Deciphering the conserved genetic loci implicated in plant disease control through comparative genomics of Bacillus amyloliquefaciens subsp. plantarum strains
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 genom...
| Main Authors: | , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2015-08-01
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| Series: | Frontiers in Plant Science |
| Subjects: | |
| Online Access: | http://journal.frontiersin.org/Journal/10.3389/fpls.2015.00631/full |
| _version_ | 1818602699112841216 |
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| author | Mohammad J Hossain Chao eRan Ke eLiu Choong-Min eRyu Cody R Rasmussen-Ivey Malachi A Williams Mohammad K Hassan Soo-Keun eChoi Haeyoung eJeong Molli eNewman Joseph W Kloepper Mark R Liles |
| author_facet | Mohammad J Hossain Chao eRan Ke eLiu Choong-Min eRyu Cody R Rasmussen-Ivey Malachi A Williams Mohammad K Hassan Soo-Keun eChoi Haeyoung eJeong Molli eNewman Joseph W Kloepper Mark R Liles |
| author_sort | Mohammad J Hossain |
| collection | DOAJ |
| description | 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- 90%, with 2,839 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 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. |
| first_indexed | 2024-12-16T13:11:25Z |
| format | Article |
| id | doaj.art-561d59f8914b4239814b7f3aac42d349 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-16T13:11:25Z |
| publishDate | 2015-08-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-561d59f8914b4239814b7f3aac42d3492022-12-21T22:30:36ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2015-08-01610.3389/fpls.2015.00631141804Deciphering the conserved genetic loci implicated in plant disease control through comparative genomics of Bacillus amyloliquefaciens subsp. plantarum strainsMohammad J Hossain0Chao eRan1Ke eLiu2Choong-Min eRyu3Cody R Rasmussen-Ivey4Malachi A Williams5Mohammad K Hassan6Soo-Keun eChoi7Haeyoung eJeong8Molli eNewman9Joseph W Kloepper10Mark R Liles11Auburn UniversityAuburn UniversityAuburn UniversitySuperbacteria Research Center, KRIBBAuburn UniversityAuburn UniversityAuburn UniversitySuperbacteria Research Center, KRIBBSuperbacteria Research Center, KRIBBAuburn UniversityAuburn UniversityAuburn UniversityTo 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- 90%, with 2,839 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 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.http://journal.frontiersin.org/Journal/10.3389/fpls.2015.00631/fullBacillusrhizospherebiocontrolBacterial spot diseasePlantarum |
| spellingShingle | Mohammad J Hossain Chao eRan Ke eLiu Choong-Min eRyu Cody R Rasmussen-Ivey Malachi A Williams Mohammad K Hassan Soo-Keun eChoi Haeyoung eJeong Molli eNewman Joseph W Kloepper Mark R Liles Deciphering the conserved genetic loci implicated in plant disease control through comparative genomics of Bacillus amyloliquefaciens subsp. plantarum strains Frontiers in Plant Science Bacillus rhizosphere biocontrol Bacterial spot disease Plantarum |
| title | Deciphering the conserved genetic loci implicated in plant disease control through comparative genomics of Bacillus amyloliquefaciens subsp. plantarum strains |
| title_full | Deciphering the conserved genetic loci implicated in plant disease control through comparative genomics of Bacillus amyloliquefaciens subsp. plantarum strains |
| title_fullStr | Deciphering the conserved genetic loci implicated in plant disease control through comparative genomics of Bacillus amyloliquefaciens subsp. plantarum strains |
| title_full_unstemmed | Deciphering the conserved genetic loci implicated in plant disease control through comparative genomics of Bacillus amyloliquefaciens subsp. plantarum strains |
| title_short | Deciphering the conserved genetic loci implicated in plant disease control through comparative genomics of Bacillus amyloliquefaciens subsp. plantarum strains |
| title_sort | deciphering the conserved genetic loci implicated in plant disease control through comparative genomics of bacillus amyloliquefaciens subsp plantarum strains |
| topic | Bacillus rhizosphere biocontrol Bacterial spot disease Plantarum |
| url | http://journal.frontiersin.org/Journal/10.3389/fpls.2015.00631/full |
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