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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

Phylogeny of PGPR Bacillus spp. evaluated in this study. (A) Neighbor joining phylogenetic tree based on gyrB sequences using B. cereus ATCC 14579T as an outgroup. (B) Maximum-likelihood phylogenetic tree of the 25 B. subtilis group strains based on 729,383 bp sequence of core genome. Two clusters belonging to B. amyloliquefaciens subsp. plantarum and B. amyloliquefaciens subsp. amyloliquefaciens are indicated by brackets.
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Figure 1: Phylogeny of PGPR Bacillus spp. evaluated in this study. (A) Neighbor joining phylogenetic tree based on gyrB sequences using B. cereus ATCC 14579T as an outgroup. (B) Maximum-likelihood phylogenetic tree of the 25 B. subtilis group strains based on 729,383 bp sequence of core genome. Two clusters belonging to B. amyloliquefaciens subsp. plantarum and B. amyloliquefaciens subsp. amyloliquefaciens are indicated by brackets.

Mentions: For phylogenetic analysis, the gyrB gene sequence for each strain (a list of the 25 strains is presented in Figure 1) was retrieved from sequence data. Strains AS43.3, FZB42, YAU B9601-Y2, CAU B946, and 5B6 were used as representative strains of B. amyloliquefaciens subsp. plantarum; strains DSM7, LL3, and TA208 were used as representative strains of B. amyloliquefaciens subsp. amyloliquefaciens. The gyrB phylogenetic tree was inferred with MEGA5.05 (Tamura et al., 2011) using Neighbor-Joining (Saitou and Nei, 1987) and Maximum Likelihood (ML) methods (Felsenstein, 1981). All positions that contained gaps or missing data were eliminated from the final dataset, resulting in 1911 bp positions of gyrB sequence. We used 729,383 bp of DNA to represent the conserved core genome found across 25 strains of the B. subtilis group, to generate a phylogenomic tree using RAxML (v 7.2.7) (Pfeiffer and Stamatakis, 2010). The phylogenomic tree was then visualized with iTOL (http://itol.embl.de) (Letunic and Bork, 2011).


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)

Phylogeny of PGPR Bacillus spp. evaluated in this study. (A) Neighbor joining phylogenetic tree based on gyrB sequences using B. cereus ATCC 14579T as an outgroup. (B) Maximum-likelihood phylogenetic tree of the 25 B. subtilis group strains based on 729,383 bp sequence of core genome. Two clusters belonging to B. amyloliquefaciens subsp. plantarum and B. amyloliquefaciens subsp. amyloliquefaciens are indicated by brackets.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 1: Phylogeny of PGPR Bacillus spp. evaluated in this study. (A) Neighbor joining phylogenetic tree based on gyrB sequences using B. cereus ATCC 14579T as an outgroup. (B) Maximum-likelihood phylogenetic tree of the 25 B. subtilis group strains based on 729,383 bp sequence of core genome. Two clusters belonging to B. amyloliquefaciens subsp. plantarum and B. amyloliquefaciens subsp. amyloliquefaciens are indicated by brackets.
Mentions: For phylogenetic analysis, the gyrB gene sequence for each strain (a list of the 25 strains is presented in Figure 1) was retrieved from sequence data. Strains AS43.3, FZB42, YAU B9601-Y2, CAU B946, and 5B6 were used as representative strains of B. amyloliquefaciens subsp. plantarum; strains DSM7, LL3, and TA208 were used as representative strains of B. amyloliquefaciens subsp. amyloliquefaciens. The gyrB phylogenetic tree was inferred with MEGA5.05 (Tamura et al., 2011) using Neighbor-Joining (Saitou and Nei, 1987) and Maximum Likelihood (ML) methods (Felsenstein, 1981). All positions that contained gaps or missing data were eliminated from the final dataset, resulting in 1911 bp positions of gyrB sequence. We used 729,383 bp of DNA to represent the conserved core genome found across 25 strains of the B. subtilis group, to generate a phylogenomic tree using RAxML (v 7.2.7) (Pfeiffer and Stamatakis, 2010). The phylogenomic tree was then visualized with iTOL (http://itol.embl.de) (Letunic and Bork, 2011).

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