DOI: 10.5061/dryad.573n5tb6z
title: Fungal, bacterial & plant biomass data: Evaluation of phenolic root exudates as stimulants of saprotrophic fungi in the rhizosphere

description: 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.
description: 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<sup>-1</sup>
 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
 (<em>pdr2 </em>and <em>sid2</em>) 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 <em>A. thaliana </em>were separated
 from each other but pooled per pot, frozen, freeze-dried and weighed. This
 resulted in the measurent of total aboveground (mg
 pot<sup>-1</sup>) and belowground dry biomass (μg
 pot<sup>-1</sup>) produced in each pot. For
 a complete description of the methods, see the published
 article.
description: Sequencing data is accessible at the European Nucleotide Archive
 - primary accession PRJEB38475, secondary accession ERP121911