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]:10.1186/s40793-017-0233-7 {PMID}:28194258
  2. 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
  3. 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]:10.1038/nmeth.4260
  4. King, A., S. Preheim, K. Bailey, M. Robeson, T. Roy Chowdhury, B. R. Crable, R. Hurt, T. Mehlhorn, K. Lowe, T. Phelps, A. Palumbo, C. Brandt, S. Brown, M. Podar, P. Zhang, W. Lancaster, F. Poole, D. Watson, M. Fields, J.-M. Chandonia, E. Alm, J. Zhou, M. Adams, T. C. Hazen, A. Arkin, and D. 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
  5. 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.
  6. 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
  7. Price M. N.; and A. P. Arkin (2017) PaperBLAST: Text-mining papers for information about homologs. bioRxiv. [doi]:1101/133041
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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. 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. Accepted
  2. Franco, L; 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
  3. 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. Submitted
  4. 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
  5. 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
  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” Environ. Microbiol. 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. 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. Submitted
  9. 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
  10. 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
  11. 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
  12. 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