Publications

Miller, S.E., Colman, A.S., and Waldbauer, J.R. (2023) Metaproteomics reveals functional partitioning and vegetational variation among permafrost-affected Arctic soil bacterial communities.  mSystems 10.1128/msystems.01238-22. [Link]

Zimmerman, A.E., Podowski, J.C., Gallagher, G.E., Coleman, M.L., and Waldbauer, J.R. (2023) Tracking nitrogen allocation to proteome biosynthesis in a marine microbial community. Nature Microbiology 8: 498–509. [Link]

Research Briefing: Following nitrogen into proteins reveals microbial community nutrient allocations. Nature Microbiology (2023). [Link] 

Wilkes, R.A., Waldbauer, J.R., Caroll, A., Nieto-Dominguez-M., Parker, D.J., Zhang, L., Guss, A.M., and Aristilde, L. (2023) Complex regulation in a Comamonas platform for diverse aromatic carbon metabolism. Nature Chemical Biology 19: 651–662. [Link]

Capovilla, G., Braakman, R., Hackl, T., Schwartzman, J., Lu, X., Yelton, A., Longnecker, K., Kido Soule, M., Thomas, E., Swarr, G., Mongera, A., Payette, J., Waldbauer, J.R., Kujawinski, E.B., Cordero, O.X., Fournier, G. and Chisholm, S.W. (2023) Chitin use by marine picocyanobacteria and the evolution of a planktonic lifestyle. Proceedings of the National Academy of Sciences 120: e2213271120. [Link]

Grim, S.L., Stuart, D.G., Aron, P., Levin, N., Kinsman-Costello, L.E., Waldbauer, J.R. and Dick, G.J. (2023) Seasonal shifts in community composition and proteome expression in a sulfur-cycling cyanobacterial mat. Environmental Microbiology. [Link]

Chiu, B.K., Waldbauer, J.R., Elling, F.J., Mete, Ö.Z., Zhang, L., Pearson, A., Eggleston, E., and Leavitt, W.D. (2023) Membrane lipid and expression responses of Saccharolobus islandicus REY15A to acid and cold stress. Frontiers in Microbiology (sec. Biology of Archaea) 10.3389/fmicb.2023.1219779. [Link]

Gonzalez-Nayeck, A.C., Grim, S.L., Waldbauer, J.R., Dick, G.J., and Pearson, A. (2023) Natural abundance carbon isotopic signatures of microbial carbon transfer in a Proterozoic analogue mat. Applied and Environmental Microbiology 89: e01870-22. [Link]

Ferreira, D., Venceslau, S., Bernardino, R., Preto, A., Zhang, L., Waldbauer, J.R., Leavitt, W., and Cardoso Pereira, I. (2023) DsrC is involved in fermentative growth and interacts directly with the FlxABCD-HdrABC complex in Desulfovibrio vulgaris Hildenborough. Environmental Microbiology. 25: 962-976 [Link]

Gallagher, G.E. and Waldbauer, J.R. (2022) Proteome expression and survival strategies of a proteorhodopsin-containing Vibrio strain under carbon and nitrogen limitation. mSystems 7: e01263-21. [Link]

Wilkes, R.A., Waldbauer J.R., and Aristilde, L. (2021) Analogous Metabolic Decoupling in Pseudomonas putida and Comamonas testosteroni Implies Energetic Bypass to Facilitate Gluconeogenic Growth. mBio 12: e03259-21. [Link]

Luxem, K.E., Krapiel, A.M.L., Zhang, L., Waldbauer, J.R., and Zhang, X. (2020) Carbon substrate re-orders relative growth of a bacterium using Mo-, V-, or Fe-nitrogenase for N2 fixation. Environmental Microbiology 22: 1397-1408. [Link]

Zimmerman, A.E., Howard-Varona, C., Needham, D.M., John, S., Worden, A.Z., Sullivan, M.B., Waldbauer, J.R., and Coleman, M.L. (2020) Metabolic and biogeochemical consequences of viral infection in aquatic systems. Nature Reviews Microbiology 18: 21-34. [Link]

Waldbauer, J.R.*, Coleman, M.L.*, Rizzo, A.D., Campbell, K.L., Lotus, J.M., and Zhang, L.C. (2019) Nitrogen sourcing during viral infection of marine cyanobacteria. Proceedings of the National Academy of Sciences 116(31):15590-15595. (*co-first authors) [Link]

Zimmerman, A.E., C. Bachy, X. Ma, S. Roux, H. Jang, M.B. Sullivan, J.R. Waldbauer, A.Z. Worden (2019) Closely-related viruses of the marine picoeukaryotic alga, Ostreococcus lucimarinus, exhibit different ecological strategies. Environmental Microbiology 21(6): 2148-2170. [Link]

Leavitt, W.D., Venceslau, S.S., Waldbauer, J., Smith, D.A., Pereira, I.A.C. and Bradley, A.S. (2019) Proteomic and Isotopic Response of Desulfovibrio vulgaris to DsrC Perturbation. Frontiers in Microbiology 10:658. doi: 10.3389/fmicb.2019.00658. [Link]

Miller, S., Rizzo A.D. and Waldbauer, J.R. (2018) Postnovo: Post-Processing Enables Accurate and FDR-Controlled De Novo Peptide Sequencing. Journal of Proteome Research 17:3671-3680. [Link]

Ma, X., Coleman, M.L. and Waldbauer, J.R. (2018) Distinct molecular signatures in dissolved organic matter produced by viral lysis of marine cyanobacteria. Environmental Microbiology 20:3001-3011. [Link]

Waldbauer, J.R., Zhang, L., Rizzo, A. and Muratore, D. (2017) diDO-IPTL: A Peptide-Labeling Strategy for Precision Quantitative Proteomics. Analytical Chemistry 89: 11498-11504. [Link]

Schwartz, M., Waldbauer, J.R., Zhang, L. and Pan, T. (2016) Global tRNA misacylation induced by anaerobiosis and antibiotic exposure broadly increases stress resistance in Escherichia coli. Nucleic Acids Research 44: 10292-10303. [Link]

Moran, M.A., Kujawinski, E.B., Stubbins, A., Fatland, R., Aluwihare, L.I., Buchan, A., Crump, B.C., Dorrestein, P.C., Dyhrman, S.T., Hess, N.J., Howe, B., Longnecker, K., Medeiros, P.M., Niggemann, J., Obernosterer, I., Repeta, D.J., Waldbauer, J.R. (2016) Deciphering ocean carbon in a changing world. Proceedings of the National Academy of Sciences 113:3143-3151. [Link]

Waldbauer, J.R.*, Rodrigue, S.*, Coleman, M.L. and Chisholm, S.W. (2012) Transcriptome and proteome dynamics of a light-dark synchronized bacterial cell cycle. PLoS ONE 7: e43432. (*co-first authors) [Link]

Waldbauer, J.R., Newman, D.K. and Summons, R.E. (2011) Microaerobic steroid biosynthesis and the molecular fossil record of Archean life. Proceedings of the National Academy of Sciences 108: 13409-13414. [Link]

Awarded the Cozzarelli Prize for Physical and Mathematical Sciences

Waldbauer, J.R., Sherman, L.S., Sumner, D.Y. and Summons, R.E. (2009) Late Archean molecular fossils from the Transvaal Supergroup record the antiquity of microbial diversity and aerobiosis. Precambrian Research 169: 28-47. [Link]

Frias-Lopez, J., Thompson, A.W., Waldbauer, J.R. and Chisholm, S.W. (2009) Use of stable isotope labeled cells to identify active grazers of picocyanobacteria in ocean surface waters. Environmental Microbiology 11: 512-525. [Link]

Martínez, A., Bradley, A.S., Waldbauer, J.R., Summons, R.E. and DeLong, E.F. (2007) Proteorhodopsin photosystem gene expression enables photophosphorylation in a heterologous host. Proceedings of the National Academy of Sciences 104: 5590-5595. [Link]

Knoll, A.H., Summons, R.E., Waldbauer, J.R. and Zumberge, J.E. (2007) The Geological Succession of Primary Producers in the Oceans. In The Evolution of Primary Producers in the Sea, P.G. Falkowski and A.H. Knoll, eds. Academic Press, p. 133-163.

Sherman, L.S., Waldbauer, J.R. and Summons, R.E. (2007) Improved methods for isolating and validating indigenous biomarkers in Precambrian rocks. Organic Geochemistry 38: 1987-2000. [Link]

Hayes, J.M. and Waldbauer, J.R. (2006) The carbon cycle and associated redox processes through time. Philosophical Transactions of the Royal Society B 361: 931-950. [Link]

Summons, R.E., Bradley, A.S., Jahnke, L.L. and Waldbauer, J.R. (2006) Steroids, triterpenoids and molecular oxygen. Philosophical Transactions of the Royal Society B 361: 951-968. [Link]

Chamberlain, C.P., Waldbauer, J.R., Fox-Dobbs, K., Newsome, S.D., Koch, P.L., Smith, D.R., Church, M.E., Chamberlain, S.D., Sorenson, K.J. and Risebrough, R. (2005) Pleistocene to recent dietary shifts in California condors. Proceedings of the National Academy of Sciences 102: 16707-16711. [Link]