Berkeley Lab

2015 Publications

Jump to: Books/Book Chapters | Legacy and Synergistic External Research

  1. Baran, R.; E.L. Brodie, J. Mayberry-Lewis, E. Hummel, U.N. Da Rocha, R. Chakraborty, B.P. Bowen, U. Karaoz, H. Cadillo-Quiroz, F. Garcia-Pichel, and T.R. Northen. (2015) Exometabolite niche partitioning among sympatric soil bacteria. Nature Communications. 6: p. [doi]: 10.1038/ncomms9289. {PMID}:26392107
  2. Barnhart, E.P.; M.A. McClure, K. Johnson, S. Cleveland, K.A. Hunt, and M.W. Fields. (2015) Potential Role of Acetyl-CoA Synthetase (acs) and Malate Dehydrogenase (mae) in the Evolution of the Acetate Switch in Bacteria and Archaea. Sci Rep. 5: p. 12498 [doi]:10.1038/srep12498. {PMID}:26235787
  3. Brewer, B.; S. M. Techtmann, N. Mahmoudi, D. Niang, S. Pfiffner, and T. C. Hazen. 2016. Co-extraction of DNA and PLFA from Soil Samples.  J. Microbiol. Methods 115:64-66. [doi]: 10.1016/j.mimet.2015.05.018
  4. Carlson, H.K.; J.V. Kuehl, A.B. Hazra, N.B. Justice, M.K. Stoeva, A. Sczesnak, M.R. Mullan, A.T. Iavarone, A. Engelbrektson, M.N. Price, A.M. Deutschbauer, A.P. Arkin, and J.D. Coates. (2015) Mechanisms of direct inhibition of the respiratory sulfate-reduction pathway by (per)chlorate and nitrate. ISME Journal. 9(6): p. 1295-305 [doi]: 10.1038/ismej.2014.216. {PMID}:25405978
  5. Christensen, G.A.; G.M. Zane, A.E. Kazakov, X. Li, D.A. Rodionov, P.S. Novichkov, I. Dubchak, A.P. Arkin, and J.D. Wall. (2015) Rex (encoded by DVU_0916) in Desulfovibrio
    vulgaris Hildenborough is a repressor of sulfate adenylyl transferase and is regulated by NADH. Journal of Bacteriology. 197(1): p. 29-39. [doi]: 10.1128/JB.02083-14.{PMID}:25313388
  6. De León, K.B.; S.M. Utturkar, L.B. Camilleri, D.A. Elias, A.P. Arkin, M.W. Fields, S.D. Brown, and J.D. Wall. (2015) Complete Genome Sequence of Pelosinus fermentans JBW45, a Member of a Remarkably Competitive Group of Negativicutes in the Firmicutes Phylum. Genome Announcements. 3(5) [doi]: 10.1128/genomeA.01090-15. {PMID}:26404608
  7. Deng, Y.; P. Zhang, Y. Qin, Q. Tu, Y. Yang, Z. He, C.W. Schadt, and J. Zhou. (2015) Network succession reveals the importance of competition in response to emulsified vegetable oil amendment for uranium bioremediation. Environmental Microbiology. [doi]: 10.1111/1462-2920.12981. {PMID}:26177312
  8. Hemme, C.L.; Q. Tu, Z. Shi, Y. Qin, W. Gao, Y. Deng, J. Van Nostrand, L. Wu, Z. He, P. S. G. Chain, S. G. Tringe, M. W. Fields, E. Rubin, J. M. Tiedje, T. C. Hazen, A.P. Arkin, and J.-Z. Zhou. (2015) Comparative metagenomics reveals impact of contaminants on groundwater microbiomes. Front. Microbiol.; 6:1205, [doi]: 10.3389/fmicb.2015.01205. {PMID}:26583008
  9. Hwang, C.; A. Copeland, S. Lucas, A. Lapidus, K. Barry, T. Glavina Del Rio, E. Dalin, H. Tice, S. Pitluck, D. Sims, T. Brettin, D.C. Bruce, J.C. Detter, C.S. Han, J. Schmutz, F.W. Larimer, M.L. Land, L.J. Hauser, N. Kyrpides, A. Lykidis, P. Richardson, A. Belieav, R.A. Sanford, F.E. Loeffler, and M.W. Fields. (2015) Complete Genome Sequence of Anaeromyxobacter sp. Fw109-5, an Anaerobic, Metal-Reducing Bacterium Isolated from a Contaminated Subsurface Environment. Genome Announcements. 3(1) [doi]: 10.1128/genomeA.01449-14. {PMID}:25614562
  10. Kazakov A.E.; L. Rajeev, A. Chenn, E.G. Luning, I. Dubchak, A. Mukhopadhyay and P.S. Novichkov. (2015) σ54-dependent Regulome in Desulfovibrio vulgaris Hildenborough. BMC Genomics. BMC Genomics 2015 V16:919. [doi]: 10.1186/s12864-015-2176-y {PMID}:26555820
  11. Korte, H.L.; A. Saini, V.V. Trotter, G.P. Butland, A.P. Arkin, and J.D. Wall. (2015) Independence of Nitrate and Nitrite Inhibition of Desulfovibrio vulgaris Hildenborough and Use of Nitrite as a Substrate for Growth. Environmental Science & Technology. 49(2): p. 924-931. [doi]: 10.1021/es504484m. {PMID}:25534748
  12. Kurczy, M.; T. Northen, S. Trauger, and G. Siuzdak (2015) Nanostructure Imaging Mass Spectrometry: The Role of Fluorocarbons in Metabolite Analysis and Yoctomole Level Sensitivity. Methods Mol Biol. 2015;1203:141-9. [doi]: 10.1007/978-1-4939-1357-2_14.
  13. Melnyk, R.A.; M.D. Youngblut, I.C. Clark, H.K. Carlson, K.M. Wetmore, M.N. Price, A.T. Iavarone, A.M. Deutschbauer, A.P. Arkin, and J.D. Coates. (2015) Novel Mechanism for Scavenging of Hypochlorite Involving a Periplasmic Methionine-Rich Peptide and Methionine Sulfoxide Reductase. MBio. 6(3): p. e00233-15. [doi]: 10.1128/mBio.00233-15. {PMID}:25968643
  14. Rajeev, L.; A. Chen, A.E. Kazakov, E.G. Luning, G.M. Zane, P.S. Novichkov, J.D. Wall, and A. Mukhopadhyay. (2015) Regulation of nitrite stress response in Desulfovibrio vulgaris Hildenborough, a model sulfate-reducing bacterium. Journal of Bacteriology [doi]: 10.1128/jb.00319-15. {PMID}:26283774
  15. Raman, A.V. and N.S. Baliga. (2015) The universe under a microscope. Environmental Microbiology Reports. 7(1): p. 11-12. [doi]: 10.1111/1758-2229.12225. {PMID}:25721591
  16. Ramos, A.R.; F. Grein, G.P. Oliveira, S.S. Venceslau, K.L. Keller, J.D. Wall, and I.A. Pereira. (2015) The FlxABCD-HdrABC proteins correspond to a novel NADH dehydrogenase/heterodisulfide reductase widespread in anaerobic bacteria and involved in ethanol metabolism in Desulfovibrio vulgaris Hildenborough. Environmental Microbiology. 17(7): p. 2288-305. [doi]: 10.1111/1462-2920.12689. {PMID}:25367508
  17. Ramsay, B.D.; C. Hwang, H.L. Woo, S.L. Carroll, S. Lucas, J. Han, A.L. Lapidus, J.-F. Cheng, L.A. Goodwin, S. Pitluck, L. Peters, O. Chertkov, B. Held, J.C. Detter, C.S. Han, R. Tapia, M.L. Land, L.J. Hauser, N.C. Kyrpides, N.N. Ivanova, N. Mikhailova, I. Pagani, T. Woyke, A.P. Arkin, P. Dehal, D. Chivian, C.S. Criddle, W. Wu, R. Chakraborty, T.C. Hazen, and M.W. Fields. (2015) High-Quality Draft Genome Sequence of Desulfovibrio carbinoliphilus FW-101-2B, an Organic Acid-Oxidizing Sulfate-Reducing Bacterium Isolated from Uranium(VI)-Contaminated Groundwater. Genome Announcements. 3(2) [doi]: 10.1128/genomeA.00092-15.{PMID}:25767232
  18. Ray, J.; R. J. Waters, J. M. Skerker, J. V. Kuehl, M. N. Price, J. Huang, R. Chakraborty, A. P. Arkin and A. Deutschbauer (2015). “Complete Genome Sequence of Cupriavidus basilensis 4G11, Isolated from the Oak Ridge Field Research Center Site.” Genome Announcements 3(3). [doi]: 10.1128/genomeA.00322-15 {PMID}:25977418
  19. Reiss, D.J.; C.L. Plaisier, W.-J. Wu, and N.S. Baliga. (2015) cMonkey2: Automated, systematic, integrated detection of co-regulated gene modules for any organism. Nucleic Acids Research. 43(13): p. e87. [doi]: 10.1093/nar/gkv300 {PMID}:25873626
  20. Sahraeian, S.M.; K.R. Luo, and S.E. Brenner. (2015) SIFTER search: a web server for accurate phylogeny-based protein function prediction. Nucleic Acids Research. 43(W1): p. W141-7. [doi]: 10.1093/nar/gkv461. {PMID}:25979264
  21. Smith, M.B.; A.M. Rocha, C.S. Smillie, S.W. Olesen, C. Paradis, L. Wu, J.H. Campbell, J.L. Fortney, T.L. Mehlhorn, K.A. Lowe, J.E. Earles, J. Phillips, S.M. Techtmann, D.C. Joyner, D.A. Elias, K.L. Bailey, R.A. Hurt, S.P. Preheim, M.C. Sanders, J. Yang, M.A. Mueller, S. Brooks, D.B. Watson, P. Zhang, Z. He, E.A. Dubinsky, P.D. Adams, A.P. Arkin, M.W. Fields, J. Zhou, E.J. Alm, and T.C. Hazen. (2015) Natural Bacterial Communities Serve as Quantitative Geochemical Biosensors. MBio. 6(3): p. e00326-15. [doi]: 10.1128/mBio.00326-15. {PMID}:25968645
  22. Swenson, T.L.; S. Jenkins, B.P. Bowen, and T.R. Northen. (2015) Untargeted soil metabolomics methods for analysis of extractable organic matter. Soil Biology & Biochemistry. 80: p. 189-198. [doi]: 10.1016/j.soilbio.2014.10.007. {WOS}:000346545800022
  23. Thompson, A.W.; M.J. Crow, B. Wadey, C. Arens, S. Turkarslan, S. Stolyar, N. Elliott, T.W. Petersen, G. van den Engh, D.A. Stahl, and N.S. Baliga. (2015) A method to analyze, sort, and retain viability of obligate anaerobic microorganisms from complex microbial communities. Journal of Microbiological Methods. 117: p. 74-7. [doi]: 10.1016/j.mimet.2015.07.009.{PMID}:26187776
  24. Thorgersen, M.P.; W.A. Lancaster, B.J. Vaccaro, F.L. Poole, A.M. Rocha, T. Mehlhorn, A. Pettenato, J. Ray, R.J. Waters, R.A. Melnyk, R. Chakraborty, T.C. Hazen, A.M. Deutschbauer, A.P. Arkin, and M.W. Adams. (2015) Molybdenum Availability is Key to Nitrate Removal in Contaminated Groundwater Environments. Applied and Environmental Microbiology. 81(15): p. 4976-83. [doi]: 10.1128/AEM.00917-15. {PMID}:25979890
  25. Wetmore, K.M.; M.N. Price, R.J. Waters, J.S. Lamson, J. He, C.A. Hoover, M.J. Blow, J. Bristow, G. Butland, A.P. Arkin, and A. Deutschbauer. (2015) Rapid Quantification of Mutant Fitness in Diverse Bacteria by Sequencing Randomly Bar-Coded Transposons. MBio. 6(3): p. e00306-15. [doi]: 10.1128/mBio.00306-15. {PMID}:25968644
  26. Yao, Y.; T. Sun, T. Wang, O. Ruebel, T. Northen, and B.P. Bowen. (2015) Analysis of Metabolomics Datasets with High-Performance Computing and Metabolite Atlases. Metabolites. 5(3): p. 431-42. [doi]: 10.3390/metabo5030431. {PMID}:26287255
  27. Zhang, P.; J.D. Van Nostrand, Z. He, R. Chakraborty, Y. Deng, D. Curtis, M.W. Fields, T.C. Hazen, A.P. Arkin, and J. Zhou. (2015) A Slow-Release Substrate Stimulates Groundwater Microbial Communities for Long-Term in Situ Cr(VI) Reduction. Environmental Science & Technology. 49(21): p. 12922-31. [doi]: 10.1021/acs.est.5b00024. {PMID}:25835088
  28. Zhang, P.; W.-M. Wu, J.D. Van Nostrand, Y. Deng, Z. He, T. Gihring, G. Zhang, C.W. Schadt, D. Watson, P. Jardine, C.S. Criddle, S. Brooks, T.L. Marsh, J.M. Tiedje, A.P. Arkin, and J. Zhou. (2015) Dynamic Succession of Groundwater Functional Microbial Communities in Response to Emulsified Vegetable Oil Amendment during Sustained In Situ U(VI) Reduction. Applied and Environmental Microbiology. 81(12): p. 4164-4172. [doi]: 10.1128/aem.00043-15. {PMID}:25862231
  29. Zhou, A.; K.L. Hillesland, Z. He, W. Schackwitz, Q. Tu, G.M. Zane, Q. Ma, Y. Qu, D.A. Stahl, J.D. Wall, T.C. Hazen, M.W. Fields, A.P. Arkin, and J. Zhou. (2015) Rapid selective sweep of pre-existing polymorphisms and slow fixation of new mutations in experimental evolution of Desulfovibrio vulgaris. ISME Journal. 9(11): p. 2360-72. [doi]: 10.1038/ismej.2015.45. {PMID}:25848870
  30. Zhou, J.; Z. He, Y. Yang, Y. Deng, S.G. Tringe, and L. Alvarez-Cohen. (2015) High-throughput metagenomic technologies for complex microbial community analysis: open and closed formats. MBio. 6(1) [doi]: 10.1128/mBio.02288-14. {PMID}:25626903

  31. Books/Book Chapters

  32. Rabus R. ; S.S. Venceslau, L. Wöhlbrand, G. Voordouw, J.D. Wall, I.A.C. Pereira. (2015) A post-genomic view of the ecophysiology, catabolism and biotechnological relevance of sulfate-reducing prokaryotes. Advances in Microbial Physiology. Book Chapter 2. Series Editor:RK. Poole [doi]: 10.1016/bs.ampbs.2015.05.002 { PMID}:26210106
  33. Fels, S.R. (2015) Development of genome-wide genetic assays in Desulfovibrio vulgaris Hildenborough. Ph.D. thesis, University of Missouri, Columbia, MO.
  34. Korte, H.L. (2015) Nitrate and nitrite growth inhibition of Desulfovibrio strains. Ph.D. thesis. University of Missouri, Columbia, MO.

  35. Legacy and Synergistic External Research

  36. Silva, L; Northen, Trent R. Exometabolomics and MSI: Deconstructing How Cells Interact to Transform Their Small Molecule Environment. Current Opinions in Biotechnology (2015), 34, 209-216. [doi]: 10.1016/j.copbio.2015.03.015 {PMID}:25855407