Intra-annual shift and deterministic assembly of root endospheric microbial communities of the grapevines

*Script_PCOA_RDA.R

Script to perform multivariate analysis - PCOA to test the effect of date sampling on the microbial composition (with random effect "individual grapevine incorporated ) for each cultivar- RDA to analyse the microbial composition differences between the cultivar (for each date)

*Script_linearMixMod.R

Script to perform univariate models (linear Mixed Models (with random effect "individual grapevine incorporated ) to test the effecto test the effect of date sampling on the microbial richness

*Matrix_Bacteria_sumup.ods

Data to perform multivariate, univariate and null model analyses on bacterial communities
-> This spreadsheet file has 9 sheets : (1) summary of the spreadsheet content and matrices information; (2) Bacterial composition for the two cultivars and the three dates tested (backup matrix) ; (3) Bacterial composition for only the Cabernet Sauvignon cultivar samples(neutral models construction); (4) Bacterial composition for only the Merlot cultivar samples(neutral models construction); (5)transposition of the matrix containing Bacterial composition for only the Cabernet Sauvignon cultivar samples (PCOA analyses); (6)transposition of the matrix containing Bacterial composition for only the Merlot cultivar samples (PCOA analyses); (7) Richness values of each Cabernet sauvignon samples for the major phyla of bacteria and condition to create the linear mixed model (random effect “pied” = individual grapevine; - fixed effect “Sampling”); (8) Richness values of each Merlot samples for the major phyla of bacteria and condition to create the linear mixed model (random effect “pied” = individual grapevine; - fixed effect “Sampling”); (9) transposition of the matrix containing Bacterial composition for the Cabernet Sauvignon and Merlot cultivars samples but for only one sampling date (S18 in this example) (RDA analyses)

*Matrix_Fungi_sumup.ods

Data to perform multivariate, univariate and null model analyses on Fungal communities
-> This spreadsheet file has 9 sheets : (1) summary of the spreadsheet content and matrices information; (2) Fungal composition for the two cultivars and the three dates tested (backup matrix) ; (3) Fungal composition for only the Cabernet Sauvignon cultivar samples(neutral models construction); (4) Fungal composition for only the Merlot cultivar samples(neutral models construction); (5)transposition of the matrix containing Fungal composition for only the Cabernet Sauvignon cultivar samples (PCOA analyses); (6)transposition of the matrix containing Fungal composition for only the Merlot cultivar samples (PCOA analyses); (7) Richness values of each Cabernet sauvignon samples for the major phyla of fungi and condition to create the linear mixed model (random effect “pied” = individual grapevine; - fixed effect “Sampling”); (8) Richness values of each Merlot samples for the major phyla of fungi and condition to create the linear mixed model (random effect “pied” = individual grapevine; - fixed effect “Sampling”); (9) transposition of the matrix containing Fungal composition for the Cabernet Sauvignon and Merlot cultivars samples but for only one sampling date (S18 in this example) (RDA analyses)

*condition_bacteria_CSM.ods

information on variables and format of sheets to perform multivariate, univariate and null model analyses on Bacterial communities
-> This spreadsheet file has 7 sheets : (1) summary of the spreadsheet content and matrices information; (2) information about each sample: type of cultivars representing the fields, date of sampling and random effect (individual grapevines sampled at the three dates); (3) condition details only for CS samples to perform PCOA analyses. To perform the PCOA on Merlot samples, refer to the (2) and use the same format of the sheet; (4) condition details only for CS samples to perform neutral models construction. To perform the neutral models on Merlot samples, refer to the (2) and use the same format of the sheet; (5) taxonomic details for CS samples to perform neutral models construction and class composition analyses; (6) taxonomic details for M samples to perform neutral models construction and class composition analyses; (7) condition details only for S18 samples to perform RDA analyses (to test the microbial composition variability between the cultivars for each date). To perform the RDA on J19 and S19 samples, refer to the (2) and use the same format of the sheet

*condition_fungi_CSM.ods

information on variables and format of sheets to perform multivariate, univariate and null model analyses on Fungal communities
-> This spreadsheet file has 7 sheets : same descripton and organisation of the sheets than the bacterial spreadsheet ("condition_bacteria_CSM.ods")