Biogeography influences plant-microbe interactions and natural soil suppressiveness to black root rot disease of tobacco

Biogeography influences natural soil suppressiveness to black root rot disease of tobacco This repositery accompanies the submitted manuscript "Biogeography influences natural soil suppressiveness to black root rot disease of tobacco". It contains the processed data of tobacco plant and soil metabolomics and tobacco rhizosphere metagenomics and amplicon sequencing and the scripts used for analyzing the data. The data and scripts are also presented in the GitLab https://gitlab.in2p3.fr/alix.catry/sps_tobacco/ hosted at the IN2P3 in Lyon. The raw genomic data used in this study are available under BioProject number PRJNA1224598, which comprises raw reads from metagenomic sequencing of the tobacco rhizosphere and raw reads from 16S and ITS amplicon sequencing of the tobacco rhizosphere. Scripts All R markdown scripts are available as HTML file to facilitate visualization of otherwise time-consuming analyses.- stats_soil_physicochemistry.Rmd: Perform statistical analyses and plot physicalchemical data of soils - Evaluate significance of differences between groups (Student's t-tests) - Correlation between symptoms and physicochemical variables - Evaluate data structure with PCA, and assess effect of soil status with PLS-DA - Assess impact of factors on soil physicochemistry (PERMANOVAs)- stats_soil_metabolomics.Rmd: Perform statistical analyses and analyze the structure of soil metabolomics data. - Compute and plot PCA of metabolomes - Assess impact of factors on soil metabolome (PERMANOVAs) - Compute and plot PLS-DA of metabolomes supervised by soil - Test correlation between metabolome distance and physical distance of soils (Mantel test)- stats_tob_disease.Rmd: Peform statistical analysis and plot figures related to diseas severity and plant health measures (biomass, plants that survived, etc.) - Effect of soil, inoculation, status, geology & geography on black root rot severity and other plant health measures (Kruskal-Wallis) - Evaluate significance of difference in severity and measures between treatments for each soil (pairwise Wilcoxon) - Plot (barplots, boxplots) plant health measures and statistical significance - Correlogram of black root rot severity and plant health measures (Spearman)- script_dada2_jki_seq13_nt.R: filter, dereplicate, merge and assign 16S amplicon sequences.- metabarcodingTobacco.Rmd: Performs statistical analyses and plots figure for the ITS and 16S metabarcoding analyses. - OTU/ASV table rarefaction - Alpha diversity: compute indices, assess impact of factors on community diversity (PERMANOVAs), boxplot representation - Beta diversity: assess impact of factors on community structure (PERMANOVAs), view community similarity between samples (NMDS), estimate correlation with physical distance of soils (Mantel test) - Get top 20 most abundant taxa and plot barplot or their relative abundance - Indicator species : identify and plot (abundance)- stats_metagenome_tobacco.Rmd: Performs statistical analyses and plots figures for metagenome data (tax. and functional annotation). - Plot abundance of SCGs by taxonomic group (Phylum, Class) and identify groups differentially abundant between supp. & cond. soils - CSS normalization of COGs, PERMANOVA and NMDS - Identification of differentially abundant COGs - Make heatmap of differentially abundant COGs- stats_bins_tobacco.Rmd: Performs statistical analyses and plots figures for the analyses of bins reconstructed from the metagenomes. - Filter bin by contamination and completion and format input files - Make taxonomy barplots for the bins - Make combined bin abundance and COG abundance heatmap - Get bins that are significantly different between soils of different status - Make heatmap for bin abundance and antiSMASH annotation cluster count - Abundance of _Pseudomonas_ bin- stats_tobacco_shoots_metabolomics.Rmd: Performs statistical analyses and plots figures for shoot metabolome data - Compute and plot PCA of metabolomes - Assess impact of factors on soil metabolome (PERMANOVAs) - Compute and plot PLS-DA of metabolomes Data Sequencing data is available under the BioProject PRJNA1224598. The geographic coordinates of soils is indicated in "geo_distance_soils.txt". Soil physicochemistry Physicochemistry measures (clay content, silt content, sand content, CEC, SAB, pH/H2O, humus, total N, P2O5, P, K2O, K, total Fe) per soil. Plant health Black root rot severity and plant health measures (fresh and dry root biomass, fresh and dry shoot biomass, mortality, number of green and damaged leaves) per soil, condition and replicate. Metabolomics Metabolomes with ion abundance per sample (soil, condition and replicate).- Tabac_NT_globale: tobacco shoot metabolome matrix with metadata- Sols_Global_avec_outliers.csv: soil metabolome matrix- variableMetadata.xlsx: retention time of ions in the metabolome matrix- Galaxy332-peakspectra.msp: Mass spectral peak library for soil metabolome (MSP formatted)- Vect_INI_trait_dim_F2.csv : metabolome metadata for tobacco shoot samples Metabarcoding - 16S - 01_rarefied_ASVs_ed_16S.txt: rarefied 16S ASV table with metadata - 08_Genus_table_sum_16S.txt: table of abundance (read count) summed by bacterial/archaeal genus with metadata - IndGenusSupFr_Co_v3.txt : 16S indicator species in French soils and control conditions, with phylum and abundance - IndGenusSupFr_Tb_v2.txt : 16S indicator species in French soils and inoc. conditions, with phylum and abundance - IndGenusSupSwiss_Co_v3.txt : 16S indicator species in Swiss soils and control conditions, with phylum and abundance - IndGenusSupSwiss_Tb_v2.txt : 16S indicator species in Swiss soils and inoculated conditions, with phylum and abundance- ITS - 01_rarefied_ASVs_ed_ITS.txt: rarefied ITS OTU table with metadata - 08_Genus_table_sum_ITS.txt: table of abundance (read count) summed by fungal genus with metadata - IndGenusSupFr_ControlOnly.txt : ITS indicator species in French soils and control conditions, with phylum and abundance - IndGenusSupFr_InocOnly.txt : ITS indicator species in French soils and inoc. conditions, with phylum and abundance - IndGenusSupSw_ControlOnly.txt : ITS indicator species in Swiss soils and control conditions, with phylum and abundance - IndGenusSupSw_InocOnly.txt : ITS indicator species in Swiss soils and inoculated conditions, with phylum and abundance Metagenomics - COG_CH_countMatrix.txt : COG abundance matrix (read count) for Swiss soils samples- Tobacco_metadata_CHs.txt: metadata for differential abundance analysis of Swiss soils samples- COG_FR_countMatrix.txt : COG abundance matrix (read count) for French soils samples- Tobacco_metadata_FR.txt: metadata for differential abundance analysis of French soils samples- COG_only_countMatrix.txt : COG abundance matrix (read count) for all samples- Tobacco_metadata_all.txt: metadata for differential abundance analysis of all samples- COG_suppressive_countMatrix.txt : COG abundance matrix (read count) for suppressive soils- Tobacco_metadata_supp.txt: metadata for differential abundance analysis of suppressive soils samples- HM_CSS_transformed_cogQ.txt: input file for heatmap of COG abundance (CSS-transformed values) and significance of differences between soil status.- df.SCG.class.txt: summed abundance (TPM) by class and SCG (PFAM id) per sample- tab.USCGs.kingdom_phylum.txt : summed abundance (TPM) by phylum and SCG (PFAM id) per sample