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Bacterial systematics and microdiversity of plant pathogenic bacteria

Taking advantage of our knowledge of ecology (coexistence of pathogenic and non-pathogenic strains) and systematics (organization into species complexes), and disregarding classifications based on pathogenicity (presence of pTi, organization into pathovars), we are contributing to the definition of the Agrobacterium genus and its component species (Singh et al. 2021; Trong et al. 2021, Nabi et al. 2022). We have also launched bacterial systematics work on the causal agent of leaf bacterial blight of lettuce and amended the taxonomy, delimiting the species Xanthomonas hortorum pv. vitians (Morinière et al. 2021).

Molecular and chemical bases of plant adaptation

Using an integrative strategy, we analyze the molecular and chemical basis of the interaction of our bacterial models with the plant by combining different techniques: analysis of the selective value and expression of genes, particularly in contact with the plant or in response to plant metabolites, as well as the plant's response, notably through metabolomic analysis and metabolite profiling.

With this approach, we show that in Agrobacterium fabrum, the functions encoded by the 7 species-specific regions define the ecological niche of A. fabrum in relation to the plant. For example, one of the species-specific islands enables the degradation of various hydroxycinnamic acids (HCAs), including ferulic acid, a major component of the plant wall. The presence of ferulic acid in the plant environment has led us to finely characterize the HCA degradation pathway and its regulation (Campillo et al. 2014; Meyer et al. 2018, Vigouroux et al. 2020).

The rhizosphere and the tumor are competitive environments for bacteria. The team is therefore interested in the mechanisms of cooperation (e.g. degradation of toxic compounds), bacterial competition (e.g. role of secretion systems, Dechèvre et al. in preparation), and cellular communication (e.g. N-acyl-homoserine lactone), which fluctuate according to biotic and abiotic conditions.

Plant tissues also represent a complex environment that the bacterium must master in order to multiply. In order to investigate the molecular basis underlying the interaction between Xanthomonas hortorum pv. vitians and lettuce, and in particular to understand the pathogen's pathogenicity, we opted for an unprejudiced Transposon insertion sequencing (Tn-seq) approach and thus established the set of genes required for the establishment of this pathogen in its host (Morinière et al. 2022).

Ecological roles of biological nanoparticles (bacterial extracellular vesicles and bacteriophages)

Our work on the adaptation of plant pathogenic bacteria to their host has encouraged us to consider the importance of bacterial extracellular vesicles in the dialogue between bacteria and the host, including the microbiota. At present, we have undertaken a detailed and exhaustive characterization of the cargo of bacterial extracellular vesicles in A. tumefaciens, as well as characterizing their impact on the plant host and its microbiota.

Understanding the pathogenicity and identifying the virulence genes of X. hortorum pv. vitians may lead to the establishment of strategies for controlling lettuce bacterial leaf disease, including innovative biocontrol solutions against these pathogens such as phage therapy, i.e. the use of bacteriophages to combat bacterial infection. Phagotherapy, in combination with phytoprotective bacteria or natural substances, is currently being developed within the team as a strategy for controlling lettuce leaf bacterial disease. These associations will be tested in the laboratory under in situ conditions, in order to propose a solution for the agro-ecological transition towards low-input, resilient systems.

Diagnosis of crown gall, grapevine scab and root hair disease

We have developed various techniques for diagnosing phytobacterial diseases such as crown gall and grapevine leaf scorch caused by bacteria of the Agrobacterium / Allorhizobium genus. These analyses are based on the isolation and identification of phytopathogenic bacteria from symptomatic tissues, the detection of virulence genes (e.g. present on the Ti virulence plasmid) from tumor-derived isolates, and the reproduction of symptoms on model plants (Habbadi et al., 2020). Complementing these traditional approaches (Koch's postulate), the team has developed a method for the detection and quantification of opines (tumor-specific constituents and perennial biomarkers of infection) by UHPLC-MS QTOF (Padilla et al. 2020).