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Comparative and genetic analysis of the four sequenced Paenibacillus polymyxa genomes reveals a diverse metabolism and conservation of genes relevant to plant-growth promotion and competitiveness.

Eastman AW, Heinrichs DE, Yuan ZC - BMC Genomics (2014)

Bottom Line: Although a variety of plant-growth promoting traits are encoded by all strains, only P. polymyxa CR1 encodes the unique nitrogen fixation cluster found in other Paenibacillus sp.This study provides an in-depth understanding of the genome architecture of this species, thus facilitating future genetic engineering and applications in agriculture, industry and medicine.Furthermore, this study highlights the current gap in our understanding of complex plant biomass metabolism in Gram-positive bacteria.

View Article: PubMed Central - PubMed

Affiliation: Southern Crop Protection & Food Research Centre, Agriculture & Agri-Food Canada, 1391 Sandford Street, London, Ontario N5V 4 T3, Canada. zyuan27@uwo.ca.

ABSTRACT

Background: Members of the genus Paenibacillus are important plant growth-promoting rhizobacteria that can serve as bio-reactors. Paenibacillus polymyxa promotes the growth of a variety of economically important crops. Our lab recently completed the genome sequence of Paenibacillus polymyxa CR1. As of January 2014, four P. polymyxa genomes have been completely sequenced but no comparative genomic analyses have been reported.

Results: Here we report the comparative and genetic analyses of four sequenced P. polymyxa genomes, which revealed a significantly conserved core genome. Complex metabolic pathways and regulatory networks were highly conserved and allow P. polymyxa to rapidly respond to dynamic environmental cues. Genes responsible for phytohormone synthesis, phosphate solubilization, iron acquisition, transcriptional regulation, σ-factors, stress responses, transporters and biomass degradation were well conserved, indicating an intimate association with plant hosts and the rhizosphere niche. In addition, genes responsible for antimicrobial resistance and non-ribosomal peptide/polyketide synthesis are present in both the core and accessory genome of each strain. Comparative analyses also reveal variations in the accessory genome, including large plasmids present in strains M1 and SC2. Furthermore, a considerable number of strain-specific genes and genomic islands are irregularly distributed throughout each genome. Although a variety of plant-growth promoting traits are encoded by all strains, only P. polymyxa CR1 encodes the unique nitrogen fixation cluster found in other Paenibacillus sp.

Conclusions: Our study revealed that genomic loci relevant to host interaction and ecological fitness are highly conserved within the P. polymyxa genomes analysed, despite variations in the accessory genome. This work suggets that plant-growth promotion by P. polymyxa is mediated largely through phytohormone production, increased nutrient availability and bio-control mechanisms. This study provides an in-depth understanding of the genome architecture of this species, thus facilitating future genetic engineering and applications in agriculture, industry and medicine. Furthermore, this study highlights the current gap in our understanding of complex plant biomass metabolism in Gram-positive bacteria.

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Global alignment of chromosomes of completely sequencedP. polymyxastrains. The local collinear block (LCB) plot was generated using the progressiveMauve algorithm using default parameters. The name of the strain represented is listed below each LCB plot. Global alignments are visualized as LCBs, which represent regions of chromosomal similarity among strains. Six LCBs were identified in the four P. polymyxa strains genomes and are coloured according to homology to LCBs of other strains. Regions without colour both within and between LCBs represent the presence of strain-specific sequence. LCBs drawn below the horizontal correspond to inversions.
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Fig2: Global alignment of chromosomes of completely sequencedP. polymyxastrains. The local collinear block (LCB) plot was generated using the progressiveMauve algorithm using default parameters. The name of the strain represented is listed below each LCB plot. Global alignments are visualized as LCBs, which represent regions of chromosomal similarity among strains. Six LCBs were identified in the four P. polymyxa strains genomes and are coloured according to homology to LCBs of other strains. Regions without colour both within and between LCBs represent the presence of strain-specific sequence. LCBs drawn below the horizontal correspond to inversions.

Mentions: A global alignment of CR1, E681, M1 and SC2 chromosomes was performed using progressiveMauve and visualized as local collinear blocks (LCBs) to glean global information into the nucleotide level similarity amongst the sequenced P. polymyxa genomes (Figure 2). The nucleotide level similarity between M1 and SC2 is markedly higher than the similarity between any other grouping of strains (compare LCB composition between M1 and SC2, Figure 2), demonstrating the close relationship of these two strains. Furthermore, the close relationship between the chromosomes of M1 and SC2 versus the more distant CR1 and E681 at the nucleotide level becomes evident, supporting our phylogeny showing the M1 and SC2 strains forming a sub-clade within the P. polymyxa species (Figure 1). Also readily apparent is dissimilarity of the CR1 chromosome compared to any other combination of strains, with many strain-specific, low-similarity regions dispersed throughout the CR1 genome (Figure 2), which are discussed later.Figure 2


Comparative and genetic analysis of the four sequenced Paenibacillus polymyxa genomes reveals a diverse metabolism and conservation of genes relevant to plant-growth promotion and competitiveness.

Eastman AW, Heinrichs DE, Yuan ZC - BMC Genomics (2014)

Global alignment of chromosomes of completely sequencedP. polymyxastrains. The local collinear block (LCB) plot was generated using the progressiveMauve algorithm using default parameters. The name of the strain represented is listed below each LCB plot. Global alignments are visualized as LCBs, which represent regions of chromosomal similarity among strains. Six LCBs were identified in the four P. polymyxa strains genomes and are coloured according to homology to LCBs of other strains. Regions without colour both within and between LCBs represent the presence of strain-specific sequence. LCBs drawn below the horizontal correspond to inversions.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4209062&req=5

Fig2: Global alignment of chromosomes of completely sequencedP. polymyxastrains. The local collinear block (LCB) plot was generated using the progressiveMauve algorithm using default parameters. The name of the strain represented is listed below each LCB plot. Global alignments are visualized as LCBs, which represent regions of chromosomal similarity among strains. Six LCBs were identified in the four P. polymyxa strains genomes and are coloured according to homology to LCBs of other strains. Regions without colour both within and between LCBs represent the presence of strain-specific sequence. LCBs drawn below the horizontal correspond to inversions.
Mentions: A global alignment of CR1, E681, M1 and SC2 chromosomes was performed using progressiveMauve and visualized as local collinear blocks (LCBs) to glean global information into the nucleotide level similarity amongst the sequenced P. polymyxa genomes (Figure 2). The nucleotide level similarity between M1 and SC2 is markedly higher than the similarity between any other grouping of strains (compare LCB composition between M1 and SC2, Figure 2), demonstrating the close relationship of these two strains. Furthermore, the close relationship between the chromosomes of M1 and SC2 versus the more distant CR1 and E681 at the nucleotide level becomes evident, supporting our phylogeny showing the M1 and SC2 strains forming a sub-clade within the P. polymyxa species (Figure 1). Also readily apparent is dissimilarity of the CR1 chromosome compared to any other combination of strains, with many strain-specific, low-similarity regions dispersed throughout the CR1 genome (Figure 2), which are discussed later.Figure 2

Bottom Line: Although a variety of plant-growth promoting traits are encoded by all strains, only P. polymyxa CR1 encodes the unique nitrogen fixation cluster found in other Paenibacillus sp.This study provides an in-depth understanding of the genome architecture of this species, thus facilitating future genetic engineering and applications in agriculture, industry and medicine.Furthermore, this study highlights the current gap in our understanding of complex plant biomass metabolism in Gram-positive bacteria.

View Article: PubMed Central - PubMed

Affiliation: Southern Crop Protection & Food Research Centre, Agriculture & Agri-Food Canada, 1391 Sandford Street, London, Ontario N5V 4 T3, Canada. zyuan27@uwo.ca.

ABSTRACT

Background: Members of the genus Paenibacillus are important plant growth-promoting rhizobacteria that can serve as bio-reactors. Paenibacillus polymyxa promotes the growth of a variety of economically important crops. Our lab recently completed the genome sequence of Paenibacillus polymyxa CR1. As of January 2014, four P. polymyxa genomes have been completely sequenced but no comparative genomic analyses have been reported.

Results: Here we report the comparative and genetic analyses of four sequenced P. polymyxa genomes, which revealed a significantly conserved core genome. Complex metabolic pathways and regulatory networks were highly conserved and allow P. polymyxa to rapidly respond to dynamic environmental cues. Genes responsible for phytohormone synthesis, phosphate solubilization, iron acquisition, transcriptional regulation, σ-factors, stress responses, transporters and biomass degradation were well conserved, indicating an intimate association with plant hosts and the rhizosphere niche. In addition, genes responsible for antimicrobial resistance and non-ribosomal peptide/polyketide synthesis are present in both the core and accessory genome of each strain. Comparative analyses also reveal variations in the accessory genome, including large plasmids present in strains M1 and SC2. Furthermore, a considerable number of strain-specific genes and genomic islands are irregularly distributed throughout each genome. Although a variety of plant-growth promoting traits are encoded by all strains, only P. polymyxa CR1 encodes the unique nitrogen fixation cluster found in other Paenibacillus sp.

Conclusions: Our study revealed that genomic loci relevant to host interaction and ecological fitness are highly conserved within the P. polymyxa genomes analysed, despite variations in the accessory genome. This work suggets that plant-growth promotion by P. polymyxa is mediated largely through phytohormone production, increased nutrient availability and bio-control mechanisms. This study provides an in-depth understanding of the genome architecture of this species, thus facilitating future genetic engineering and applications in agriculture, industry and medicine. Furthermore, this study highlights the current gap in our understanding of complex plant biomass metabolism in Gram-positive bacteria.

Show MeSH
Related in: MedlinePlus