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Abstract:
Members of the Pseudomonas genus of gram-negative bacteria are often highly abundant in the plant microbiota. While some species or isolates have been described as pathogenic, others are beneficial to host plants or merely commensals. In this study, we focus on the evolution of a focused collection of plant-associated Pseudomonas strains, to better characterize the factors governing plant colonization by members of this taxon. We collected 1,524 Pseudomonas isolates from wild Arabidopsis thaliana plants, over several years and sites near Tübingen, Germany. We sequenced and assembled the genomes of these bacterial isolates and inferred their pan-genome, based on ortholog groups. Out of the 72,397 ortholog groups specified, only 1.3% belonged to the bacterial ‘core genome’, while 36.3% were unique to individual isolates - suggesting high variability in isolates’ gene content. Next, we grouped closely-related strains (determined by their genome-wide average nucleotide identity, ANI) and compared the gene content within and between groups. By comparing these closely-related isolates, we discovered genomic islands that varied among isolates and we characterized their function and evolutionary dynamics. We found that pathogenicity levels can vary even among closely-related strains, allowing us to further associate genomic islands with strain pathogenicity. Finally, we describe our strategy for functional tests of genomic islands that are associated with microbe-microbe interactions. Taken together, our results demonstrate that focusing on the evolution of closely-related strains, which are co-colonizing the same plant population, can shed light on the complex host-microbe and microbe-microbe interactions shaping the plant microbiome.
