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Successional Trajectories of Rhizosphere Bacterial Communities over Consecutive Seasons.

Shi S, Nuccio E, Herman DJ, Rijkers R, Estera K, Li J, da Rocha UN, He Z, Pett-Ridge J, Brodie EL, Zhou J, Firestone M - MBio (2015)

Bottom Line: Succession in the rhizosphere was characterized by a significant decrease in both taxonomic and phylogenetic diversity relative to background soil communities, driven by reductions in both richness and evenness of the bacterial communities.Plant roots selectively stimulated the relative abundance of Alphaproteobacteria, Betaproteobacteria, and Bacteroidetes but reduced the abundance of Acidobacteria, Actinobacteria, and Firmicutes.The reproducibility of rhizosphere succession and the apparent phylogenetic conservation of rhizosphere competence traits suggest adaptation of the indigenous bacterial community to this common grass over the many decades of its presence.

View Article: PubMed Central - PubMed

Affiliation: Department of Environmental Science, Policy and Management, University of California, Berkeley, California, USA Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA.

No MeSH data available.


PCoA analysis of bulk/residual soil and rhizosphere microbial community associated with Avena fatua grown in microcosms for 12 weeks in two seasons, based on the Bray distance metric. The percent value for each axis represents the proportion of total variation explained. Circles and triangles represent samples from seasons 1 and 2, respectively. Solid symbols indicate rhizosphere soils, and open symbols indicate the bulk/residual soils. Samples collected at weeks 0, 3, 6, 9, and 12 are shown in black, green, yellow, blue, and red, respectively. Large crosses indicate the centroid of rhizosphere treatment at different plant growth stages in corresponding colors.
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fig2: PCoA analysis of bulk/residual soil and rhizosphere microbial community associated with Avena fatua grown in microcosms for 12 weeks in two seasons, based on the Bray distance metric. The percent value for each axis represents the proportion of total variation explained. Circles and triangles represent samples from seasons 1 and 2, respectively. Solid symbols indicate rhizosphere soils, and open symbols indicate the bulk/residual soils. Samples collected at weeks 0, 3, 6, 9, and 12 are shown in black, green, yellow, blue, and red, respectively. Large crosses indicate the centroid of rhizosphere treatment at different plant growth stages in corresponding colors.

Mentions: Across the 288 samples analyzed, a total of 153,504 OTUs were obtained after randomly resampling Illumina 16S sequence reads to the same depth (11,914 sequences per sample). However, this sequencing depth was not sufficient to document the vast diversity of the bacterial community in this natural soil ecosystem (see Fig. S1 in the supplemental material). To assess the dynamics of bacterial community structure over time, a principal coordinate analysis (PCoA) based on the Bray distance metric was conducted (Fig. 2). The composition of rhizosphere bacterial communities differed significantly (P < 0.01, Adonis) from bulk/residual soil communities in both seasons (Fig. 2). Rhizosphere bacterial communities exhibited successional patterns in which the rhizosphere community gradually diverged from bulk/residual soil communities as the plants grew (P < 0.01, Adonis). In addition, samples collected from the two seasons showed a clear and significant (P < 0.01, Adonis) separation. Interestingly, within each season, bulk soil samples clustered much more closely together than the rhizosphere samples (Fig. 2). In general, the dispersion among replicates of bulk bacterial communities did not change over time (0.362 to 0.369). However, in season 1, the dispersion in replicated rhizosphere bacterial communities generally increased over time with plant growth (from 0.375 to 0.417 [Fig. 2]). The source of this increased dispersion in the season 1 rhizosphere community composition was further explored by comparing the variation in plant shoot biomass (at each sampling time in season 1) and the dispersion of the associated rhizosphere community. The dispersion in the rhizosphere bacterial communities correlated strongly (Pearson’s r2 = 0.99, P < 0.01) with the variation in plant shoot biomass (see Fig. S2). Although the dispersion in rhizosphere communities in season 2 was larger than that in the residual soil communities (0.300 and 0.280, respectively; P < 0.05) (Fig. 2), it was similar across plant growth stages (0.294 to 0.302) and did not show significant correlations with the variation of plant biomass.


Successional Trajectories of Rhizosphere Bacterial Communities over Consecutive Seasons.

Shi S, Nuccio E, Herman DJ, Rijkers R, Estera K, Li J, da Rocha UN, He Z, Pett-Ridge J, Brodie EL, Zhou J, Firestone M - MBio (2015)

PCoA analysis of bulk/residual soil and rhizosphere microbial community associated with Avena fatua grown in microcosms for 12 weeks in two seasons, based on the Bray distance metric. The percent value for each axis represents the proportion of total variation explained. Circles and triangles represent samples from seasons 1 and 2, respectively. Solid symbols indicate rhizosphere soils, and open symbols indicate the bulk/residual soils. Samples collected at weeks 0, 3, 6, 9, and 12 are shown in black, green, yellow, blue, and red, respectively. Large crosses indicate the centroid of rhizosphere treatment at different plant growth stages in corresponding colors.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4526712&req=5

fig2: PCoA analysis of bulk/residual soil and rhizosphere microbial community associated with Avena fatua grown in microcosms for 12 weeks in two seasons, based on the Bray distance metric. The percent value for each axis represents the proportion of total variation explained. Circles and triangles represent samples from seasons 1 and 2, respectively. Solid symbols indicate rhizosphere soils, and open symbols indicate the bulk/residual soils. Samples collected at weeks 0, 3, 6, 9, and 12 are shown in black, green, yellow, blue, and red, respectively. Large crosses indicate the centroid of rhizosphere treatment at different plant growth stages in corresponding colors.
Mentions: Across the 288 samples analyzed, a total of 153,504 OTUs were obtained after randomly resampling Illumina 16S sequence reads to the same depth (11,914 sequences per sample). However, this sequencing depth was not sufficient to document the vast diversity of the bacterial community in this natural soil ecosystem (see Fig. S1 in the supplemental material). To assess the dynamics of bacterial community structure over time, a principal coordinate analysis (PCoA) based on the Bray distance metric was conducted (Fig. 2). The composition of rhizosphere bacterial communities differed significantly (P < 0.01, Adonis) from bulk/residual soil communities in both seasons (Fig. 2). Rhizosphere bacterial communities exhibited successional patterns in which the rhizosphere community gradually diverged from bulk/residual soil communities as the plants grew (P < 0.01, Adonis). In addition, samples collected from the two seasons showed a clear and significant (P < 0.01, Adonis) separation. Interestingly, within each season, bulk soil samples clustered much more closely together than the rhizosphere samples (Fig. 2). In general, the dispersion among replicates of bulk bacterial communities did not change over time (0.362 to 0.369). However, in season 1, the dispersion in replicated rhizosphere bacterial communities generally increased over time with plant growth (from 0.375 to 0.417 [Fig. 2]). The source of this increased dispersion in the season 1 rhizosphere community composition was further explored by comparing the variation in plant shoot biomass (at each sampling time in season 1) and the dispersion of the associated rhizosphere community. The dispersion in the rhizosphere bacterial communities correlated strongly (Pearson’s r2 = 0.99, P < 0.01) with the variation in plant shoot biomass (see Fig. S2). Although the dispersion in rhizosphere communities in season 2 was larger than that in the residual soil communities (0.300 and 0.280, respectively; P < 0.05) (Fig. 2), it was similar across plant growth stages (0.294 to 0.302) and did not show significant correlations with the variation of plant biomass.

Bottom Line: Succession in the rhizosphere was characterized by a significant decrease in both taxonomic and phylogenetic diversity relative to background soil communities, driven by reductions in both richness and evenness of the bacterial communities.Plant roots selectively stimulated the relative abundance of Alphaproteobacteria, Betaproteobacteria, and Bacteroidetes but reduced the abundance of Acidobacteria, Actinobacteria, and Firmicutes.The reproducibility of rhizosphere succession and the apparent phylogenetic conservation of rhizosphere competence traits suggest adaptation of the indigenous bacterial community to this common grass over the many decades of its presence.

View Article: PubMed Central - PubMed

Affiliation: Department of Environmental Science, Policy and Management, University of California, Berkeley, California, USA Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA.

No MeSH data available.