Berkeley Lab
Bringing Science Solutions to the World
Berkeley Lab

2020 Publications

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

Jump to: Submitted/In Review Manuscripts


  1. Carlson, H. K.; L.M. Lui, M. N. Price, A. E. Kazakov, A.V. Carr, J. V. Kuehl, T.K. Owens, T. Nielsen, A.P. Arkin, A.M. Deutschbauer (2020) Selective carbon sources influence the end-products of microbial nitrate respiration. ISME Journal [doi]:1038/s41396-020-0666-7
  2. Moon J-W.; C.J. Paradis, D.C. Joyner, F. von Netzer, E.L. Majumder, E. Dixon, M. Podar, X. Ge, P.J. Walian, H.J. Smith, X. Wu, G.M. Zane, K.S. Walker, M.P. Thorgersen, F.L. Poole II, L.M. Lui, B.G. Adams, K.B. De León, S.S. Brewer, D.E. Williams, K.A. Lowe, M. Rodriguez, Jr., T.L. Mehlhorn, S.M. Pfiffner, R. Chakraborty, A.P. Arkin, J.D. Wall, M.W. Fields, M.W.W. Adams, D.A. Stahl, D.A. Elias a and T. C. Hazen* (2020) Integrated characterization of subsurface media from locations up- and down-gradient of a  uranium-contaminated aquifer. Chemosphere. https://doi.org/10.1016/j.chemosphere.2020.126951
  3. Rajeev, L.; M.E. Garber, A.Mukhopadhyay (2020) Tools to map target genes of bacterial two-component system response regulators. Environmental Microbiology Reports. [doi]: 1111/1758-2229.12838
  4. Tian, R; D. Ning, Z. He, P. Zhang, S.J. Spencer, S. Gao, W. Shi, L. Wu, Y. Zhang, Y. Yang, B. G. Adams, A.M. Rocha, B.L. Detienne, K.A. Lowe, D.C. Joyner, D.M. Klingeman, A.P. Arkin, M.W. Fields, T.C. Hazen, D.A. Stahl, E.J. Alm, J. Zhou (2020) Small is mighty: adaptation of Patescibacteria to groundwater environment drives their genome simplicity. Microbiome. ISME Journal [doi]:1186/s40168-020-00825-w
  5. Submitted/In Review Manuscripts

  6. Camilleri L.J. and Matthew W. Fields (2020) Growth Effects of Sulfopyruvate and Sulfoacetate on the Sulfate-Reducing Bacterium, Desulfovibrio vulgarisHildenborough, and the Methanogenic Archaeon Methanococcus maripaludis  Letters in Applied Microbiology. Submitted
  7. Carim, S.; AL. Azadeh, AE. Kazakov, MN. Price, PJ. Walian, R. Chakraborty, A.M. Deutschbauer, VK. Mutalik*, Adam P. Arkin* (2020) Identification of Genetic Factors Involved in Sensitivity to Tailocins. bioRxiv. Submitted
  8. Kempher, M.L; X. Tao R. Song B. Wu D. A. Stahl J. D. Wall A. Zhou J. Zhou (2020) Effects of genetic and physiological divergence on the evolution of a sulfate-reducing bacterium under elevated temperature. mBio. Submitted
  9. Kothari, A.; S. Roux, H. Zhang, A. Prieto, J-M Chandonia, S. Spencer, X. Wu, A M. Deutschbauer, A. P. Arkin, E J. Alm, R. Chakraborty, A Mukhopadhyay (2020) Ecogenomics of groundwater viruses suggests niche differentiation linked to specific environmental tolerance. mBio. Submitted
  10. Lui, L.M.; T.N. Nielsen, A.P. Arkin (2020) A method for achieving complete microbial genomes and better quality bins from metagenomics data. bioRxiv. Submitted
  11. Majumder, E. L.-W.; E.O. Billings, H. P. Benton, A. Palermo, R. L. Martin, C. Guijas, M. M. Rinschen, X. Domingo-Almenara, J. R. Montenegro-Burke, G. Siuzdak* (2020) Cognitive Analysis of Metabolomics Data for Systems Biology. Molecular Systems Biology. Submitted
  12. Mutalik, VK; B.A. Adler, H.S. Rishi, D. Piya, C. Zhong, B. Koskella, R. Calendar, P.S. Novichkov, M.N. Price, A.M. Deutschbauer, A.P. Arkin (2020) High-throughput mapping of the phage resistance landscape in E. coli. bioRxiv [doi]:1101/2020.02.15.951020
  13. Ning, D.; M. Yuan, L. Wu, Y. Zhang, X. Guo, X. Zhou, Y. Yang, A. P. Arkin, M. K. Firestone, and J. Zhou (2020) A quantitative framework reveals the ecological drivers of grassland soil microbial community assembly in response to warming. Nature Communications. Submitted
  14. Paradis, C.J.; J. I. Miller, J-W. Moon, S.J. Spencer, L.M. Lui, J.D. Van Nostrand, D. Ning, A.D. Steen, L.D. McKay, A.P. Arkin, J-Z. Zhou, E.J. Alm, T.C. Hazen (2020) In situ demonstration of sustained adaptation of a natural microbial community to remove nitrate from groundwater. Environmental Science & Technology. Submitted
  15. Price M.N.; and A.P. Arkin (2020) Short Methionine Synthases. bioRxiv. Submitted
  16. Price M.N.; A.M. Deutschbauer, and A.P. Arkin (2020) GapMind: Automated annotation of amino acid biosynthesis. bioRxiv [doi]:10.1101/741918
  17. Shi, W.L.; Q. Ma, F.Y. Pan, Y.P. Fan, M.L. Kempher, D.L. Ning, J.D. Wall, A.F. Zhou, J-Z. Zhou (2019) Genetic basis of chromate stress tolerance revealed by experimental evolution of genetically diverse sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. The ISME Journal. Submitted
  18. Wilpiszeski, R.L.; C.M. Gionfriddo, A.M. Wymore J.W. Moon, K.A. Lowe, M. Podar, S.R. Elorfi, D.C. Joyner, A.V. Palumbo, M.W. Fields, T.C. Hazen, M.W.W. Adams, F. Poole III, R. Chakraborty, Y. Fan, J.D. Van Nostrand, J-Z. Zhou, A.P. Arkin, D.A. Elias (2020) Using in-field bioreactors to monitor microbial community dynamic shifts with geochemical perturbations. bioRxiv. [doi]:1101/2020.04.16.044594 Submitted
  19. Wu, L; Y Yang, D Ning, Q Gao, H Yin, N Xiao, B.Y. Zhou, S Chen, Q He, and J-Z. Zhou (2019) A Process Models-Based Quantitative Framework For Assessing Community Assembly Mechanisms. Nature Ecology & Evolution. Submitted
  20. Wu, X.; S.J. Spencer, E.J. Alm, J. Voriskova, R. Chakraborty (2020) Capturing the Diversity of Subsurface Microbiota – Choice of Carbon Source for Microcosm Enrichment and Isolation of Groundwater Bacteria. bioRxiv. Submitted https://www.biorxiv.org/node/152948.full
  21. Books/Book Chapters

  22. Louie, K.; S. Kosina, Y. Hu, H. Otani, M. de Raad, A. Kuftin, N. Mouncey, B. Bowen, and T. Northen. Mass spectrometry for natural product discovery. Comprehensive Natural Products III: Chemistry and Biology (in press)