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Verticillium  wilt causes severe yield losses in a broad range of economically important crops worldwide. As many soil fumigants have a severe environmental impact, new biocontrol strategies are needed. Members of the genus  Bacillus  are known as plant growth-promoting bacteria (PGPB) as well as biocontrol agents of pests and diseases. In this study, we isolated 267  Bacillus  strains from root-associated soil of field-grown tomato plants. We evaluated the antifungal potential of 20 phenotypically diverse strains according to their antagonistic activity against the two phytopathogenic fungi  Verticillium dahliae  and  Verticillium longisporum . In addition, the 20 strains were sequenced and phylogenetically characterized by multi-locus sequence typing (MLST) resulting in 7 different  Bacillus thuringiensis  and 13  Bacillus weihenstephanensis  strains. All  B. thuringiensis  isolates inhibited  in vitro  the tomato pathogen  V. dahliae  JR2, but had only low efficacy against the tomato-foreign pathogen  V. longisporum  43. All  B. weihenstephanensis  isolates exhibited no fungicidal activity whereas three  B. weihenstephanensis  isolates showed antagonistic effects on both phytopathogens. These strains had a rhizoid colony morphology, which has not been described for  B. weihenstephanensis  strains previously. Genome analysis of all isolates revealed putative genes encoding fungicidal substances and resulted in identification of 304 secondary metabolite gene clusters including 101 non-ribosomal polypeptide synthetases and 203 ribosomal-synthesized and post-translationally modified peptides. All genomes encoded genes for the synthesis of the antifungal siderophore bacillibactin. In the genome of one  B. thuringiensis  strain, a gene cluster for zwittermicin A was detected. Isolates which either exhibited an inhibitory or an interfering effect on the growth of the phytopathogens carried one or two genes encoding putative mycolitic chitinases, which might contribute to antifungal activities. This indicates that chitinases contribute to antifungal activities. The present study identified  B. thuringiensis  isolates from tomato roots which exhibited  in vitro  antifungal activity against  Verticillium  species.

Bacillus thuringiensis and Bacillus weihenstephanensis Inhibit the Growth of Phytopathogenic Verticillium Species