Environmental long read amplicons of soil fungi across Podzol soil profile

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亦存在 2 筆延伸集的資料表。延伸集中的紀錄補充核心集中紀錄的額外資訊。 每個延伸集資料表中資料筆數顯示如下。

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如何引用

研究者應依照以下指示引用此資源。:

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

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此資料的發布者及權利單位為 Biology Section, Uppsala University。 This work is licensed under a Creative Commons Attribution (CC-BY 4.0) License.

GBIF 註冊

此資源已向GBIF註冊，並指定以下之GBIF UUID: 2148b949-ef4e-465c-b706-48e9f29e0a15。  Biology Section, Uppsala University 發佈此資源，並經由GBIF Sweden同意向GBIF註冊成為資料發佈者。

關鍵字

Occurrence

聯絡資訊

地理涵蓋範圍

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.

時間涵蓋範圍

計畫資料

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.

參與計畫的人員:

取樣方法

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).

方法步驟描述:

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.

引用文獻

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

額外的詮釋資料