ps.RDS

The arbuscular mycorrhizal fungi (AMF; Glomeromycota) diversity in a single agricultural field in western Germany was characterized using Illumina MiSeq paired-end amplicon sequencing of the 28S rRNA D1D2 region using a nested-PCR first targeting the small subunit-internal transcribed spacer-large subunit (SSU-ITS-LSU) region using a mixture of Glomeromycota-specific primers (SSUmAf-LSUmAr followed by SSUmCf-LSUmBr) and then using LR2rev (5'-GAAAAGAACTTTGAAAA-3')-LR3 (5'-CCGTGTTTCAAGACGGG-3'). The field is a plot experiment which has been performed at campus Klein–Altendorf near Bonn, Germany and was planted with <em>Cichorium intybus</em> L. at the time of sampling. The soil is characterized as Haplic Luvisol. Soil samples were collected across two orthogonal environmental gradients. A horizontal gradient consisted of different soil compartments: the drilosphere (defined as maximal 1mm coating of earthworm holes), rhizosphere (maximal 2 mm root-adhering soil), and bulk soil. A vertical gradient of soil depth (hereafter referred to as layer), consisted of two levels : the topsoil layer (at 10–30 cm depth) and the subsoil layer (at 60–75 cm depth) in each of the soil compartments. Each combination (layer * compartment) was replicated three times, resulting in 18 communities. Denoised, chimera-free, non-singleton exact sequence variants (ESVs) were obtained using DADA2 in R. AMF ESVs were searched using BLAST against reference Glomeromycota sequences. Taxonomic assignment was done for queries having at least 90% of sequence similarity, 90% of sequence coverage, and a minimum e-value of 10e50 against their closest reference. Raw paired-end fastq read files are accessible at the European Nucleotide Archive (ENA) under study project accession number PRJEB54814. The analysed dataset including the ESV count table, ESV taxonomy, and sample metadata is available as a phyloseq{} R object saved in .RDS R format (in the software R, use readRDS() function to load the phyloseq{} R object).