Berkeley Lab
Bringing Science Solutions to the World
Berkeley Lab

2019 Publications

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

Jump to: Legacy and Synergistic External Research


  1. Couradeau, E.; J. Sasse, D. Goudeau, N. Nath, R. Chakraborty, T.C. Hazen, B.P. Bowen, R.R. Malmstrom and T.R. Northen (2019) Probing the active fraction of soil microbiomes using BONCAT-FACS. Nature Communications. [doi]:10.1038/s41467-019-10542-0 {PMID}:31235780 PMCID:PMC6591230
  2. Day, L.A.; K.B. De León, M.L. Kempher, J. Zhou and J.D. Wall (2019) Complete Genome Sequence of Desulfovibrio desulfuricans IC1, a Sulfonate-Respiring Anaerobe. Microbiology Resource Announcements. [doi]:10.1128/MRA.00456-19 {PMID}:31371536 PMCID:PMC6675984
  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 Fragment Annotation for Untargeted Metabolomics. American Chemical Society Analytical Chemistry. [doi]:10.1021/acs.analchem.8b03126 {PMID}:30681830 PMCID:PMC6637741
  4. Erbilgin, O.; O. Rübel, K.B. Louie, M. Trinh, M. de Raad, T. Wildish, D. Udwary, C. Hoover, S. Deutsch, T.R. Northen and B.P. Bowen (2019) MAGI: A Method for Metabolite Annotation and Gene Integration. American Chemical Society Analytical Chemistry. [doi]:10.1021/acschembio.8b01107 {PMID}:30896917
  5. Kothari, A.; Y.-W. Wu, M. Charrier, L. Rajeev, A.M. Rocha, C.J. Paradis, T.C. Hazen, S.W. Singer and A. Mukhopadhyay (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 {PMID}:30808697 PMCID:PMC6391923
  6. Kothari, A.; D. Soneja, A. Tang, H. Carlson, A.M. Deutschbauer and A. Mukhopadhyay (2019) Native plasmid-encoded mercury resistance genes are functional and demonstrate natural transformation in environmental bacterial isolates. mSystems. [doi]:10.1128/mSystems.00588-19 {PMID}:31848306 PMCID:PMC6918032
  7. Krantz, G.P.; K. Lucas, E.L.-W. Majumder, L.T Hoang, R. Avci, G. Siuzdak and M.W. Fields (2019) Bulk phase resource ratio alters carbon steel corrosion rates and endogenously produced extracellular electron transfer mediators in a sulfate-reducing biofilm. Biofouling. [doi]:10.1080/08927014.2019.1646731 {PMID}:31402749
  8. 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 in bacteria. Nature Communications. [doi]:10.1038/s41467-018-08177-8 {PMID}:30659179 PMCID:PMC6338753 
  9. Ning, D.; Y. Deng, J.M. Tiedje and 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 {PMID}:31391302 PMCID:PMC6708315
  10. Price, M.N.; J. Ray, A.T. Iavarone, H.K. Carlson, E.M. Ryan, R.R. Malmstrom, A.P. Arkin and A.M. Deutschbauer (2019) Oxidative Pathways of Deoxyribose and Deoxyribonate Catabolism. mSystems. [doi]:10.1128/mSystems.00297-18 {PMID}:30746495 PMCID:PMC6365646
  11. Price, M.N.; and A.P. Arkin (2019) Curated BLAST for Genomes. mSystems. [doi]:10.1128/mSystems.00072-19 {PMID}:30944879 PMCID:PMC6435814
  12. Rajeev, L.; E.G. Luning, G.M. Zane, T.R. Juba, A.E. Kazakov, P. Novichkoc, J.D. Wall and A. Mukhopadhyay (2019) LurR is a regulator of the central lactate oxidation pathway in sulfate-reducing Desulfovibrio species. Public Library of Science ONE. [doi]:10.1371/journal.pone.0214960 {PMID}:30964892 PMCID:PMC6456213
  13. Shi, Z.; H. Yin, J.D. Van Nostrand, J.W. 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 Ultrasensitive and Quantitative Detection of Microbial Populations in Complex Communities. International Society for Microbial Ecology Journal. [doi]:10.1128/mSystems.00296-19 {PMID}:31213523 PMCID:PMC6581690
  14. Thorgersen, M.P.; X. Ge, F.L. Poole II, M.N. Price, A.P. Arkin and 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 {PMID}:31253673 PMCID:PMC6696972
  15. Vuono, D.C.; R.W. Read, J. Hemp, B.W. Sullivan, J.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 {PMID}:30723459 PMCID:PMC6349771
  16. Zelaya, A.; A. Parker, K.L. Bailey, P. Zhang, J. Van Nostrand, D. Ning, D.A. Elias, J. Zhou, T.C Hazen, A.P Arkin and M.W. Fields (2019) High spatiotemporal variability of bacterial diversity over short time scales with unique hydrochemical associations within a shallow aquifer. Water Research. [doi]:10.1016/j.watres.2019.114917 {PMID}:31387058
  17. Legacy and Synergistic External Research

  18. McKay, L.J.; M. Dlakić, M.W. Fields, T.O. Delmont, A.M. Eren, Z.J. Jay, K.B. Klingelsmith, D. Rusch and W.P. Inskeep (2019) Co-occurring genomic capacity for anaerobic methane metabolism and dissimilatory sulfur metabolisms discovered in the Korarchaeota. Nature Microbiology. [doi]:10.1038/s41564-019-0362-4 {PMID}:30833730