Computational approach to identify novel genomic features conferring high fitness in Bacillus atrophaeus CNY01 and Bacillus velezensis AK-0 associated with plant growth promotion (PGP) in apple

• Published in: BMC plant biology 2024-11, Vol.24 (1), p.1127-13, Article 1127
• Main Authors: Das, Vandana Apurva, Gautam, Budhayash, Yadav, Pramod Kumar, Varadwaj, Pritish Kumar, Wadhwa, Gulshan, Singh, Satendra
• Format: Article
• Language: English
• Subjects: Antibiotic resistance; Apple; Apples; Bacillus (Bacteria); Bacillus - genetics; Bacillus - physiology; Bacillus atrophaeus; Bacillus velezensis; Bioinformatics; Biological evolution; Comparative genomic analysis; Computational biology; Computational Biology - methods; Deoxyribonucleic acid; DNA; DNA motif; Fruits; Gene transfer; Genes; Genetic analysis; Genetic aspects; Genetic diversity; Genetic Fitness; Genome, Bacterial; Genomes; Genomic analysis; Genomic island (GI); Genomic Islands; Genomics; Genomics - methods; Genotype & phenotype; Growth; Horizontal gene transfer (HGT); Horizontal transfer; Malus - genetics; Malus - microbiology; Metabolic pathways; Microbiological research; Microorganisms; Ontology; Pathogenicity; Pathogens; Physiological aspects; Plant diseases; Plant growth; Plant growth promotion (PGP); Prophage; Strains (organisms); Sustainable development
• ISSN: 1471-2229; 1471-2229
• DOI: 10.1186/s12870-024-05795-x

A comparative genomic analysis approach provides valuable information about genetic variations and evolutionary relationships among microorganisms, aiding not only in the identification of functional genes responsible for traits such as pathogenicity, antibiotic resistance, and metabolic capabilities but also in enhancing our understanding of microbial genomic diversity and their ecological roles, such as supporting plant growth promotion, thereby enabling the development of sustainable strategies for agriculture. We used two strains from different Bacillus species, Bacillus velezensis AK-0 and Bacillus atrophaeus CNY01, which have previously been reported to have PGP activity in apple, and performed comparative genomic analysis to understand their evolutionary process and obtain a mechanistic understanding of their plant growth-promoting activity. We identified genomic features such as mobile genetic elements (MGEs) that encode key proteins involved in the survival, adaptation and growth of these bacterial strains. The presence of genomic islands and intact prophage DNA in Bacillus atrophaeus CNY01 and Bacillus velezensis AK-0 suggests that horizontal gene transfer has contributed to their diversification and acquisition of adaptive traits, enhancing their evolutionary advantage. We also identified novel DNA motifs that are associated with key physiological processes and metabolic pathways.