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

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Os dados deste recurso de ocorrência foram publicados como um Darwin Core Archive (DwC-A), que é o formato padronizado para compartilhamento de dados de biodiversidade como um conjunto de uma ou mais tabelas de dados. A tabela de dados do núcleo contém 3.984 registros.

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.

Versões

A tabela abaixo mostra apenas versões de recursos que são publicamente acessíveis.

Como citar

Pesquisadores deveriam citar esta obra da seguinte maneira:

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

Direitos

Pesquisadores devem respeitar a seguinte declaração de direitos:

O editor e o detentor dos direitos deste trabalho é South African National Biodiversity Institute. This work is licensed under a Creative Commons Attribution (CC-BY 4.0) License.

GBIF Registration

Este recurso foi registrado no GBIF e atribuído ao seguinte GBIF UUID: b9aab537-db65-4b7c-ab35-0a4877703dde. South African National Biodiversity Institute publica este recurso, e está registrado no GBIF como um publicador de dados aprovado por South African Biodiversity Information Facility.

Palavras-chave

Occurrence; Specimen

Contatos

Jean-Baptiste Ramond

Provedor Dos Metadados ●
Originador ●
Ponto De Contato

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

jean-baptiste.ramond@up.ac.za

0124206980

Mahlatse Kgatla

Processador

FBIP Data Specialist

SANBI

2 Cussonia Avenue, Brummeria

0184 Pretoria

Gauteng

ZA

m.kgatla@sanbi.org.za

0128435196

http://fbip.co.za/contact/

Cobertura Geográfica

South Africa (Northern Cape and Limpopo Province)

Coordenadas delimitadoras	Sul Oeste [-30,168, 16,908], Norte Leste [-24,495, 27,499]

Cobertura Taxonômica

Diversities of microbiomes

Reino	Fungi, Bacteria

Cobertura Temporal

Data Inicial / Data final	2017-02-28 / 2017-03-31

Dados Sobre o Projeto

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

Título	FBIP: Diversities of microbiomes from South African arid and natural soils
Identificador	FBIS160422162807
Financiamento	Foundational Biodiversity Information Programme
Descrição da Área de Estudo	South Africa (Northern Cape and Limpopo Province)

O pessoal envolvido no projeto:

Jean-Baptiste Ramond

Pesquisador Principal

Métodos de Amostragem

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.

Área de Estudo	South Africa (Northern Cape and Limpopo Province)
Controle de Qualidade	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).

Área de Estudo

South Africa (Northern Cape and Limpopo Province)

Controle de Qualidade

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).

Descrição dos passos do método:

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

Metadados Adicionais

Identificadores alternativos	http://ipt.sanbi.org.za/iptsanbi/resource?r=fbip11