The Microbiome and Evolution

We are investigating the importance of the microbiome and the holobiont in evolution. To test this, we are experimentally evolving the model plant, Arabidopsis thaliana in conjunction with a synthetic microbial community. Plant genetic diversity is supplied with a set of A. thaliana recombinant inbred lines. The synthetic microbial community is composed of bacteria, fungi, and other eukaryotes. These microbes were isolated from the tissues and rhizosphere of A. thaliana growing in the field.


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

infected crop cultivars from the ongoing adaptation experiment



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.


The evolution of resistance to pathogens

Plant pathogen interactions have been thought to undergo arms race dynamics, where there is consistant, dynamic turnover of resistance alleles – R genes – in the host, and avirulence alleles in the pathogen. If this were the case, resistance alleles segregating in natural populations should be relatively young.

However, over a decade ago we learned that, instead, R genes in plants are frequently maintained as ancient, balanced polymorphisms. Through field trials with transgenic A. thaliana lines, we have demonstrated that large fitness costs are associated with R genes experiencing balancing selection for presence/absence polymorphisms.

Not all R genes experiencing balancing selection are presence/absence polymorphisms. We are interested in how ecological and evolutionary forces combine to shape patterns of variation at RPS2, an R gene under balancing selection for disease resistance and susceptibility which is present in all natural populations of A. thaliana sequenced to date.

We have conducted a field trial with transgenic A. thaliana lines differing in only the native allele of RPS2 that they contain. We found that there was no cost of carrying a resistant allele of RPS2 in the field; instead, having any allele of RPS2 was beneficial in the field relative to a mutant that lacked RPS2.

High fitness benefit of RPS2 presence in the absence of pathogen!

Currently we are trying to understand the fitness benefit of RPS2 presence. We are exploring whether RPS2 has some alternative function, aside from the previously known resistance to avrRpt2, which gives plants with RPS2 a fitness benefit relative to plants that don’t. To support our field results, we are also determining if variation in RPS2 is associated with any fitness changes in the Recombinant Inbred Lines phenotyped by Ben Brachi.

To explore the benefit of RPS2 presence, we first asked if there was a difference in metabolome between plants with RPS2 and plants without.  We used mass spectrometry to look at the metabolomes of our transgenic lines with and without RPS2, but we found no convincing differences between these lines. We are now using RNAseq to further characterize differences between these different transgenic lines.

We are also exploring the prevalence of homologs of avrRpt2, the avirulence gene that interacts with RPS2, in the environment. Diffuse interactions with common avirulence genes in other species may help to explain the maintenance of RPS2 in all accessions. Though we did not detect avrRpt2 using PCR for any of our field samples, these PCRs may not have picked up other homologs of avrRpt2. A weak homolog of avrRpt2 seems to be present in dot blots of most P. syringae strains from the Midwestern US; if RPS2 can recognize this homolog, it may explain the consistent presence of RPS2 and the fitness benefit of RPS2 presence.

Though we expected that R genes without presence-absence polymorphisms should not carry high fitness costs of resistance, we were surprised that the presence of RPS2 carried a substantial fitness benefit. We think understanding this benefit may help us understand the difference between R genes are under balancing selection for presence/absence polymorphisms and those that always present.