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Structure and function of the bacterial root microbiota in wild and domesticated barley.

Bulgarelli D, Garrido-Oter R, Münch PC, Weiman A, Dröge J, Pan Y, McHardy AC, Schulze-Lefert P - Cell Host Microbe (2015)

Bottom Line: To investigate the structural and functional diversification among these communities, we employed a combination of 16S rRNA gene profiling and shotgun metagenome analysis of the microbiota associated with wild and domesticated accessions of barley (Hordeum vulgare).Strikingly, protein families assigned to these same traits showed evidence of positive selection.Our results indicate that the combined action of microbe-microbe and host-microbe interactions drives microbiota differentiation at the root-soil interface.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany; Division of Plant Sciences, College of Life Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK.

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The Barley Rhizosphere and Root Microbiota Are Gated CommunitiesAverage relative abundance (RA ± SEM) of the five most abundant (A) phyla and (B) families in soil, rhizosphere, and root samples as revealed by the 16S rRNA gene ribotyping. For each sample type, the number of replicates is n = 6. Stars indicate significant enrichment (FDR, p < 0.05) in the rhizosphere and root samples compared to bulk soil. Vertical lines denote a simultaneous enrichment of the given taxa in all three barley accessions. Only taxa with a RA > 0.5% in at least one sample were included in the analysis.
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fig1: The Barley Rhizosphere and Root Microbiota Are Gated CommunitiesAverage relative abundance (RA ± SEM) of the five most abundant (A) phyla and (B) families in soil, rhizosphere, and root samples as revealed by the 16S rRNA gene ribotyping. For each sample type, the number of replicates is n = 6. Stars indicate significant enrichment (FDR, p < 0.05) in the rhizosphere and root samples compared to bulk soil. Vertical lines denote a simultaneous enrichment of the given taxa in all three barley accessions. Only taxa with a RA > 0.5% in at least one sample were included in the analysis.

Mentions: Taxonomic classification of the OTU-representative sequences to phylum level highlighted that Actinobacteria, Bacteroidetes, and Proteobacteria largely dominate the barley rhizosphere and root communities, where 88% and 96% of the pyrosequencing reads, respectively, were assigned to these three phyla. Of note, other members of the soil biota, such as Firmicutes and Chloroflexi, were virtually excluded from the plant-associated assemblages (Figure 1). The enrichment of members of the phylum Bacteroidetes significantly discriminated rhizosphere and root samples from bulk soil samples irrespective of the accession tested (moderated t test, false discovery rate-adjusted [FDR], p value < 0.05; Figure 1) At family level, Comamonadaceae, Flavobacteriaceae, and Rhizobiaceae designated a conserved barley microbiota whose enrichment differentiated the rhizosphere and root communities from bulk soil irrespective of the accessions tested (moderated t test, FDR, p < 0.05; Figure 1). Of note, the enrichment of a fourth family, Oxalobacteraceae, also significantly discriminated between root samples and unplanted soil in wild, landrace, and modern accessions (moderated t test, FDR < 0.05; Figure 1). Taken together, these results highlight a shift in community composition at the barley root-soil interface, which progressively differentiated the rhizosphere and root bacterial assemblages from the surrounding soil biota.


Structure and function of the bacterial root microbiota in wild and domesticated barley.

Bulgarelli D, Garrido-Oter R, Münch PC, Weiman A, Dröge J, Pan Y, McHardy AC, Schulze-Lefert P - Cell Host Microbe (2015)

The Barley Rhizosphere and Root Microbiota Are Gated CommunitiesAverage relative abundance (RA ± SEM) of the five most abundant (A) phyla and (B) families in soil, rhizosphere, and root samples as revealed by the 16S rRNA gene ribotyping. For each sample type, the number of replicates is n = 6. Stars indicate significant enrichment (FDR, p < 0.05) in the rhizosphere and root samples compared to bulk soil. Vertical lines denote a simultaneous enrichment of the given taxa in all three barley accessions. Only taxa with a RA > 0.5% in at least one sample were included in the analysis.
© Copyright Policy - CC BY-NC-ND
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4362959&req=5

fig1: The Barley Rhizosphere and Root Microbiota Are Gated CommunitiesAverage relative abundance (RA ± SEM) of the five most abundant (A) phyla and (B) families in soil, rhizosphere, and root samples as revealed by the 16S rRNA gene ribotyping. For each sample type, the number of replicates is n = 6. Stars indicate significant enrichment (FDR, p < 0.05) in the rhizosphere and root samples compared to bulk soil. Vertical lines denote a simultaneous enrichment of the given taxa in all three barley accessions. Only taxa with a RA > 0.5% in at least one sample were included in the analysis.
Mentions: Taxonomic classification of the OTU-representative sequences to phylum level highlighted that Actinobacteria, Bacteroidetes, and Proteobacteria largely dominate the barley rhizosphere and root communities, where 88% and 96% of the pyrosequencing reads, respectively, were assigned to these three phyla. Of note, other members of the soil biota, such as Firmicutes and Chloroflexi, were virtually excluded from the plant-associated assemblages (Figure 1). The enrichment of members of the phylum Bacteroidetes significantly discriminated rhizosphere and root samples from bulk soil samples irrespective of the accession tested (moderated t test, false discovery rate-adjusted [FDR], p value < 0.05; Figure 1) At family level, Comamonadaceae, Flavobacteriaceae, and Rhizobiaceae designated a conserved barley microbiota whose enrichment differentiated the rhizosphere and root communities from bulk soil irrespective of the accessions tested (moderated t test, FDR, p < 0.05; Figure 1). Of note, the enrichment of a fourth family, Oxalobacteraceae, also significantly discriminated between root samples and unplanted soil in wild, landrace, and modern accessions (moderated t test, FDR < 0.05; Figure 1). Taken together, these results highlight a shift in community composition at the barley root-soil interface, which progressively differentiated the rhizosphere and root bacterial assemblages from the surrounding soil biota.

Bottom Line: To investigate the structural and functional diversification among these communities, we employed a combination of 16S rRNA gene profiling and shotgun metagenome analysis of the microbiota associated with wild and domesticated accessions of barley (Hordeum vulgare).Strikingly, protein families assigned to these same traits showed evidence of positive selection.Our results indicate that the combined action of microbe-microbe and host-microbe interactions drives microbiota differentiation at the root-soil interface.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany; Division of Plant Sciences, College of Life Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK.

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Related in: MedlinePlus