Similar diversity but distinct composition: Soil fungal communities after fire and clear-cutting in boreal forests

Data and code for: Similar diversity but distinct composition: Soil fungal communities after fire and clear-cutting in boreal forests This repository contains the data and R scripts to reproduce the figures and supplementary tables of the manuscript. Manuscript Buness, V., Gangiah, T. K., Lindahl, B. D., Sundqvist, M. K., Josefsson, T., Estensen, A., Metcalfe, D. B., Nilsson, M.-C., Gundale, M. J. Similar diversity but distinct composition: Soil fungal communities after fire and clear-cutting in boreal forests. (in review) Affiliations: Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, Umeå, Sweden Department of Soil Science, Swedish University of Agricultural Sciences, Uppsala, Sweden Ecogain AB, Umeå, Sweden Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden Author affiliations: Vincent Buness (1), Tamlyn K. Gangiah (2), Björn D. Lindahl (2), Maja K. Sundqvist (1), Torbjörn Josefsson (1,3), Andreas Estensen (3), Daniel B. Metcalfe (4), Marie-Charlotte Nilsson (1), Michael J. Gundale (1). Dataset citation Buness, V., Gangiah, T. K., Lindahl, B. D., Sundqvist, M. K., Josefsson, T., Estensen, A., Metcalfe, D. B., Nilsson, M.-C., Gundale, M. J. Data and code for "Similar diversity but distinct composition: Soil fungal communities after fire and clear-cutting in boreal forests". Zenodo. https://doi.org/10.5281/zenodo.20408466 Contents . ├── data/ │ ├── succession_data.xlsx Stand-level data (36 stands) │ ├── OTU_table_final_assignment.xlsx Fungal OTU table with guild assignments │ └── Soil_fertility_PCA.xlsx Soil fertility PCA scores per stand ├── scripts/ │ ├── A_-_Figure_1.R Figure 1 and Table S1 │ ├── B_-_Figure_2.R Figure 2 and Table S2 │ ├── C_-_Figure_3.R Figure 3 and Table S3 │ └── D_-_Figure_4.R Figure 4 and Table S4 ├── output/ Supplementary tables are written here └── README.md What each script produces A_-_Figure_1.R: species richness trajectories (total, EcM, red-listed) along the two chronosequences. GAMs, ANOVA and Tukey tests. Figure 1, Table S1. B_-_Figure_2.R: guild succession and early/late EcM dynamics, including the permutation test for very-late EcM species. Figure 2, Table S2. C_-_Figure_3.R: community-environment relationships (NMDS, PERMANOVA, envfit) for the total community and each guild. Figure 3, Table S3. D_-_Figure_4.R: environmental trajectories and fungal guild niches. Figure 4, Table S4. Each script is independent and reads the data files directly. They can be run in any order. Data files succession_data.xlsx: one row per stand (n = 36). Columns include stand ID, management (M = managed clear-cut, F = unmanaged fire), time since disturbance, species richness metrics, guild richness and abundance, soil variables (pH, NO3, NH4, C:N ratio), host abundance (EcM and ErM), and per-stand OTU abundances. OTU_table_final_assignment.xlsx: fungal OTUs with taxonomy, guild assignment, and read counts per subplot. Used by scripts B and C. Soil_fertility_PCA.xlsx: soil fertility PCA scores (PC1) per stand, used as a covariate in script D. How to run Download and unzip the repository. Open R with the working directory set to the repository root (the folder containing this README), for example via setwd() or an RStudio project. Run any script. Each one loads its data from data/, draws its figure, and writes its supplementary table to output/. Paths in the scripts are relative (data/ and output/), so no editing is needed as long as the working directory is the repository root. Software Analyses were run in R (version 4.5.0). The scripts use the following packages: tidyverse, dplyr, tidyr, ggplot2, readxl, mgcv, vegan, patchwork, cowplot, ggrepel, ggsignif, openxlsx. Install them with: install.packages(c("tidyverse", "readxl", "mgcv", "vegan", "patchwork", "cowplot", "ggrepel", "ggsignif", "openxlsx")) (dplyr, tidyr and ggplot2 are part of tidyverse; grid is part of base R.) License This work is licensed under the Creative Commons Attribution 4.0 International (CC BY 4.0) license. It allows re-distribution and re-use of the licensed work on the condition that the creator is appropriately credited. Contact Vincent Buness ([e-mail]) and Michael Gundale ([e-mail]), Department of Forest Ecology and Management, Swedish University of Agricultural Sciences (SLU), Umeå, Sweden, are the owners of this dataset.