Comparative Genomics Identified a Genetic Locus in Plant-Associated Pseudomonas Spp. that Is Necessary for Induced Systemic Susceptibility
This week we profile a recent publication in mBio from the laboratory of Dr. Cara
Haney (pictured, front row right) at the Michael Smith Laboratories and UBC.
Can you provide a brief overview of your lab’s current research focus?
“Symbiosis” means “living together”: sometimes the outcome of host-microbe associations is pathogenic, while in other cases both the host and microbe benefit. The Haney Lab is broadly interested in how bacteria co-exist with plants and animals, and the factors that affect whether the interaction is beneficial or harmful for the host. We study bacteria in the genus Pseudomonas, which includes human and plant pathogens (i.e. P. aeruginosa and P. syringae respectively) and animal and plant commensals (i.e. P. fluorescens). We primarily use the model plant, Arabidopsis, which is a host for diverse Pseudomonas spp. To identify the genes required for bacteria to colonize plants, or that are associated with positive or negative health outcomes for the plant, we use genetic and molecular approaches, combined with high-throughput assays, and next-generation sequencing. We are interested in both basic mechanisms that regulate host-microbiome and host-pathogen interactions, and to translating these findings to improving agricultural sustainability and treatment of chronic infections.
What is the significance of the findings in this publication?
Bacteria that live in communities associated with plants and animals (microbiomes) can have diverse effects on health of their hosts, yet the genetic and molecular bases of these effects have largely remained elusive. Plant root-associated microbes can promote plant growth and induce systemic resistance (ISR) to foliar pathogens. While ISR is well described in the literature, we previously identified strains of root-associated Pseudomonas spp. that promote plant growth but unexpectedly induced systemic susceptibility (ISS) rather than ISR to plant leaf pathogens. This paper demonstrates that the ISS-inducing phenotype is common among root-associated Pseudomonas spp. Comparing the genomes of closely-related bacteria that do and do not trigger ISS, we identified a single genetic locus that is unique to ISS strains. We generated a clean deletion of the 11-gene ISS locus and found that it is necessary for ISS. This work demonstrates that growth-promoting strains of Pseudomonas may have unanticipated consequences for plant immunity, and this is critical to consider when the plant microbiome is engineered for agronomic improvement.
What are the next steps for this research?
The functions of the predicted genes in the ISS locus are not apparent based on similarity to genes of known function, which made this project both interesting and challenging. We found that a subset of the genes in the locus were previously implicated in pathogenesis in animals. We also found that some, but not all, contribute to colonization. The next steps will involve further characterization of the individual genes in the ISS locus to determine their involvement in ISS and host colonization, and characterize their molecular and biochemical function.
This work was funded by:
This work was supported by an NSERC Discovery Grant (NSERC-RGPIN-2016-04121) and a Seeding Food Innovation grant from George Weston Ltd. awarded to Cara Haney. Additional support came from a Life Sciences Research Foundation Fellowship from the Simons Foundation awarded to Ryan Melnyk, a fellowship from China Postdoctoral Science Foundation awarded to Yi Song a Chinese Graduate Scholarship Council award to Yang Liu, and an NSERC CGS-M award to Zhexian Liu.