May 2020
Five files:
Comma-separated values file showing the population dynamics data presented in Figures 1, S1, and S2. Columns are as follows: 'replicate' indicates replicate (values a, b, c, d, e, f); timepoint indicates transfer number, with 0 indicating the start of the experiment; trt is a two-digit treatment code describing plasmid, mercury, and natural community treatment, with the first digit indicating plasmid status (1 = no pQBR plasmid added, 2 = pQBR57, 3 = pQBR103) and the second digit indicating mercury and natural community status (1 and 4 = 0 µg/g, 2 and 5 = 16 µg/g, 3 and 6= 64 µg/g; 1, 2, 3 = P. fluorescens SBW25 alone; 4, 5, 6 = with natural community); plasmid indicates starting plasmid treatment (values 'plasmid-', 'pQBR57', 'pQBR103'); mercury indicates mercury treatment (added mercury concentration in Hg2+ µg/g); enc indicates addition or not of natural community (values 'alone' or 'with_enc'); type indicates the population being measured (values are 'SBW25_total' = P. fluorescens SBW25; 'SBW25_hgr' = mercury-resistant P. fluorescens SBW25; 'ENC' = natural community; 'ENC_hgr' = mercury-resistant natural community); density is the density in cfu/g soil estimated from plate counts.
Short-read sequencing data associated with this project is available at the European Nucleotide Archive PRJEB34647. A table linking samples with metadata is provided in the file SOILCOM_Short_Read_Data.csv.
Sample analysis scripts in Rmarkdown format are provided at raw .Rmd and formatted .html files in subdirectories in SOILCOM_Analysis_Scripts.zip. Along with the raw data they can reproduce the figures and statistics presented in the manuscript.
The following tables represent the output of processing the short-read sequencing data described above. They are provided in a compressed .zip archive, SOILCOM_amplicon_processed_data.zip. Intermediate files used in their production, as well as sample analysis scripts, are provided in SOILCOM_amplicons.zip.
Data presented in Figure 3, showing Faith's phylogenetic diversity for the analysed populations.
Data presented in Figure S3, showing Pielou's evenness for the analysed populations.
Data presented in Figure S3, showing Shannon's H for the analysed populations.
Distance matrix used to prepare Figure 4, showing unweighted UniFrac distances between populations. Columns and rows are named using the trt format described above.
Distance matrix used to prepare Figure S4, showing Bray-Curtis distances between populations. Columns and rows are named using the trt format described above.
Distance matrix used to prepare Figure S4, showing weighted UniFrac distances between populations. Columns and rows are named using the trt format described above.
Table showing ASV counts for each population that was used to prepare Figure 6. Populations (columns) are named using the trt format described above, rows refer to unique ASV identifiers that can be interpreted taxonomically using 6_epic_taxonomy.tsv.
Taxonomy assignments for ASVs using the GreenGenes database.
Distance matrix used to prepare Figure S6, showing Bray-Curtis distances between populations. Columns and rows are named using the trt format described above.
Distance matrix used to prepare Figure S6, showing unweighted UniFrac distances between populations. Columns and rows are named using the trt format described above.
Distance matrix used to prepare Figure S6, showing weighted UniFrac distances between populations. Columns and rows are named using the trt format described above.