説明
Forests and woodlands in the Guineo-Sudanian transition zone contain many tree species that form symbiotic interactions with ectomycorrhizal (ECM) fungi, which facilitate plant growth by increasing nutrient and water uptake. Despite their importance for ecosystem functioning and anthropogenic use, diversity and distribution of ECM fungi is severely under-documented in West Africa. We conducted a broad regional sampling across five West African countries using soil eDNA to characterize the ECM as well as the total soil fungal community in two vegetation types dominated by ECM host tree species. Sequencing of the entire ITS region and much of the LSU region allows us to infer a phylogeny for all detected soil fungal species. This data resource contain amplicon sequence variants (ASVs) generated from the dataset using the procedure established in Kalsoom-Khan et al. (2020) after accessing general read quality and ensuring that the majority of reads fell within the expected length (1-2 kb). In brief, raw sequence reads were filtered and trimmed, and PacBio-type chimeras were detected and removed using the tool cutadapt. Amplicons sequenced in reverse were reverse complemented. Reads were filtered using DADA2, discarding sequences with more than 3 expected errors as well as those with a length outside the range of 1200–1800 bases. Filtered sequences were then denoised using DADA2, with complete pooling and an increased alignment band size of 32. Singleton ASVs are not included in DADA2 denoising output. De novo chimera detection and removal were also performed in DADA2, with a minimum parent overabundance of 3.5 and allowing detection of chimeras with a single base difference from their parent sequence. 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、6,144 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, Furneaux B, Meidl P (2024). Soil fungal communities of ectomycorrhizal dominated woodlands across West Africa. Version 1.6. Biology Section, Uppsala University. Occurrence dataset. https://www.gbif.se/ipt/resource?r=ps155_westafrica_asv&v=1.6
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。 This work is licensed under a Creative Commons Attribution (CC-BY 4.0) License.
GBIF登録
このリソースをはGBIF と登録されており GBIF UUID: 26d7ac29-8e7e-4449-985b-2f12b6ec282f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; Observation
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
https://orcid.org/0000-0002-7003-5941
- メタデータ提供者 ●
- 最初のデータ採集者
- PhD student
- Evolutionsbiologiskt centrum, Norbyvägen 18D
- メタデータ提供者 ●
- 最初のデータ採集者
- Master student
- Evolutionsbiologiskt centrum, Norbyvägen 18D
- 論文著者
- PhD student
- 論文著者
- Professor
- 論文著者
- Professor
- 論文著者
- Professor
- 論文著者
- Professor
- 論文著者
- Professor
- 論文著者
- Associate professor
- Norbyvägen 18D
- 論文著者
- PhD student
- Norbyvägen 18D
地理的範囲
A total of seven locations with nine sites were sampled: Kota Waterfall (KOTA-G and KOTA-W) in Benin, Kou Forest Reserve (KOUF-G) and Niangoloko Forest Reserve (NIAN-W) in Burkina Faso, Farako Forest Reserve (FA01-W and FA15-W) in Mali, Bissandougou Forest Reserve (BISS-W) and Moussaya Forest Reserve (MOUS-W) in Guinea and Kouadianikro Forest Reserve (KDNK-W) in Ivory Coast.
| 座標（緯度経度） | 南 西 [7.624, -10], 北 東 [11.24, 2.725] |
|---|
生物分類学的範囲
N/A
| Kingdom | Fungi |
|---|---|
| Phylum | Mortierellomycota, Entorrhizomycota, Mucoromycota, Glomeromycota, Ascomycota, Rozellomycota, Basidiomycota, Chytridiomycota |
| Class | Geminibasidiomycetes, Rhizophydiomycetes, Paraglomeromycetes, Tremellomycetes, Atractiellomycetes, Mortierellomycetes, Microbotryomycetes, Glomeromycetes, Pezizomycotina_cls_Incertae_sedis, Dothideomycetes, Eurotiomycetes, Lecanoromycetes, Umbelopsidomycetes, Sordariomycetes, Saccharomycetes, Lobulomycetes, Geoglossomycetes, Mucoromycotina_cls_Incertae_sedis, Mucoromycetes, Rhizophlyctidomycetes, Archaeorhizomycetes, Agaricomycetes, Cystobasidiomycetes, Rozellomycotina_cls_Incertae_sedis, Pezizomycetes, Leotiomycetes, Orbiliomycetes |
| Order | Gigasporales, GS23, Agaricomycetes_ord_Incertae_sedis, Auriculariales, Mucoromycotina_ord_Incertae_sedis, Leotiomycetes_ord_Incertae_sedis, Sordariales, Rhizophlyctidales, Orbiliales, Onygenales, Microascales, Jahnulales, Cystofilobasidiales, Sebacinales, Geminibasidiales, Corticiales, Geoglossales, Acrospermales, Mortierellales, Helotiales, Mucorales, Agaricales, GS11, Trechisporales, Geastrales, Pleosporales, Umbelopsidales, Pezizales, Glomerales, Polyporales, Sporidiobolales, Mycosphaerellales, Eurotiales, Capnodiales, Eurotiomycetes_ord_Incertae_sedis, Hymenochaetales, Xylariales, Lecanorales, Russulales, Atractiellales, Hypocreales, Botryosphaeriales, Tremellales, Chaetothyriales, Venturiales, Peltigerales, Muyocopronales, GS36, Mytilinidales, Tubeufiales, Magnaporthales, Thelephorales, Rhizophydiales, Lobulomycetales, Saccharomycetales, Boletales, Sakaguchiales, Archaeorhizomycetales, Paraglomerales, Cantharellales, Cystobasidiales, Dothideales, Diaporthales |
時間的範囲
| 開始日 / 終了日 | 2018-06-22 / 2018-07-11 |
|---|
プロジェクトデータ
説明がありません
| タイトル | Soil fungal communities of ectomycorrhizal dominated woodlands across West Africa |
|---|---|
| ファンデイング | National Geographic Society as part of exploration grant #CP-126R-17 Bioinformatic analysis was possible thanks to the National Bioinformatics Infrastructure Sweden (NBIS) and enabled by resources provided by the Swedish Na- tional Infrastructure for Computing (SNIC), partially funded by the Swedish Research Council through grant agreement no. 2018-05973. |
| Study Area Description | Field collections were carried out during June and July of 2018 in five West African countries: Benin, Burkina Faso, Mali, Guinea and Ivory Coast. A total of seven locations with nine sites were sampled: Kota Waterfall (KOTA-G and KOTA-W) in Benin, Kou Forest Reserve (KOUF-G) and Niangoloko Forest Reserve (NIAN-W) in Burkina Faso, Farako Forest Reserve (FA01-W and FA15-W) in Mali, Bissandougou Forest Reserve (BISS-W) and Mous- saya Forest Reserve (MOUS-W) in Guinea and Kouadianikro Forest Reserve (KDNK- W) in Ivory Coast |
| 研究の意図、目的、背景など（デザイン） | Sites were selected op- portunistically from natural areas where ECM host trees were present, with relatively uniform vegetation and slope. |
収集方法
Two soil samples were collected roughly one meter on either side of each selected tree, using a small sterilized spade to collect the top 5 cm of soil, after which the two samples were pooled and homogenized. A sub-sample of around 250 mg of soil was placed in a separate 2.0 ml tube containing 750 ml of field lysis and preservation buffer (Zymo Research Xpedition) and homogenized in the field using a portable bead beater, and was used for DNA extraction (Zymo Research Soil/Fecal DNA mini-prep). Approximately 1500 bp of the rDNA from soil DNA extracts was amplified using the primer set ITS1 and LR5. Both primers were indexed for multiplexing to allow pooling of the samples during sequencing. The pooled library was sent for sequencing at Uppsala Genome Center (Sweden) using two cells on a Sequel system (Pacific Biosciences, Menlo Park, CA, USA).
| Study Extent | Field collections were carried out during June and July of 2018 in five West African countries: Benin, Burkina Faso, Mali, Guinea and Ivory Coast. Sites were selected opportunistically from natural areas where Ectomycorrhizal (ECM) host trees were present, with relatively uniform vegetation and slope. In each plot, ten trees with Ectomycorrhizal (ECM) symbiosis were chosen in proportion to the relative abundance of ECM tree species in the plot, while ensuring that each species in the plot was represented at least once, and that all sampled trees were at least eight meters apart. |
|---|
Method step description:
- Raw sequence reads were filtered and trimmed, and PacBio-type chimeras were detected and removed using the tool cutadapt. Amplicons sequenced in reverse were reverse complemented. Reads were filtered using DADA2, discarding sequences with more than 3 expected errors as well as those with a length outside the range of 1200–1800 bases. Filtered sequences were then denoised using DADA2, with complete pooling and an increased alignment band size of 32. Singleton ASVs are not included in DADA2 denoising output. De novo chimera detection and removal were also performed in DADA2, with a minimum parent overabundance of 3.5 and allowing detection of chimeras with a single base difference from their parent sequence.; https://doi.org/10.3897/mycokeys.81.66249"
書誌情報の引用
- https://doi.org/10.3897/mycokeys.81.66249
追加のメタデータ
| 代替識別子 | 26d7ac29-8e7e-4449-985b-2f12b6ec282f |
|---|---|
| https://www.gbif.se/ipt/resource?r=ps155_westafrica_asv |