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Deciphering the conserved genetic loci implicated in plant disease control through comparative genomics of Bacillus amyloliquefaciens subsp. plantarum.

Hossain MJ, Ran C, Liu K, Ryu CM, Rasmussen-Ivey CR, Williams MA, Hassan MK, Choi SK, Jeong H, Newman M, Kloepper JW, Liles MR - Front Plant Sci (2015)

Bottom Line: Comparative genomic analyses of B. amyloliquefaciens strains identified genes that are linked with biological control and colonization of roots and/or leaves, including 73 genes uniquely associated with subsp. plantarum strains that have predicted functions related to signaling, transportation, secondary metabolite production, and carbon source utilization.Although B. amyloliquefaciens subsp. plantarum strains contain gene clusters that encode many different secondary metabolites, only polyketide biosynthetic clusters that encode difficidin and macrolactin are conserved within this subspecies.This study defines genomic features of PGPR strains and links them with biocontrol activity and with host colonization.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, Auburn University Auburn, AL, USA.

ABSTRACT
To understand the growth-promoting and disease-inhibiting activities of plant growth-promoting rhizobacteria (PGPR) strains, the genomes of 12 Bacillus subtilis group strains with PGPR activity were sequenced and analyzed. These B. subtilis strains exhibited high genomic diversity, whereas the genomes of B. amyloliquefaciens strains (a member of the B. subtilis group) are highly conserved. A pairwise BLASTp matrix revealed that gene family similarity among Bacillus genomes ranges from 32 to 90%, with 2839 genes within the core genome of B. amyloliquefaciens subsp. plantarum. Comparative genomic analyses of B. amyloliquefaciens strains identified genes that are linked with biological control and colonization of roots and/or leaves, including 73 genes uniquely associated with subsp. plantarum strains that have predicted functions related to signaling, transportation, secondary metabolite production, and carbon source utilization. Although B. amyloliquefaciens subsp. plantarum strains contain gene clusters that encode many different secondary metabolites, only polyketide biosynthetic clusters that encode difficidin and macrolactin are conserved within this subspecies. To evaluate their role in plant pathogen biocontrol, genes involved in secondary metabolite biosynthesis were deleted in a B. amyloliquefaciens subsp. plantarum strain, revealing that difficidin expression is critical in reducing the severity of disease, caused by Xanthomonas axonopodis pv. vesicatoria in tomato plants. This study defines genomic features of PGPR strains and links them with biocontrol activity and with host colonization.

No MeSH data available.


Related in: MedlinePlus

LC-MS spectra for metabolites from cell-free supernatants of (A) wild-type B. amyloliquefaciens AP193, and (B) its isogenic dfnD mutant, when grown in TSB for 72 h. Note that in negative ion mode that only the deprotonated form of oxydifficidin was detected in bacterial culture supernatants at a m/z 559.3.
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Figure 4: LC-MS spectra for metabolites from cell-free supernatants of (A) wild-type B. amyloliquefaciens AP193, and (B) its isogenic dfnD mutant, when grown in TSB for 72 h. Note that in negative ion mode that only the deprotonated form of oxydifficidin was detected in bacterial culture supernatants at a m/z 559.3.

Mentions: We further confirmed that the AP193ΔdfnD and Δsfp mutants lacked synthesis of difficidin by conducting LC-MS analysis of the cell-free TSB culture supernatants from wild-type AP193 and each of these mutants. As reported previously, only the deprotonated form of oxydifficidin was detectable in bacterial supernatants using MS in the negative mode ([M – H]− = 559.3) (Chen et al., 2006), with a molecular mass of 559.3 detected in supernatants of the wild-type AP193 culture but not observed from the culture of the ΔdfnD mutant (Figure 4) or from the Δsfp mutant (data not shown). The ΔsrfAA mutant exhibited difficidin synthesis as in the wild-type AP193 culture (data not shown). These findings demonstrate the importance of difficidin in the biocontrol activity of subsp. plantarum strains against plant pathogens.


Deciphering the conserved genetic loci implicated in plant disease control through comparative genomics of Bacillus amyloliquefaciens subsp. plantarum.

Hossain MJ, Ran C, Liu K, Ryu CM, Rasmussen-Ivey CR, Williams MA, Hassan MK, Choi SK, Jeong H, Newman M, Kloepper JW, Liles MR - Front Plant Sci (2015)

LC-MS spectra for metabolites from cell-free supernatants of (A) wild-type B. amyloliquefaciens AP193, and (B) its isogenic dfnD mutant, when grown in TSB for 72 h. Note that in negative ion mode that only the deprotonated form of oxydifficidin was detected in bacterial culture supernatants at a m/z 559.3.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4538294&req=5

Figure 4: LC-MS spectra for metabolites from cell-free supernatants of (A) wild-type B. amyloliquefaciens AP193, and (B) its isogenic dfnD mutant, when grown in TSB for 72 h. Note that in negative ion mode that only the deprotonated form of oxydifficidin was detected in bacterial culture supernatants at a m/z 559.3.
Mentions: We further confirmed that the AP193ΔdfnD and Δsfp mutants lacked synthesis of difficidin by conducting LC-MS analysis of the cell-free TSB culture supernatants from wild-type AP193 and each of these mutants. As reported previously, only the deprotonated form of oxydifficidin was detectable in bacterial supernatants using MS in the negative mode ([M – H]− = 559.3) (Chen et al., 2006), with a molecular mass of 559.3 detected in supernatants of the wild-type AP193 culture but not observed from the culture of the ΔdfnD mutant (Figure 4) or from the Δsfp mutant (data not shown). The ΔsrfAA mutant exhibited difficidin synthesis as in the wild-type AP193 culture (data not shown). These findings demonstrate the importance of difficidin in the biocontrol activity of subsp. plantarum strains against plant pathogens.

Bottom Line: Comparative genomic analyses of B. amyloliquefaciens strains identified genes that are linked with biological control and colonization of roots and/or leaves, including 73 genes uniquely associated with subsp. plantarum strains that have predicted functions related to signaling, transportation, secondary metabolite production, and carbon source utilization.Although B. amyloliquefaciens subsp. plantarum strains contain gene clusters that encode many different secondary metabolites, only polyketide biosynthetic clusters that encode difficidin and macrolactin are conserved within this subspecies.This study defines genomic features of PGPR strains and links them with biocontrol activity and with host colonization.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, Auburn University Auburn, AL, USA.

ABSTRACT
To understand the growth-promoting and disease-inhibiting activities of plant growth-promoting rhizobacteria (PGPR) strains, the genomes of 12 Bacillus subtilis group strains with PGPR activity were sequenced and analyzed. These B. subtilis strains exhibited high genomic diversity, whereas the genomes of B. amyloliquefaciens strains (a member of the B. subtilis group) are highly conserved. A pairwise BLASTp matrix revealed that gene family similarity among Bacillus genomes ranges from 32 to 90%, with 2839 genes within the core genome of B. amyloliquefaciens subsp. plantarum. Comparative genomic analyses of B. amyloliquefaciens strains identified genes that are linked with biological control and colonization of roots and/or leaves, including 73 genes uniquely associated with subsp. plantarum strains that have predicted functions related to signaling, transportation, secondary metabolite production, and carbon source utilization. Although B. amyloliquefaciens subsp. plantarum strains contain gene clusters that encode many different secondary metabolites, only polyketide biosynthetic clusters that encode difficidin and macrolactin are conserved within this subspecies. To evaluate their role in plant pathogen biocontrol, genes involved in secondary metabolite biosynthesis were deleted in a B. amyloliquefaciens subsp. plantarum strain, revealing that difficidin expression is critical in reducing the severity of disease, caused by Xanthomonas axonopodis pv. vesicatoria in tomato plants. This study defines genomic features of PGPR strains and links them with biocontrol activity and with host colonization.

No MeSH data available.


Related in: MedlinePlus