Comparative seasonal abundance and diversity of populations of the Pseudomonas syringae and Soft Rot Pectobacteriaceae species complexes throughout the Durance River catchment from its French Alps sources to its delta

Flowing surface waters (rivers, creeks, streams) are integrators of biological, chemical and physical processes occurring in a catchment and they link catchment land cover from the headwaters to the outlet. The dynamics of human and animal pathogens in catchments have been widely studied in a large variety of contexts allowing the optimization of disease risk reduction. In parallel, there is an emerging awareness that crop pathogens might also be disseminated via surface waters especially when they are used for irrigation. However, there are no studies on the extent to which potential plant pathogens are present – nor about their dynamics - along the full course of a catchment. We do not know if they are confined to regions close to crops or if they are present throughout a catchment. Here we have compared the seasonal dynamics of populations of the Pseudomonas syringae (Psy) and the Soft Rot Pectobacteriaceae (SRP) species complexes along a 270 km stretch of the Durance River from the upstream alpine reaches to the downstream agricultural production areas at the confluence with the Rhone River at Avignon. Among 168 samples collected at 21 sites in fall, winter, spring and summer of 2016 and 2017, Psy strains were detected at all sampling sites and in 156 of the samples at population densities up to 105 bacteria L−1. In contrast, SRP strains were detected in 98 of the samples, mostly from the southern part of the river, at population densities that did not exceed 3 × 104 bacteria L−1. Among the aquatic parameters that were characterized at each sampling site (total culturable bacteria, temperature, conductivity, concentrations of dissolved organic carbon (DOC), P043−, NH4+, N02− and N03−), temperature was the only factor that explained a significant amount of the variability in population size for both species complexes. Psy densities decreased with increasing temperature whereas SRP densities increased with increasing temperature. River-borne populations of SRP were composed mainly of Pectobacterium versatile and P. aquaticum that have little known epidemiological importance. Only a few strains of Pectobacterium and Dickeya species reputed for their epidemiological impact were observed. In contrast, Psy populations at all sites were dominated by a genetic lineage of phylogroup 2 known from other studies for its broad host range and its geographic and habitat ubiquity. These results suggest that strains of SRP with pathogenic potential to plants have lower competence for saprophytic survival (in freshwaters) than do potentially pathogenic strains of Psy and that their presence in river water is probably much more dependent on specific vegetative sources than are pathogenic strains of Psy. Nevertheless, their vegetative sources have not yet been identified. We discuss how to incorporate knowledge of the abundance and diversity of these two groups of plant pathogens in river water into a strategy for anticipating risk for disease outbreaks on crops in a catchment