Selection on soil microbiomes reveals reproducible impacts on plant function

Abstract

Soil microorganisms found in the root zone impact plant growth and development, but the potential to harness these benefits is hampered by the sheer abundance and diversity of the players influencing desirable plant traits. Here, we report a high level of reproducibility of soil microbiomes in altering plant flowering time and soil functions when partnered within and between plant hosts. We used a multi-generation experimental system using Arabidopsis thaliana Col to select for soil microbiomes inducing earlier or later flowering times of their hosts. We then inoculated the selected microbiomes from the tenth generation of plantings into the soils of three additional A. thaliana genotypes (Ler, Be, RLD) and a related crucifer (Brassica rapa). With the exception of Ler, all other plant hosts showed a shift in flowering time corresponding with the inoculation of early- or late-flowering microbiomes. Analysis of the soil microbial community using 16 S rRNA gene sequencing showed distinct microbiota profiles assembling by flowering time treatment. Plant hosts grown with the late-flowering-associated microbiomes showed consequent increases in inflorescence biomass for three A. thaliana genotypes and an increase in total biomass for B. rapa. The increase in biomass was correlated with two- to five-fold enhancement of microbial extracellular enzyme activities associated with nitrogen mineralization in soils. The reproducibility of the flowering phenotype across plant hosts suggests that microbiomes can be selected to modify plant traits and coordinate changes in soil resource pools.

Figure 1

Soil microbiota group together primarily by flowering time treatment and controls. Heatmap of log absolute abundance of all taxa. Classification, dendrograms and order of samples and taxa were determined by the Prediction Analysis for Microarrays in the R statistical package. The color key at the top left includes a frequency histogram of number of OTUs at each expression level. Vertical columns represent samples mapping primarily into ‘Control', EF and LF treatment groups. The ‘control' serves as a profile of the surviving and residual microbiota endemic in the soils after steam-sterilization and without inoculation of additional microbiota. Although the heatmap showed strong clustering by treatment, eight samples were misclassified representing an error rate of 0.075.

Figure 2

Family-level taxa uniquely associated with EF/LF time groups and controls. (a) Ternary plot of OTUs showing the percent of each OTU's observations present in each group (EF, LF and Control) across different plant hosts. For example, a point's position within the ‘0.8' triangle at the ‘EF' corner of the ternary plot indicates that 80% of all observations of that OTU occur within the EF group. Diameter of plotted points corresponds to relative abundance of the OTU. Compartments of the dotted grid correspond to 20% increments. (b) List of taxonomy at the family level corresponding to OTUs of points falling within the 80% compartment of each group.

Figure 3

Unweighted UniFrac distances show separation of the EF/LF-associated microbiome treatments and controls by microbial taxa. Principle coordinates analysis of unweighted UniFrac distances generated from 16 S rRNA sequence data obtained from the rhizosphere soils of the plant hosts. Unweighted UniFrac distances are insensitive to relative abundance of observed OTUs and instead reveal patterns and differences in the presence/absence of taxa. Samples were rarefied to an even sampling depth of 12 000 seqs per sample. The orange points refer to LF microbiomes, the blue points are the EF microbiomes and the red points are the control microbiomes. Percentages on each axis represent the percent variation explained by the PCs.

Figure 4

Flowering time, reproductive biomass and potential extracellular enzyme activity show consistent changes across plant hosts. (a) Days to flowering of each plant host after inoculation with EF and LF microbiomes. (b) Reproductive biomass for the A. thaliana genotypes and total biomass for B. rapa. (c) Potential extracellular enzyme activity in soils across plant hosts. Enzyme activity associated with N mineralization is represented by the sum of leucine aminopeptidase, N-acetyl glucosaminidase and phenol oxidase (Sinsabaugh, 2010). Enzyme activity is measured in nmol per gram soil per hour. Values reported are from a standard least squares regression model including control values as a covariate (analysis of covariance). Plant host abbreviations correspond to B. rapa (BR) and the four A. thaliana genotypes Rld (RLD), Ler (LER), Col-0 (COL) and Be (BE). Asterisks denote statistical significance at P<0.05. Error bars represent s.e.m.