説明
Since Linnaeus's time, the Kungsängen Nature Reserve has drawn frequent visitors because of its vegetation including the largest population of Fritillaria meleagris L. in Sweden. The reserve is a meadow with an abrupt moisture transition, where the wetter part has a Carex acuta dominated plant community with low species richness, visually distinct from the drier part, which has a species rich plant community including a high density of Fritillaria meleagris. To investigate the link between plant and below-ground micro-eukaryotic communities, we amplified and sequenced the ITS and LSU regions of the rDNA operon (1500 bp) from soil using PacBio SMRT sequencing, and evaluated three different methods for generation of operational taxonomic units. We found distinct communities associated with wet and mesic-dry soil conditions but estimated richness was not so different. Both soil conditions host communities dominated by protists, a large fraction of which were taxonomically assigned to Ciliphora (Alveolata), while 30-40% of all reads were assigned to kingdom Fungi. Ecological patterns were consistently recovered irrespective of the read clustering method used. However, different clustering methods affect the taxonomic and phylogenetic resolution of community characterization with implications for how well members of the micro-eukaryotic communities can be recognized in the data. This data resource contain amplicon sequence variant (ASV) sequences generated with DADA2 using the Ampliseq pipeline (https://nf-co.re/ampliseq). This dataset was published via the SBDI ASV portal (https://asv-portal.biodiversitydata.se/).
データ レコード
この オカレンス（観察データと標本) リソース内のデータは、1 つまたは複数のデータ テーブルとして生物多様性データを共有するための標準化された形式であるダーウィン コア アーカイブ (DwC-A) として公開されています。 コア データ テーブルには、1,117 レコードが含まれています。
拡張データ テーブルは2 件存在しています。拡張レコードは、コアのレコードについての追加情報を提供するものです。 各拡張データ テーブル内のレコード数を以下に示します。
この IPT はデータをアーカイブし、データ リポジトリとして機能します。データとリソースのメタデータは、 ダウンロード セクションからダウンロードできます。 バージョン テーブルから公開可能な他のバージョンを閲覧でき、リソースに加えられた変更を知ることができます。
バージョン
次の表は、公にアクセス可能な公開バージョンのリソースのみ表示しています。
引用方法
研究者はこの研究内容を以下のように引用する必要があります。:
Rosling A, Eshghi Sahraei S, Furneaux B, Kluting K, Zakieh M (2024). Kungsängen soil microbial communities. Version 1.7. Biology Section, Uppsala University. Occurrence dataset. https://www.gbif.se/ipt/resource?r=pb363_kungsangen_otu_a&v=1.7
権利
研究者は権利に関する下記ステートメントを尊重する必要があります。:
パブリッシャーとライセンス保持者権利者は Biology Section, Uppsala University。 To the extent possible under law, the publisher has waived all rights to these data and has dedicated them to the Public Domain (CC0 1.0). Users may copy, modify, distribute and use the work, including for commercial purposes, without restriction.
GBIF登録
このリソースをはGBIF と登録されており GBIF UUID: d850eb3d-d7e2-48f9-b6c1-cf1136a50bbbが割り当てられています。 GBIF Sweden によって承認されたデータ パブリッシャーとして GBIF に登録されているBiology Section, Uppsala University が、このリソースをパブリッシュしました。
キーワード
Occurrence
連絡先
- メタデータ提供者 ●
- 最初のデータ採集者 ●
- 連絡先
- Associate Professor
- Evolutionsbiologiskt centrum, Norbyvägen 18D
- +46184716444
http://orcid.org/0000-0002-7003-5941
- メタデータ提供者
- PhD student
- Evolutionsbiologiskt centrum, Norbyvägen 18D
- 最初のデータ採集者
- PhD student
- Evolutionsbiologiskt centrum, Norbyvägen 18D
- 最初のデータ採集者
- PhD student
- Evolutionsbiologiskt centrum, Norbyvägen 18D
- 最初のデータ採集者
- Associate Professor
- Evolutionsbiologiskt centrum, Norbyvägen 18D
- メタデータ提供者
- Associate Professor
- Evolutionsbiologiskt centrum, Norbyvägen 18D
地理的範囲
Kungsängen Nature Reserve (N59°50’, E17°40’) is a 12.5-hectare reserve in a larger meadow located in the south of Uppsala, Sweden, along the east shore of the Fyris River. Soil samples were taken across an abrupt moisture transition that divides the meadow community into a Carex acuta dominated plant community with low species richness in the wetter part, which is visually distinct from the mesic-dry part that has a species rich grass-dominated plant community including a high frequency of F. meleagris.
| 座標（緯度経度） | 南 西 [59.836, 17.661], 北 東 [59.837, 17.663] |
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時間的範囲
| 開始日 | 2016-06-07 |
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プロジェクトデータ
説明がありません
| タイトル | Kungsängen soil microbial communities |
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プロジェクトに携わる要員:
- 研究代表者
収集方法
Soil samples were taken with a soil corer when possible (5cm diameter x 10 cm depth), or with a hand shovel when soil was to wet (sampling depth and volume estimated to correspond to that of the soil cores). Soil samples were individually placed in plastic bags and kept on ice during sampling before storage at 4degC over night. The day after, soils were homogenized in the plastic bags and subsamples were transferred to 15ml conical centrifuge tubes and frozen at -20degC prior to freeze drying. Approximately 250 to 500 mg of freeze-dried soil was used for total DNA extraction. The entire ITS and partial LSU regions of rDNA, approximately 1500 bp, was amplified using a modified ITS1 primer and the LR5 primer. Both primers were indexed for multiplexing to allow pooling of the samples during sequencing. The pooled library was sequenced at SciLifeLab/NGI (Uppsala, Sweden) on the PacBio RSII sequencing platform.
| Study Extent | Soil samples were collected on June 7th, 2016, at Kungsängen Nature Reserve (N59°50’, E17°40’). Samples were taken from five locations 30 m apart on each side of the soil moisture transition border separated by 30 m across the transition border. |
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Method step description:
- Sequence denoising and ASV creation was performed with DADA2 using the nfcore/ampliseq pipeline (https://nf-co.re/ampliseq), commit 5adaf23d7f. Taxonomy assignment was based on the ITS2 region and performed according to https://docs.biodiversitydata.se/analyse-data/molecular-tools/#taxonomy-annotation, using nf-core/ampliseq commit e1bdbfb623 and the database unite-alleuk=8.3 (UNITE general FASTA release for Eukaryotes - Version 8.3, https://doi.org/10.15156/BIO/1280127)
追加のメタデータ
| 代替識別子 | d850eb3d-d7e2-48f9-b6c1-cf1136a50bbb |
|---|---|
| https://www.gbif.se/ipt/resource?r=pb363_kungsangen_otu_a |