Environmental long read amplicons of soil fungi across Podzol soil profile

Dataset type

This dataset that contains primary occurrence data for species.

Description

Soil samples were collected in mid-October 2013 from Ivantjärnsheden field station in Jädraås (60°49‘N, 16°30’E, altitude 185 m), a well-documented field site in central Sweden (Persson, 1980) with Pinus sylvestris L. overstory and an understory of ericaceous dwarf shrubs (Calluna vulgaris (L.) Hull and Vaccinium vitis-ideae L.) and mosses (Dicranum majus Turner and Pleurozium schreberi (Bridel) Mitten). To account for small-scale variability in soil fungal communities we collected 5 soil cores (5 cm diameter and 15 cm deep) in each of 12 plots in the since terminated experiment IhII (9802) (Axelsson & Bråkenhielm, 1980). After visually dividing the plot into four quadrats one core were taken from the middle of each quadrat and from the middle of the plot after peeling back the top shrub and moss layer (incl. most of the litter layer). Soil cores were separated into visually distinct podzol soil layers: organic soil (O), mineral elluvial soil (E) and mineral illuvial soil (B) before pooling the layers for each plot. From each composite soil sample two sub-samples of approximately 0.5 g wet weight were collected for DNA extraction. Approximately 1500 bp of the rDNA from all soil DNA extracts was amplified using the primer set ITS1F (Gardes & Bruns, 1993) and LR5 (Hopple Jr & Vilgalys, 1994). A total of 5, 8 and 3 samples successfully amplified for O, E and B horizons, respectively (Table S1). PCR products from the separate soil horizons were pooled to generate three amplicon libraries (SwO, SwE and SwB) for sequencing at SciLifeLab/NGI (Uppsala, Sweden) on a PacBio RS II system (Pacific Biosciences, Menlo Park, CA, USA).

This dataset was published via the SBDI ASV portal.

Geographic Description

Soil samples were collected from Ivantjärnsheden field station in Jädraås (60°49‘N, 16°30’E, altitude 185 m), in an area of around 150x150 m.

Methods

Data analysis is described in more detail in Kalsoom-Khan et al. 2020 (DOI: 10.1186/s43008-020-00045-9). In short, raw sequence reads were filtered and trimmed using the tool cutadapt (Martin 2011; version 1.18) to de-multiplexed reads based on the forward and reverse barcodes, to keep only reads with both primers present, and to remove the actual primer sequences from the reads. Amplicons sequenced in reverse were reverse complemented before continuing the analyses. Amplified sequence variants (ASVs) were generated using DADA2 (Callahan et al. 2016; version 1.9.3). Default parameters were used for filtering the reads, but discarding sequences with more than 12 "expected errors" (maxEE=12). The tool ITSx (Bengtsson-Palme et al. 2013; version 1.1-beta) was used to extract the ITS2 region of ribosomal rDNA within each ASV, which was then used for taxonomy assignment.

Type of content

Includes: Point occurrence data.

Citation

Rosling A, Urbina H, Kluting K, Eshghi Sahraei S (2024). Environmental long read amplicons of soil fungi across Podzol soil profile. Version 1.11. Biology Section, Uppsala University. Occurrence dataset. https://www.gbif.se/ipt/resource?r=sbdi-asv-1&v=1.11

Rights

This work is licensed under a Creative Commons Attribution (CC-BY) 4.0 License.

Digitised records

Metadata last updated on 2024-11-04 07:34:53.0