P-278 - Evolution of Arabidopsis thaliana-associated Pseudomonas and Sphingomonas Strains

Tuesday, July 15, 2025

09:55 - 11:30

Location: Confex Hall 3

Population Biology, Ecology & Genomics

Presenting Author(s)

HA

Haim Ashkenazy

Max Planck Institute for Biology Tuebingen
Tuebingen, Baden-Wurttemberg, Germany

Author(s)

SR

Sheila Roitman

Max Planck Institute for Biology Tuebingen
Tuebingen, Baden-Wurttemberg, Germany
OS

Or Shalev

Max Planck Institute for Biology Tuebingen
Tuebingen, Baden-Wurttemberg, Germany
TK

Talia Karasov, PhD

University of Utah
Salt Lake City, UT, USA
DL

Derek Lundberg

Research group leader
Swedish University of Agricultural Sciences
Uppsala, Uppsala Lan, Sweden
MN

Manuela Neumann

Max Planck Institute for Biology Tuebingen
Tuebingen, Baden-Wurttemberg, Germany
DW

Detlef Weigel

Max Planck Institute for Biology
Tübingen, Baden-Wurttemberg, Germany

Members of the bacterial genera Pseudomonas and Sphingomonas are often highly abundant in the leaf-associated plant microbiota. In this study, we focus on the evolution of a local collection of plant-associated Pseudomonas and Sphingomonas strains, to better characterize the factors governing plant colonization by members of these taxa.

We collected 1,524 Pseudomonas isolates and 425 Sphingomonas 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. The pan-genome suggests high variability in isolates’ gene content, where only a small fraction of the ortholog groups belongs to the ‘core genome’.

Next, we grouped closely-related strains (determined by their genome-wide average nucleotide identity) 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 further identify genomic islands shared between Pseudomonas and Sphingomonas isolates.

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.