arens, A. López García de Lomana, A.V. Raman, D.A. Stahl, and N.S. Baliga. (2017) Robustness of a model microbial community emerges from population structure among single cells of a clonal population. Environmental Microbiology. [doi]:1111/1462-2920.13764. {PMID}:28419704
  12. Thorgersen, M. P., Lancaster, W. A., Rajeev, L., Ge, X., Vaccaro, B. J., Poole, F. P., Arkin, A. P., Mukhopadhyay, A. and Adams, M. W. W. (2017) “A highly expressed high molecular weight S-layer complex of Pelosinus strain UFO1 binds uranium” Applied and Environmental Microbiology 83(4). pii: e03044-16.[doi]:1128/AEM.03044-16. {PMID}:27913415
  13. Turkarslan, S., A.V. Raman, A.W. Thompson, C.E. Arens, M.A. Gillespie, F. von Netzer, K.L. Hillesland, S. Stolyar, A. López García de Lomana, D.J. Reiss, D. Gorman-Lewis, G.M. Zane, J.A. Ranish, J.D. Wall, D.A. Stahl, and N.S. Baliga. (2017) Mechanism for microbial population collapse in a fluctuating resource environment. Molecular Systems Biology. 13(3): p. 919[doi]:15252/msb.20167058. {PMID}:28320772
  14. Warth B.; N. Levin, D. Rinehart, H.P. Benton, J. Teijaro, and G. Siuzdak (2017) Metabolizing Data in the Cloud. Trends in Biotechnology. [doi]:1016/j.tibtech.2016.12.010 {PMID}:28117091
  15. Wu, X; A.M. Deutschbauer, A.E. Kazakov, K.M. Wetmore, B.A. Cwick, R.M. Walker, P.S. Novichkov, A.P. Arkin, R. Chakraborty. (2017) Draft Genome Sequences of Two Janthinobacterium strains, Isolated from Pristine Groundwater Collected from Oak Ridge Field Research Center. Genome Announcements. 5:e00582-17; [doi]:1128/genomeA.00582-17
  16. Zhang, P.; Z. He, J.D. Van Nostrand, Y. Qin, Y. Deng, L. Wu, Q. Tu, J. Wang, C.W. Schadt, M.W. Fields, T.C. Hazen, A.P. Arkin, D.A. Stahl, and J. Zhou. (2017) Dynamic succession of groundwater sulfate-reducing communities during prolonged reduction of uranium in a contaminated aquifer. Environmental Science and Technology. [doi]:1021/acs.est.6b02980 {PMID}:28300407

Submitted/In Review Manuscripts

  1. Franco, S. Steinbeisser, and M.W. Fields (2017) Chromium reduction under nutrient limiting conditions by the sulfate reducing bacterium Desulfovibrio vulgaris. Applied and Environmental Microbiology. Submitted
  2. He Z, Zhang P, Rocha AM, Wu L, Tu Q, Qin Y, Curtis D, Van Nostrand JD, Wu L, Alm EJ, Fields MW, Elias DA, Stahl DA, Hazen TC, Arkin AP, Adams PD, and Zhou J (2017) Groundwater microbial functional diversity predicts environmental contamination and ecosystem functioning. ISME Journal. Accepted
  3. Kempher, M.L; A.S. Burns, P.S. Novichkov, K.S. Bender. (2017) Characterization Of A Dual Functioning Small RNA/Riboswitch In Desulfovibrio Vulgaris Hildenborough. Nucleic Acids Research. Submitted
  4. Lancaster, W.A.; M.P. Thorgersen, B.J. Vaccaro, A.E. Kazakov, M.N. Price, K.M. Wetmore, A.M. Deutschbauer, P.S. Novichkov, A.P. Arkin and M.W.W. Adams (2017) Responses of Pseudomonas stutzeri RCH2 to Toxic Concentrations of Chromium and Uranium. Environmental Microbiology. Submitted
  5. Paradis, C. J., L. D. McKay, E. Perfect, J. D. Istok, and T. C. Hazen. (2017) Push-pull tests for estimating effective porosity: expanded analytical solution and in situ application. Hydrogeology Journal. Accepted
  6. Thorgersen, M.P; W.A. Lancaster, X. Ge, G. Zane, K.M. Wetmore, B.J. Vaccaro, F.L. Poole, A.M. Deutschbauer, A.P. Arkin, J.D. Wall and M.W.W. Adams (2017) “Mechanisms of Uranium and Chromium Toxicity in Pseudomonas stutzeri RCH2 Grown Under Anaerobic Nitrate-Reducing Conditions” Environmental Microbiology. Submitted
  7. Vaccaro, B.J.; W.A. Lancaster, and M.W.W. Adams (2017) Molybdenum and Mineral Depletion in Aluminum and Iron Contaminated Environments: Effects on Eutrophication and the Nitrogen Cycle. International Society for Microbial Ecology. Submitted
  8. Zelaya A; A. Parker, K. L. Bailey , P. Zhang, J. Van Nostrand, D.A. Elias, J. Zhou, M.W. Fields (2017) High temporal variability in bacterial populations and association networks of an undisturbed, pristine aquifer. ISME J. Submitted
  9. Zeng, L; E. Wooton, D.A. Stahl, P.J. Walian. (2017) Identification and Characterization of the Major Porin of Desulfovibrio vulgaris Hildenborough. Journal of Bacteriology. Submitted
  10. Zhou A., Lau R., Baran R. B., Ma J., Shi W., He Z., Tu Q., Qin Y., Shi Z., Kempher M. L., Zane G. M. Z., Wu L., Bowen B., Northen T., Hillesland K. L., von Netzer F., Gorman-Lewis D., Stahl D. A., Wall J. D., Arkin A. P., Zhou J. Working title: Mostly restored basal changes and altered adaptation-derived salt stress response and genomic changes in experimentally evolved Desulfovibrio vulgaris Hildenborough. In revision
  11. Zhou J., Ning D. Stochastic Community Assembly: Does It Matter in Microbial Ecology? Microbiology and Molecular Biology Reviews, 2017. In revision.

Books/Book Chapters


Legacy and Synergistic External Research