Data Sets and Analyses

• ch_and_pp (Caldwell House and Passion Puddle)
• PM_Year1 (Princeton Meadows Year 1)
• PM_Year2 (Princeton Meadows Year 2)
• core_microbiomes (include data from sets above plus Huang et al, 2020 datasets)
• evolution_analysis (includes data from rice and Arabidopsis studies)
• other_figures (code to create NJ map figure)
• plastid_ratio_analysis (code used to analyze DAB t0 reads)
• data-* (figures and files used in manuscript)
• q2_analysis_using_R.R (R functions used to analyze data)

Workflow

• upload fastq libraries
• use q2 to process fastq libraries and generate feature tables, diversity metrics, taxa barplots
• use R to analyze q2 output and create visualizations
• use R to perform differential abundance analysis using ALDEx2

Citation

If this was helpful please cite:

Acosta, K., Xu, J., Gilbert, S., Denison, E., Brinkman, T., Lebeis, S. and Lam, E., 2020. Duckweed hosts a taxonomically similar bacterial assemblage as the terrestrial leaf microbiome. PloS one, 15(2), p.e0228560.