Joy Bergelson

Plant-pathogen dynamics, evolutionary genetics, coevolution, microbial ecology

Microbe-host coevolution

Even though pathogens enjoy the advantage of rapid generation times and enormous population sizes, hosts don’t typically die of infection in nature. Why not? We have discovered the prevalence of ancient balanced polymorphisms segregating at plant R-genes in Arabidopsis, indicating the preservation of particular resistance alleles. Our efforts to understand how selection maintains such a balanced polymorphism revealed an important role of community context, including microbes sharing a focal host as well as alternative hosts for a focal pathogen.  We are thus exploring this complexity to understand how plants and pathogens interact in realistic community contexts. Our current focus is on how the interactions and coevolution of microbes influences microbiome development, plant health/fitness, and the evolution of resistance among shared hosts.

Microbial networks and communities

Plants harbor diverse arrays of microbes that can impact host phenotypes and fitness. Greater insights into the ecological forces that structure these microbial communities are needed to develop effective strategies to promote host health and resist pathogen invasion. We use GWAS mapping to determine the host factors that shape microbial communities growing within Arabidopsis thaliana and use controlled experiments to test the importance of candidate host factors in shaping microbial communities. In a recent collaboration with the laboratories of Detlef Weigel and Fabrice Roux, we are exploring species interactions with the aim of understanding community assembly across host genotypes, and are embarking on efforts to understand the factors that make microbial communities robust. Ultimately, our goal is to enhance plant resistance by identifying conditions that favor protective microbes.

Genomics of adaptation

A long-term focus of our laboratory has been to build genetic resources and tools in Arabidopsis thaliana and its associated microbes. In collaboration with the Magnus Nordborg lab, we have established that A. thaliana has patterns of linkage disequilibrium well suited for GWAS mapping and have genotyped sets of accessions to allow mapping by members of the community. We have made extensive collections of A. thaliana accessions and made these publically available and have collected tens of thousands of isolates from within plant leaves. We are currently making use of these resources for genome-wide studies of local adaptation in Arabidopsis thaliana, as well as targeted studies of the molecular evolution of focal plant and microbial traits such as resistance to suites of natural enemies, virulence across hosts, chemical defense and tolerance to abiotic stress. A recent collaboration with the Manyuan Long laboratory begins to explore the functional role played by new genes in Arabidopsis and rice, again with an eye towards the genetic basis of adaptation.

Genomics and systems biology, Evolution, ecology and environmental biology

• MiCROP Science Advisory Board, Wageningen, The Netherlands
• CEPLAS Science Advisory Board, Cologne, Germany
• TULIP Science Advisory Board, INRA Toulouse, France
• Novo Nordisk Scientific Advisory Board, Denmark
• International Advisory Board, Plant Sciences, The Netherlands
• European Research Council
• Blavatnik National Award for Young Scientists
• Multinational Arabidopsis steering committee on Natural Variation

• Bergelson, J, Kreitman, K, Petrov, D, Sanchez, A and M Tikhonov. 2021. Functional biology in its natural context: a search for emergent simplicity. eLife 10:e67646. DOI: 10.7554/eLife.67464
• Bergelson, J, Brachi, B, Roux, F and F Vailleau. 2021. Assessing the potential to harness the microbiome through plant genetics. Current Opinions in Biotechnology 70:167-173.
• Koskella, B and J Bergelson. 2020. The study of host microbiome (co)evolution across levels of selection. Philosophical Transactions of the Royal Society B 375(1808): DOI:10.1098/rstb.2019.0604.
• Bergelson, J, Mittelstrass, J and MW Horton. 2019. Characterizing both bacteria and fungi improves understanding of the Arabidopsis root microbiome. Scientific Reports 9:24 DOI:10.1038/s41598-018-37208-z.
• Wang, M, Roux, F, Huard-Chauveau, C, Lee, H, Meyer, C, Roby, D, Mc-Peek*, MS and J Bergelson*. 2018. Two-way mixed-effects methods for joint association analysis using both host and pathogen genomes. Proceedings of the National Academy of Sciences, www.pnas.org/cgl/doi/10.1073/pnas.1710980115.          
• MacQueen, A, Sun, X and J Bergelson. 2016. Genetic architecture and pleiotropy shape costs of Rps2 mediated resistance in Arabidopsis thaliana. Nature Plant 2: 16110 doi:10.1038/nplants.2016.110
• 1001 Genomes Consortium. 2016. 1135 genomes reveal the global pattern of polymorphism in Arabidopsis thaliana. Cell 166: 481-491.
• Horton, MW, Bodenhausen, N, Beilsmith, K, Meng, D, Muegge, B, Subramanian, S, Vetter, MM, Vilhkálmsson, BJ, Nordborg, M, Gordon, J and J Bergelson. 2014. Genome-wide association study of Arabidopsis thaliana’s leaf microbial community. Nature Communications 5: 5320 doi: 10.1038/ncomms6320.
• Karasov, TL, Kniskern, JM, Gao, L, DeYoung, BJ, Ding, J, Ullrich, D, Lastra, R, Nallu, S, Innes, RW, Barrett, LG, Hudson, RR and J Bergelson. 2014. The long-term maintenance of a resistance polymorphism through diffuse interactions. Nature 512 (7515): 436-440.
• Horton, MW, Hancock, AM, Huang, YS, Toomajian, C, Atwell, S, Auton, A, Muliyati, NW, Platt, A, Sperone, FG, Vilhkálmsson, BJ, Nordborg, M, Borevitz, JO and J Bergelson. 2012. Genome-wide pattern of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel. Nature Genetics 44(2): 212-216.
• Hancock, AM, Brachi, B, Faure, N, Horton, MW, Jarymowycz, LB, Sperone, FG, Toomajian, C, Roux, F and J Bergelson. 2011. Adaptation to climate across the Arabidopsis thaliana genome. Science 334: 83-86.
• Barrett, L, Bell, T, Dwyer, G and J Bergelson. 2011. Cheating, trade-offs and the evolution of aggressiveness in a natural pathogen population. Ecology Letters doi: 10.1111/j.1461-0248.2011.01687.x.
• Kniskern, JM, Barrett, LG and J Bergelson. 2010. Maladaptation in wild populations of the generalist plant pathogen Pseudomonas syringae. Evolution 65 (3): 818-830.
• Atwell, S, Huang, Y, Vilhkálmsson, BJ, Willems, G, Horton, M, Li, Y, Meng, D, Platt, A, Tarone, A, Hu, TT, Jiang, R, Muliyati, NW, Zhang, X, Amer, MA, Baxter, I, Brachi, B, Chory, J, Dean, C, Debieu, M, de Meaux, J, Ecker, JR, Faure, N, Kniskern, JM, Jones, JDG, Michael, T, Nemri, A, Roux, F, Salt, DE, Tang, C, Todesco, M, Traw, MB, Weigel, D, Marjoram, P, Borevitz, JO, Bergelson*, J and M Nordborg*. 2010. Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature 465 (7298): 627-631
• Bakker, E, Toomajian, C, Kreitman, M and J Bergelson. 2006. A genome-wide survey of R gene polymorphisms in Arabidopsis. The Plant Cell 18:1803-1818.
• Nordborg, M, Hu, T, Ishino, Y, Toomajian, C, Jhaveri, J, Bakker, E, Calabrese, Gladstone, J, Goyal R, P, Jakobsson, M, Jhaveri, J, Kim, S, Padhukasahasram, B, Plagnol, V, Rosenberg, N, Schultz, V, Stevens, C, Shah, C, Wall, J, Wang, J, Zheng, H, Zhao, K, Kreitman, M and J Bergelson. 2005. The pattern of polymorphism in Arabidopsis thaliana. PLoS Biology 3(7): e196.
• Tian, D, Traw, MB, Chen J, Kreitman, M and J Bergelson. 2003. Fitness costs of R-gene-mediated resistance in Arabidopsis thaliana. Nature 423: 74-77.
• Bergelson, J, Kreitman, M, Stahl, EA and D Tian.  2001. Evolutionary dynamics of plant R-genes. Science 292: 2281-2285.
• Stahl, E, Dwyer, G, Mauricio, R, Kreitman, M and J Bergelson. 1999. Dynamics of disease resistance polymorphism at the Rpm1 locus of Arabidopsis.  Nature 400: 667-671.