Berkeley Lab

2019 Publications

Jump to: Submitted/In Review Manuscripts | Books/Book Chapters | Legacy and Synergistic External Research

  1. Couradeau E.; J. Sasse, D. Goudeau, N. Nath, R. Chakraborty, T.C. Hazen, B.. Bowen, R.R. Malmstrom, T.R. Northen (2019) Challenging our view of the active fraction of soil microbiomes using BONCAT-FACS-Seq. Nature Communication. [doi]:10.1038/s41467-019-10542-0
  2. Day, L.A.; K.B. De León, M.L. Kempher, J. Zhou, J.D. Wall (2019) Complete Genome Sequence of Desulfovibrio desulfuricans IC1, a Sulfonate-Respiring Anaerobe. Microbiology Resource Announcements. [doi]: 10.1128/MRA.00456-19
  3. Domingo-Almenara, X.; J. R. Montenegro-Burke, C. Guijas, E. L.-W. Majumder, H. P. Benton and G. Siuzdak (2019) Autonomous METLIN-guided in-source fragmentation detection increases annotation confidence in untargeted metabolomics. ACS Analytical Chemistry. [doi]:10.1021/acs.analchem.8b03126
  4. Erbilgin O; O. Rübel, KB. Louie, M. Trinh, M. DeRaad, T. Wildish, D. Udwary, C. Hoover, S. Deutsch, T. Northen*, B.P. Bowen (2019) MAGI: Metabolite, annotation, and gene integration to efficiently link metabolomics data to (meta)genome sequencing. ACS Analytical Chemistry. [doi]:10.1021/acschembio.8b01107
  5. Kothari A, Wu Y-W, Charrier M, Rajeev L, Rocha AM, Paradis CJ, Hazen TC, Singer SW, Mukhopadhyay A. (2019) Large Circular Plasmids from Groundwater Plasmidomes Span Multiple Incompatibility Groups and Are Enriched in Multimetal Resistance Genes. mBio. [doi]:10.1128/mBio.02899-18
  6. Mutalik, V.K.; P.S. Novichkov, M.N. Price, T.K. Owens, M. Callaghan, S. Carim, A.M. Deutschbauer, and A.P. Arkin (2019) Dub-seq: dual-barcoded shotgun expression library sequencing for high-throughput characterization of functional traits. Nature Communication. [doi]:10.1038/s41467-018-08177-8
  7. Ning, D.; Y. Deng, J. M. Tiedje, J. Zhou (2019) A General Framework for Quantitatively Assessing Ecological Stochasticity. Proceedings of the National Academy of Sciences of the United States of America. [doi]:10.1073/pnas.1904623116
  8. Price, M. N.; J. Ray, A. T. Iavarone, H. K. Carlson, E. M. Ryan, R. R. Malmstrom, A. P. Arkin, A. M. Deutschbauer (2019) An Oxidative Pathway of Deoxyribose Catabolism. mSystems. [doi]:10.1128/mSystems.00297-18
  9. Price M.N.; and A.P. Arkin (2019) Curated BLAST for Genomes. mSystems. [doi]:10.1128/mSystems.00072-19
  10. Rajeev L, Luning EG, Zane GM, Juba TR, Kazakov AE, Novichkoc P, Wall J, Mukhopadhyay A* LurR is a regulator of the central lactate oxidation pathway in sulfate-reducing Desulfovibrio species. PLOS ONE 2019. [doi]:10.1371/journal.pone.0214960
  11. Thorgersen, M.P; X. Ge , F.L. Poole, II; M.N. Price, A.P. Arkin, M.W.W. Adams (2019) Nitrate-Utilizing Microorganisms Resistant to Multiple Metals from the Heavily Contaminated Oak Ridge Reservation. Applied and Environmental Microbiology. [doi]:10.1128/AEM.00896-19
  12. Vuono, D.C., R.W. Read, J. Hemp, B.W. Sullivan, A. Arnone, I. Neveux, R.R. Blank, E. Loney, D. Miceli, M-K.H.. Winkler, R. Chakraborty, D.A. Stahl, and J.J. Grzymski.   (2019) Resource concentration modulates the fate of dissimilated nitrogen in a dual-pathway Actinobacterium. Frontiers in Microbiology.  [doi]:10.3389/fmicb.2019.00003
  13. Zelaya A; A. Parker, K. L. Bailey, P. Zhang, J. Van Nostrand, D.A. Elias, J. Zhou, M.W. Fields (2019) High temporal variability in bacterial populations and association networks of an undisturbed, pristine aquifer. Water Res. [doi]:10.1016/j.watres.2019.114917

Submitted/In Review Manuscripts

  1. Camilleri L.J. and Matthew W. Fields.  Growth Effects of Sulfopyruvate and Sulfoacetate on the Sulfate-Reducing Bacterium, Desulfovibrio vulgarisHildenborough, and the Methanogenic Archaeon Methanococcus maripaludis  Letters in Applied Microbiology. Submitted
  2. Kempher, M.L; A.S. Burns, P.S. Novichkov, K.S. Bender. (2019) Characterization Of A Dual Functioning Small RNA/Riboswitch In Desulfovibrio Vulgaris Hildenborough. mBio. Submitted
  3. Krantz, GP; K. Lucas, E. L-W. Majumder, L.T Hoang, R. Avci, G. Siuzdak, M.W Fields (2019) Bulk phase resource ratio alters metal corrosion rates and extracellular electron transfer mediators in a sulfate-reducing. Biofouling. Revision
  4. 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* (2019) Cognitive Analysis of Metabolomics Data for Systems Biology. Molecular Systems Biology. Submitted
  5. 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* (2019) Integrated characterization of subsurface media from locations up- and down-gradient of a  uranium-contaminated aquifer. bioRxiv. https://www.biorxiv.org/content/10.1101/712562v1
  6. Paradis, C.J.; W. Reimus, R.H. Johnson, D.M. Mackay, L.D. McKay, T.C. Hazen (2019) Single-well injection-drift test to estimate groundwater velocity. Groundwater. Accepted
  7. Shi, Z.; H Yin, JD Van Nostrand, JW Voordeckers, Q Tu, Y Deng, M Yuan, A Zhou, P Zhang, N Xiao, D Ning, Z He, L Wu, and J Zhou (2019) Functional gene array-based ultra-sensitive and quantitative detection of microbial populations in complex communities. International Society for Microbial Ecology Journal. Submitted
  8. Wu, X.; S.J. Spencer, E.J. Alm, J. Voriskova, R. Chakraborty
    (2019) Capturing the Diversity of Subsurface Microbiota – Choice of Carbon Source for Microcosm Enrichment and Isolation of Groundwater Bacteria. bioRxiv. https://www.biorxiv.org/node/152948.full

Books/Book Chapters

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Legacy and Synergistic External Research

  1. McKay, L.J., M. Dlakić, M.W. Fields, T.O. Delmont, A. Murat Eren, Z.J. Jay, K.B. Klingelsmith, D. Rusch, and W.P. Inskeep. (2019) Co-occurring genomic capacity for anaerobic methane metabolism and dissimilatory sulfite reduction discovered in the Korarchaeota. Nature Microbiology. Accepted