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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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Co-occurrence network of the PBFC genes for the 25 PGPR genomes.The genes are depicted with a colored circle according to their encoded function. Each co-occurrence is represented by an edge linking the corresponding genes and materialized by a line (based on Fisher exact test; P < 0.05). Several PBFC genes found in PGPR (i.e. pqqF, pqqG, budC, nirK, ppdC and acdS) did not display significant co-occurrence with any other(s).
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f1: Co-occurrence network of the PBFC genes for the 25 PGPR genomes.The genes are depicted with a colored circle according to their encoded function. Each co-occurrence is represented by an edge linking the corresponding genes and materialized by a line (based on Fisher exact test; P < 0.05). Several PBFC genes found in PGPR (i.e. pqqF, pqqG, budC, nirK, ppdC and acdS) did not display significant co-occurrence with any other(s).

Mentions: In the 25 sequenced PGPR strains, which belonged to the genera Azospirillum, Rhizobium/Agrobacterium (Alphaproteobacteria), Azoarcus, Burkholderia, (Betaproteobacteria), and Enterobacter, Klebsiella, Pantoea, Pseudomonas, Serratia, (Gammaproteobacteria), the PBFC genes were found in 2 (for gene ppdC) to 20 (pqqBCDE) of the genomes (Table 1). The PGPR strains harbored from 1 (i.e. acdS in Burkholderia ‘cepacia' 383 and B. phytofirmans PSJN) to 14 of the 23 PBFC genes studied (in P. protegens Pf-5, P. brassicacearum NFM421 and P. fluorescens F113), which gave 7.5 ± 3.1 PBFC genes per strain (Supplementary Fig. S1a). The exact test of Fisher (P < 0.05) evidenced that phlACBD and hcnABC significantly occurred together in certain PGPR strains (Fig. 1) i.e. pseudomonads. Three other separate groups of co-occurring genes were identified, i.e. budAB and ipdC, the operon nifHDK and the clustered genes pqqBCDE. No other significant co-occurrence of PBFC genes was found.


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)

Co-occurrence network of the PBFC genes for the 25 PGPR genomes.The genes are depicted with a colored circle according to their encoded function. Each co-occurrence is represented by an edge linking the corresponding genes and materialized by a line (based on Fisher exact test; P < 0.05). Several PBFC genes found in PGPR (i.e. pqqF, pqqG, budC, nirK, ppdC and acdS) did not display significant co-occurrence with any other(s).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f1: Co-occurrence network of the PBFC genes for the 25 PGPR genomes.The genes are depicted with a colored circle according to their encoded function. Each co-occurrence is represented by an edge linking the corresponding genes and materialized by a line (based on Fisher exact test; P < 0.05). Several PBFC genes found in PGPR (i.e. pqqF, pqqG, budC, nirK, ppdC and acdS) did not display significant co-occurrence with any other(s).
Mentions: In the 25 sequenced PGPR strains, which belonged to the genera Azospirillum, Rhizobium/Agrobacterium (Alphaproteobacteria), Azoarcus, Burkholderia, (Betaproteobacteria), and Enterobacter, Klebsiella, Pantoea, Pseudomonas, Serratia, (Gammaproteobacteria), the PBFC genes were found in 2 (for gene ppdC) to 20 (pqqBCDE) of the genomes (Table 1). The PGPR strains harbored from 1 (i.e. acdS in Burkholderia ‘cepacia' 383 and B. phytofirmans PSJN) to 14 of the 23 PBFC genes studied (in P. protegens Pf-5, P. brassicacearum NFM421 and P. fluorescens F113), which gave 7.5 ± 3.1 PBFC genes per strain (Supplementary Fig. S1a). The exact test of Fisher (P < 0.05) evidenced that phlACBD and hcnABC significantly occurred together in certain PGPR strains (Fig. 1) i.e. pseudomonads. Three other separate groups of co-occurring genes were identified, i.e. budAB and ipdC, the operon nifHDK and the clustered genes pqqBCDE. No other significant co-occurrence of PBFC genes was found.

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