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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

Phylogenetic distribution of genes along Proteobacteria phylogeny.Internal circles: presence of a gene is indicated by a grey square and absence by a white square. Taxonomically coherent groups with the same gene content were collapsed for sake of clarity. Biovars are indicated for Rhizobium leguminosarum and pathovars for Pseudomonas syringae.
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f3: Phylogenetic distribution of genes along Proteobacteria phylogeny.Internal circles: presence of a gene is indicated by a grey square and absence by a white square. Taxonomically coherent groups with the same gene content were collapsed for sake of clarity. Biovars are indicated for Rhizobium leguminosarum and pathovars for Pseudomonas syringae.

Mentions: The distribution of certain PBFC genes according to bacterial ecological type could, at least in part, reflect taxonomic properties. This is indicated by the occurrence of PBFC genes in taxa restricted to a given ecological type (Fig. 3). In particular, ppdC was only retrieved in certain Azospirillum PGPR and Bradyrhizobium in the endophyte/symbiont category. For many PBFC genes, however, their occurrence within a taxon was related to species/strain ecology. This was the case for phlACBD (Pseudomonas PGPR), hcnABC (all Pseudomonas types except phytopathogens), and nifHDK (mainly in PGPR and endophytes/symbionts from various proteobacterial taxa). The relation to ecology, if any, was not as strong for ipdC and budAB (Enterobacteriaceae), acdS (all Burkholderiaceae considered and various Alphaproteobacteria and Gammaproteobacteria), nirK and pqq genes (various Proteobacteria corresponding to several ecological types).


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)

Phylogenetic distribution of genes along Proteobacteria phylogeny.Internal circles: presence of a gene is indicated by a grey square and absence by a white square. Taxonomically coherent groups with the same gene content were collapsed for sake of clarity. Biovars are indicated for Rhizobium leguminosarum and pathovars for Pseudomonas syringae.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f3: Phylogenetic distribution of genes along Proteobacteria phylogeny.Internal circles: presence of a gene is indicated by a grey square and absence by a white square. Taxonomically coherent groups with the same gene content were collapsed for sake of clarity. Biovars are indicated for Rhizobium leguminosarum and pathovars for Pseudomonas syringae.
Mentions: The distribution of certain PBFC genes according to bacterial ecological type could, at least in part, reflect taxonomic properties. This is indicated by the occurrence of PBFC genes in taxa restricted to a given ecological type (Fig. 3). In particular, ppdC was only retrieved in certain Azospirillum PGPR and Bradyrhizobium in the endophyte/symbiont category. For many PBFC genes, however, their occurrence within a taxon was related to species/strain ecology. This was the case for phlACBD (Pseudomonas PGPR), hcnABC (all Pseudomonas types except phytopathogens), and nifHDK (mainly in PGPR and endophytes/symbionts from various proteobacterial taxa). The relation to ecology, if any, was not as strong for ipdC and budAB (Enterobacteriaceae), acdS (all Burkholderiaceae considered and various Alphaproteobacteria and Gammaproteobacteria), nirK and pqq genes (various Proteobacteria corresponding to several ecological types).

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