Drought and host selection influence bacterial community dynamics in the grass root microbiome

Abstract

Root endophytes have been shown to have important roles in determining host fitness under periods of drought stress, and yet the effect of drought on the broader root endosphere bacterial community remains largely uncharacterized. In this study, we present phylogenetic profiles of bacterial communities associated with drought-treated root and rhizosphere tissues of 18 species of plants with varying degrees of drought tolerance belonging to the Poaceae family, including important crop plants. Through 16S rRNA gene profiling across two distinct watering regimes and two developmental time points, we demonstrate that there is a strong correlation between host phylogenetic distance and the microbiome dissimilarity within root tissues, and that drought weakens this correlation by inducing conserved shifts in bacterial community composition. We identify a significant enrichment in a wide variety of Actinobacteria during drought within the roots of all hosts, and demonstrate that this enrichment is higher within the root than it is in the surrounding environments. Furthermore, we show that this observed enrichment is the result of an absolute increase in Actinobacterial abundance and that previously hypothesized mechanisms for observed enrichments in Actinobacteria in drought-treated soils are unlikely to fully account for the phenomena observed here within the plant root.

Figure 1

(a) Density plots of Shannon’s Diversity in drought (yellow) and control (samples) for each combination of sample type (soil, rhizosphere, root) and time point (early, late). Asterisks indicate drought treatment groups that were significantly different from the respective control group by anlaysis of variance (ANOVA) and Tukey's post hoc tests. (b) Principal coordinate plot for all samples generated using the Bray–Curtis distance; samples are colored for each combination of sample type and treatment. (c) Percent of variance explained by each factor as determined by canonical analysis of principal coordinates (CAPS) using the Bray–Curtis distance for remaining three experimental factors (species, time point and replicate), performed separately for each pairwise combination of sample type and treatment. The y-axis indicates the fraction of variance explained, and the shade of the bar indicates the significance. Error bars indicate a 95% bootstrap confidence interval around each fraction of variance explained.

Figure 2

(a) The relative abundance of each of the top nine most abundant bacterial classes for each pairwise combination of sample type, time point and treatment. (b) The fold enrichment under drought of each of the top nine most abundant bacterial classes for each pairwise combination of sample type and time point. (c) Heatmap displaying the fold enrichment under drought (yellow) or control (blue) in roots for all bacterial genera (x-axis) belonging to the top nine most abundant classes and identified as statistically enriched in either drought or control treatments through indicator species analysis. Enrichment is shown independently for each of the 19 host species (y-axis). The class that each genus belongs to is indicated by the colored bar above its name (colors represent the same class as in (a) and (b)). Enrichment is shown independently for each of the 19 host species (y-axis). Abbreviations correspond to host species as follows (Out=Solanum lycopersicum, Et=Eragrostis tef, Pa=Pennisetum americanum, Zm=Zea mays, Bb=Bothriochloa bladhii, Ms=Miscanthus sinensis, Sn=Sorghastrum nutans, Sl=Sorghum laxiflorum, SbH=Sorghum bicolor H, SbA=Sorghum bicolor A, Bd=Brachypodium distachyon, Fa=Festuca arundinaceae, As=Avena sativa, Hv=Hordeum vulgare, Sc=Secale cereale, Tm=Triticum monococcum, Tt=Triticum turgidum, TaG=Triticum aestivum G, TaB=Triticum aestivum B).

Figure 3

Phylogenetic tree of all Actinobacteria genera identified as indicators of drought treatment in any sample type. The inner ring indicates the five orders these genera belong to; the second, third and fourth innermost rings indicate the degree of log₁₀ fold enrichment in the soil, rhizosphere and root, respectively (legend at bottom). Darker shades of color indicate greater enrichment, whereas white indicates no significant enrichment. The outer ring indicates the log₁₀ abundance of each genus in all samples.

Figure 4

(a) Phylogenetic tree for the 18 grass lineages used in this experiment, constructed from an alignment of three conserved full-length chloroplast gene sequences (rbcL, matK, trnK); nodes for C3 grasses are colored in shades of blue, and C4 grasses are colored in shades of red. (b) The Mantel’s R coefficient is plotted for pairwise comparisons of host phylogenetic distance and microbiome distance for each pairwise combination of sample type, treatment and time point. To maintain sample evenness across the surveyed phylogenetic breadth of host species, C3 and C4 clades were analyzed separately with the inclusion of a single member from the other clade and the outgroup species. The shade of each bar indicates the significance. (c) The Mantel’s R coefficient is plotted for pairwise comparisons of field distance and microbiome distance for each pairwise combination of sample type, treatment and time point. The shade of each bar indicates the significance.

Figure 5

(a) Heatmap displaying the percent of overlap between the taxa common to the root microbiome of each host with every other host; lighter shades of blue represent less overlap, while darker shades represent more. Host species identifiers are the first letter of the genus and species (e.g. Zm for Zea mays). (b) The size of the list of common taxa as the number of OTUs identified as member of each list for each of the 19 host species.