Michelle Afkhami


248 Cox Neuroscience & Health Annex

Phone: (305) 284-3973
E-mail: afkhami@bio.miami.edu

Lab Website


  • 2016-present, Assistant Professor, University of Miami, Biology Department
    2013-2015, Postdoctoral Fellow, Department of Ecology and Evolutionary Biology, University of Toronto & Plant Sciences Department, Michigan State University
    2007-2013, Ph.D. in Population Biology, University of California Davis
    2006-2007, M.S. in Ecology and Evolutionary Biology, Rice University
    2002-2006, B.S. in Ecology and Evolutionary Biology, Rice University


  • 2018, University of Miami College of Arts and Sciences Award for Recognition of Scholarly Achievement
    2012, Dean’s Mentorship Award, College of Biological Sciences, UC Davis
    2011, 2014,  Achievement Rewards for College Scientists Award
    2011, 2012, Hardman Foundation Award (for research on native plants)
    2006, Julian Huxley Best Thesis Award, Dept. of EEB at Rice University
    2006, Phi Beta Kappa


  • 2018, Provost Research Award
    2018, Microbial Effects on Everglades Tree Islands Grant, South Florida Water Management District
    2017, ULINK Fellows Award for Interdisciplinary Research (coPI)
    2017, Interactive Effects of Hurricanes & Habitat Fragmentation on Ecological Interactions Grant
    2017, Preparedness and Recovery of Living Plant Collections Grant (coPI)
    2017, Provost Research Award
    2014, NSF Postdoctoral Fellowship, Plant Genome Initiative
    2014, NSERC Banting Postdoctoral Fellowship (Declined)
    2013-2014, University of Toronto Departmental Postdoctoral Fellowship
    2013, NSF Postdoctoral Fellowship, Plant Genome Initiative (Declined)
    2010-2013, NSF Doctoral Dissertation Improvement Grant
    2007-2011, NSF Graduate Student Research Fellowship
    2009,  Mildred E. Mathias Research Grant
    2008, 2009, 2010, 2011, UC Davis Center for Population Biology Travel and Research Grants
    2006-2007, Houston Livestock Show and Rodeo Endowed Fellowship


  • Species Interactions, Ecology, Evolutionary Biology, Genomics, Conservation, Microbes, Sustainable Agriculture


My lab studies the ecology, evolution, and genomics of species interactions at scales ranging from genes to communities using a combination of long term field and greenhouse experiments, mathematical modeling, and laboratory-based molecular methods. While our research spans all types of interactions, we are especially interested in positive species associations and often work with plant-microbial mutualisms, such as rhizobia, mycorrhizal fungi, and fungal endophytes. Much of our research is aimed at understanding the mechanisms underlying how mutualisms work and integrating these associations into the broader foundations of ecology and evolution.

For example, we ask questions like “Can mutualism cause range expansions into new habitats?”, “What is the impact of microbial mutualisms on plant and herbivore community diversity?”, “How do complex multispecies mutualisms impact fitness and what is the genomic basis of these effects?”, “Can mutualists also act as reproductive manipulations?”, “Does mutualism drive diversification of plant radiations?”, and “Can we improve sustainable agriculture through use of natural species interactions?”  Some of our current projects investigate:
(1) the role of fungal endophytes in plant population persistence across species ranges and in the resilience of communities to wildfires in California,
(2) how plant-soil feedbacks impact the demography and conservation of rare species in Florida, and
(3) the genomic basis of plant and microbial performance in a tripartite interaction between legumes, rhizobia, and mycorrhizal fungi.
Please see the lab website (link available above) for more details on our research and contact me if you are interested in joining us.


  • I teach BIL330 (Ecology) and BIL331 (Ecology lab) as well as an inquiry-based hands-on lab through HHMI for freshman and sophomores that integrates biology and chemistry to look at bioprospecting with tree microbiomes.
  • Some of my goals as a teacher are to train students to think critically, engage with the natural world, and to link classroom knowledge to its source. Toward these goals, my classes incorporate realistic lab and field modules, hands-on experience with data, exposure to the primary literature, and/or inquiry-based learning to complement traditional lectures when possible.


  • Key -- *undergraduate mentee, **graduate mentee, ***postdoctoral mentee
  • David, A.S.***, K.B. Thapa Magar*, & M.E. Afkhami (2018) Microbial Mitigation-Exacerbation Continuum: A novel framework for microbiome effects on hosts in the face of stress. Ecology. 99: 517-523.
  • S. Palakurty*, J.R. Stinchcombe, & M.E. Afkhami. (2018) Cooperation and Coexpression: How coexpression networks shift in response to multiple mutualists. Molecular Ecology. Special Issue on “The Host-Associated Microbiome: Pattern, Process,
  • and Function” 27:1860-1873. doi.org/10.1111/mec.14550
  • Afkhami, M.E., D.L. Mahler, J.H. Burns, M.G. Weber, M.F., Wojciechowski, J. Sprent & S.Y. Strauss. (2018) Symbioses with nitrogen-fixing bacteria: Nodulation and phylogenetic data across legume genera. Ecology. 99: 502.
  • Afkhami, M.E. & J.R. Stinchcombe. (2016) Multiple mutualist effects on genomewide expression in the tripartite association between Medicago truncatula, nitrogen-fixing bacteria, and mycorrhizal fungi. Molecular Ecology. 25: 4946-4962.
  • Afkhami, M.E., & S.Y. Strauss. (2016) Native fungal endophytes suppress an exotic dominant and increase plant diversity over small and large spatial scales. Ecology. 97: 1159-1169.
  • Afkhami, M.E., P.J. McIntyre, & S.Y. Strauss. (2014) Mutualist-mediated effects on species’ range limits across large geographic scales. Ecology Letters. 17: 1265-1273. (Recommended by Faculty 1000)