Data and R scripts for: Pioneer plant legacies gate biodiversity-productivity coupling under coal-gangue stress

Overview This repository contains all R scripts, input data, and analysis outputs required to reproduce the figures and statistical results in the manuscript. The analysis was performed with R 4.5.2. Repository structure . ├── README.md # This file ├── Figure2_conditioning_plant_traits.R # Figure 2: Phase-I pioneer plant traits ├── Figure3_BEF.R # Figure 3: Phase-II richness-productivity ├── Figure4.R # Figure 4: Heavy metal analysis ├── Figure5_profile.R # Figure 5: Phase-I functional-gene profiles ├── FigureS1_TableS2.R # Figure S1 & Table S2: Soil properties ├── FigureS2_PCoA.R # Figure S2: Microbial community PCoA ├── data/ │ ├── phase1_plant_traits.txt # Phase-I plant trait measurements │ ├── phase1_soil_properties.txt # Phase-I soil physicochemical properties │ ├── phase2_community_biomass.txt # Phase-II community biomass data │ ├── gangue_metal_concentrations.txt # Coal gangue heavy metal concentrations (8 elements, 4 samples) │ ├── plant_metal_concentrations.txt # Plant tissue metal concentrations (8 elements, 5 species) │ ├── metagenomic_sample_metadata.txt # Sample metadata for metagenomic sequencing (30 samples) │ ├── bacteria_absolute_abundance.txt # Bacterial absolute abundance matrix (GTDB) │ ├── fungi_absolute_abundance.txt # Fungal absolute abundance matrix (NCBI NR) │ └── profile/ # Functional gene annotation profiles │ ├── phi.txt # PHI-base pathogen-associated genes │ ├── vfdb.txt # VFDB virulence factor genes │ ├── bacmet.txt # BacMet metal resistance genes │ ├── ncycdb.txt # NCycDB nitrogen-cycling genes │ └── pcycdb.txt # PCycDB phosphorus-cycling genes └── log/ # Analysis outputs and session info ├── R_sessionInfo_Figure3.txt # R session info (Figure 3) ├── R_sessionInfo_Figure5.txt # R session info (Figure 5) ├── R_sessionInfo_FigureS2.txt # R session info (Figure S2) ├── TableS2.txt # Substrate basic properties (Table S2) ├── figure3A_conditioning_comparisons.csv ├── figure3B_lrr_comparisons.csv ├── figure3c_composition_adjusted_slopes.csv ├── tableS3_phase2_mixed_model.csv ├── figure5_functional_category_totals.csv ├── figure5_pathogen_nutrient_index.csv └── figureS2_hellinger_euclidean_permanova.csv Running the scripts All scripts accept a working-directory-independent invocation from the repository root: Rscript code/Figure3_BEF.R Rscript code/FigureS2_PCoA.R Rscript code/Figure2_conditioning_plant_traits.R Rscript code/Figure4.R Rscript code/FigureS1_TableS2.R Rscript code/Figure5_profile.R Each script reads from code/data/, writes intermediate outputs to code/log/, and saves publication-quality figures to figures/ (PDF, TIFF, and/or JPG). The figure output path is ../figures/ relative to the script location (within code/). Figure-to-script mapping Figure Script Key packages Figure 2 Figure2_conditioning_plant_traits.R tidyverse, emmeans, multcomp, cowplot, patchwork, ggtext Figure 3 Figure3_BEF.R lme4, lmerTest, emmeans, multcomp, patchwork Figure 4 Figure4.R tidyverse, viridis, patchwork Figure 5 Figure5_profile.R data.table, agricolae, patchwork Figure S1 & Table S2 FigureS1_TableS2.R tidyverse, emmeans, multcomp, cowplot, patchwork, ggtext Figure S2 FigureS2_PCoA.R vegan, patchwork Data description Phase I (soil conditioning) phase1_plant_traits.txt: Pot-level plant traits (Number, Height, Root_Length, Biomass) after 65 days of growth. Columns: Pot, Substrate, Species, Number, Height, Root_Length, Biomass. phase1_soil_properties.txt: Pot-level soil physicochemical properties after Phase I. Columns: Pot, Substrate, Species, pH, EC (μS/cm), OM (g/kg), AP (mg/kg), AN (mg/kg), TN (g/kg), TP (g/kg). metagenomic_sample_metadata.txt: Sample mapping for metagenomic sequencing (30 biological samples, 5 per treatment). Columns: SampleID, Name, Plant, Substrate. bacteria_absolute_abundance.txt / fungi_absolute_abundance.txt: Absolute abundance matrices (rows = taxonomic IDs, columns = SampleID) used for PCoA. profile/*.txt: Functional gene annotation tallies per sample for five databases (PHI-base, VFDB, BacMet, NCycDB, PCycDB). Phase II (biodiversity assay) phase2_community_biomass.txt: Pot-level species data for the Phase II biodiversity assay (480 pots, 20 species combinations × 6 legacy matrices × 4 replicates). Columns: Pot, Substrate, Training, Diversity, Sp_combination, Species, Number, Height, Root_Length, Biomass. Heavy metals gangue_metal_concentrations.txt: Heavy metal concentrations (mg/kg) in four coal gangue samples for 8 elements (Cd, Hg, As, Pb, Cr, Cu, Ni, Zn). Columns: Sample, Element, Content. plant_metal_concentrations.txt: Shoot tissue metal concentrations (mg/kg) for five species grown on coal gangue, plus Medicago sativa on clean soil. Columns: Pot, Species_abbr, Species, Treatment, Element, Content. R session information The log/ directory contains R_sessionInfo_*.txt files documenting the exact R version, platform, and package versions used for each analysis. Key packages: lme4 / lmerTest: linear mixed models with Satterthwaite df emmeans / multcomp: estimated marginal means and Tukey-adjusted comparisons vegan: Hellinger transformation, Euclidean distance, PERMANOVA data.table: memory-efficient profile aggregation (>1 million annotation rows) ggplot2 / patchwork: publication figures License This dataset is made available under the Creative Commons Attribution 4.0 International (CC BY 4.0) license. If you use these data or code, please cite the associated manuscript.