A pioneer in microbiome research: Arabidopsis as a model for rhizosphere microbial community assembly?

With decades of experience in the field of root nodule symbiosis, our lab at the Wageningen University has recently broadened its interest to include plant-associated microbial communities. We quantified and compared the rhizosphere effect of the model plant Arabidopsis.

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Under the surface, thousands of microbial species together make up the soil microbiome, which is one of the most diverse communities on earth. In the soil close to the plant root (rhizosphere), and to a greater extent inside plant roots (endorhizosphere), these communities are markedly different from bulk soil, a phenomenon referred to as the “rhizosphere effect”. Often, these plant-associated microbiomes are beneficial to plant, and the strength of the rhizosphere effect is plant host specific. This suggests that the capacity of plants to shape the root microbiome has differentially evolved.

To study the mechanisms underlying the rhizosphere effect, good genetic resources of the host plant are indispensable. From this point of view, Arabidopsis thaliana (Arabidopsis) is an ideal host plant. However, the fugitive, “pioneering” life history of Arabidopsis might correlate with a relatively weak rhizosphere effect. Since Arabidopsis is among other plant species now widely used as a blueprint to understand how plant species may steer their rhizosphere microbiome composition, our lab raised the question how adequate Arabidopsis is for this type of research.

To answer this question, we teamed up with researchers from the Terrestrial Ecology group, at the Netherlands Institute of Ecological Research (NIOO-KNAW). This resulted in a unique possibility to use an ecological site in the Netherlands, where Arabidopsis remained part of the ecosystem’s vegetation because of the open soil patches created by ploughing activity of wild pigs. We reasoned that this created a very good possibility to compare the rhizosphere effect of Arabidopsis with several other plant species. To do so, we set up both a lab and a field experiment with soil from this area and we selected eight other plant species, with varying successional position.

By 16S and ITS meta-amplicon sequencing analysis, we determined the shifts in microbial communities from bulk soil to rhizosphere and endorhizosphere of all the selected plants. Combined with data of enriched and depleted microbial taxa, we were able to quantify the (relative) rhizosphere effect of Arabidopsis. We found that the rhizosphere effect in the endorhizosphere of Arabidopsis is similar compared to later successional plants, for both bacterial and fungal taxa. However, the microbial community in the rhizosphere of Arabidopsis shows the closest similarity to the bulk soil community, indicating a smaller rhizosphere effect. This holds especially for true for fungal taxa. Most highly abundant taxa enriched in the other plant species were also enriched in Arabidopsis, indicating that although the rhizosphere effect of Arabidopsis might be lower, it still reflects a core plant-associated community. By comparing the rhizosphere of Arabidopsis with other plant species, we aim to position this important model plant in the emerging field of microbiome research.

Arrows from soil to either rhizosphere or endorhizosphere indicate the change in the community as measured by affected microbial taxa (OTUs), i.e. the rhizosphere effect. Percentages indicate the number of affected OTUs relative to the average of the other plant species.

Martinus Schneijderberg

PhD, Wageningen University and Research