ps.beforeLULU.all.RDS

The cercozoan diversity in a single agricultural field in western Germany was characterized using Illumina MiSeq paired-end amplicon sequencing of the 18S rRNA V4 region using a nested-PCR with the forward primers S616F_Cerco and S616F_Eocer and the reverse primers S963R_Cerco and S947R Cerco (see doi: 10.1093/femsec/fiz04). 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 cercozoan exact sequence variants (ESVs) were obtained using DADA2 in R. Cercozoan ESVs were identified against the PR2 database using the Naive Bayesian Classifier, at a minimum bootstrap confidence threshold of 100%. Raw paired-end fastq read files are accessible at the European Nucleotide Archive (ENA) under study project accession number PRJEB30791. 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).