The Diversity and Abundance of Soft Rot Along the Durance River Stream in the Southeast of France Revealed by Multiple Seasonal Surveys.

Although irrigation water is frequently assessed for the presence of plant pathogens, large spatial and temporal surveys that provide clues on the diversity and circulation of pathogens are missing. We evaluate the diversity of soft rot (SRP) of the genera and over 2 years in a temperate, mixed-use watershed. The abundance of isolated strains correlates with the agricultural gradient along the watershed with a positive correlation found with temperature, nitrate, and dissolved organic carbon water concentration. We characterized 582 strains by amplification and sequencing of the A gene. Multilocus sequence analysis, performed with three housekeeping genes for 99 strains, and core genome analysis of 38 sequenced strains, confirmed for all the strains but one, the taxonomic assignation obtained with the sole A sequence. spp. (549 isolates) were far more abundant than spp. (33 isolates). spp. were only observed in the lower part of the river when water temperature was >19°C, and we experimentally confirmed a decreased fitness of several spp. at 8°C in river water. dominates the spp. and and . dominate the spp., but their repartition along the watershed was different, with . being the only species regularly recovered all along the watershed. Excepting . , the and spp. responsible for disease outbreak on crops were less abundant or rarely detected. This work sheds light on the various ecological behaviors of different SRP types in stream water and indicates that SRP occupation is geographically structured.