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

Occurrence
Latest version published by South African National Biodiversity Institute on Dec 10, 2020 South African National Biodiversity Institute
Publication date:
10 December 2020
License:
CC-BY 4.0

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Description

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

Data Records

The data in this occurrence resource has been published as a Darwin Core Archive (DwC-A), which is a standardized format for sharing biodiversity data as a set of one or more data tables. The core data table contains 3,984 records.

This IPT archives the data and thus serves as the data repository. The data and resource metadata are available for download in the downloads section. The versions table lists other versions of the resource that have been made publicly available and allows tracking changes made to the resource over time.

Versions

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How to cite

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

Rights

Researchers should respect the following rights statement:

The publisher and rights holder of this work is South African National Biodiversity Institute. This work is licensed under a Creative Commons Attribution (CC-BY 4.0) License.

GBIF Registration

This resource has been registered with GBIF, and assigned the following GBIF UUID: b9aab537-db65-4b7c-ab35-0a4877703dde.  South African National Biodiversity Institute publishes this resource, and is itself registered in GBIF as a data publisher endorsed by South African Biodiversity Information Facility.

Keywords

Occurrence; Specimen

Contacts

Jean-Baptiste Ramond
  • Metadata Provider ●
  • Originator ●
  • Point Of Contact
Research Fellow
University of Pretoria
Centre for Microbial Ecology and Genomics (CMEG), Natural Science Building 2 Office 3-20, Hatfied Campus, Lynwood Road
0083 Pretoria
Gauteng
ZA
0124206980
Mahlatse Kgatla
  • Processor
FBIP Data Specialist
SANBI
2 Cussonia Avenue, Brummeria
0184 Pretoria
Gauteng
ZA
0128435196
http://fbip.co.za/contact/

Geographic Coverage

South Africa (Northern Cape and Limpopo Province)

Bounding Coordinates South West [-30.168, 16.908], North East [-24.495, 27.499]

Taxonomic Coverage

Diversities of microbiomes

Kingdom Fungi, Bacteria

Temporal Coverage

Start Date / End Date 2017-02-28 / 2017-03-31

Project Data

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
Identifier FBIS160422162807
Funding Foundational Biodiversity Information Programme
Study Area Description South Africa (Northern Cape and Limpopo Province)

The personnel involved in the project:

Jean-Baptiste Ramond
  • Principal Investigator

Sampling Methods

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:

  1. 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

Additional Metadata