Environmental long read amplicons of soil fungi across Podzol soil profile

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Comment citer

Les chercheurs doivent citer cette ressource comme suit:

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

Droits

Les chercheurs doivent respecter la déclaration de droits suivante:

L’éditeur et détenteur des droits de cette ressource est Biology Section, Uppsala University. Ce travail est sous licence Creative Commons Attribution (CC-BY) 4.0.

Enregistrement GBIF

Cette ressource a été enregistrée sur le portail GBIF, et possède l'UUID GBIF suivante : 2148b949-ef4e-465c-b706-48e9f29e0a15.  Biology Section, Uppsala University publie cette ressource, et est enregistré dans le GBIF comme éditeur de données avec l'approbation du GBIF Sweden.

Mots-clé

Occurrence

Contacts

Couverture géographique

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.

Couverture temporelle

Données sur le projet

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). Ref Axelsson B, Bråkenhielm S. 1980. Investigation sites of the Swedish coniferous forest project - biological and physiological features. In: Persson T ed. Structure and Function of Northern Coniferous Forests - An Ecosystem Study. Arlöv, Sweden: Berlings, 25 - 64. Gardes M, Bruns TD. 1993. ITS primers with enhanced specificity for basidiomycetes‐application to the identification of mycorrhizae and rusts. Molecular Ecology 2(2): 113-118. Hopple Jr JS, Vilgalys R. 1994. Phylogenetic relationships among coprinoid taxa and allies based on data from restriction site mapping of nuclear rDNA. Mycologia 86(1): 96-107. Persson, T, ed . 1980. Structure and function of northern coniferous forests – an ecosystem study. Ecological Bulletins 32. Stockholm, Sweden.

Les personnes impliquées dans le projet:

Méthodes d'échantillonnage

We collected 5 soil cores (5 cm diameter and 15 cm deep) in each of 12 plots 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. This sampling rendered a total of 36 soil samples that were separately homogenized in ziplock bags before separating a 15 mL sample from each that was transported back to the laboratory on ice and stored at -20°C. 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). 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).

Description des étapes de la méthode:

1. 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.

Citations bibliographiques

1. Kalsoom Khan, F., Kluting, K., Tångrot, J. et al. Naming the untouchable – environmental sequences and niche partitioning as taxonomical evidence in fungi. IMA Fungus 11, 23 (2020). https://doi.org/10.1186/s43008-020-00045-9

Métadonnées additionnelles