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Analysis of genes contributing to plant-beneficial functions in Plant Growth-Promoting Rhizobacteria and related Proteobacteria.

Bruto M, Prigent-Combaret C, Muller D, Moënne-Loccoz Y - Sci Rep (2014)

Bottom Line: Here, this issue was targeted using 23 genes contributing directly or indirectly to established PGPR effects, based on genome sequence analysis of 304 contrasted Alpha- Beta- and Gammaproteobacteria.Most of the 23 genes studied were also found in non-PGPR Proteobacteria and none of them were common to all 25 PGPR genomes studied.However, ancestral character reconstruction indicated that gene transfers -predominantly ancient- resulted in characteristic gene combinations according to taxonomic subgroups of PGPR strains.

View Article: PubMed Central - PubMed

Affiliation: 1] Université de Lyon, F-69622, Lyon, France [2] Université Lyon 1, Villeurbanne, France [3] CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France.

ABSTRACT
The positive effects of root-colonizing bacteria cooperating with plants lead to improved growth and/or health of their eukaryotic hosts. Some of these Plant Growth-Promoting Rhizobacteria (PGPR) display several plant-beneficial properties, suggesting that the accumulation of the corresponding genes could have been selected in these bacteria. Here, this issue was targeted using 23 genes contributing directly or indirectly to established PGPR effects, based on genome sequence analysis of 304 contrasted Alpha- Beta- and Gammaproteobacteria. Most of the 23 genes studied were also found in non-PGPR Proteobacteria and none of them were common to all 25 PGPR genomes studied. However, ancestral character reconstruction indicated that gene transfers -predominantly ancient- resulted in characteristic gene combinations according to taxonomic subgroups of PGPR strains. This suggests that the PGPR-plant cooperation could have established separately in various taxa, yielding PGPR strains that use different gene assortments. The number of genes contributing to plant-beneficial functions increased along the continuum -animal pathogens, phytopathogens, saprophytes, endophytes/symbionts, PGPR- indicating that the accumulation of these genes (and possibly of different plant-beneficial traits) might be an intrinsic PGPR feature. This work uncovered preferential associations occurring between certain genes contributing to phytobeneficial traits and provides new insights into the emergence of PGPR bacteria.

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Related in: MedlinePlus

Reconstruction of acquisitions and losses of PBFC genes in relation to evolutionary history of sequenced bacteria.When different strains of the same species had the same PBFC gene profile, only one representative strain was kept in the Maximum-Likelihood tree to avoid redundant information. Acquisitions are indicated by a blue arrow with a circle and losses by a red arrow with a triangle.
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f5: Reconstruction of acquisitions and losses of PBFC genes in relation to evolutionary history of sequenced bacteria.When different strains of the same species had the same PBFC gene profile, only one representative strain was kept in the Maximum-Likelihood tree to avoid redundant information. Acquisitions are indicated by a blue arrow with a circle and losses by a red arrow with a triangle.

Mentions: All 23 genes appeared at least once in a distant ancestor of the species studied (Fig. 5). ipdC, ppdC and phlACBD are clade specific; ipdC appeared in the last common ancestor (LCA) of Pantoea and Erwinia genera, ppdC in the LCA of Azospirillum brasilense and the LCA of Bradyrhizobium strains ORS78 and BTAi1, and phlACBD in the LCA of Pseudomonas fluorescens F113 and Pseudomonas brassicacearum NFM421 and the LCA of Pseudomonas protegens Pf-5. budABC appeared in the LCA of Enterobacteriaceae; budAB are clade specific but budC was acquired at least 7 times in other clades. The pqqBCDEFG genes appeared in the LCA of the Pseudomonas; pqqG, pqqF and pqqBCDE were acquired respectively 4, 5 and 15 times by other taxa. At the extreme, nifHDK underwent at least 18 acquisitions and acdS (which appeared in the Burkholderiaceae LCA) 21 acquisitions, in both cases across the three phyla considered.


Analysis of genes contributing to plant-beneficial functions in Plant Growth-Promoting Rhizobacteria and related Proteobacteria.

Bruto M, Prigent-Combaret C, Muller D, Moënne-Loccoz Y - Sci Rep (2014)

Reconstruction of acquisitions and losses of PBFC genes in relation to evolutionary history of sequenced bacteria.When different strains of the same species had the same PBFC gene profile, only one representative strain was kept in the Maximum-Likelihood tree to avoid redundant information. Acquisitions are indicated by a blue arrow with a circle and losses by a red arrow with a triangle.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4151105&req=5

f5: Reconstruction of acquisitions and losses of PBFC genes in relation to evolutionary history of sequenced bacteria.When different strains of the same species had the same PBFC gene profile, only one representative strain was kept in the Maximum-Likelihood tree to avoid redundant information. Acquisitions are indicated by a blue arrow with a circle and losses by a red arrow with a triangle.
Mentions: All 23 genes appeared at least once in a distant ancestor of the species studied (Fig. 5). ipdC, ppdC and phlACBD are clade specific; ipdC appeared in the last common ancestor (LCA) of Pantoea and Erwinia genera, ppdC in the LCA of Azospirillum brasilense and the LCA of Bradyrhizobium strains ORS78 and BTAi1, and phlACBD in the LCA of Pseudomonas fluorescens F113 and Pseudomonas brassicacearum NFM421 and the LCA of Pseudomonas protegens Pf-5. budABC appeared in the LCA of Enterobacteriaceae; budAB are clade specific but budC was acquired at least 7 times in other clades. The pqqBCDEFG genes appeared in the LCA of the Pseudomonas; pqqG, pqqF and pqqBCDE were acquired respectively 4, 5 and 15 times by other taxa. At the extreme, nifHDK underwent at least 18 acquisitions and acdS (which appeared in the Burkholderiaceae LCA) 21 acquisitions, in both cases across the three phyla considered.

Bottom Line: Here, this issue was targeted using 23 genes contributing directly or indirectly to established PGPR effects, based on genome sequence analysis of 304 contrasted Alpha- Beta- and Gammaproteobacteria.Most of the 23 genes studied were also found in non-PGPR Proteobacteria and none of them were common to all 25 PGPR genomes studied.However, ancestral character reconstruction indicated that gene transfers -predominantly ancient- resulted in characteristic gene combinations according to taxonomic subgroups of PGPR strains.

View Article: PubMed Central - PubMed

Affiliation: 1] Université de Lyon, F-69622, Lyon, France [2] Université Lyon 1, Villeurbanne, France [3] CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France.

ABSTRACT
The positive effects of root-colonizing bacteria cooperating with plants lead to improved growth and/or health of their eukaryotic hosts. Some of these Plant Growth-Promoting Rhizobacteria (PGPR) display several plant-beneficial properties, suggesting that the accumulation of the corresponding genes could have been selected in these bacteria. Here, this issue was targeted using 23 genes contributing directly or indirectly to established PGPR effects, based on genome sequence analysis of 304 contrasted Alpha- Beta- and Gammaproteobacteria. Most of the 23 genes studied were also found in non-PGPR Proteobacteria and none of them were common to all 25 PGPR genomes studied. However, ancestral character reconstruction indicated that gene transfers -predominantly ancient- resulted in characteristic gene combinations according to taxonomic subgroups of PGPR strains. This suggests that the PGPR-plant cooperation could have established separately in various taxa, yielding PGPR strains that use different gene assortments. The number of genes contributing to plant-beneficial functions increased along the continuum -animal pathogens, phytopathogens, saprophytes, endophytes/symbionts, PGPR- indicating that the accumulation of these genes (and possibly of different plant-beneficial traits) might be an intrinsic PGPR feature. This work uncovered preferential associations occurring between certain genes contributing to phytobeneficial traits and provides new insights into the emergence of PGPR bacteria.

Show MeSH
Related in: MedlinePlus