Rhizosphere bacterial community changes and plant growth promoters in a Brassica rapa timeseries
Authors: Scott A. Klasek, Marcus T. Brock, W. John Calder, Hilary G. Morrison, Cynthia Weinig, and Loïs Maignien
Manuscript status: In review, January 2022
There’s a lot of code scattered across a lot of different documents here:
Sequence processing R script here - from fastq files to phyloseq objects
Graphing plant growth across the timeseries
Barplots of highly abundant ASVs across treatments, including soil inoculum, and some alpha diversity plots over time, here
Ordinations and beta-diversity
Biomarker detection with DESeq2 (differentially abundant ASVs across blocks, time, treatment, and combinations thereof)
Some preliminary PGP-associations before controlling PA and biomass by days grown.
GLM LASSO workflow test version 1
An update to the GLM LASSO function (contains some helpful notes too)
ASVs on PA data and PA residuals
ASVs on growth rates
Modules and networks on all growth data except RGR (also includes supplemental figure of rank/prevalence/abundance plots for all sample groups, this is a hearty one)
Modules with RGR data
Scrambling to test for false positives
All multivariate models
All univariate models (this one is too big to show as a .md, so it’s a raw file)
Miscellaneous investigations into growth-associated ASVs including their connectivity, barplots across time, and supplemental figure of time-biomarkers
Final figures 1 and 2 plus supplementals of growth differences across blocks & block biomarkers
Final figures 3 and 5 plus some interaction plots of two growth-associated ASVs
Final figure 4 dominant growth-associated ASVs over time, and supplemental of all Flavo abundances across treatment and time
Final figure 6 - networks
I couldn’t find the docs where I plotted supplemental figures RGR rates over time/treatment or barplots of SBC inoculum and major class-level taxonomies across time/treatment. Will add those once I find them and remember to update this document…
The phyloseq object containing ASV raw read counts and all sample metadata (associated plant growth measurements) of is available here.
The NCBI bioproject where raw (fastq) sequence data from this project can be found here.
Supplementary data and tables from this project are available in this figshare collection.
We referred to the Disrupted treatment as “Autoclaved” in most of the analysis.