Indigenous soil bacteria: an alternative strategy to protect against potato diseases

Potato has been present in Europe for more than 500 years and has become one of the major crops. Although significant improvements have been made in term of selection and agricultural practices, potato crops are still facing the burden of bacterial diseases such as tuber soft rot (Pectobacterium carotovorum), common scab (Streptomyces scabies) and fungal diseases such as tuber dry rot (Fusarium solani), black scurf (Rhizoctonia solani), early blight (Alternaria solani) and potato late blight (Phytophthora infestans), this latter being the major pathogen in terms of yield losses. Both disease pressure and exploitation profitability enforce farmers to use large amounts of pesticides that lead to important economic and environmental costs. However, the strengthening of European policies regarding the limited use of pesticides forces producers to find sustainable alternatives. A suitable solution is an Integrated Pest Management (IPM), which promotes prevention means, purposeful fertilizations and/or alternative crop protection strategies. These strategies have led to study and use microbial agents due to their antagonistic abilities and their competence to induce natural plant defenses. The present study aims at characterizing indigenous bacteria (Bacillus spp. and Pseudomonas spp.) associated with potato-agrosystems for diseases biocontrol. From a large collection of more than 2,000 strains isolated from Belgian soils, 54 Bacillus spp. and 16 Pseudomonas spp. have been selected for further characterization. The bacteria were identified by sequencing their 16S RNA genes and, for some, their gyrase genes. PCR screenings were then performed to identify potential virulent genetic determinants and to list the genes associated with known bioactive molecules. The results indicated that none of the studied Bacillus strains displayed a potential pathogenicity towards vertebrates or plants. Genes associated with different bioactive molecules such as lipopeptides, bacteriocins or siderophores were also revealed. Beside preliminary genetic characterization, in vitro tests showed promising antagonistic activities of the bacterial collection against the following potato pathogens: P. infestans, F. solani, A. solani, R. solani, P. carotovorum and S. scabies. The most promising strains are currently further characterized through whole genome sequencing, in vitro antagonistic activities and field assays to assess their bona fide antagonistic potentials and to better understand the mechanisms involved in their antagonistic activities.