Computational Biologist
Computational Biologist


Amy Zimmerman is a microbial ecologist in the Computational Biology group and on the Systems Biology team at PNNL. She is a key member of PNNL’s Soil Microbiome Science Focus Area project. Her research focuses on understanding the ecological and evolutionary mechanisms that govern microbial interactions and contributions to biogeochemical processes by applying quantitative molecular and bioinformatic approaches. Her research experience spans the tree of life, from viruses to bacteria to unicellular eukaryotes.

Prior to joining PNNL, Zimmerman was a research scientist in the Molecular Biogeochemistry group at the University of Chicago, an assistant professor of Biology at Roosevelt University in Chicago, and a postdoctoral researcher in the Molecular Microbial Ecology group at the Monterey Bay Aquarium Research Institute in California.

Disciplines and Skills

  • Microbial interactions and functional diversity
  • Microbial contributions to geochemical cycles


  • PhD in Ecology and Evolutionary Biology, University of California, Irvine
  • BA in Biology, Point Loma Nazarene University

Affiliations and Professional Service

  • American Association for the Advancement of Science
  • American Society for Microbiology
  • American Geophysical Union

Awards and Recognitions

  • Max Goldenberg Foundation Grant Awardee (2017)
  • ASM-LINK Undergraduate Faculty Research Initiative Fellow (2017)
  • Edward Steinhaus Teaching Awardee (2012)
  • National Science Foundation GK-12 Fellow (2009 - 2011)



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


  • 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. 2920.14608


  • Mouginot C., A.E. Zimmerman, J.A. Bonachela, H. Fredricks, S.D. Allison, B.A.S. Van Mooy, A.C. Martiny. 2015. “Resource allocation by the marine cyanobacterium Synechococcus WH8102 in response to different nutrient supply ratios.” Limnology and Oceanography 60(5): 1634-1641.
  • Worden, A.Z., M.J. Follows, S.J. Giovannoni, S. Wilken, A.E. Zimmerman, and P.J. Keeling. 2015. “Rethinking the marine carbon cycle: Factoring in the multifarious lifestyles of microbes.” Science 347(6223): 1257594.


  • Zimmerman, A.E., S.D. Allison, and A.C. Martiny. 2014. “Phylogenetic constraints on elemental stoichiometry and resource allocation in heterotrophic marine bacteria.” Environmental Microbiology 16(5): 1398–1410.
  • Zimmerman, A.E., A.C. Martiny, M.W. Lomas and S.D. Allison. 2014. “Phosphate supply explains variation in nucleic acid allocation but not C:P stoichiometry in the western North Atlantic.” Biogeosciences 11: 1599-1611.


  • Zimmerman, A.E., A.C. Martiny, and S.D. Allison. 2013. “Microdiversity of extracellular enzyme genes among sequenced prokaryotic genomes.” The ISME Journal 7(6): 1187-1199.


  • Cummings, D.E., A.E. Zimmerman, K.R. Unruh, and S. Spring. 2010. “Influence of microbially reducible Fe(III) on the bacterial community structure of estuarine surface sediments.” Geomicrobiology Journal 27(4): 292-302.