Limits...
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

Antimicrobial activities of Bacillus sp. AP193 and its mutants ΔsrfAA, defective in surfactin expression, ΔdfnD, defective in difficidin expression, and Δsfp, defective in the expression of multiple secondary metabolites (including difficidin) against plant pathogens Pseudomonas syringe pv. tabaci, Rhizobium radiobacter, Xanthomonas axonopodis pv. vesicatoria and Xanthomonas axonopodis pv. campestris as demonstrated with an agar diffusion assay.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4538294&req=5

Figure 3: Antimicrobial activities of Bacillus sp. AP193 and its mutants ΔsrfAA, defective in surfactin expression, ΔdfnD, defective in difficidin expression, and Δsfp, defective in the expression of multiple secondary metabolites (including difficidin) against plant pathogens Pseudomonas syringe pv. tabaci, Rhizobium radiobacter, Xanthomonas axonopodis pv. vesicatoria and Xanthomonas axonopodis pv. campestris as demonstrated with an agar diffusion assay.

Mentions: Antimicrobial activities of strain AP193 and its mutants AP193ΔdfnD (deficient in the production of difficidin), AP193ΔsrfAA (deficient in surfactin production), and AP193Δsfp (unable to produce polyketide or lipopepetide due to a deletion of sfp gene encoding 4′-phosphopantetheinyl transferase) were tested against plant pathogens Pseudomonas syringe pv. tabaci, Rhizobium radiobacter, Xanthomonas axonopodis pv. vesicatoria, and Xanthomonas axonopodis pv. campestris. The AP193 wild type strain demonstrated strong antimicrobial activity, whereas the AP193Δsfp mutant was devoid of an inhibitory effect against those plant pathogens (Figure 3), underlining the contribution of lipopeptides and/or polyketides in the bioactivity of AP193. This also indicates that the dipeptide bacilysin, whose synthesis is independent of Sfp, was not involved in antagonistic activity expressed in vitro. The AP193ΔsrfAA mutant conferred antimicrobial activity similar to wild-type to P. syringe pv. tabaci, R. radiobacter, X. axonopodis pv. vesicatoria, and X. axonopodis pv. campestris (Figure 3), suggesting that surfactin has no putative role in the antibacterial activity of AP193 against those plant pathogens under the conditions tested in this study. These findings also demonstrated that surfactin neither influences the antimicrobial compound biosynthesis in AP193 nor does it inhibit antibacterial activities of the antibacterial compounds produced by AP193. Difficidin acts as the major antibiotic in antagonism of AP193 against plant pathogens P. syringe pv. tabaci, R. radiobacter, X. axonopodis pv. vesicatoria, and X. axonopodis pv. campestris as indicated by the lack of the inhibitory effect of the AP193ΔdfnD mutant against those plant pathogens (Figure 3).


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)

Antimicrobial activities of Bacillus sp. AP193 and its mutants ΔsrfAA, defective in surfactin expression, ΔdfnD, defective in difficidin expression, and Δsfp, defective in the expression of multiple secondary metabolites (including difficidin) against plant pathogens Pseudomonas syringe pv. tabaci, Rhizobium radiobacter, Xanthomonas axonopodis pv. vesicatoria and Xanthomonas axonopodis pv. campestris as demonstrated with an agar diffusion assay.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 3: Antimicrobial activities of Bacillus sp. AP193 and its mutants ΔsrfAA, defective in surfactin expression, ΔdfnD, defective in difficidin expression, and Δsfp, defective in the expression of multiple secondary metabolites (including difficidin) against plant pathogens Pseudomonas syringe pv. tabaci, Rhizobium radiobacter, Xanthomonas axonopodis pv. vesicatoria and Xanthomonas axonopodis pv. campestris as demonstrated with an agar diffusion assay.
Mentions: Antimicrobial activities of strain AP193 and its mutants AP193ΔdfnD (deficient in the production of difficidin), AP193ΔsrfAA (deficient in surfactin production), and AP193Δsfp (unable to produce polyketide or lipopepetide due to a deletion of sfp gene encoding 4′-phosphopantetheinyl transferase) were tested against plant pathogens Pseudomonas syringe pv. tabaci, Rhizobium radiobacter, Xanthomonas axonopodis pv. vesicatoria, and Xanthomonas axonopodis pv. campestris. The AP193 wild type strain demonstrated strong antimicrobial activity, whereas the AP193Δsfp mutant was devoid of an inhibitory effect against those plant pathogens (Figure 3), underlining the contribution of lipopeptides and/or polyketides in the bioactivity of AP193. This also indicates that the dipeptide bacilysin, whose synthesis is independent of Sfp, was not involved in antagonistic activity expressed in vitro. The AP193ΔsrfAA mutant conferred antimicrobial activity similar to wild-type to P. syringe pv. tabaci, R. radiobacter, X. axonopodis pv. vesicatoria, and X. axonopodis pv. campestris (Figure 3), suggesting that surfactin has no putative role in the antibacterial activity of AP193 against those plant pathogens under the conditions tested in this study. These findings also demonstrated that surfactin neither influences the antimicrobial compound biosynthesis in AP193 nor does it inhibit antibacterial activities of the antibacterial compounds produced by AP193. Difficidin acts as the major antibiotic in antagonism of AP193 against plant pathogens P. syringe pv. tabaci, R. radiobacter, X. axonopodis pv. vesicatoria, and X. axonopodis pv. campestris as indicated by the lack of the inhibitory effect of the AP193ΔdfnD mutant against those plant pathogens (Figure 3).

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