Lysobacter capsici AZ78 has considerable potential for biocontrol of phytopathogenic microorganisms. However, lack of information about genetic cues regarding its biological characteristics may slow down its exploitation as a biofungicide. In order to obtain a comprehensive overview of genetic features, the L. capsici AZ78 genome was sequenced, annotated and compared with the phylogenetically related pathogens Stenotrophomonas malthophilia K729a and Xanthomonas campestris pv. campestris ATCC 33913. Whole genome comparison, supported by functional analysis, indicated that L. capsici AZ78 has a larger number of genes responsible for interaction with phytopathogens and environmental stress than S. malthophilia K729a and X. c. pv. campestris ATCC 33913. Genes involved in the production of antibiotics, lytic enzymes and siderophores were specific for L. capsici AZ78, as well as genes involved in resistance to antibiotics, environmental stressors, fungicides and heavy metals. The L. capsici AZ78 genome did not encompass genes involved in infection of humans and plants included in the S. malthophilia K729a and X. c. pv. campestris ATCC 33913 genomes, respectively. The L. capsici AZ78 genome provides a genetic framework for detailed analysis of other L. capsici members and the development of novel biofungicides based on this bacterial strain.
Omics technologies have had a tremendous impact on underinvestigated genera of plant disease biocontrol agents such as Lysobacter. Strong evidence of the association between Lysobacter spp. and the rhizosphere has been obtained through culture-independent methods, which has also contributed towards highlighting the relationship between Lysobacter abundance and soil suppressiveness. It is conceivable that the role played by Lysobacter spp. in soil suppressiveness is related to their ability to produce an impressive array of lytic enzymes and antibiotics. Indeed, genomics has revealed that biocontrol Lysobacter strains share a vast number of genes involved in antagonism activities, and the molecular pathways underlying how Lysobacter spp. interact with the environment and other micro-organisms have been depicted through transcriptomic analysis. Furthermore, omics technologies shed light on the regulatory pathways governing cell motility and the biosynthesis of antibiotics. Overall, the results achieved so far through omics technologies confirm that the genus Lysobacter is a valuable source of novel biocontrol agents, paving the way for studies aimed at making their application in field conditions more reliable.
Biological interactions in the microbial communities of the rhizosphere continuously shape the gene expression patterns of each individual microorganism. A dual RNA-Seq approach was applied to obtain a comprehensive overview of the molecular mechanisms activated during the interaction between the biocontrol rhizobacterium Lysobacter capsici AZ78 and the soilborne phytopathogenic oomycete Phytophthora infestans. The RNA-Seq transcriptional profile of L. capsici AZ78 was characterized by up-regulation of genes concerned in the biogenesis of type 4 pilus and lytic enzymes, involved, respectively, in host colonization and subsequent attack of the P. infestans cell wall. The activation of detoxification processes allowed L. capsici AZ78 to overcome the attempted defense processes of P. infestans. Moreover, the genes involved in antibiotic biosynthesis were up-regulated in L. capsici AZ78 and caused cell death in P. infestans, with the activation of putative apoptotic processes. The consequences of P. infestans cell death resulted in the down-regulation of primary metabolic pathways, such as carbohydrates, nucleic acids and protein metabolisms. Overall, the mechanism of action of L. capsici AZ78 was related to parasitism and predatory activities that cause the death of P. infestans.
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