說明
To decipher edaphic microbial communities' diversities in South African natural terrestrial environments located in different aridity zones using phylogenetic/barcoding and shot-gun metagenomes
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版本
以下的表格只顯示可公開存取資源的已發布版本。
如何引用
研究者應依照以下指示引用此資源。:
Ramond J (2020): FBIP: Diversities of microbiomes from South African arid and natural soils. v1.0. South African National Biodiversity Institute. Dataset/Occurrence. http://ipt.sanbi.org.za/iptsanbi/resource?r=fbip11&v=1.0
權利
研究者應尊重以下權利聲明。:
此資料的發布者及權利單位為 South African National Biodiversity Institute。 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: b9aab537-db65-4b7c-ab35-0a4877703dde。 South African National Biodiversity Institute 發佈此資源，並經由South African Biodiversity Information Facility同意向GBIF註冊成為資料發佈者。
關鍵字
Occurrence; Specimen
聯絡資訊
- 元數據提供者 ●
- 出處 ●
- 連絡人
- 處理者
地理涵蓋範圍
South Africa (Northern Cape and Limpopo Province)
| 界定座標範圍 | 緯度南界 經度西界 [-30.168, 16.908], 緯度北界 經度東界 [-24.495, 27.499] |
|---|
分類群涵蓋範圍
Diversities of microbiomes
| Kingdom | Fungi, Bacteria |
|---|
時間涵蓋範圍
| 起始日期 / 結束日期 | 2017-02-28 / 2017-03-31 |
|---|
計畫資料
To decipher edaphic microbial communities' diversities in South African natural terrestrial environments located in different aridity zones using phylogenetic/barcoding and shot-gun metagenomes
| 計畫名稱 | FBIP: Diversities of microbiomes from South African arid and natural soils |
|---|---|
| 辨識碼 | FBIS160422162807 |
| 經費來源 | Foundational Biodiversity Information Programme |
| 研究區域描述 | South Africa (Northern Cape and Limpopo Province) |
參與計畫的人員:
- 研究主持人
取樣方法
Three different soil biotopes will be sampled from each of the 4 National Parks (Namaqualand, Richtersveld, Kgalagadi and Marakele NPs). 4 true replicates (~300g each) from each biotope will be collected at the vertices of a 50m perpendicular cross. Each true replicate sample will correspond to a mixture of 5 pseudo-replicates taken within a 1m2 quadrat. A total of 48 (4x4x3) individual soil samples are thus expected.
| 研究範圍 | South Africa (Northern Cape and Limpopo Province) |
|---|---|
| 品質控管 | Quality filtering and OTU clustering were done simultaneously using USEARCH 61 (Edgar 2010). During quality filtering the short sequences, chimeras and duplicate sequences were removed. Chimeras were filtered out by de novo and reference based methods using UCHIME (Ashelford et al, 2005; Edgar et al, 2011). High quality paired-end forward reads (sequenced DNA molecule in the 5’-3’ direction) were then used to determine the sequencing depth of each metagenome in read alignment mode using Nonpareil v2.4. This program estimates the average sequence coverage by read redundancy (Rodriguez and Konstantinidis, 2014). |
方法步驟描述:
- Arid edaphic community barcoding: Soil metagenomic DNA extractions will be performed using commercial kits and send for 16S rRNA gene (Bacteria/Archaea) and ITS region (Fungi) Illumina MiSeq barcoding to a commercial company Shotgun metagenome sequencing: This approach involves the DNA sequencing of the whole microbial communities followed by intense computational analyses leading, notably, to the phylogenetic assignments of metabolic pathways and genes [7]. The Illumina HiSeq platform of a commercial company will be used and paired-end sequencing performed