Supplementary Data and Appendix: Niche Flattening in Factory Cultivation of Edible Fungi

Title: Supplementary Data and Appendix: Niche Flattening in Factory Cultivation of Edible Fungi Description: This deposit contains the complete supplementary materials and empirical data supporting the findings of the associated study on niche flattening and system resilience in factory cultivation of edible fungi. Contents This package includes four components: Enterprise IoT and Production Data (Layer I & II) Minute-level environmental records (temperature, relative humidity, CO₂, illumination) from two Guizhou facilities (Xuerong Bijie, Guiwang Daozhen, 2022–2024) Batch-linked yield and quality records for 510 production batches Audited cross-regional metrics from seven domestic production bases (2016–2024), including capital intensity, energy intensity, water intensity, and biological efficiency Microbiome and Species Distribution Data (Layer III & IV) Processed ASV (amplicon sequence variant) tables from NCBI SRA, covering factory facilities in the Netherlands, Japan, South Korea, and China (168 samples) Functional guild annotations (FUNGuild) and alpha diversity indices Spatially thinned occurrence records (~45,000) for 12 wild edible fungi species from GBIF MaxEnt model outputs and bioclimatic variable sets (WorldClim 2.1) Model Parameters and Diversity Indices Calibrated parameters for the coupled ODE system (10 dynamic parameters with prior ranges and posterior distributions) Environmental Heterogeneity Index (EHI) calculations for factory and natural forest systems Chesson's σ and κ approximations Functional diversity (FD) and functional redundancy index (FRI) for all samples Reproducibility Scripts R scripts for EHI computation (compute_EHI.R) R scripts for ODE simulation and bifurcation analysis (ode_simulation.R) File Structure File Description F1_Data_Environment_Yield.xlsx IoT environmental data, batch yield records, cross-base corporate metrics, MaxEnt occurrences F2_Data_Microbiome.xlsx ASV table, taxonomic assignments, MaxEnt summary F3_Model_Parameters.xlsx ODE parameters, diversity indices (Shannon H, FD, FRI) F4_Scripts_EHI_ODE.zip R scripts for EHI calculation and system dynamics simulation F5_Figures.zip All main figures (Figure 1–4) in TIFF format F6_README.txt Overview and data availability statement Raw Data Availability Raw ITS2 amplicon FASTQ files are available at NCBI SRA under BioProjects: PRJNA1173348 (Netherlands) PRJNA1082792 (Japan) PRJNA1325705 (South Korea) PRJNA1259403 (China) GBIF occurrence records and WorldClim rasters are publicly accessible via standard APIs. Usage Notes All data have been preprocessed and quality-controlled as described in Appendix A of the associated paper. Scripts require R v4.3.2+ with packages: vegan, lme4, deSolve, sensitivity For questions or troubleshooting, please contact the corresponding author. License CC BY 4.0