Whole Genome Sequencing and Comparative Genomics of Two Nematicidal <i>Bacillus</i> Strains Reveals a Wide Range of Possible Virulence Factors

Abstract

<i>Bacillus firmus</i> nematicidal bacterial strains are used to control plant parasitic nematode infestation of crops in agricultural production. Proteases are presumed to be the primary nematode virulence factors in nematicidal <i>B. firmus</i> degrading the nematode cuticle and other organs. We determined and compared the whole genome sequences of two nematicidal strains. Comparative genomics with a particular focus on possible virulence determinants revealed a wider range of possible virulence factors in a <i>B. firmus</i> isolate from a commercial bionematicide and a wild type <i>Bacillus</i> sp. isolate with nematicidal activity. The resulting 4.6 Mb <i>B. firmus</i> I-1582 and 5.3 Mb <i>Bacillus</i> sp. ZZV12-4809 genome assemblies contain respectively 18 and 19 homologs to nematode-virulent proteases, two nematode-virulent chitinase homologs in ZZV12-4809 and 28 and 36 secondary metabolite biosynthetic clusters, projected to encode antibiotics, small peptides, toxins and siderophores. The results of this study point to the genetic capability of <i>B. firmus</i> and related species for nematode virulence through a range of direct and indirect mechanisms.