Arabidopsis thaliana and Pseudomonas Pathogens Exhibit Stable Associations over Evolutionary Timescales

Abstract

SummaryCrop disease outbreaks are often associated with clonal expansions of single pathogenic lineages. To determine whether similar boom-and-bust scenarios hold for wild pathosystems, we carried out a multi-year, multi-site survey of Pseudomonas in its natural host Arabidopsis thaliana. The most common Pseudomonas lineage corresponded to a ubiquitous pathogenic clade. Sequencing of 1,524 genomes revealed this lineage to have diversified approximately 300,000 years ago, containing dozens of genetically identifiable pathogenic sublineages. There is differentiation at the level of both gene content and disease phenotype, although the differentiation may not provide fitness advantages to specific sublineages. The coexistence of sublineages indicates that in contrast to crop systems, no single strain has been able to overtake the studied A. thaliana populations in the recent past. Our results suggest that selective pressures acting on a plant pathogen in wild hosts are likely to be much more complex than those in agricultural systems.

Combining whole genome shotgun sequencing and rDNA amplicon analyses to improve detection of microbe-microbe interaction networks in plant leaves

“…Jugendhaus Einsiedel (JUG) around Tübingen, Germany [15,55] , in four distinct sampling batches which also had different processing details, representing our evolving pipeline.…”

Legacy of prior host and soil selection on rhizobial fitness in planta

“…; Karasov et al. ). High‐coverage pooled sequencing together with bioinformatic estimation of strain frequencies provide a means to assess selection acting on multistrain populations (Kessner et al.…”

The tomato Pto gene confers resistance to Pseudomonas floridensis, an emergent plant pathogen with just nine type III effectors

“…A recent study of the microbiota (i.e. both beneficial and pathogenic bacteria) present on wild Arabidopsis populations in Europe found dozens of Pseudomonas 'operational taxonomic units' (OTUs) present on both leaf surfaces and in the apoplast of this plant species (Karasov et al, 2018). The wild plants did not exhibit obvious disease symptoms, suggesting that some of the bacteria might exist as latent pathogens.…”

“…The wild plants did not exhibit obvious disease symptoms, suggesting that some of the bacteria might exist as latent pathogens. In fact, under controlled inoculation conditions in the greenhouse, a large number of the isolates were able to multiply and cause disease on Arabidopsis (Karasov et al, 2018). Interestingly, only one type III effector gene, avrE, was broadly conserved in these pathogenic strains.…”