Pseudomonas syringae is a phytopathogenic bacterium responsible for the emergence of diseases of fruit trees, including the recent outbreak of bacterial canker of kiwifruit caused P. syringae pv. actinidiae. Our goal is to develop the process of ecological engineering in plant health in orchards. The study of these bacterial diseases caused by Pseudomonas syringae gain from our experience acquired over the years on the bacteria blight of cantaloupe caused also by P. syringae.

The in-depth knowledge of environmental populations of P. syringae  generated by our team has led us to question the classical framework of P. syringae classification that was initially structured around pathovars. This new framework and our very large strain collection led us to develop quick, affordable and robust PCR tools to facilitate identification of P. syringae and characterization of its population structure in various contexts.

Bacterial cankers caused by Pseudomonas syringae in orchards (apricot, kiwifruit)

The kiwifruit canker due to P. syringae pv. actinidiae represent an important economic issue worldwide. In France, means of control of bacterial canker consist of copper treatments and preventive measures in order to reduce the spread of bacteria within and between orchards.

Our research is focused on the study of the role of orchard ground cover plants in the emergence of fruit tree diseases:

• simultaneous study of P. syringae communities associated with ground covers and fruit trees from apricot and kiwifruit orchards chosen for their health status (healthy, diseased, or disease emergence)
• study of different ground cover management practices (bare soil, ground cover in inter-rows, ground cover in inter-rows and tree rows)

The ground cover plants and orchard weeds host abundant P. syringae communities, however the role of ground covers in the emergence of fruit tree diseases remains ignored. Simultaneous study of ground cover and fruit tree P. syringae communities highlight bacterial exchanges between these two compartments because of the presence of genetically correlated strains in both of them

A new framework for the classification of the Pseudomonas syringae complex

• based on systematic characterization (phenotypic and genotypic) of about 800 strains of P. syringae selected from our collection to represent the full range of known diversity of this bacterium. We delimited and described 13 phylogroups of P. syringae of which 5 were new. The sequence of a single housekeeping gene (citrate synthase) is sufficient for classifying over 97% of the strains into the phylogroups.
• this new framework and our very large strain collection led us to develop quick, affordable and robust PCR tools. By comparative genomics, primers were designed to identify as P. syringae any new isolate in a PCR without the need for subsequent sequencing. Likewise, primers specific to each phylogroup were designed.

Berge, O., Monteil, C., Bartoli, C., Chandeysson, C., Guilbaud, C., Sands, D. C., Morris, C. E. (2014). A user's guide to a data base of the diversity of Pseudomonas syringae and its application to classifying strains in this phylogenetic complex. Plos One, 9, e105547. DOI : 10.1371/journal.pone.0105547 https://hal.inrae.fr/hal-02640865 Guilbaud, C., Morris, C. E., Barakat, M., Ortet, P., Berge, O. (2016). Isolation and identification of Pseudomonas syringae facilitated by a PCR targeting the whole P. syringae group. FEMS microbiology ecology, 92, fiv146 . DOI : 10.1093/femsec/fiv146https://hal.inrae.fr/hal-02632676 Morris, C. E., Lamichhane, J. R., Nikolic, I., Stanković, S., Moury, B. (2019). The overlapping continuum of host range among strains in the Pseudomonas syringae complex. Phytopathology Research, 1:4, 16 p. DOI : 10.1186/s42483-018-0010-6 https://hal.inrae.fr/hal-02621367v1