Genomic sequencing of fourteen Bacillus thuringiensis isolates: Insights into geographic variation and phylogenetic implications

Authors: Blackburn, Michael - Mike; Sparks, Michael; MISHRA, RUCHIR - University Of Florida; BONNING, BRYONY - University Of Florida

Submitted to: BMC Research Notes
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/20/2023
Publication Date: 7/4/2023
Citation: Blackburn, M.B., Sparks, M., Mishra, R., Bonning, B.C. 2023. Genomic sequencing of fourteen Bacillus thuringiensis isolates: Insights into geographic variation and phylogenetic implications. BMC Research Notes. https://doi.org/10.1186/s13104-023-06411-1.
DOI: https://doi.org/10.1186/s13104-023-06411-1

Interpretive Summary: Historically, Bacillus thuringiensis (Bt) is the most widely used microbial insecticide worldwide, and remains so today. Due to the dominance of two varieties of Bt used for insect control, many types of Bt identified in early research have been largely ignored in the years since, and there little published information about their complete pesticidal protein profiles. Using modern genomic sequencing methods, we have sequenced the genomes of fourteen Bt isolates from an extensive collection at the Invasive Insect Biocontrol and Behavior Laboratory in Beltsville , MD. Based on the sequence data, the isolates could be assigned to varieties within the framework of early serotyping identification methods, their pesticidal proteins identified, and genetic distances between isolates determined by modern genomic alignment methods. The isolates were found to represent the classical Bt serovars kurstaki, israelensis, toumanoffi, pakistani, thuringiensis, entomocidus, and finitimus. Pesticidal protein profiles were found to be identical among members of the same variety, despite the fact that the isolates were geographically diverse. Genetic distances between the isolates indicated that the isolates represent several distinct species of Bacillus. This information is valuable to those studying Bt as a living organism, and the isolates are now among the most highly characterized Bt available for research.

Technical Abstract: Genomic sequencing of fourteen geographically diverse crystalliferous Bacillus was performed on both PacBio and Illumina platforms. The genome assemblies were used to determine the pesticidal protein profiles of the isolates, and to assign the isolates to Bacillus cereus multilocus sequence types, predict their placement within the classical Bacillus thuringiensis (Bt) serotyping system, and to assess phylogenetic distances between the isolates and Bacillus thuringiensis serotype strains by calculating digital DNA-DNA hybridization (dDDH) values among the isolates. Based on these experiments, the isolates were determined to be likely representatives of Bt serovars kurstaki, pakistani, toumanoffi, israelensis, thuringiensis, entomocidus, and finitimus. Within a predicted serovar, pesticidal protein profiles were found to be identical, despite the geographic diversity of the isolates. While the dDDH values calculated for pairwise comparisons of the isolates and their apparent corresponding Bt serotype strain were, as expected, quite high (>97%), dDDH comparisons with other serotype strains were often surprisingly low, and suggest unrecognized taxa within Bt and the Bacillus cereus sensu lato.