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Researchers should cite this work as follows:
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
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South Africa (Northern Cape and Limpopo Province)
|Bounding Coordinates||South West [-30.168, 16.908], North East [-24.495, 27.499]|
Diversities of microbiomes
|Start Date / End Date||2017-02-28 / 2017-03-31|
To decipher edaphic microbial communities' diversities in South African natural terrestrial environments located in different aridity zones using phylogenetic/barcoding and shot-gun metagenomes
|Title||FBIP: Diversities of microbiomes from South African arid and natural soils|
|Funding||Foundational Biodiversity Information Programme|
|Study Area Description||South Africa (Northern Cape and Limpopo Province)|
The personnel involved in the project:
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.
|Study Extent||South Africa (Northern Cape and Limpopo Province)|
|Quality Control||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).|
Method step description:
- 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 . The Illumina HiSeq platform of a commercial company will be used and paired-end sequencing performed