README

This repository contains all the data and code used for Kosmopoulos, Batstone-Doyle, & Heath (2023).

• greenhouse_coinoc.csv contains the raw data generated by the greenhouse experiment, used to create Figure 2
• greenhouse_N_add.csv contains the raw data generated by the nitrogen-addition experiment, used to create Figure 3
• coinoculation.Rmd contains all the code to reproduce Figures 2 & 3
• tp_ep.Rdata contains the saved endpoint measurements after reformatting the data in greenhouse_coinoc.csv
• dada2_deseq2.Rmd contains all the code to reproduce Figures 4 & S1
  • NOTE: To fully execute the code to produce these figures and reproduce Figures 4 & S1, you must obtain the raw 16S V3-V4 amplicon reads used in this analysis. These files can be found online from the National Center for Biotechnology Information under BioProject PRJNA1077341. Alternatively, if you choose to forego reproducing the initial steps in this workflow (from filtering & trimming raw sequence reads through sequence dereplication) you can load dadaFs.RDS and dadaRs.RDS to obtain previously generated dada2 objects for these data.
• dadaFs.RDS, dadaRs.RDS see note above
• 16S_metadata.csv contains all the metadata for the tissue occupancy experiment used to generate Figures 4 & S1

The controls directory contains tables and plots used to compare controls vs treatment groups in greenhouse_coinoc.csv

The treated directory contains tables and plots used to compare inoculation treatments in greenhouse_coinoc.csv. It also contains intermediate files used to generate Figure 2.

The Nadd directory contains tables and plots used to compare nitrogen-addition groups in greenhouse_N_add.csv. It also contains intermediate files used to generate Figure 3.

The 16S directory contains intermediate files, test results, and plots used in the analysis of the 16S amplicon data used to generate Figures 4 & S1. Within, there is ASV.fasta which is a fasta-formatted file of the ASV inferred from the amplicon data.