Supplementary files
Creators: name: Kudjordjie, Enoch Narh
name: Desmedt, Willem
name: Kyndt, Tina
name: Nicolaisen, Mogens
name: Peters, Reuben J.
name: Vestergård, Mette
Publisher: name: figshare
Year: 2025
Subjects: classificationCode: 310703
subject: Microbial ecology

description: Supplementary files for the article Phytoalexin diterpenoids shape rice root microbiomes and their associations with root parasitic nematodesEnoch Narh Kudjordjie1, Willem Desmedt2,3,4, Tina Kyndt2, Mogens Nicolaisen1, Reuben J. Peters5*, Mette Vestergård1*1Department of Agroecology, Faculty of Technical Sciences, Aarhus University, Slagelse 4200, Denmark.2VIB Center for Plant Systems Biology, Ghent 9052, Belgium.3Research Group Epigenetics and Defence, Department of Biotechnology, Ghent University, Ghent 9000, Belgium; 4Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium.5Roy J. Carver Department of Biochemistry, Biophysics &amp; Molecular Biology, Iowa State University, Ames, IA 50011, USA.*Correspondence: Reuben J. Peters (rjpeters@iastate.edu); Mette Vestergård (mvestergard@agro.au.dk)<br>Supplementary figures Fig. S1. (A) bacterial and (B) fungal sequence reads and OTUs in samples used in this study. Rarefaction curves showing the coverage of (C) bacterial and (D) fungal OTU richness (species richness in number of OTUs) as a function of sequencing depth (sample size in number of reads). Fig. S2. Bacterial Shannon diversity in root and rhizosphere of WT and mutant rice at A) 17 and B) 28 dpt. Fungal alpha diversity (Observed and Shannon) in root and rhizosphere of WT and mutant rice at C) 17 and D) 28 dpt. Fig. S3. Microbial community composition in soil and rice lines. Principal Coordinates Analysis (PCoA) of rice WT and mutants A) bacterial and B) fungal communities. Analysis was performed using datasets from both 17 and 28 dpt. Fig. S4. Principal Coordinates Analysis of microbial communities in rice WT and mutants using Bray-Curtis dissimilarity distances. PCoA plots of bacterial community in root and rhizosphere at A) 17 and B) 28 dpt. PCoA plots of fungal community in root and rhizosphere at A) 17 and B) 28 dpt. Fig. S5. Differentially abundant (log2 fold change) microbial genera in the rhizosphere of Kitaake (wildtype rice) and mutants. Differentially abundant A) bacterial and B) fungal genera between Kitaake (red) and individual mutants (green) at 17 dpt. Data are represented by log fold change (shown as a column), ±SE (shown as error bars) derived from the ANCOM-BC model. The significance of test is indicated as ***for p &lt; 0.001, ** for p &lt; 0.01 and * for p &lt; 0.05. Fig. S6. Differentially abundant (log2 fold change) microbial genera in the rhizosphere of Kitaake (wildtype rice) and mutants. Differentially abundant A) bacterial and B) fungal genera between Kitaake (red) and individual mutants (green) at 28 dpt. Data are represented by log fold change (shown as a column), ±SE (shown as error bars) derived from the ANCOM-BC model. The significance of test is indicated as ***for p &lt; 0.001, ** for p &lt; 0.01 and * for p &lt; 0.05. Fig. S7. Differentially abundant (log2 fold change) microbial genera in the rhizosphere of cps2 (red) and cps4 (green). Differentially abundant A) bacterial and B) fungal genera between Kitaake and individual mutants at 28 dpt. Data are represented by log fold change (shown as a column), ±SE (shown as error bars) derived from the ANCOM-BC model. The significance of test is indicated as ***for p &lt; 0.001, ** for p &lt; 0.01 and * for p &lt; 0.05. Fig. S8. Differentially abundant (log2 fold change) root bacterial taxa between cps2 (red) and cps2/4 (green) at A)17dpt and B) 28dpt and fungal genera at C) 17dpt and D) 28dpt. Data are represented by log fold change (shown as a column), ±SE (shown as error bars) derived from the ANCOM-BC model. The significance of test is indicated as ***for p &lt; 0.001, ** for p &lt; 0.01 and * for p &lt; 0.05. Fig. S9. Differentially abundant (log2 fold change) root bacterial taxa between cps4 (red) and cps2/4 (green) at A)17dpt and B) 28dpt and fungal genera at C) 17dpt and D) 28dpt. Data are represented by log fold change (shown as a column), ±SE (shown as error bars) derived from the ANCOM-BC model. The significance of test is indicated as ***for p &lt; 0.001, ** for p &lt; 0.01 and * for p &lt; 0.05. Fig. S10. Differentially abundant (log2 fold change) rhizosphere bacterial taxa between cps2 (red) and cps2/4 (green) at A)17dpt and B) 28dpt and fungal genera at C) 17dpt and D) 28dpt. Data are represented by log fold change (shown as a column), ±SE (shown as error bars) derived from the ANCOM-BC model. The significance of test is indicated as ***for p &lt; 0.001, ** for p &lt; 0.01 and * for p &lt; 0.05. Fig. S11. Differentially abundant (log2 fold change) rhizosphere bacterial taxa between cps4 (red) and cps2/4 (green) at A)17dpt and B) 28dpt and fungal genera at C) 17dpt and D) 28dpt. Data are represented by log fold change (shown as a column), ±SE (shown as error bars) derived from the ANCOM-BC model. The significance of test is indicated as ***for p &lt; 0.001, ** for p &lt; 0.01 and * for p &lt; 0.05. Fig. S12. Heat map of microbial-nematode associations in rice WT and mutants. Both microbes that correlated positively and negatively with M. graminicola were used for the visualization. Fig. S13. Heat map of microbial-nematode associations in rice WT and mutants. Only microbes that positively correlated with M. graminicola were used for the visualization. Supplementary Tables Table S1: Primer sets used in this study for the amplification of bacterial 16S rRNA V5-7 genes. Multiplex identifiers (MID) are indicated in bold in forward primer (799F). Table S2: Mean, median and range of reads per compartment for fungal and bacterial libraries at different days post inoculation (DPI). Table S3: Permutation analysis of variance (PERMANOVA) using “adonis” test on Bray-Curtis distance matrices for bacterial and fungal community dissimilarity assessment using 1000 permutations. Table S4: PERMANOVA (pairwise-adonis) between rice mutants cps2 and cps4.