Additional file 1 of Effects of above ground pathogen infection and fungicide application on the root-associated microbiota of apple saplings
Creators: name: Becker, Maximilian Fernando
name: Klueken, A. Michael
name: Knief, Claudia
Publisher: name: figshare
Year: 2024
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Plant Biology

description: Additional file 1. Table S1. The hierarchies in each of the trials with the number of samples. Total read number after quality filtering, mean number of reads per sample and the number of samples remaining after quality filtering. Table S2. Differences in beta diversity of the root-associated bacterial community of apple saplings in the L- and T-compartment inoculated with two different pathogens and sampled at different timepoints. The disease severity, the height of the plant and the number of leaves was measured at each timepoint. Effect sizes were assessed by ANOSIM based on DEICODE distance matrices. Significant resultsare printed bold. Table S3. Differences in beta diversity of the root-associated bacterial community of apple saplings in the L- and T-compartment treated with two different pathogens and sampled at different timepoints. Effect sizes were assessed by PERMANOVA based on DEICODE distance matrices. Significant resultsare printed bold. Table S4. Dispersion of the root-associated bacterial community of young apple plants between different treatments at different timepoints in the L- and T-compartment. The different treatments included inoculations with either V. inaequalisor P. leucotricha and an uninoculated control. Effect sizes were assessed by PERMDISP and Tukey’s test based on DEICODE distance matrices and p-values adjusted after multiple comparison. Significant results are printed bold. Figure S1. Composition of the root-associated bacterial community of apple plants as revealed by 16S rRNA gene amplicon sequencing in the temporal trial. The relative abundance of bacterial families in samples from three different treatments sampled at different days after inoculation in the loosely associated and tightly associated compartment is shown. Phyla and their families with &lt; 2% relative abundance in the respective treatment were grouped as “Other”. Figure S2. Differential abundance analysis of genera in the L- and T-compartment in dependence on pathogen infection 40 days after inoculation compared to 0 DAI based on ANCOM-BC. Plants were either inoculated with V. inaequalisor P. leucotricha and are shown besides an uninoculated control treatment. The heatmap shows the coefficients obtained from the ANCOM-BC log-linear model divided by their standard error. The colour code indicates differential abundances of genera between the two timepoints with red indicating an increase in relative abundance at 40 DAI compared to 0 DAI. A “*” is shown if ANCOM-BC showed significant differences using the adjusted p-value in this comparison. The mean relative abundances of the taxa are displayed at 40 DAI in percent. In the L‑compartment, most identified genera of the pathogen inoculated plants belong to the phylum Proteobacteria, e.g., unclassified members of the Comamonadaceae, Moraxellaceae, Morganellaceae, Sphingomonadaceae and Xanthomonadaceae. In the control plants, several Acidobacteriota such as Acidipila, Bryobacter or Bryocella were significantly decreased in relative abundance at 40 DAI, though not in the inoculated plants. Only few observations like these were made in the T-compartment with Edaphobacter, Acidibacter and unclassified members of Methylophilaceae and Micropepsaceae being significantly increased in the inoculated plants 40 DAI, but not in the control plants. Figure S3. Composition of the root-associated bacterial community of apple plants as revealed by 16S rRNA gene amplicon sequencing in the mixed trial. The relative abundance of bacterial families in samples from three different treatments at three different timepoints in the loosely associated and tightly associated compartment is shown. Phyla and their families with &lt; 2% relative abundance in the respective treatment were grouped as “Other”. Figure S4. Variation in beta diversity of differently treated apple saplings at timepoint 3 in the L-compartment and T-compartment. Variation is presented based on constrained analysis of principle coordinates using DEICODE distance matrices; it is constrained by the variables treatment and disease severity. Plants were either inoculated with P. leucotricha and left untreated or were additionally treated with a synthetic fungicide, or they underwent a treatment with water as control. The different treatments are shown in different colors, and disease severity is illustrated by different symbol sizes, rated on a 0-5 scale with 0 = healthy plants and 5 = plants having multiple leaves entirely covered with mycelium and with leaves close to senescence. Figure S5. Boxplots showing the differences between two different treatments to an untreated control group for the L-compartment and T-compartment at TP3 based on DEICODE distances. Significant differences were calculated with pairwise Kruskal-Wallis tests.