Understanding our environment

Jim Bever

Senior Scientist, Kansas Biological Survey
Foundation Distinguished Professor of Ecology and Evolutionary Biology
Primary office:
Takeru Higuchi Hall 35

Academic degrees
Ph.D., Duke University, 1992
M.S., Biology, University of Michigan, 1987
B.S., Biology (Honors), University of Illinois, 1984

Program affiliation
Bever/Schultz Research Laboratory

Area(s) of specialization
Microbial interactions and pathogenesis

Research interests
I am interested in testing basic ecological and evolutionary processes occurring within plants and their associated fungi. Much of the conceptual basis of ecology and evolution was developed with animals in mind. Plants and fungi differ from animals in important ways, including their motility, their nutrient acquisition systems and their genetic systems. Conceptual frameworks building on these peculiarities can be very useful in exploring the dynamics of populations and communities of plants and fungi. Developing, testing, and exploring the implications of these models and has been the goal of my work.

Maintenance of diversity in plant communities
We have found that dynamics within the soil community can be a major driver of dynamics within the plant community. The presence of a particular plant host changes the composition of the soil community and the change in soil community composition often decreases the growth rate of their host plant. Through this negative feedback on plant growth, the dynamics within the soil community can directly contribute to the maintenance of diversity within plant communities and populations. We have found that these negative feedbacks can result from accumulation of host-specific soil pathogens, specifically fungal pathogens in the genus Pythium. However, host-specific shifts in the composition of mutualistic mycorrhizal fungi and of soil bacteria also generate these feedbacks.

Ecology of arbuscular mycorrhizal fungi
We have been particularly interested in the ecological and evolutionary dynamics between plants and their mutualistic mycorrhizal fungi. The roots of most plant species form symbiotic associations with arbuscular mycorrhizal fungi, which facilitate their uptake of soil minerals. We have found communities of AM fungi to be very diverse and that individual fungal species are ecologically distinct. We are accumulating evidence that the dynamics and diversity within the AM fungal community can play an important role in determining the diversity and composition of plant communities.

Restoration of native plant diversity after disturbance
The original tallgrass prairie that dominated the Midwest was fantastically diverse. Unfortunately, much of this community type has been lost due to agricultural development. Efforts to replant agricultural fields into prairie have met some success, but the original diversity has not been restored. We are evaluating whether the degradation of the soil community, particularly the community of mycorrhizal fungi, limits the success of restorations. We find support for an important role of native mycorrhizal fungi and find that restoration of this native diversity can have cascading benefits for ecosystem functions, including reduced erosion.

Genetics of arbuscular mycorrhizal fungi
Arbuscular mycorrhizal fungi are thought to reproduce solely through the asexual processes of hyphal growth and production of asexual spores. However, we have found substantial amounts of heritable variation within single populations of these fungi. In culturing these fungi, we have found evidence of an unusual mechanism of inheritance within these fungi in which variable nuclei segregate through dividing and growing hyphae. New combinations of nuclei can then be created through hyphal fusion. We are developing and testing the implications of these genetic processes.

Evolution of mutualism within the plant-AM fungal interaction
The evolution of mutualism between plants and their belowground symbionts is not adequately explained by current evolutionary theory. Because the delivery of benefit to the host likely involves some cost to the symbiont, symbionts that provide reduced benefit to their host would be expected to increase in frequency, leading to the dissolution of the mutualism. We have demonstrated this expected decline in mutualism in our observation of negative feedback on plant growth through changes in the composition of the mycorrhizal mutualism. The processes that might prevent the dissolution of the mutualism has been an unresolved question in evolutionary ecology. We have identified the conditions through which plants can influence the direction of evolution in their symbionts through preferential allocation. We have used carbon labeling experiments to demonstrate preferential allocation to the more mutualistic fungi and have found that this preferential allocation results in increased fitness of the more mutualistic fungi provided there is sufficient spatial structure.

Other topics of interest
Students in our lab are addressing a diversity of issues within ecology and evolution, including interspecific competition among AM fungi, AM fungal systematics, ecology of multitrophic interactions, factors affecting plant community invasibility, evolution of virulence in microbial pathogens, and the evolution of plant dependence on mycorrhizal fungi.

Selected publications

Koziol, L., and J.D. Bever.  2016. The missing link in grassland restoration: arbuscular mycorrhizal fungi inoculation increases plant diversity and accelerates succession.  Journal of Applied Ecology.  10.1111/1365-2664.12843

Steidinger, B.S., and J.D. Bever.  2016.  Host discrimination in modular mutualisms:  a theoretical framework for meta-populations of mutualists and cheaters.  Proceedings of the Royal Society of London, B.  283: 20152428.  http://dx.doi.org/10.1098/rspb.2015.2428.

Ji, B. and J. D. Bever.  2016.  Plant preferential allocation and fungal reward decline with soil phosphorus enrichment: implications for evolution of the arbuscular mycorrhizal mutualism.  Ecosphere7:e01256. 10.1002/ecs2.1256

Barrett, Luke G., Peter C. Zee, James D. Bever, Joseph T. Miller, Peter H. Thrall.  2016.   Evolutionary history shapes patterns of specificity in Acacia-rhizobial mutualisms.  Evolution.  70: 1473-1485.

House, Geoffrey L., Saliya Ekanayake, Yang Ruan, Ursel Schütte, Wittaya Kaonongbua, Geoffrey Fox, Yuzhen Ye, James D. Bever.  2016.  Sequence variation in the nuclear ribosomal RNA gene within isolates of arbuscular mycorrhizal fungi: Tests of phylogeny and clustering methodologies.  Applied and Environmental Microbiology.  82:16 4921-4930.

Koziol, L., and J. D. Bever.  2016.  AMF, phylogeny and succession: specificity of plant response to arbuscular mycorrhizal fungal species increases with succession.  Ecosphere.  7:e01555.

Bever, J.D.  2015.  Preferential allocation, physio-evolutionary feedbacks, and the stability and environmental patterns of mutualism between plants and their root symbionts.  New Phytologist.  205: 1503–1514

Zheng, C., Baoming Ji, Junling Zhang, Fusuo Zhang, James D. Bever. 2015.  Shading decreases plant carbon preferential allocation toward most effective mycorrhizal mutualist.  New Phytologist.  205: 361-368

Cheeke, Tanya E., Ursel M. Schütte, Chris Hemmerich, Mitchell B. Cruzan, Todd N. Rosenstiel, and James D. Bever. 2015. Spatial variation and heterogeneity in the field has a greater effect on the composition of AMF communities than Bt genetic insertion. Molecular Ecology.  24, 2580–2593.

Koziol, E. and J.D. Bever.  2015.  Mycorrhizal response trades off with plant growth rate and increases with plant successional status.  Ecology.  96:1478–1484.

Bauer, J.T., K.M.L. Mack, and J.D. Bever.  2015.  Plant-soil feedbacks as drivers of succession: Evidence from remnant and restored tallgrass prairies.  Ecosphere. (9):158. http://dx.doi.org/10.1890/ES14-00480.1

Middleton, Elizabeth, Sarah Richardson, Liz Koziol, Corey E. Palmer, Zhanna Yermakov, Jeremiah A. Henning, Peggy A. Schultz, and James D. Bever.  2015.  Locally-adapted arbuscular mycorrhizal fungi improve vigor and resistance to herbivory of native prairie plant species.  Ecosphere 6:276. http://dx.doi.org/10.1890/ES15-00152.1

Bever, J.D., S. Mangan, and H. Alexander.  2015.  Pathogens maintain plant diversity.  Annual Review of Ecology and Systematics.  46: 305-325.

Morton, Elise R, Thomas G. Platt, Clay Fuqua, and James D. Bever.  2014.  Non-additive costs and interactions alter the competitive dynamics of co-occurring ecologically distinct plasmids. Proceedings of the Royal Society of London.  281: 20132173.

Larimer, A., K. Clay and J.D. Bever.  2014.  Synergism and context dependency of interactions between arbuscular mycorrhizal fungi and rhizobia with a prairie legume.  Ecology.  95: 1045–1054.

Zee, P.C., and J.D. Bever.  2014.  Joint evolution of  kin recognition and cooperation in spatially structured rhizobium populations.  PLOS ONE.  9:e95141.

Steidinger, B.S. and J.D. Bever. 2014.  The coexistence of hosts with different abilities to discriminate against cheater partners: an evolutionary game theory approach to the stability of cheating and mutualisms.  American Naturalist.  183: 762-770.              

Mack, K.M.L., and J.D. Bever.  2014.  Strength of feedback determines relative abundance in plant communities:  Theoretical considerations of the scale of dispersal and the scale and strength of feedback.  Journal of Ecology.  102: 1195–1201.

Bever, James D., Linda M. Broadhurst and Peter H. Thrall.  2013.  Microbial phylotype composition and diversity predicts ecological function and plant-soil feedbacks.  Ecology Letters.  16: 167–174. 

Middleton, E. and J D. Bever.  2012.  Inoculation with a native soil community advances succession in a grassland restoration.  Restoration Ecology.  20: 218-226


Johnson, D.J., Beaulieu, W.T., Bever, J.D. and Clay, K.  2012.  Conspecific negative density dependence and forest diversity. Science.  336: 904-907.

Platt, Thomas Gene, Clay Fuqua, and James D. Bever. 2012. Public goods and resource competition determine the fitness of Agrobacterium tumefaciens’ virulence plasmid.  Evolution.  66: 1953–1965.

Bever, J.D., T.G. Platt. E.R. Morton.  2012.  Microbial population and community dynamics on plant roots and their feedbacks on plant communities.  Annual Review of Microbiology.  66:265–83

Duchicela, J., K.M. Vogelsang, W. Kaonongbua, E. Middleton, P.A. Schultz, and J.D. Bever.  2012.  Non-native plants and soil microbes contribute to reduced soil aggregate stability in disturbed N. American grasslands.  New Phytologist.  196: 212–222.

Bever, James D., Ian A. Dickie, Evelina Facelli, Jose M. Facelli, John Klironomos, Mari Moora, Matthias C. Rillig, William D. Stock, Mark Tibbett, Martin Zobel. 2010.  Rooting Theories of Plant Community Ecology in Microbial Interactions.  Trends in Ecology and Evolution. 25:  468–478.

Mangan S.A., Schnitzer S.A., Herre E.A., Mack, K., Valencia, M., Sanchez, E., and Bever, J.D.  2010.  Negative plant-soil feedback predicts tree-species relative abundance in a tropical forest.  Nature.  466, 752-755. 

Bever, J.D., S. Richardson, B.M. Lawrence, J. Holmes and M. Watson.  2009.  Preferential Allocation to Beneficial Symbiont with Spatial Structure Maintains Mycorrhizal Mutualism.  Ecology Letters.  12: 13–21. 

Seifert, E.K., J.D. Bever, and J. M Maron.  2009.  Evidence for evolution of reduced mycorrhizal dependence during plant invasion.  Ecology.  90: 1055–1062.

Vogelsang, K.M., and J.D. Bever.  2009.  Mycorrhizal densities decline in association with non-native plants and contribute to plant invasion.  Ecology.  90: 399-407.