Michelle E. Afkhami

Associate Professor

(305) 284-1796
Locator Code:


Research Interests

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 plants and their microbiomes. Much of our research is aimed at understanding the mechanisms underlying how mutualisms work and what structures microbiomes, with the goal of integrating these associations into the broader foundations of ecology, evolution, genomics, and conservation.

For example, we ask questions like “How do complex multispecies mutualisms impact fitness and what is the genomic basis of these effects?”, “How does environmental stress alter microbial gene expression and microbiome composition, and what are the consequences of these shifts for plant population dynamics and community structure?”, “Can mutualistic symbionts cause range expansions into new habitats?”, “Do microbial landscapes drive plant distributions and metapopulation dynamics that underpin them?”, “Can microbial 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 genomic basis of plant and microbial performance in a tripartite interaction between legumes, rhizobia, and mycorrhizal fungi.

(2) how soil microbial communities impact the population and metapopulation dynamics, as well as conservation, of rare species in Florida, and
(3) how habitat fragmentation and the urban matrix alter plant microbiomes with cascading effects on herbivore and pollinator communities.

(4) microbial mitigation of salinity and hydrological stress of mangroves and Everglades tree islands.

(5) functional responses of microbial communities to disturbance and stress using metatranscriptomics and single cell sequencing technologies.

Please see the lab website (link available above) for more details on our research and contact me if you are interested in joining us.

Teaching Interests

In the fall, I teach upper level ‘Ecology’ course and lab which teach principals of Biology from genes to ecosystems and includes trips to local ecosystems (e.g. Everglades National Park). In Spring, I teach the HHMI (Howard Hughes Medical Institute) integrated biology-chemistry laboratory course, which offers an authentic research experience to freshman and sophomores. 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.



2013Ph.D. Population Biology, University of California Davis
2007M.S. Ecology and Evolutionary Biology, Rice University
2006B.S. Ecology and Evolutionary Biology, Rice University

LIST OF SPECIALTIES: Species Interactions | Ecology | Evolutionary Biology | Genomics | Conservations | Microbes | Sustainable Agriculture

LIST OF SPECIALTIES: Species Interactions | Ecology | Evolutionary Biology | Genomics | Conservations | Microbes | Sustainable Agriculture

Professional Experience

2016 - Assistant Professor, University of Miami, Biology Department
2013 - 2015Postdoctoral Fellow, Department of Ecology and Evolutionary Biology, University of Toronto & Plant Sciences Department, Michigan State University

Honors & Acknowledgements

2019, Faculty Mentor of the Year, UM School of Graduate Studies
2019, NSF Division of Environmental Biology Research Grant
2019, Department of Energy’s Joint Genome Institute Research Grant (coPI)
2018, Recognition of Scholarly Achievement Award, UM College of Arts and Sciences
2018, Everglades Research Grant, South Florida Water Management District
2018, Provost Research Award
2017, Provost Research Award
2017, ULINK Fellows Award, Interdisciplinary Research
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)
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)
2010-2013, NSF Doctoral Dissertation Improvement Grantv
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
2006, Julian Huxley Best Thesis Award, Dept. of EEB at Rice University
2006, Phi Beta Kappa


Afkhami, M.E., B.K. Almeida, D.J. Hernandez, K.N. Kiesewetter & D.P. Revillini "Tripartite microbial mutualisms: Linking mechanism and fitness effects of inter-microbial interactions on plants" Plant Biology 56 28-36 (2020).

David, A.D., E.S. Menges, K.B. Thapa-Magar, C.A. Searcy & M.E. Afkhami "Do plant-microbe interactions support the Stress Gradient Hypothesis?" Ecology 101 8 (2020).

David, A.S., P.F. Quintana-Ascencio, E.S. Menges, K.B. Thapa-Magar, M.E. Afkhami & C.A. Searcy "Soil microbiomes underlie population persistence of an endangered plant species" The American Naturalist 194 488-494 (2019).

Hernandez, D., K. Kiesewetter, S. Palakurty, J. Stinchcombe & M.E. Afkhami "Synergism and symbiosis: Unpacking complex species interactions using transcriptomic approaches" The Model Legume Medicago truncatula (Wiley Publishers . 2020).

Rudgers, J.A., M.E. Afkhami, L. Bell-Dereske, Y.A Chung, K. Crawford, S.N Kivlin, M. Mann & M. Nunez Annual Review of Ecology, Evolution, and Systematics Climate disruption of plant-microbe interactions (In Press).