Soil fungal communities differ between shaded and sun-intensive coffee plantations in El Salvador

We collected soil samples from a sun coffee system, shade coffee system, and nearby forest from Izalco, Sonsonate, El Salvador. At each coffee system, we collected soil samples from the surface (upper) and 10 cm below the surface (lower), and from the coffee plant drip line (drip line) and the walkway between two plants (walkway). Forest samples were collected from the soil surface only. We used high-throughput ITS meta-barcode sequencing to characterize soil fungal communities and assigned fungal taxa to functional guilds using FUNGuild. Dataset includes R code for main analyses (coffee_R.R). Main files to bring in for that code are the feature table (ASV x sample matrix) = "table-with-taxonomy2.biom", metadata file = "sample_metadata_coffee_final2.txt", tree file = "tree.nwk". Second R file is for the analyses after funguild categories were assigned (coffee_R_funguild.R). The same files are brought in except the taxonomy file to use is "coffee_taxonomy_funguild.csv" which has the funguild assignments.

本研究从萨尔瓦多松索纳特省伊萨尔科地区的露天咖啡种植园、遮阴咖啡种植园及周边森林中采集土壤样本。在各咖啡种植园中，分别从表层（上层）、地表下10 cm处（下层）、咖啡植株滴水线以及两植株间的步道采集土壤样本；森林土壤样本仅采集自地表层。本研究采用高通量内转录间隔区（ITS）元条形码测序技术表征土壤真菌群落，并通过FUNGuild工具将真菌类群归类至功能菌群。本数据集包含核心分析所用的R代码（coffee_R.R），运行该代码需导入的主要文件包括：特征表（扩增子序列变异体-样本矩阵，即ASV x sample matrix）"table-with-taxonomy2.biom"、元数据文件"sample_metadata_coffee_final2.txt"以及系统发育树文件"tree.nwk"。第二个R脚本（coffee_R_funguild.R）用于完成功能菌群分类后的分析，所需导入文件与上述一致，仅需将分类学文件替换为包含功能菌群注释信息的"coffee_taxonomy_funguild.csv"。