Community Assembly and Stability in the Root Microbiota During Early Plant Development

Abstract

Little is known about how community composition in the plant microbiome is affected by events in the life of a plant. For example, when the plant is exposed to soil, microbial communities may be an important factor in root community assembly. We conducted two experiments asking whether the composition of the root microbiota in mature plants could be determined by either the timing of root exposure to microbial communities or priority effects by early colonizing microbes. Timing of microbial exposure was manipulated through an inoculation experiment, where plants of different ages were exposed to a common soil inoculum. Priority effects were manipulated by challenging roots with established microbiota with an exogenous microbial community. Results show that even plants with existing microbial root communities were able to acquire new microbial associates, but that timing of soil exposure affected root microbiota composition for both bacterial and fungal communities in mature plants. Plants already colonized were only receptive to colonizers at 1 week post-germination. Our study shows that the timing of soil exposure in the early life stages of a plant is important for the development of the root microbiota in mature plants.

Keywords: Setaria viridis; bacteria; fungi; plant microbiome; priority effects; root microbiota; soil exposure.

Figure 1

Schematic overview of Experiment 1: Window of opportunity. At each harvest, root samples of Setaria viridis were collected. Harvest 1 controls for community composition prior to inoculation and includes plants of representing different developmental stages (flowering, budding, non-reproducing mature plant, seedling, and seed). Harvest 2 was collected 2 weeks after inoculation to control for the length of exposure to the inoculum, and Harvest 3 was collected when the plant was 12 weeks old to control for the age of the plant. The age of the plants at the time of harvest is listed in the diagram.

Figure 2

Different root microbial communities may develop in the plant roots if the initial community is resistant or sensitive to perturbation (colors represent different microbial taxa). In a resistant community, the progression of community development would continue in the same direction regardless of exposure to an exogenous soil (A,B). In a sensitive community, the introduction of an exogenous soil would cause a shift in community composition (C,D).

Figure 3

Alpha diversity measures of observed species richness in bacterial (A) and fungal (B) communities in roots harvested prior to (Harvest 1), or 2 weeks after (Harvest 2) exposure to soil. Each dot represents a sample. Soil exposure to an un-colonized root led to a significant increase in bacterial (t = −4.29, p = 0.0001) but not fungal (t = 1.15, p = 0.26) richness. ***indicates p < 0.001.

Figure 4

Compositional differences in bacterial (A) and fungal (B) communities of roots harvested immediately prior to, and 2 weeks after, exposure to soil. Bacterial communities differed significantly between roots harvested before and after inoculation (pseudo-F = 2.89, p = 0.0001). There was also a difference between fungal communities in roots harvested before and after inoculation (pseudo-F = 1.57, p = 0.03). Dots represent pairwise differences (measured as Bray–Curtis distances).

Figure 5

Average relative abundance of sequences belonging to bacterial (A) and fungal (B) orders, compared between samples harvested before (Harvest 1) and after inoculation (Harvest 2). For Harvest 1 and Harvest 2, the bars show an average community composition based on a combination of all samples from that harvest. Sequences were classified to the level of orders, and orders representing less than 1% of the community have been grouped as “Other.”

Figure 6

Alpha diversity measures of bacterial (A) and fungal (B) communities in 12-week-old roots that were exposed to soil at different developmental stages. Each dot represents a sample, and the variation among samples is calculated using observed Operational Taxonomic Unit (OTU) richness. Timing of exposure had no effect of the community composition of mature plants (F = 0.66, p = 0.59) or fungal (F = 1.55, p = 0.26).

Figure 7

Compositional differences in bacterial (A) and fungal (B) communities of roots harvested at 12 weeks. Plants inoculated at different developmental stages hosted distinct bacterial (Pseudo-F = 1.45, p = 0.008) and fungal communities (pseudo-F = 1.38, p = 0.03). Dots represent pairwise differences (measured as Bray–Curtis distances).

Figure 8

Observed species richness of bacterial (A) and fungal (B) root communities among roots exposed to resident (1) or exogenous (2) soils at different ages (a, b, and c). There was an overall decrease in bacterial richness over the course of the experiment, but no significant difference in richness between plants of the same age but with different soil exposure. For fungal communities, results show no significant difference between plants with different soil exposures. These observations were in accordance with Duncan test results (significant differences indicated by different lowercase letters).

Figure 9

Compositional differences in bacterial (A) and fungal (B) communities of roots across age classes [seeds (a), 1-week-old seedlings (b), or 2-weeks-old seedlings (c)] and exposure to either resident soil (1) or exogenous soil (2). For bacteria, root communities differed among plants harvested at different ages, but there was no clear distinction between plants with different soil exposure harvested at the same age. For fungi, there is no clear separation between samples with different soil exposure of any age. These trends were confirmed in PERMANOVA comparisons of the Bray–Curtis dissimilarities (Supplementary Table S6).

Figure 10

Observed species richness of bacterial (A) and fungal (B) root communities among harvests. (Harvest 1 = 4 weeks. Harvest 2 = 5 weeks, and Harvest 3 = 12 weeks) that were exposed to resident soil exogenous soil. Bacterial richness decreased significantly between Harvests 1 and 2. For fungi, there was no significant change in richness between harvests. ***indicates p < 0.001.