Key microbial taxa in the rhizosphere of sorghum and sunflower grown in crop rotation

Oberholster, Tanzelle; Vikram, Surendra; Cowan, Don A.; Valverde, Angel

Key microbial taxa in the rhizosphere of sorghum and sunflower grown in crop rotation

Oberholster, Tanzelle; Vikram, Surendra; Cowan, Don A.; Valverde, Angel

Date: 2018-05

Abstract:

Microbes are key determinants of plant health and productivity. Previous studies have characterized the rhizosphere microbiomes of numerous plant species, but little information is available on how rhizosphere microbial communities change over time under crop rotation systems. Here, we document microbial communities in the rhizosphere of sorghum and sunflower (at seedling, flowering and senescence stages) grown in crop rotation in four different soils under field conditions. A comprehensive 16S rRNA-based amplicon sequencing survey revealed that the differences in alpha-diversity between rhizosphere and bulk soils changed over time. Sorghum rhizosphere soil microbial diversity at flowering and senescence were more diverse than bulk soils, whereas the microbial diversity of sunflower rhizosphere soils at flowering were less diverse with respect to bulk soils. Sampling time was also important in explaining the variation in microbial community composition in soils grown with both crops. Temporal changes observed in the rhizosphere microbiome were both plant-driven and due to seasonal changes in the bulk soil biota. Several individual taxa were relatively more abundant in the rhizosphere and/or found to be important in maintaining rhizosphere microbial networks. Interestingly, some of these taxa showed similar patterns at different sampling times, suggesting that the same organisms may play the same functional/structural role at different plant growth stages and in different crops. Overall, we have identified prominent microbial taxa that might be used to develop microbiome-based strategies for improving the yield and productivity of sorghum and sunflower.

Description:

Supplementary data Fig. S1. a) Average Good's coverage estimates (%) and b) rarefaction curves. BS, bulk soil; RS, rhizosphere soil. S, seedling; F, flowering; H, harvest. LB, Limpopo black; LR, Limpopo red; FN, Free State new; FO, Free State old.

Supplementary data Fig. S2. PCoA of soil parameters at pre-planting, using Euclidean distances with standardized data, and PERMANOVA tables. P-values were obtained after correction for multiple comparisons using Benjamini-Hochberg discovery rate. LB, Limpopo black; LR, Limpopo red; FN, Free State new; FO, Free State old.

Supplementary data Fig. S3. Faith's phylogenetic diversity (PD) at pre-planting. Different letters indicate significant differences in PD (Wilcoxon-Mann-Whitney P < 0.05) between soils. LB, Limpopo black; LR, Limpopo red; FN, Free State new; FO, Free State old.

Supplementary data Fig. S4. PCoA of soil bacterial communities at pre-planting, using weighted UniFrac distances, and PERMANOVA tables. P-values were obtained after correction for multiple comparisons using Benjamini-Hochberg discovery rate. LB, Limpopo black; LR, Limpopo red; FN, Free State new; FO, Free State old.

Supplementary data Fig. S5. Faith's phylogenetic diversity (PD), richness and Chao1 estimator. Least-square mean for each crop (So, sorghum; Su, sunflower) is plotted with ± 1 s.e of the mean. Different letters indicate significant differences (ANOVA P < 0.05).

Supplementary data Fig. S6. PCoA of post-planting soil bacterial communities, using weighted UniFrac distances, and PERMANOVA tables. LB, Limpopo black; LR, Limpopo red; FN, Free State new; FO, Free State old. So, sorghum; Su, sunflower.

Supplementary data Fig. S7. PCoA of post-planting soil parameters, using Euclidean distances with standardized data, and PERMANOVA tables. LB, Limpopo black; LR, Limpopo red; FN, Free State new; FO, Free State old. So, sorghum; Su, sunflower.

Supplementary data Fig. S8. Soil chemistry. All concentrations are expressed in mg/kg.

Supplementary data Fig. S9. Relative abundance over time of the nine most abundant phyla. PP, pre-planting; S, seedling; F, flowering; H, harvest.

Supplementary data Fig. S10. Abundance of the phyla enriched in each habitat type (bulk and rhizosphere soils). S, seedling; F, flowering; H, harvest.

Supplementary data Fig. S11. Relative abundance over time of the ten most abundant families. PP, pre-planting; S, seedling; F, flowering; H, harvest.

Supplementary data Fig. S12. Abundance of the families enriched in each habitat type (bulk and rhizosphere soils).

Supplementary data Fig. S13. Rhizosphere networks a) sorghum at seedling, b) sorghum at flowering, c) sorghum at harvest, d) sunflower at seedling, e) sunflower at flowering, f) sunflower at harvest. C, connectors; MH, module hubs; NH, network hubs. Bacteria are depicted as ellipses and archaea as squares.

Supplementary data Table S1. Good's coverage estimates indicating percentage of OTUs sampled. (https://ars.els-cdn.com/content/image/1-s2.0-S0048969717335969-mmc1.txt)

Supplementary data Table S2. . Soil chemistry. All concentrations are expressed in mg/kg. (https://ars.els-cdn.com/content/image/1-s2.0-S0048969717335969-mmc2.txt)

Supplementary data Table S3. OTUs (137 in total) showing relative abundances higher than 0.1%. These OTUs represented 43.3% of the total number of reads and belonged to the bacterial phyla Proteobacteria, Actinobacteria, Bacteroidetes and the archaeal phylum Crenarchaeota. (https://ars.els-cdn.com/content/image/1-s2.0-S0048969717335969-mmc3.txt)

Supplementary data Table S4. Differentially abundant OTUs (Bulk soil vs Rhizosphere soil). (https://ars.els-cdn.com/content/image/1-s2.0-S0048969717335969-mmc4.txt)

Supplementary data Table S5. Key rhizosphere OTUs. Defined as those found in greater abundance in the rhizosphere compared to the bulk soil in at least two growth stages and/or being module hubs, networks hubs and connectors in rhizosphere networks. (https://ars.els-cdn.com/content/image/1-s2.0-S0048969717335969-mmc5.txt)

Show full item record