Research Summary

Plants roots are surrounded by communities of microbes (i.e. the “rhizosphere microbiome”); these microbes influence plant growth, development, and disease resistance. Using the model plant Arabidopsis and its associated bacteria, such as Pseudomonas fluorescens, our lab studies the genetic and environmental factors that regulate plant-microbiome associations.


1. Uncovering how microbes, including Pseudomonas fluorescens, can colonize a host despite the presence of an intact immune system.
2. Identifying plant genes that shape microbiome community.
3. Identifying bacterial and plant genes that affect the functional outputs of the microbiome.
4. Identifying conserved mechanisms across Pseudomonas species that are required for association with diverse hosts.


Dr. Cara Haney is an associate professor and Canada Research Chair in Molecular mechanisms in host-microbiome interactions in the Department of Microbiology & Immunology at the University of British Columbia in Vancouver, Canada. Prior to joining the UBC faculty in 2016, she was a postdoctoral fellow at Harvard Medical School. Her lab uses high throughput screening combined with genetic and genomic approaches to identify the genetic basis of beneficial traits in plant-microbiome interactions. Her research focuses on elucidating basic mechanisms in host-microbiome interactions, and in finding sustainable solutions for agronomically important challenges in the face of a changing climate.


Canada Research Chair in Molecular mechanisms in host-microbiome interactions
Cystic Fibrosis Canada Early Career Investigator


1. Song, Y., Wilson, A., Zhang, X.C., Thoms, D., Sohrabi, R., Song, S., Geissmann, Q., Liu, Y., Walgren, L., He, S.Y. and Haney, C.H.* (2021). FERONIA restricts Pseudomonas in the rhizosphere microbiome via regulation of reactive oxygen species. Nature Plants.

2. Harting, R.#, Nagel, A.#, Nesemann, K., Höfer, A.M., Kusch, H.,, Stanley, C.E., Stöckli, M., Kaever, A., Hoff, H., Stanke, M., deMello, A.J., Künzler, M., Haney, C. H., Braus-Stromeyer, S.A., Braus, G.H.* (2021). Pseudomonas strains induce transcriptional and morphological changes and reduce root colonization of Verticillium spp. Frontiers in Microbiology. #Equal contributions.

3. Song, S., Liu, Y., Wang, N.R., and Haney, C. H.* (2021). Mechanisms in plant-microbiome interactions: lessons from model systems. Current Opinion in Plant Biology. (Cover Image).

4. Thoms, D., Liang, Y., and Haney, C. H.* (2021). Maintaining symbiotic homeostasis: How do plants engage with beneficial microorganisms while at the same time restricting pathogens? Molecular-plant microbe interactions.

5. Vishwanathan, K., Zienkiewicz, K., Liu, Y., Janz, D., Feussner, I., Polle, A.*, and Haney, C. H*. (2020). Ectomycorrhizal fungi induce systemic resistance against insects on a non-mycorrhizal plant in a CERK1-dependent manner. New Phytologist.

6. Wang, N and Haney, C.H.* (2020). Harnessing the genetic potential of the plant microbiome. The Biochemist.

7. Beskrovnaya, P.#, Melnyk, R. A.#, Liu, Z., Liu, Y., Higgins, M. A., Song, Y., Ryan, K., and Haney, C. H*. (2020) Comparative genomics identified a genetic locus in plant-associated Pseudomonas spp. that is necessary for induced systemic susceptibility. mBIO. 11:e00575-20. #Equal contributions.

8. Yu, K., Liu, Y., Tichelaar, R., Savant, N., Lagendijk, E., van Kuijk, S.J.L., Stringlis, I.A., van Dijken, A.J.H., Pieterse, C.M.J., Bakker, P.A.H.M, Haney, C.H. and Berendsen, R.L. (2019). Plant-beneficial Pseudomonas spp. suppress local root immune responses by gluconic acid-mediated lowering of environmental pH. Current Biology. Doi: 10.1016/j.cub.2019.09.015.

9. Melnyk, R.A., Hossain, S.S. and Haney, C. H.* (2019). Convergent gain and loss of genomic islands drives lifestyle changes in plant-associated bacteria. ISME. doi: 10.1038/s41396-019-0372-5

10. Liu, Z. X., Beskrovnaya, P., Melnyk, R. A., Hossain, S. S., Khorasani,S., O’Sullivan, L.R., Wiesmann, C. L., Bush, B., Richard, J. D. and Haney, C. H*. (2018). A genome-wide screen identifies genes in rhizosphere-associated Pseudomonas required to evade plant defenses. mBio. doi: 10.1128/mBio.00433-18

11. Haney, C. H*., Weismann, C. L., Shapiro, L., Melnyk, R.A., O’Sullivan, L., Khorasani, S., Xiao, L., Han, J., Bush, J., Carrillo, J, Pierce, N., Ausubel, F.M. (2017). Rhizosphere-associated Pseudomonas induce systemic resistance to herbivores at the cost of susceptibility to bacterial pathogens. Molecular Ecology. doi: 10.1111/mec.14400 (*corresponding author)

12. Haney, C.H., Samuel, B. S., Bush, J and Ausubel, F.M. (2015). Associations with rhizosphere bacteria can confer an adaptive advantage to plants. Nature Plants. 1(6): 1-9. (IF: 13.3)

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