Pan-genome analysis and molecular docking unveil the biocontrol potential of Bacillus velezensis VB7 against Phytophthora infestans

Kadiri, Mahendra; Sevugapperumal, Nakkeeran; Nallusamy, Saranya; Ragunathan, Janani; Ganesan, Malathi Varagur; Al‐Farraj, Saleh A.; Ansarif, Mohammad Javed; Sayyed, R. Z.; Lim, Hooi Ren; Show, Pau Loke

doi:10.1016/j.micres.2022.127277

Cited by 30 publications

(7 citation statements)

References 64 publications

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“…From our analysis, we demonstrated that L. irui has an open genome since the pan/core genome profiles tend to increase and decrease, respectively, with the addition of new genomes. Similar results have been noted in previous genomic studies of related Bacillus species, including B. subtillis (Brito et al 2018 ) and B. velezensis (Kadiri et al 2023 ).…”

Section: Discussionsupporting

confidence: 90%

Comparative genomics reveals insights into the potential of Lysinibacillus irui as a plant growth promoter

Hilário,

Gonçalves,

Matos

et al. 2024

Appl Microbiol Biotechnol

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Members of the genus Lysinibacillus attract attention for their mosquitocidal, bioremediation, and plant growth-promoting abilities. Despite this interest, comprehensive studies focusing on genomic traits governing plant growth and stress resilience in this genus using whole-genome sequencing are still scarce. Therefore, we sequenced and compared the genomes of three endophytic Lysinibacillus irui strains isolated from Canary Island date palms with the ex-type strain IRB4-01. Overall, the genomes of these strains consist of a circular chromosome with an average size of 4.6 Mb and a GC content of 37.2%. Comparative analysis identified conserved gene clusters within the core genome involved in iron acquisition, phosphate solubilization, indole-3-acetic acid biosynthesis, and volatile compounds. In addition, genome analysis revealed the presence of genes encoding carbohydrate-active enzymes, and proteins that confer resistance to oxidative, osmotic, and salinity stresses. Furthermore, pathways of putative novel bacteriocins were identified in all genomes. This illustrates possible common plant growth-promoting traits shared among all strains of L. irui. Our findings highlight a rich repertoire of genes associated with plant lifestyles, suggesting significant potential for developing inoculants to enhance plant growth and resilience. This study is the first to provide insights into the overall genomic signatures and mechanisms of plant growth promotion and biocontrol in the genus Lysinibacillus. Key points • Pioneer study in elucidating plant growth promoting in L. irui through comparative genomics. • Genome mining identified biosynthetic pathways of putative novel bacteriocins. • Future research directions to develop L. irui-based biofertilizers for sustainable agriculture.

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Section: Discussionsupporting

confidence: 90%

Comparative genomics reveals insights into the potential of Lysinibacillus irui as a plant growth promoter

Hilário,

Gonçalves,

Matos

et al. 2024

Appl Microbiol Biotechnol

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“…Strain JIN4 showed positive reactions in the catalase test, starch hydrolysis, VP, gelatin liquefaction, nitrate reduction, H2S production, citrate utilization, lecithin enzyme activity, cellulolytic activity and fermentation utilization tests for glucose, D-mannose, D-fructose, and D-xylose; whereas, it was negative for the oxidase reaction, MR test, malonate utilization, D-galactose and D-arabinose utilization. JIN4 was significantly similar to Bacillus subtilis (Manju & Shanmugam, 2013;Moawia et al, 2016;Kadiri et al, 2023) based on characteristic reactions.…”

Section: Physiological and Biochemical Resultsmentioning

confidence: 63%

Isolation, identification, and genome of a Bacillus velezensis JIN4 exhibiting biocontrol activity against kiwifruit bacterial canker

Zhao,

Zhai,

et al. 2023

Preprint

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Kiwifruit bacterial canker is a devastating disease in production. This study aimed to screen antagonistic bacteria that might be used to control this disease. Strain JIN4 showed significant antifungal activity against Pseudomonas syringae pv. Actinidiae (Psa) and seven other phytopathogenic bacteria isolated from kiwifruit branches. Based on morphological, physiological, and biochemical characteristics, 16S rDNA sequence analysis, and gyrA sequence analysis, JIN4 was identified as Bacillus velezensis. In field prevention experiments, the control efficiency of strain JIN4 reached 60.22%. Our results indicate that B. velezensis JIN4 has broad-spectrum antifungal resistance, and its genome contains many genes encoding enzymes involved in the synthesis of antimicrobial metabolites. In addition, JIN4 has three antibiotic-resistance genes and a cluster of nine genes used in the synthesis of secondary metabolites with antimicrobial activity. In conclusion, B. velezensis JIN4 can be used as a potential biocontrol agent against kiwifruit bacterial canker, but further work is required to improve its efficacy.

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“…With the addition of more genome assemblies, the core genome size decreased while the pan-genome size increased. The “open form” idea of Heap law ( Kadiri et al, 2023 ) was reflected as more orthologous families were included in the analysis ( Figure 3B ). On the whole, the pan-genome encompassed 9,539 orthogroups, of which 6,683 (70.06%) had been converged as the core genome, while the remaining were variable and exhibited the PAV feature, which was an important source of genetic divergence and diversity, as well as having profound effects on phenotypic variations ( Wang et al, 2014 ).…”

Section: Resultsmentioning

confidence: 99%

Insight into the phylogeny and metabolic divergence of Monascus species (M. pilosus, M. ruber, and M. purpureus) at the genome level

et al. 2023

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BackgroundSpecies of the genus Monascus are economically important and widely used in the production of food colorants and monacolin K. However, they have also been known to produce the mycotoxin citrinin. Currently, taxonomic knowledge of this species at the genome level is insufficient.MethodsThis study presents genomic similarity analyses through the analysis of the average nucleic acid identity of the genomic sequence and the whole genome alignment. Subsequently, the study constructed a pangenome of Monascus by reannotating all the genomes and identifying a total of 9,539 orthologous gene families. Two phylogenetic trees were constructed based on 4,589 single copy orthologous protein sequences and all the 5,565 orthologous proteins, respectively. In addition, carbohydrate active enzymes, secretome, allergic proteins, as well as secondary metabolite gene clusters were compared among the included 15 Monascus strains.ResultsThe results clearly revealed a high homology between M. pilosus and M. ruber, and their distant relationship with M. purpureus. Accordingly, all the included 15 Monascus strains should be classified into two distinctly evolutionary clades, namely the M. purpureus clade and the M. pilosus-M. ruber clade. Moreover, gene ontology enrichment showed that the M. pilosus-M. ruber clade had more orthologous genes involved with environmental adaptation than the M. purpureus clade. Compared to Aspergillus oryzae, all the Monascus species had a substantial gene loss of carbohydrate active enzymes. Potential allergenic and fungal virulence factor proteins were also found in the secretome of Monascus. Furthermore, this study identified the pigment synthesis gene clusters present in all included genomes, but with multiple nonessential genes inserted in the gene cluster of M. pilosus and M. ruber compared to M. purpureus. The citrinin gene cluster was found to be intact and highly conserved only among M. purpureus genomes. The monacolin K gene cluster was found only in the genomes of M. pilosus and M. ruber, but the sequence was more conserved in M. ruber.ConclusionThis study provides a paradigm for phylogenetic analysis of the genus Monascus, and it is believed that this report will lead to a better understanding of these food microorganisms in terms of classification, metabolic differentiation, and safety.

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Pan-genome analysis and molecular docking unveil the biocontrol potential of Bacillus velezensis VB7 against Phytophthora infestans

Cited by 30 publications

References 64 publications

Comparative genomics reveals insights into the potential of Lysinibacillus irui as a plant growth promoter

Comparative genomics reveals insights into the potential of Lysinibacillus irui as a plant growth promoter

Isolation, identification, and genome of a Bacillus velezensis JIN4 exhibiting biocontrol activity against kiwifruit bacterial canker

Insight into the phylogeny and metabolic divergence of Monascus species (M. pilosus, M. ruber, and M. purpureus) at the genome level

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