Analysis code and data for "Long-term annual growing-season fire reduces plant diversity and homogenizes soil fungal communities in a longleaf pine savanna"

This repository contains raw and processed data, metadata, and R code for the manuscript: Long-term annual growing-season fire reduces plant diversity and homogenizes soil fungal communities in a longleaf pine savanna. Repository contents README.txt file Raw and/or processed community data tables Metadata Taxonomic assignment tables R scripts used for statistical analyses and figure generation Supplementary code/figures associated with the manuscript The study examined the effects of prescribed fire regimes on fungal, bacterial, and plant communities in a longleaf pine ecosystem at three sites within the Jones Center at Ichauway, Georgia, USA. Treatments included annual growing-season prescribed fire and maintenance fire regimes (1-2 year fires). Vegetation and soil samples were collected from 60 plots across three field sites (DL, FOJ, and TOA). Amplicon sequencing targeted fungal ITS2 and bacterial 16S rRNA gene regions. Fungal ITS2 sequences were generated using primers fITS7/ITS4 and bacterial 16S rRNA gene sequences targeted the V4 region using primers 515F/806R. Sequence data were processed using DADA2 within QIIME2 (version 2022.11). Taxonomy was assigned using the UNITE and SILVA databases. Sequence processing and downstream analyses were conducted in R and included alpha diversity, beta diversity, indicator species analyses, functional guild analyses, and community composition analyses. Raw sequencing reads are available through the NCBI Sequence Read Archive (SRA) under accession number: PRJNA1469031.