The rhizosphere microbial community of crop plants in intensively managed arable soils is strongly dominated by bacteria, especially in the initial stages of plant development. In order to establish more diverse and balanced rhizosphere microbiomes, as seen for wild plants, crop variety selection could be based on their ability to promote growth of saprotrophic fungi in the rhizosphere. We hypothesized that this can be achieved by increasing the exudation of phenolic acids, as generally higher fungal abundance is observed in environments with phenolic-rich inputs, such as exudates of older plants and litter leachates. To test this, a rhizosphere simulation microcosm was designed to establish gradual diffusion of root exudate metabolites from sterile sand into arable soil. With this system, we tested the fungus-stimulating effect of eight phenolic acids alone or in combination with primary root metabolites. Ergosterol-based fungal biomass measurements revealed that most phenolic acids did not increase fungal abundance in the arable soil layer. These results were supported by comparison of fungal biomass in the rhizosphere of wild type Arabidopsis thaliana plants and mutants with altered phenolic acid metabolism. Salicylic acid was the only phenolic acid that stimulated a higher fungal biomass in the arable soil layer of microcosms, but only when combined with a background of primary root metabolites. However, no such stimulation of rhizosphere fungi was seen for a salicylic acid-overproducing A. thaliana mutant. For three phenolic acid treatments (chlorogenic acid, salicylic acid, vanillic acid) fungal and bacterial community compositions were analyzed using amplicon sequencing. Despite having little effect on fungal biomass, phenolic acids combined with primary metabolites promoted a higher relative abundance of soil-borne fungi with the ability to invade plant roots (Fusarium, Trichoderma and Fusicolla spp.) in the simulated rhizosphere. Bacterial community composition was also affected by these phenolic acids. Although this study indicates that phenolic acids do not increase fungal biomass in the rhizosphere, we highlight a potential role of phenolic acids as attractants for root-colonizing fungi.

The data was collected from two experiments.

The first experiment (Exp. 1) was carried out in two-compartment microcosms, which were used to simulate diffusion of root exudates into arable soil. This set-up is referred throughout this study as "simulated rhizosphere microcosm". With it we investigated the effect of eight phenolic acids on abundance fungi and bacteria. Eight phenolic acids (vanillic acid, syringic acid, gallic acid, salicylic acid, chlorogenic acid, nicotinic acid, ferulic acid, cinnamic acid) were applied alone and in combination with primary metabolites (PM). The soil was sampled from the simulated rhizosphere. Ergosterol was extracted from the soil samples and sand samples with the Bååth method and measured with an LC-MS-MS. Ergosterol values (μg ergosterol g^-1 soil) were used as a proxy for fungal biomass. DNA was extracted from soil samples and 16S qPCR was performed in order to quantify the abundance of bacteria. Fungal biomass was quantified for all treatments, whereas bacterial abundance was quantified only for the control, vanillic acid and salicylic acid (with and without primary metabolites) treatments.

In the second experiment (Exp. 2), two A. thaliana mutant lines with altered phenolics exudation patterns (pdr2 and sid2) and two wild-type A. thaliana lines (Col-0 and Col-8) were grown in an arable soil. Fungal biomass was measured in the rhizosphere of these plants at two developmental stages, using the same methods of ergosterol extraction and measurement as in Exp. 1. Roots and shoots of A. thaliana were separated from each other but pooled per pot, frozen, freeze-dried and weighed. This resulted in the measurent of total aboveground (mg pot^-1) and belowground dry biomass (μg pot^-1) produced in each pot.

For a complete description of the methods, see the published article.

Sequencing data is accessible at the European Nucleotide Archive - primary accession PRJEB38475, secondary accession ERP121911