Stability and succession of the rhizosphere microbiota depends upon plant type and soil composition

Abstract

We examined succession of the rhizosphere microbiota of three model plants (Arabidopsis, Medicago and Brachypodium) in compost and sand and three crops (Brassica, Pisum and Triticum) in compost alone. We used serial inoculation of 24 independent replicate microcosms over three plant generations for each plant/soil combination. Stochastic variation between replicates was surprisingly weak and by the third generation, replicate microcosms for each plant had communities that were very similar to each other but different to those of other plants or unplanted soil. Microbiota diversity remained high in compost, but declined drastically in sand, with bacterial opportunists and putative autotrophs becoming dominant. These dramatic differences indicate that many microbes cannot thrive on plant exudates alone and presumably also require carbon sources and/or nutrients from soil. Arabidopsis had the weakest influence on its microbiota and in compost replicate microcosms converged on three alternative community compositions rather than a single distinctive community. Organisms selected in rhizospheres can have positive or negative effects. Two abundant bacteria are shown to promote plant growth, but in Brassica the pathogen Olpidium brassicae came to dominate the fungal community. So plants exert strong selection on the rhizosphere microbiota but soil composition is critical to its stability. microbial succession/ plant-microbe interactions/rhizosphere microbiota/selection.

Figure 1

Experimental design of multi-generation plant growth. Autoclaved sand or compost (90% by volume) was inoculated with Bawburgh grass soil (10% by volume) for the first generation of plant growth. In generations two and three, soil (25% by volume) from the previous generation was used as an inoculum. Bawburgh grass soil constituted 10, 2.5 and 0.6% (volume) in successive generations. Identical treatment was given to unplanted controls for three generations. After 4 weeks growth plants were harvested and DNA isolated from the rhizosphere for ARISA and 454Flx analysis of the microbiota.

Figure 2

Different model and crop plants grown in sand and compost establish distinct rhizosphere microbiota. (a) Sand: ARISA analysis of first generation of plants. (b) Sand: 454Flx pyrosequencing analysis of bacteria from all three generations. (c) Compost: 454Flx pyrosequencing analysis of bacteria from three generations of model plants. (d) Compost: 454Flx pyrosequencing analysis of bacteria from three generations of crop plants. Data shown as n multi-dimensional scaling plots (based on Bray–Curtis dissimilarity), which lack axes and where each data point represents one plant microbiota.

Figure 3

The effect on the bacterial rhizosphere microbiota of plants grown in sand compared with compost. Each sphere represents a single OTU, size represents abundance, position corresponds to the relative abundance in the three rhizospheres and colour reflects the rhizosphere abundance relative to unplanted soil calculated for each generation separately. Please refer to Supplementary Figure S6 for an example explanation. (a) Bacterial microbiota of model plants grown in sand. (b) Bacterial microbiota of model plants grown in compost. (c) Bacterial microbiota of crop plants grown in compost. Only OTUs with a relative abundance of greater than 0.1% were used. Achromobacter xylosoxidans (Ax), Acidovorax (A), Arthrobacter sp. (Asp), Massilia (M), Pseudomonas (P), Rhizobium (three separate OTUs are annotated) (R), Rhodopseudomonas (Rh), Rodanobacter (Ro), Solirubrobacter (So) Stenotrophomonas (S) and Arabidopsis (A), Medicago (M), Brachypodium (B), Brassica (Br), Pisum (P), Triticum (W) and generation (1, 2, 3).

Figure 4

An invasion of Olpidium brassicae on Brassica rapa corresponds with increased abundance of Massilia. The black line represents O. brassicae abundance and bars represent abundance of the genus Massilia. B. rapa was grown for three generations on compost, A. thaliana (A), M. truncatula (M), Brassica distachyon (B), B. rapa (Br), Pisum sativum (P), Triticum aestivum (W), unplanted control (U), generation (1, 2, 3). The abundance of Massilia and Olpidium in Brassica rhizospheres was compared against other rhizospheres using t-tests. Grey and black stars represent statistical significance result for Massilia and Olpidium abundance, respectively. *P<0.05, a-absent. Error bars represent the standard error calculated from three biological replicates.