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

• Published in: Molecular genetics and genomics : MGG Vol. 297; no. 4; pp. 1063 - 1079
• Main Authors: Bach, Evelise, Rangel, Caroline Pinto, Ribeiro, Igor Daniel Alves, Passaglia, Luciane Maria Pereira
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer Berlin Heidelberg 01-07-2022; Springer Nature B.V
• Subjects: Acetoin; Adaptation; Animal Genetics and Genomics; Antifungal activity; Bacilli; Bacillus pumilus; Bacillus safensis; Biochemistry; Biofilms; Biomedical and Life Sciences; Biotechnology; Canola; Chemoreceptors; Deoxyribonucleic acid; DNA; Genomes; Genomic analysis; Human Genetics; Hybridization; Life Sciences; Microbial Genetics and Genomics; Original Article; Plant Genetics and Genomics; Polyamines; Priestia megaterium; Secondary metabolites; Siderophores; Species; Pangenome; Plant-associated features; Biotechnological potential; Bacillus pumilus; Bacillus safensis; Priestia megaterium
• DOI: 10.1007/s00438-022-01907-0
• EISSN: 1617-4623
• ISSN: 1617-4615

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
.