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Pangenome analyses of Bacillus pumilus, Bacillus safensis, and Priestia megaterium exploring the plant-associated features of bacilli strains isolated from canola

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Abstract

Previous genome mining of the strains Bacillus pumilus 7PB, Bacillus safensis 1TAz, 8Taz, and 32PB, and Priestia megaterium 16PB isolated from canola revealed differences in the profile of antimicrobial biosynthetic genes when compared to the species type strains. To evaluate not only the similarities among B. pumilus, B. safensis, and P. megaterium genomes but also the specificities found in the canola bacilli, we performed comparative genomic analyses through the pangenome evaluation of each species. Besides that, other genome features were explored, especially focusing on plant-associated and biotechnological characteristics. The combination of the genome metrics Average Nucleotide Identity and digital DNA–DNA hybridization formulas 1 and 3 adopting the universal thresholds of 95 and 70%, respectively, was suitable to verify the identification of strains from these groups. On average, core genes corresponded to 45%, 52%, and 34% of B. pumilus, B. safensis, and P. megaterium open pangenomes, respectively. Many genes related to adaptations to plant-associated lifestyles were predicted, especially in the Bacillus genomes. These included genes for acetoin production, polyamines utilization, root exudate chemoreceptors, biofilm formation, and plant cell-wall degrading enzymes. Overall, we could observe that strains of these species exhibit many features in common, whereas most of their variable genome portions have features yet to be uncovered. The observed antifungal activity of canola bacilli might be a result of the synergistic action of secondary metabolites, siderophores, and chitinases. Genome analysis confirmed that these species and strains have biotechnological potential to be used both as agricultural inoculants or hydrolases producers. Up to our knowledge, this is the first work that evaluates the pangenome features of P. megaterium.

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Funding

This work was supported by Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Brazil, which provided EB’s postdoctoral scholarship (Grant number 155771/2018-3).

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  1. Departamento de Genética, Instituto de Biociências, Universidade Federal Do Rio Grande Do Sul (UFRGS), IB-UFRGS, Av. Bento Gonçalves 9500, Porto Alegre, 91501-970, Brazil

    Evelise Bach, Caroline Pinto Rangel, Igor Daniel Alves Ribeiro & Luciane Maria Pereira Passaglia

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EB was involved in conceptualization, methodology, investigation, formal analysis, editing, literature review, and writing; CPR was involved in investigation and validation; IDAR was involved in investigation and literature review; LMPP supervised this work. All authors read, revised, and approved the manuscript.

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Bach, E., Rangel, C.P., Ribeiro, I.D.A. et al. Pangenome analyses of Bacillus pumilus, Bacillus safensis, and Priestia megaterium exploring the plant-associated features of bacilli strains isolated from canola. Mol Genet Genomics 297, 1063–1079 (2022). https://doi.org/10.1007/s00438-022-01907-0

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