Plant-specific selection of drought-resistant biological control agents against soil-borne pathogens

Desert agriculture is a strongly growing field of land use. However, emerging problems with soil-borne pathogens limit the yield. Biological control agents (BCAs), which are able to suppress soil-borne pathogens, are promising candidates for plant protection but for desert application specific, drought-resistant strains are required. Here we report a stepwise selection procedure of BCAs from one of the most prominent organic desert farms SEKEM in Egypt. In a first step, we characterized the bacterial and fungal communities of the target habitat - the rhizospheres and endorhiza of medical plants (Matricaria chamomilla L., Calendula officinalis L. and Solanum distichum Schumach. & Thonn.). The bacterial communities were highly different - for the plant species as well as for both investigated microenvironments. The fungal community was less discriminative but characterized by phytopathogens. In a cultivation-dependent approach, isolates from all parts were obtained and characterized by their anti-phytopathogenic potential against fungi (Fusarium culmorum, Rhizoctonia solani, Verticillium dahliae), bacteria (Ralstonia solanacearum) and nematodes. In parallel, genotypic diversity was analysed by ARDRA and BOX-PCR. Both procedures resulted in the selection of 46 unique, broad-spectrum antagonists. However, their diversity was low: 89% of the selected strains belonged to the Bacillus/Paenibacillus cluster. Bacillus subtilis (subsp. subtilis and spizizenii) was the main species identified in cultures and also a dominant band in soil, rhizosphere and endorhiza in microbial fingerprints. Furthermore, using a metagenomic approach, it was shown that Firmicutes and especially Bacillus was enriched in SEKEM soil in comparison with the surrounding desert. In contrast, from the original desert soil, diverse antagonistic Streptomyces strains were selected.