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
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
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).
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:
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.
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).
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
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.
University of Chicago, Dept. of Ecology & Evolution