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2015 Publications

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

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. [doi]:10.1038/ncomms9289 {PMID}:26392107 PMCID:PMC4595634 
  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. Scientific Reports. [doi]:10.1038/srep12498 {PMID}:26235787 PMCID:PMC4522649
  3. Brewer, B.; S.M. Techtmann, N. Mahmoudi, D. Niang, S. Pfiffner and T.C. Hazen (2015) Co-extraction of DNA and PLFA from Soil Samples. Journal of Microbiological Methods. [doi]:10.1016/j.mimet.2015.05.018 {PMID}:26027542
  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. International Society for Microbial Ecology Journal. [doi]:10.1038/ismej.2014.216 {PMID}:25405978 PMCID:PMC4438318 
  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. [doi]:10.1128/JB.02083-14 {PMID}:25313388 PMCID:PMC4288696
  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. [doi]:10.1128/genomeA.01090-15 {PMID}:26404608 PMCID:PMC4582584
  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.D. 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. Frontiers in Microbiology. [doi]:10.3389/fmicb.2015.01205 {PMID}:26583008 PMCID:PMC4628106
  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. [doi]:10.1128/genomeA.01449-14 {PMID}:25614562 PMCID:PMC4319575
  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. BioMed Central Genomics. [doi]:10.1186/s12864-015-2176-y {PMID}:26555820 PMCID:PMC4641369
  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. [doi]:10.1021/es504484m {PMID}:25534748
  12. Kurczy, M.; T.R. Northen, S. Trauger and G. Siuzdak (2015) Nanostructure Imaging Mass Spectrometry: The Role of Fluorocarbons in Metabolite Analysis and Yoctomole Level Sensitivity. Methods in Molecular Biology. [doi]:10.1007/978-1-4939-1357-2_14 {PMID}:25361674 PMCID:PMC4755109
  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. [doi]:10.1128/mBio.00233-15 {PMID}:25968643 PMCID:PMC4436054 
  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 PMCID:PMC4621071
  15. Raman, A.V.; and N.S. Baliga (2015) The universe under a microscope. Environmental Microbiology Reports. [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. [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. [doi]:10.1128/genomeA.00092-15 {PMID}:25767232 PMCID:PMC4357754
  18. Ray, J.; R.J. Waters, J.M. Skerker, J.V. Kuehl, M.N. Price, J. Huang, R. Chakraborty, A.P. Arkin and A.M. Deutschbauer (2015) Complete Genome Sequence of Cupriavidus basilensis 4G11, Isolated from the Oak Ridge Field Research Center Site. Genome Announcements. [doi]:10.1128/genomeA.00322-15 {PMID}:25977418 PMCID:PMC4432324
  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. [doi]:10.1093/nar/gkv300 {PMID}:25873626 PMCID:PMC4513845
  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. [doi]:10.1093/nar/gkv461 {PMID}:25979264 PMCID:PMC4489292 
  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 Jr., 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. [doi]:10.1128/mBio.00326-15 {PMID}:25968645 PMCID:PMC4436078 
  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. [doi]:10.1016/j.soilbio.2014.10.007
  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. [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.W. Adams (2015) Molybdenum Availability is Key to Nitrate Removal in Contaminated Groundwater Environments. Applied and Environmental Microbiology. [doi]:10.1128/AEM.00917-15 {PMID}:25979890 PMCID:PMC4495186
  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.M. Deutschbauer (2015) Rapid Quantification of Mutant Fitness in Diverse Bacteria by Sequencing Randomly Bar-Coded Transposons. mBio. [doi]:10.1128/mBio.00306-15 {PMID}:25968644 PMCID:PMC4436071 
  26. Yao, Y.; T. Sun, T. Wang, O. Ruebel, T.R. Northen and B.P. Bowen (2015) Analysis of Metabolomics Datasets with High-Performance Computing and Metabolite Atlases. Metabolites. [doi]:10.3390/metabo5030431 {PMID}:26287255 PMCID:PMC4588804
  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. [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. [doi]:10.1128/aem.00043-15 {PMID}:25862231 PMCID:PMC4524159
  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. International Society for Microbial Ecology Journal. [doi]:10.1038/ismej.2015.45 {PMID}:25848870 PMCID:PMC4611501 
  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. [doi]:10.1128/mBio.02288-14 {PMID}:25626903 PMCID:PMC4324309 

  31. Books/Book Chapters

  32. Rabus, R.; S.S. Venceslau, L. Wöhlbrand, G. Voordouw, J.D. Wall and I.A.C. Pereira (2015) A post-genomic view of the ecophysiology, catabolism and biotechnological relevance of sulfate-reducing prokaryotes. Advances in Microbial Physiology.  Editor: R.K. 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.
    https://hdl.handle.net/10355/46854
  34. Korte, H.L. (2015) Nitrate and nitrite growth inhibition of Desulfovibrio strains. Ph.D. thesis. University of Missouri, Columbia, MO. https://mospace.umsystem.edu/xmlui/handle/10355/48213

  35. Legacy and Synergistic External Research

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