A genomic and transcriptomic approach to characterize a novel biocontrol bacterium Lysobacter capsici AZ78

In the European Union (EU) the authorization of new active substances based on microbial agents is strictly regulated by several Regulations of the European Commission. A large amount of information is needed to achieve the authorization as: a) phylogenetic characterization, b) virulence traits; c) efficacy; d) mechanism of action; e) secondary metabolites production; f) toxic effects on the environment, human and animal. In the last years, there is an increasing interest in biopesticides based on microbial strains, including the bacterial genus Lysobacter, because of its biocontrol features. Specifically, L. capsici AZ78 is can effectively control phytopathogenic oomycetes, such as Plasmopara viticola e Phytophthora infestans. Although, some information about the biocontrol activity of the Lysobacter genus is available, the data that can be used to complete the registration dossier of L. capsici AZ78 are few. Therefore, the aim of the study was to characterize L. capsici AZ78. The genome of L. capsici AZ78 was sequenced and compared with two close-related pathogenic bacteria to confirm the lack of virulence factors to plant and human. The genome of L. capsici AZ78 includes a broad range of specific genes encoding lytic enzyme and in vitro trials confirmed the lytic activity on different substrates. The genome annotation showed the presence of genes involved in the biosynthesis of antibiotics and the antimicrobial activity of L. capsici AZ78 was tested in vitro against bacteria, oomycetes and fungi. The genome mining allowed the identification of genes encoding Type 4 Pilus (T4P), an interestingly motility mechanism that is involved in the host colonization, such as fungal hyphae. Moreover, the identification of a compound that positively modulates the expression of T4P genes and increases the bacterial efficacy against P. viticola, could be an important information for the final formulation of the bacterium. Genes involved in the resistance to environmental stressors and in the environmental fitness of L. capsici AZ78 under field conditions, were identified. Finally, the analysis of the L. capsici AZ78 transcriptome provided a complete overview of the mechanism of action displayed by the bacterium in the interaction with P. infestans. In conclusion the scientific literature produced during this work includes information that can speed up the preparation of the registration dossier of L. capsici AZ78.