Emily Zakem

(Bold font indicates Zakem group member)

Sun, X., C. Frey, D. McCoy, M. Spieler, C. Kelly, A. Maloney, E. Garcia-Robledo, M. Lehmann, B. Ward, and E. J. Zakem. Mechanistic understanding of nitrate reduction as the dominant production pathway of nitrous oxide in marine oxygen minimum zones (in press) Nature Communications

Buchanan, P. J., X. Sun, J. L. Weissman, D. McCoy, D. Bianchi, and E. J. Zakem. Oxygen intrusions sustain aerobic nitrite-oxidizing bacteria in anoxic marine zones. Science 388 (6751): 1069-1074 (2025) doi:10.1126/science.ado0742

Zakem, E. J., J. McNichol, J. L. Weissman, Y. Raut, L. Xu, E. R. Halewood, C. A. Carlson, S. Dutkiewicz, J. A. Fuhrman, and N. M. Levine. Functional biogeography of marine microbial heterotrophs. Science 388 (6749): eado5323 (2025) doi:10.1126/science.ado5323

Xu, L., E. J. Zakem, and J. L. Weissman. Improved maximum growth rate prediction from microbial genomes by integrating phylogenetic information. Nature Communications 16: 4256 (2025) doi:10.1038/s41467-025-59558-9

Levine, N. M., H. Alexander, E. M. Bertrand, V. J. Coles, S. Dutkiewicz, S. G. Leles, and E. J. Zakem. Microbial Ecology to Ocean Carbon Cycling: From Genomes to Numerical Models. Annual Review of Earth and Planetary Sciences 53 (2025) doi:10.1146/annurev-earth-040523-020630

Sun, X., P. J. Buchanan, I. H. Zhang, M. S. Roman, A. R. Babbin, and E. J. Zakem. Ecological dynamics explain modular denitrification in the ocean. Proceedings of the National Academy of Sciences 121: e2417421121 (2024) doi:10.1073/pnas.2417421121

Fadum, J. M., E. K. Hall, E. Litchman, and E. J. Zakem. The aquaculture industry as a global network of perturbation experiments. Limnology and Oceanography Letters, 9 (4): 317-323 (2024) doi:10.1002/lol2.10384

Lennon, J. T., R. Z. Abramoff, S. D. Allison, R. M. Burckhardt, K. M. DeAngelis, J. P. Dunne, S. D. Frey…E. J. Zakem. “Priorities, opportunities, and challenges for integrating microorganisms into Earth system models for climate change prediction.” Mbio 15: e00455-24 (2024) doi:10.1128/mbio.00455-24

Proctor, C., Coupel, P., Casciotti, K., Tremblay, J.E., Zakem, E., Arrigo, K.R. and Mills, M.M. Light, ammonium, pH, and phytoplankton competition as environmental factors controlling nitrification. Limnology and Oceanography, 68:  1490-1503 (2023) doi:10.1002/lno.12359

Liu, L., Chen, M., Wan, X.S., Du, C., Liu, Z., Hu, Z., Jiang, Z.P., Zhou, K., Lin, H., Shen, H., Zhao, D., … Zakem, E. J., … and Zhang, Y. Reduced nitrite accumulation at the primary nitrite maximum in the cyclonic eddies in the western North Pacific subtropical gyre. Science Advances, 9, eade2078 (2023) doi:10.1126/sciadv.ade2078

Zakem, E. J., B. Bayer, W. Qin, A. E. Santoro, Y. Zhang, and N. M. Levine. Controls on the relative abundances and rates of nitrifying microorganisms in the ocean. Biogeosciences 19: 5401-5418 (2022) doi:10.5194/bg-19-5401-2022

Nguyen, T. H., E. J. Zakem, A. Ebrahimi, J. Schwartzman, T. Caglar, K. Amarnath, U. Alcolombri, F. J. Peaudecerf, T. Hwa, R. Stocker, O. X. Cordero, and N. M. Levine. Microbes contribute to setting the ocean carbon flux by altering the fate of sinking particulates. Nature Communications 13: 1657 (2022) doi:10.1038/s41467-022-29297-2

Follet, C. L., S. Dutkiewicz, F. Ribalet, E. J. Zakem, D. Caron, E. V. Armbrust, and M. J. Follows. Trophic interactions with heterotrophic bacteria limit the range of Prochlorococcus. Proc. Natl. Acad. Sci. 119: e2110993118 (2022) doi:10.1073/pnas.2110993118

Zakem, E. J., B. B. Cael, and N. M. Levine. A unified theory for organic matter accumulation. PNAS 118 (6): e2016896118 (2021) doi:10.1073/pnas.2016896118  Commentary: Repeta, D. J. Unifying chemical and biological perspectives of carbon accumulation in the environment. PNAS 118 (11): e2100935118 (2021) doi:10.1073/pnas.2100935118

Zakem, E. J., J. Lauderdale, R. Schlitzer, and M. J. Follows. A flux-based threshold for anaerobic activity in the ocean. Geophysical Research Letters (2021) doi:10.1029/2020GL090423

Zakem, E. J., M. F. Polz, and M. J. Follows. Redox-informed models of global biogeochemical cycles. Nature Communications (Perspective) 11: 5680 (2020) doi:10.1038/s41467-020-19454-w

Walworth, N. G., E. J. Zakem, J. P. Dunne, S. Collins, and N. M. Levine. Microbial evolutionary strategies in a dynamic ocean. PNAS 117 (11): 5943-5948 (2020) doi:10.1073/pnas.1919332117

Zhang, Y., W. Qin, L. Hou, E. J. Zakem, X. Wan, Z. Zhao, L. Liu, K. A. Hunt, N. Jiao, S. Kao, K. Tang, X. Xie, J. Shen, Y. Li, M. Chen, X. Dai, C. Liu, W. Deng, M. Dai, A. E. Ingalls, D. A. Stahl, and G. Herndl. Nitrifier adaptation to low energy flux controls inventory of reduced nitrogen in the dark. PNAS 117 (9): 4823-4830 (2020) doi:10.1073/pnas.1912367117

Wu, P., E. J. Zakem, S. Dutkiewicz, and Y. Zhang. Biomagnification of methylmercury in a marine plankton ecosystem. Environmental Science & Technology 54 (9): 5446-5455 (2020) doi: 10.1021/acs.est.9b06075

Zakem, E. J., A. Al-Haj, M. J. Church, G. L. van Dijken, S. Dutkiewicz, S. Q. Foster, R. W. Fulweiler, M. M. Mills, and M. J. Follows. Ecological control of nitrite in the upper ocean. Nature Communications 9: 1206 (2018) doi: 10.1038/s41467-018-03553-w

Zakem, E. J. and M. J. Follows. A theoretical basis for a nanomolar oxygen concentration. Limnology and Oceanography 62 (2): 795-805 (2016) doi: 10.1002/lno.10461 

Badgley, C., J. Moghtader, E. Quintero, E. Zakem, M. J. Chappell, K. Aviles-Vazquez, A. Samulon, and I. Perfecto. Organic agriculture and the global food supply. Renewable Agriculture and Food Systems 22: 86-108 (2007)

C. Badgley, S. Nelson, N. Beranek, and E. Zakem. Microwear analysis of squirrel teeth. Journal of Vertebrate Paleontology 25 (3): 33A (2005) 

Nelson, S., C. Badgley, and E. Zakem. Microwear in modern squirrels in relation to diet. Palaeontologia Electronica 8 (1): 14A (2005)