Tag Archives: pseudomonas

Epigenetics of trans-generational defense Induction

Some of the best evidence for environmentally induced epigenetic inheritance comes from studies of pathogen infection in A. thaliana. When infected by the common laboratory strain of the bacterial pathogen Pseudomonas syringae (DC3000), A. thaliana plants undergo extensive DNA methylation changes that regulate defense gene expression. Furthermore, some of these induced methylation changes can be transmitted to offspring, trans-generationally ‘priming’ offspring for more effective defense responses when they encounter similar pathogens.

However, plants in nature are typically subject to simultaneous infection by pathogens that induce different defense responses. The defense systems activated by different pathogens may even antagonize each other via hormonal crosstalk. The effects of such co-infection on DNA methylation patterns and trans-generational defense priming remain entirely unexplored, as does the extent of host genetic variation for these epigenetic responses.

To address these issues, we generated A. thaliana lineages with different histories of bacterial infection across generations. This framework enables several key determinations, including the specific DNA methylation changes that are induced in parents by single- versus co-infection, which of these changes are inherited by offspring, and how inherited methylation changes influence offspring defense responses when offspring are infected. To date, we have characterized the genome-wide DNA methylomes of the founding (parental) plants of these lineages, which were infected by the natural bacterial pathogens Pseudomonas syringae (Michigan strain NP29.1A) and P. viridiflava (Michigan strain RMX3.1B),separately and in combination (i.e., co-infection).

Co-infections with pathogenic and beneficial bacteria

Our preliminary experimental data reveals that coinfection has exceptionally strong impacts on pathogen performance in Arabidopsis. To test for these effects, we conducted infections consisting of a luciferase-labeled focal strain of P. viridiflava that was separately co-inoculated with each of 60 randomly chosen strains from the P. syringae complex. At 36 hours post-inoculation, luciferase activity (i.e., photon counts) in each infected plant was measured to quantify abundance of the focal strain. This was replicated in triplicate for two different focal strains. Four aspects of these results are favorable for the proposed work:

  • First, the effects of coinfection on pathogen performance are large. The mean abundance of both focal strains differed by two orders of magnitude between the most and least favorable coinfection combinations.
  • Second, these effects are highly consistent and dwarf experimental noise. The identity of the coinfecting strain explained over 70% of the variance in focal strain abundance in our experiments (linear mixed model, abundance ~ coinfecting strain + batch effect covariates), and this effect was statistically significant (P < 1e-16).
  • Third, our data indicate the potential for both costs and benefits to coinfection, depending on the identity of the coinfecting strains. In 40% of the pairwise coinfection combinations, the focal strain grew to a higher abundance than when singly inoculated; conversely, in 60% of cases, its abundance decreased relative to single infections.
  • Fourth, the two focal strains differed in how their abundance was affected by the coinfecting strains (aforementioned linear mixed model; focal strain x coinfecting strain interaction, P < 0.001). This underscores the importance of accounting for genotype x genotype interactions, as we propose to do, when predicting infection outcomes.
Figure 1. Experimental system for plant growth and infections. Above, gnotobiotic Arabidopsis in plant growth (MS) media in 24-well microplates. Below, from left: a lightly, moderately, and heavily diseased plant, 36 hours after infection with P. viridiflava strains differing in pathogenicity
Figure 2. Pairwise co-infections strongly shape pathogen performance in gnotobiotic Arabidopsis. The abundance of two luciferase-tagged strains of P. viridiflava (strain p13.G4, “b”; strain p25.A12, “c”) were measured 36 hours after co-inoculation with each of 60 different strains from the P. syringae complex, whose phylogenetic relationship is shown in “a”. Abundances of the two focal strains in each pairwise co-infection are expressed relative to their abundance in single infections. Effects on focal strain abundance are expressed as log10 units of photon counts/second.

Local adaptation and the accessory genome in an endemic plant-pathogen

infected crop cultivars from the ongoing adaptation experiment

 

ABSTRACT

Genetic variation is fodder for evolution, and microbial plant-pathogens have it in spades. The Pseudomonas syringae genome is characterized by many rare “accessory” genes that co-occur with “core” genes found in all individuals. In fact, accessory genes outnumber core genes 2:1, even though accessory genes are not essential for survival. Moreover, there is tremendous variation in the gene content of P. syringae; isolates from different crop species, for example, differ in gene content by ~32% (Karasov et al. 2017). Whether these strain-specific genes have adaptive potential remains unknown; they may simply be a consequence of high rates of mutation and lateral gene transfer, even if purifying selection to remove deleterious variants is strong. Another, not mutually exclusive possibility is that accessory genes are maintained by positive selection as pathogens adapt to alternative hosts. Indeed, local adaptation has been hypothesized to explain the presence of rare alleles in P. syringae, which causes major agricultural loss in multiple crop species each year. To address these hypotheses, I have paired a set of P. syringae isolates with their original hosts of isolation. I first test for local adaptation by comparing the in planta fitness of each isolate in its own, and in each other’s, native host. Next, I ask to what degree strain-specific genes influence adaptive patterns by using Tn-seq to track the in planta gene frequencies of each pathogen over the course of infection in each host. From this combination of experiments, we will learn to what extent host ecology influences genome evolution and virulence in P. syringae; this is important not only to inform our understanding of the selective process, but also to fields concerned with the emergence and spread of infectious disease.

P. syringae transposon mutants!

Evolution of pathogenicity and intraspecific interactions in Pseudomonas syringae

The high selective pressures involved in the “arms race” between plants and their pathogens drives rapid evolution of genes involved in immunity on the host side and virulence on the pathogen side (Alcázar et al., 2011). However, plants are not typically infected by individual pathogens: they interact with a community of inter- and intraspecifically diverse microbes that also experience competitive pressures from one another. How these interactions among microbes affect their ability to cause disease and how the host plant influences the microbial community it harbors remain open questions for investigation.

Researchers have observed that P. syringae is a common natural pathogen of A. thaliana and that resistance to P. syringae infection varies among different A. thaliana accessions (Jakob et al., 2002). Recent work has shown that  P. syringae strains isolated from A. thaliana leaf tissue are not only genetically diverse but also differ in their degree of virulence: many isolates harbor a polymorphism in the type three secretion system (T3SS), losing the ability to cause disease (Barrett et al., 2011; Kniskern et al., 2011). Such strains show increased growth in plant tissue when co-inoculated with other P. syringae isolates harboring an intact T3SS. This result suggests a model where non-pathogenic strains engage in “cheating” through taking advantage of the nutrients released from host cells infected by pathogenic strains (Barrett et al., 2011).

Works cited

Alcázar, R., Reymond, M., Schmitz, G., and de Meaux, J. (2011). Genetic and evolutionary perspectives on the interplay between plant immunity and development. Curr. Opin. Plant Biol. 14, 378–384.

Barrett, L.G., Bell, T., Dwyer, G., and Bergelson, J. (2011). Cheating, trade-offs and the evolution of aggressiveness in a natural pathogen population. Ecol. Lett. 14, 1149–1157.

Jakob, K., Goss, E.M., Araki, H., Van, T., Kreitman, M., and Bergelson, J. (2002). Pseudomonas viridiflava and P. syringae–natural pathogens of Arabidopsis thaliana. Mol. Plant Microbe Interact. 15, 1195–1203.

Kniskern, J.M., Barrett, L.G., and Bergelson, J. (2011). Maladaptation in wild populations of the generalist plant pathogen Pseudomonas syringae. Evolution 65, 818–830.