FBIP: Diversities of microbiomes from South African arid and natural soils

Jean-Baptiste Ramond1, Mahlatse Kgatla2

1 University of Pretoria, Centre for Microbial Ecology and Genomics (CMEG), Natural Science Building 2 Office 3-20, Hatfied Campus, Lynwood Road, 0083, Pretoria, South Africa; 2 SANBI, 2 Cussonia Avenue, Brummeria, 0184, Pretoria, South Africa

Corresponding author(s): Jean-Baptiste Ramond (jean-baptiste.ramond@up.ac.za)

Received {date}; Revised {date}; Accepted {date}; Published {date}

Citation: Combination of authors, year of data paper publication (in parentheses), Title, Journal Name, Volume, Issue number (in parentheses), and doi of the data paper.

Resource Citation

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

Abstract

To decipher edaphic microbial communities' diversities in South African natural terrestrial environments located in different aridity zones using phylogenetic/barcoding and shot-gun metagenomes

Keywords: Occurrence, Specimen

Project details

Project title: FBIP: Diversities of microbiomes from South African arid and natural soils
Personnel: Jean-Baptiste Ramond
Funding: Foundational Biodiversity Information Programme
Study area descriptions/descriptor: South Africa (Northern Cape and Limpopo Province)

Data published through GBIF: http://ipt.sanbi.org.za/iptsanbi/resource?r=fbip11

Taxonomic coverage

General taxonomic coverage description: Diversities of microbiomes
Taxonomic ranks
Kingdom: Fungi, Bacteria

Spatial coverage

General spatial coverage: South Africa (Northern Cape and Limpopo Province)
Coordinates: 30°10'5.6''S and 24°29'43.54''S Latitude; 16°54'27.4''E and 27°29'57.78''E Longitude 

Temporal coverage: February 28, 2017 - March 31, 2017

Methods

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 [7]. The Illumina HiSeq platform of a commercial company will be used and paired-end sequencing performed
Study extent description: South Africa (Northern Cape and Limpopo Province)
Sampling description: 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.
Quality control description: 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).

Datasets

Dataset description
Object name: Darwin Core Archive FBIP: Diversities of microbiomes from South African arid and natural soils
Character encoding: UTF-8
Format name: Darwin Core Archive format
Format version: 1.0
Distribution: http://ipt.sanbi.org.za/iptsanbi/archive.do?r=fbip11
Publication date of data: 2020-12-10
Language: English
Licences of use: Creative Commons Attribution (CC-BY) 4.0 License

Metadata language: English
Date of metadata creation: 2020-12-03
Hierarchy level: Dataset