(57.) Revillini, D.,*** C. Mothes,*** B. Almeida,** K.T. Charlton, S. Koontz, A.S. David, M.E. Afkhamiϕ, & C.A Searcyϕ. (In Review) The microbial landscape: soil microbiome properties predict plant distributions. ISME Journal. (5-year Impact factor =12.5) **= graduate mentee, ***=postdoc mentee, ϕ=equal senior authors
(56.) Li, C, M.E. Afkhami, Y. Shi, H. Nie, R. Xue, L. Sun, Z. Jia, S. Ma, X. Zhang, L. Zhai, X. Chen, Y. Yuan, J. Jiang, J. Lin, S.X. Chang, B. Zhang, X. Liu, and J. Zhang. (In Review) Microbial inoculations enhance soil aggregation via root exudate-mediated microbial processes. Soil Biology and Biochemistry. (Impact factor =11.5)
(55.) Cuprewich, S.A. K.M. Barbour, M.E. Afkhami, K.M.T. Lynn, A. Romero-Olivares, C. Aguilar-Trigueros, P. Chaveri, C. Egan, V. Norros, K. Peay, R. Ramos, R. Stephens, L. Ward, & V.B Chaudhary. (Minor Revisions) One hundred unanswered questions on the dispersal ecology of fungi. Ecology. (Impact factor =4.3)
(54.) Reyes, A.L.** and M.E. Afkhami. (In Review) How Small Plastic Particles Affect Tiny Organisms in the Soil. Frontiers for Young Minds. **graduate student mentee
(53.) Zhang, T. R. Guo, J. Xu, S. Ma, X. Jiang, H. Wang, M. Wang, L. Zhang, Y. Gao, L. Shi, J. Guo, Y. Gao, and M.E. Afkhami (In Review) Phosphorus addition reduces community stability by affecting the symbiotic relationship between plants and arbuscular mycorrhizal fungi. Ecology Letters. (5-year Impact factor =9.8)
(52.) Moreira Camara Fernandes, V., N. Pietrasiak, M.E. Afkhami, and J.A. Rudgers. (In Revision) Hierarchical Response Framework to Mitigate Soil Degradation in Drylands under Climate Change. Drylands.
*Invited Perspectives Article.
Published or Accepted
51. Li, V.**, J. Fowler***, A.S. David, S.Y. Strauss, C.A. Searcy, & M.E. Afkhami (2026) Climate variability reduces mutualists that increase long-term population persistence across host species range. Nature Ecology and Evolution. In Press. (5-year Impact factor =16.6) **graduate student mentees and postdoc mentee
50. Afkhami, M.E., A. Classen, C. Dice, D. Hernandez, V. Li**, A. Rawstern**, J.A. Rudgers, J.R. Stinchcombe, K. Crawford (2026) Unravelling complexity in climate change effects on beneficial plant–microbe interactions: Mechanisms, resilience, & future directions. Invited “Tansley Review” for New Phytologist. 249 (1) 93-113. doi.org/10.1111/nph.70644. (5-year Impact factor =10.5) **graduate student mentees
49. Katula, A.M.,** N.C. Johnson, V.B. Chaudhary, M.E. Afkhami (2026) Multilevel selection theory explains context-dependent mycorrhizal functioning. Invited Special Issue Article for Frontiers in Microbiomes. In Press. **= graduate mentee
48. Rudgers, J.A., M.E. Afkhami, et al. Integration and Future Directions: The Causes and Consequences of Dryland Ecosystem Transitions. (2026) Dryland Ecotones under Climate Variability in the American Southwest: Long-Term Research of the Sevilleta LTER Program. Ed. J. A. Rudgers and A. E. Bermudez. Oxford University Press, Oxford, UK. In Press.
47. Hernandez, D.J.**, G.B. Pohlmann*, and M.E. Afkhami. (2025) Gene family expansions provide molecular flexibility required for context-dependent species interactions. Ecology Letters. e70213. doi: 10.1111/ele.70213 (5-year Impact factor =9.8). *undergraduate mentee and **graduate student mentees
46. Revillini, D.***, C.A Searcyϕ, and M.E. Afkhamiϕ. (2025) 50-year fire legacy regulates soil microbial carbon and nutrient cycling responses to new fire. Soil Biology and Biochemistry. 208: 109868. doi:10.1016/j.soilbio.2025.109868 (Impact factor =9.8) ***postdoc mentee
45. Rawstern, A.**, L.J. Carbajal*, T.J. Slade*, and M.E. Afkhami. (2025) Non-additive interactions between multiple mutualists and host plant genotype simultaneously promote increased plant growth and pathogen defence. Plant, Cell, and Environment. Early View; 1-18. doi:10.1111/pce.15631 (Impact factor =7.95) Special issue on “Legumes: Adaptions and Interactions with the Environment” *undergraduate mentee and **graduate student mentee
44. Li, V.** and M.E. Afkhami. (2025) Past Stress Shapes Microbial Benefits to Plants in the Future. Frontiers for Young Minds. 13: 1481801. doi: 10.3389/frym.2025.1481801 **graduate student mentee
43. Rawstern, A.H.**, Hernandez, D.J.**, and M.E. Afkhami. (2025) Central taxa are keystone microbes during early succession. Ecology Letters. 28 (1) e70031. doi:10.1111/ele.70031 (Impact factor =9; preprint/article downloaded >3000 times and cited 8 times) **graduate student mentees
42. Zhang, B., Y. Yuan, M. Zu, K.M. Pajerowska-Mukhtar, M.E. Afkhami, A. Hastings, J. Qiu, and J. Zhang. (Accepted) Microbial effects on invasive grass’ response to water and nutrient stress. Elementa: Science of the Anthropocene. (Impact factor =4.6; Available on Research Square: doi: 10.21203/rs.3.rs-117418/v1)
41. Kiesewetter, K.N.**, A.H. Rawstern**, E. Cline, G.R. Ortiz**, F. Santamaria, C. Coronado, F.H. Sklar, and M.E. Afkhami. (2025) Microbes in Reconstructive Restoration: Divergence in Constructed and Natural Tree Island Soil Fungi Affects Tree Growth. Ecological Applications. 35(1): e70007. doi:10.1002/eap.70007 (Impact factor=5.1) **graduate student mentees
40. Hay, E.M.***, M.E. Afkhamiϕ, C.A. Searcyϕ. (2025) What drives birdsong evolution? Frontiers for Young Minds. 13: 1461108:1-8. doi:10.3389/frym.2025.1461108 ***postdoc mentee and ϕindicates co-senior authors
39. Almeida, B.K.**, E. Tran*, and M.E. Afkhami. (2024) Phyllosphere fungal diversity generates pervasive nonadditive effects on plant performance. New Phytologist. 243: 2416-2429. doi: 10.1111/nph.19792 (Impact factor =10.3) *undergrad mentee and **graduate student mentee
–Feature commentary on our paper by B.K. Whitaker: “Diversity in the phyllosphere – greater than the sum of its parts?” New Phytologist. 243: 2050-2051. doi: 10.1111/nph.19907
38. Afkhami, M.E. (2023) Past microbial stress benefits tree resilience. Science. 380 (6647): 798-799. doi: 10.1126/science.adi1594 (available here)
37. Hernandez, D.J.** , K.N. Kiesewetter**, B.K. Almeida**, D.P. Revillini***, M.E. Afkhami. (2023) Multidimensional specialization and generalization are pervasive in soil prokaryotes. Nature Ecology and Evolution. doi: 10.1038/s41559-023-02149-y. **graduate student and ***postdoctoral mentees
36. Revillini, D***., A.L. Reyes Gonzalez**, L.D. Knecht, P. Allen*, C. Vigo*, A.D David***, E.S Menges, C.A. Searcy ϕ, and M.E. Afkhami ϕ. (2023) Press allelopathy effects select soil microbiomes that mitigates plant performance. New Phytologist. doi: 10.1111/nph.19249 *undergraduate, **graduate, and ***postdoctoral mentees
35. David, A.D.***, Hernandez, D.**, E.S. Menges, V. Sclater, C.A. Searcyϕ, and M.E. Afkhamiϕ. (2023) Heterogeneous landscape promotes distinct microbial communities in an imperiled scrub ecosystem. Mycologia. 115: 739-748, doi: 10.1080/00275514.2023.2258268. **graduate student and ***postdoctoral mentees (Selected for “Best Papers of 2023” on 12th Annual Best Papers list by Stanford faculty — https://web.stanford.edu/~fukamit/papers2023.htm)
34. Kiesewetter, K.N**, L. Otano Velazco*, and M.E. Afkhami (2023) Fragmentation disrupts microbial effects on native plant community productivity. .Journal of Ecology. 111: 1292-1307. doi: 10.1111/1365-2745.14097 *undergraduate and **graduate student mentees
33. Schardl, C., M.E. Afkhami, P. Gundel, L. Iannone, C. Young, R. Creamer, D. Cook. (2023) Diversity of seed endophytes: Causes and implications. The Mycota. Vol 5: Plant Relationships. Ed. B. Scott and C. Mesarich. Ed. B. Scott. Springer Press
32. Revillini, D***., A.D David***, K. Main, E.S Menges, M.E. Afkhamiϕ, C.A. Searcyϕ. (2022) Microbiome-mediated response to pulse fire disturbance outweighs the effects of fire legacy on plant performance. New Phytologist. 233: 2071-2082. doi:10.1111/nph.17689 (Cover Art) ***postdoctoral mentees, ϕindicates cosenior authors
31. Subedi, S.C.***, P. Allen*, R. Vidales, L. Sternberg, M. Ross, M.E. Afkhami. (2022) Salinity legacy: Foliar microbiome’s history affects mutualist-conferred salinity tolerance. Ecology. 103: e3679. doi:10.1002/ecy.3679. *undergraduate and ***postdoctoral mentees
30. Almeida, B.K.**, E. Cline, F. Sklar, and M.E. Afkhami. (2022) Hydrology shapes microbial communities and microbiome-mediated growth of an Everglades tree island species. Restoration Ecology. e13677. doi:10.1111/rec.13677 **graduate student mentee
29. Kiesewetter, K.N** and M.E. Afkhami (2021) Microbiome-mediated effects of habitat fragmentation on native plant performance. New Phytologist. . 232: 1823-1838. doi:10.1111/nph.17595 **graduate student mentee
28. Afkhami, M.E., M. Friesen & J.R. Stinchcombe. (2021) Multiple Mutualism Effects generate synergistic selection and strengthen fitness alignment in the interaction between legumes, rhizobia, and mycorrhizal fungi. Ecology Letters. In Press. https://doi.org/10.1111/ele.13814
27. Hernandez, D.**, A.D. David***, E.S. Menges, C.A. Searcyϕ, and M.E. Afkhamiϕ. (2021) Environmental stress destabilizes microbial networks. The ISME Journal. https://doi.org/10.1038/s41396-020-00882-x **graduate student mentee, ***postdoc mentee, ϕindicates co-senior authors (Recognized as most cited 2021 paper in ISME Journal as part of special collection “Celebrating 15 Years of The ISME Journal”; “Hot Cited” paper on Web of Science; ISME Journal 2021 Best Paper Award Honorable Mention; Winner of Best 2021 UM Graduate Student Paper Award)
26. Afkhami, M.E., B.K. Almeida**, D.J. Hernandez**, K.N. Kiesewetter**, and D.P. Revillini***. (2020) Tripartite mutualisms as models for understanding plant–microbial interactions. Special Issue on “Biotic Interactions” in Current Opinion in Plant Biology. 56: 28-36. doi: doi.org/10.1016/j.pbi.2020.02.003. (Cover Art) **graduate student and ***postdoc mentee (Note all authors contributed equally)
25. Rudgers, J.A., M.E. Afkhami, L Bell-Dereske, Y.A Chung, K. Crawford, S.N Kivlin, M. Mann, and M. Nunez. (2020) Climate Disruption of Plant-Microbe Interactions. Annual Review of Ecology, Evolution, and Systematics. 51(1): 561-586
24. David, A.D.***, E.S. Menges, K.B. Thapa-Magar*, C.A. Searcyϕ and M.E. Afkhamiϕ. (2020) Do plant-microbe interactions support the Stress Gradient Hypothesis? Ecology. 101(8): e03081.10.1002/ecy.3081. *postbac and ***postdoc mentee ϕindicates co-senior authors
23. Almeida, B.K.**, M.S. Ross, S.L. Stoffella, J.P. Sah, E. Cline, F. Sklar, and M.E. Afkhami (2020) Diversity and structure of soil fungal communities across experimental Everglades tree islands. Diversity. Invited special issue on “Fungal Diversity”. 12, 324: 1-17. **graduate student mentee
22. Carscadden, K.A., N.C. Emery, C.A. Arnillas, M.E. Afkhami, D. Gravel, S.W. Livingstone, J.J. Wiens, and M.W. Cadotte. (2020) Broadening the horizons of niche breadth research. Quarterly Review of Biology. 95 (3): 179-214.
21. Almeida, B.K.**, M. Garg, M. Kubat, & M.E. Afkhami. (2020) Not that kind of tree: Decision trees inform the relative importance of morphological traits for plant databases. Applications in Plant Sciences. Special Issue on ‘Machine Learning in Plant Biology’. 8:1-7. doi.org/10.1002/aps3.11379. **graduate student mentee
20. Quintana-Ascencio, P.F., E.S. Menges, G. Cook, J. Ehrlén, and M.E. Afkhami. (2020) Drivers of demography: past challenges and a promise for a changed future. Demographic Methods across the Tree of Life. Eds. R. Salguero-Gomez and M. Gamelon. Oxford University Press. Accepted.
19. Hernandez, D.**, K. Kiesewetter**, S. Palakurty*, J. Stinchcombe, and M.E. Afkhami. (2020) Synergism and symbiosis: Unpacking complex species interactions using transcriptomic approaches. in The Model Legume Medicago truncatula. Ed. F.J. de Bruijn. Wiley Publishers. (In Press) *undergraduate mentee ** graduate mentee
18. Zanne, A.E., K. Abarenkov, M.E. Afkhami, et al. (2020) Fungal functional ecology: Bringing a trait-based approach to plant-associated fungi. Biological Reviews. 95: 409-433. doi.org/10.1111/brv.12570.
17. David, A.S.*** P. Quintana-Ascencio, E. Menges, K. Thapa-Magar*, M.E. Afkhamiϕ, C.A.S. Searcyϕ. (2019) Soil microbiomes underlie population persistence of an endangered plant species. The American Naturalist. 194:488-494. doi.org/10.1086/704684. *postbac and ***postdoc mentee ϕindicates co-senior authors
16. 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 (Cover Art) *undergraduate mentee
15. 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 doi: 10.1002/ecy.2153 ** & * indicate equal authorship of postdoc and postbac mentees
14. 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. doi:10.1002/ecy.2110.
13. Batstone, R. T.*, K. A. Carscadden*, M. E. Afkhami, & M. E. Frederickson. (2018) Using niche breadth theory to explain generalization in mutualisms. Ecology. 99: 1039-1050. doi.org/10.1002/ecy.2188 + indicates equal graduate student coauthors
12. Afkhami, M.E. & J.R. Stinchcombe. (2016) Multiple Mutualist Effects on genome-wide expression in the tripartite association between Medicago truncatula, nitrogen-fixing bacteria, and mycorrhizal fungi. Molecular Ecology. 25: 4946-4962.
**To see a nice article on our paper click here.
11. 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.
10. Jones, E.I., M.E. Afkhami, E. Akcay, J.L. Bronstein, R. Bshary, M.E. Frederickson, K.D. Heath, J. Hoeksema, J. Ness, S. Pankey, S.S. Porter, J.L. Sachs, K. Scharnagl, & M.L. Friesen. (2015) Cheaters must prosper: Reconciling theoretical and empirical perspectives on cheating in mutualism. Ecology Letters. 18:1270–1284. (Cover Art)
9. 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 F1000. ** To see this great article on our paper click here.
8. Charlton, N.D., K.D. Craven, M.E. Afkhami, B.A. Hall*, S.R. Ghimire, & C.A. Young. (2014) Interspecific hybridization and bioactive alkaloid variation increases diversity in endophytic Epichloë species of Bromus laevipes. FEMS Microbiology Ecology. 90: 276-289. *undergraduate
7. Afkhami, M.E., J.A. Rudgers, & J.J. Stachowicz. (2014) Multiple Mutualist Effects: Conflict and synergy in multispecies mutualisms. Ecology. 95: 833-844.
6. Gorischek, A.M.*, M.E. Afkhami, E.K. Seifert, & J.A. Rudgers. (2013) Fungal symbionts as manipulators of reproductive biology. The American Naturalist. 181: 562-570. *undergraduate **Covered by Science News: Pennisi, E. (March 2013) Fungus get off my lawn.
5. Afkhami, M. E. (2012) Fungal endophyte-grass symbioses are rare in the California floristic province and other regions with Mediterranean-influenced climates. Fungal Ecology special issue. 5: 345-352.
4. Afkhami, M. E. & J. A Rudgers. (2009) Endophyte-mediated resistance to herbivores depends on herbivore identity in the wild grass, Festuca subverticillata. Environmental Entomology. 38: 1086-1095.
3. Rudgers, J.A., M. E. Afkhami, M. A. Rúa, A. J. Davitt, S. Hammer, & V. M. Huguet. (2009) A fungus among us: broad patterns of endophyte distribution in the grasses. Ecology. 90(6): 1531-1539.
2. Afkhami, M. E. & J. A. Rudgers. (2008) Symbiosis Lost: Imperfect vertical transmission of fungal endophytes in grasses. The American Naturalist. 172(3): 405-416.
1. Afkhami, M. E. & J. E. Strassmann. (2007) Adult Yellow-crowned Night-herons face in opposite directions at the nest. The Wilson Journal of Ornithology. 119(4):747–749.
COMPLETE OR IN PREP MANUSCRIPTS
Stemle, L.R., R.B. Rumelt, S.L. Clements, M.E. Afkhami, A.S. David, and C.A. Searcy. (Complete Draft) Traits that Facilitate Invasion of Native Habitat. Target Journal: Global Change Biology. (Submission Summer 2025)
Fowler, J.C.***, G. Pohlmann*, E. Hay***, V. Li**, Z. Meadors*, A. Reyes**, C. Searcyϕ, and M.E. Afkhamiϕ. (Completed Manuscript) Do microbial effects on hosts vary across life stage and vital rate? A meta-analysis. Target Journal: Ecology Letters. (Submission Fall 2025)
Hernandez, D.J.** and M.E. Afkhami. (Completed Draft) Microbiomes under stress: Microbiomes and the stress gradient hypothesis. Target Journal: Trends in Ecology and Evolutionary Biology. (Submission Fall 2025)
Hay, E.***, C.A. Searcy, and M.E. Afkhami. (Completed Manuscript) Fungal symbioses accelerate niche evolution of plants. Target Journal: Nature Ecology and Evolution. (Submission Jan 2026)
Schardl, C.L., P. Nagabhyru, A. Tapia, N. Moore, J.W. Jaromczyk, P.J. Calie, M.E. Afkhami, C.A. Searcy, D.D. Cook, R. Creamer, T. Sterling, S. Florea (In Prep) Genetic, functional and phylogenetic diversity of plants and seed-borne endophytes. Target Journal: New Phytologist. (Submission Winter 2026)
Kiesewetter, K.N.** & M.E. Afkhami. (In Prep) Fragmentation-generated edge effects shape microbiome diversity, composition, and functional roles. Target Journal: Ecology. (Submission expected spring 2026)
For citation statistics, see google scholar.
AFKHAMI LAB 