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2018 Publications

(Paper highlighted as: Impact factor >8.0, ** of outstanding interest, partial funding)

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  1. Carlson, H.K.; M.N. Price, M. Callaghan, A. Aaring, R. Chakraborty, H. Liu, A.P. Arkin and A.M. Deutschbauer (2018) The selective pressures on the microbial community in a metal-contaminated aquifer. International Society for Microbial Ecology Journal. [doi]:10.1038/s41396-018-0328-1 {PMID}:30523276 PMCID:PMC6461962
  2. Christensen, G.A.; J.W. Moon, A.M. Veach, J.J. Mosher, A.M. Wymore, J.D. van Nostrand, J. Zhou, T.C. Hazen, A.P. Arkin and D.A. Elias (2018) Use of in-field bioreactors demonstrate groundwater filtration influences planktonic bacterial community assembly, but not biofilm composition. Public Library of Science ONE. [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 and J.D. Wall (2018) Unintended laboratory-driven evolution reveals genetic requirements for biofilm formation by Desulfovibrio vulgaris Hildenborough. mBio. [doi]:10.1128/mBio.01696-17 {PMID}:29042504 PMCID:PMC5646257
  4. Duncombe, T.A.; M. De Raad, B.P. Bowen, A.K. Singh and T.R. Northen (2018) Insulator Nanostructure Desorption Ionization Mass Spectrometry. Analytical Chemistry. [doi]:10.1021/acs.analchem.8b01989 {PMID}:30063326
  5. Flowers, J.; M. Richards, B. Meyer, N.S. Baliga and 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 {PMID}:29377633
  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 {PMID}:29429007 PMCID:PMC5847207
  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 {PMID}:29341298
  8. Ge, X.; B.J. Vaccaro, M.P. Thorgersen, F.L. Poole, E.L. Majumder, G.M. Zane, K.B. De Leon, A.L. Lancaster, J. Moon, K.A. Lowe, C.J. Paradis, D.C. Joyner, F. von Netzer, D.A. Stahl, P.D. Adams, A.P. Arkin, J.D. Wall, T.C. Hazen and M.W.W. Adams (2018) Iron- and Aluminum-Induced Depletion of Molybdenum in Acidic Environments Impedes the Nitrogen Cycle. Environmental Microbiology. [doi]:10.1111/1462-2920.14435 {PMID}:30289197
  9. He, Z.; P. Zhang, L. Wu, A.M. Rocha, Q. Tu, Z. Shi, B. Wu, Y. Qin, J. Wang, Q. Yan, D. Curtis, D. Ning, J.D. Van Nostrand, L. Wu, Y. Yang, D.A. Elias, D.B. Watson, M.W.W. Adams, M.W. Fields, E.J. Alm, T.C. Hazen, P.D. Adams, A.P. Arkin and J. Zhou (2018) Microbial Functional Gene Diversity Predicts Groundwater Contamination and Ecosystem Functioning. mBio. [doi]:10.1128/mBio.02435-17 {PMID}:29463661 PMCID:PMC5821090
  10. Justice, N.B.; A. Sczesnak, T.C. Hazen and A.P. Arkin (2018) Environmental Selection, Dispersal, and Organism Interactions Shape Community Assembly in High-Throughput Enrichment Culturing. Applied and Environmental Microbiology. [doi]:10.1128/AEM.01253-17 {PMID}:28778896 PMCID:PMC5626985
  11. Kosina, S.M.; A.M. Greiner(NERSC), R.K. Lau, S. Jenkins, R. Baran, B.P. Bowen and T.R. Northen (2018) Web of Microbes (WoM): a curated microbial exometabolomics database for linking chemistry and microbes. BioMed Central Microbiology. [doi]:10.1186/s12866-018-1256-y
  12. Liu, H.; and A.M. Deutschbauer (2018) Rapidly moving new bacteria to model-organism status. Current Opinion in Biotechnology. [doi]:10.1016/j.copbio.2017.12.006 {PMID}:29316481
  13. Liu, H.; M.N. Price, R.J. Waters, J. Ray, H.K. Carlson, J.S. Lamson, R. Chakraborty, A.P. Arkin and A.M. Deutschbauer (2018) Magic pools: parallel assessment of transposon delivery vectors in bacteria. mSystems. [doi]:10.1128/mSystems.00143-17 {PMID}:29359196 PMCID:PMC5768790
  14. Otwell, A.E.; A.L. García de Lomana, S.M. Gibbons, M.V. Orellana and N.S. Baliga (2018) Systems biology approaches towards predictive microbial ecology. Environmental Microbiology. [doi]:10.1111/1462-2920.14378 {PMID}:30106224
  15. Paradis, C.J.; R. Dixon, L.M. Lui, A.P. Arkin, J.C. Parker, J.D. Istok, E. Perfect, L.D. McKay and T.C. Hazen (2018) Improved method for estimating reaction rates during push-pull tests. Ground Water. [doi]:10.1111/gwat.12770 {PMID}:29656383
  16. Paradis, C.J.; J. Moon, D.A. Elias, L.D. McKay and 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 {PMID}:30201555
  17. Price, M.N.; G.M. Zane, J.V. Kuehl, R.A. Melnyk, J.D. Wall, A.M. Deutschbauer and A.P. Arkin (2018) Filling Gaps in Bacterial Amino Acid Biosynthesis Pathways with High-throughput Genetics. Public Library of Science Genetics. [doi]:10.1371/journal.pgen.1008106 {PMID}:30943208 PMCID:PMC6447180
  18. 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 and A.M. Deutschbauer (2018) Mutant Phenotypes for Thousands of Bacterial Genes of Unknown Function. Nature. [doi]:10.1038/s41586-018-0124-0 {PMID}:29769716
  19. Rajeev, L.; M.E. Garber, G.M. Zane, M.N. Price, I. Dubchak, J.D. Wall, P.S. Novichkov, A. Mukhopadhyay and A.E. Kazakov (2018) A new family of transcriptional regulators of tungstoenzymes and molybdate/tungstate transport. Environmental Microbiology. [doi]:10.1111/1462-2920.14500 {PMID}:30536693
  20. Smith H.J.; A.J. Zelaya, K.B. De León, R. Chakraborty, D.A. Elias, T.C. Hazen, A.P. Arkin, A.B. Cunningham and M.W. Fields (2018) Impact of hydrologic boundaries on microbial planktonic and biofilm communities in shallow terrestrial subsurface environments. Federation of European Microbial Societies Microbiology Ecology. [doi]:10.1093/femsec/fiy191 {PMID}:30265315 PMCID:PMC6192502
  21. Wu,X.; L. Wu, Y. Liu, P. Zhang, Q. Li, J. Zhou, N.J. Hess, T.C. Hazen, W. Yang and R. Chakraborty (2018) Microbial interactions with dissolved organic matter drive carbon dynamics and community succession. Frontiers in Microbiology. [doi]:10.3389/fmicb.2018.01234 {PMID}:29937762 PMCID:PMC6002664
  22. Zeng, L.; E. Wooton, D.A. Stahl and P.J. Walian (2018) Identification and Characterization of the Major Porin of Desulfovibrio vulgaris Hildenborough. Journal of Bacteriology. [doi]:10.1128/JB.00286-17 {PMID}:28874410 PMCID:PMC5686591
  23. 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 {PMID}:29138306 PMCID:PMC5686539

  24. Books/Book Chapters

  25. De Raad, M.; T.R. Northen and B.P. Bowen (2018) Analysis and interpretation of mass spectrometry imaging datasets. Book chapter in CAC Vol 82: Data Analysis for Omic Sciences: Methods and Applications. Editors: J. Jaumot, C. Bedia and R. Tauler. [doi]:10.1016/bs.coac.2018.06.006
  26. Hazen, T.C. (2018) Chapter: Cometabolic Bioremediation. Consequences of Microbial Interactions with Hydrocarbons, Oils, and Lipids: Biodegradation and Bioremediation, Handbook of Hydrocarbon and Lipid Microbiology. Editor: R. Steffan. [doi]:10.1007/978-3-319-44535-9_5-1
  27. Hazen, T.C. (2018) Chapter: In Situ: Groundwater Bioremediation. Consequences of Microbial Interactions with Hydrocarbons, Oils, and Lipids: Biodegradation and Bioremediation, Handbook of Hydrocarbon and Lipid Microbiology. Editor: R. Steffan. [doi]:10.1007/978-3-319-44535-9_11-1