FBIP: Survey of invertebrate and microbial diversity of the Prince Edward Islands system

Occurrence
Latest version published by South African National Biodiversity Institute on Mar 31, 2021 South African National Biodiversity Institute
Publication date:
31 March 2021
License:
CC-BY 4.0

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Description

Environmental metagenomic data generated from sequencing amplicon of in-shore, off-shore and plant-associated soil microbial communities of the sub-Antarctic Prince Edward and Marion Islands

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 14,021 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

The table below shows only published versions of the resource that are publicly accessible.

How to cite

Researchers should cite this work as follows:

Dorrington R (2021): FBIP: Survey of invertebrate and microbial diversity of the Prince Edward Islands system. v1.0. South African National Biodiversity Institute. Dataset/Occurrence. http://ipt.sanbi.org.za/iptsanbi/resource?r=fbip111&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: 5c23cc27-be23-48fe-bd70-a0cef232138d.  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; Sagina procumbens; Azorella selago; plant rhizosphere; soil microbial communities; Penicillium; Trichoderma; Ascomycetes; Specimen; Prince Edward Islands (Marion and Prince Edward); polar ecosystems; climate change; biodiversity survey; Invertebrates; microbials; terrestrial habitats

Contacts

Rosemary Dorrington
  • Metadata Provider
  • Originator
  • Point Of Contact
Professor
Rhodes University
Room 515, Biological Sciences Building, Prince Alfred Road
6140 Grahamstown
Eastern Cape
ZA
+27 46 6038442
Mahlatse Kgatla
  • Distributor
Data Quality Specialist
SANBI
2 Cussonia Avenue
0184 Pretoria
Gauteng
ZA
0128435196

Geographic Coverage

Prince Edward and Marion Islands

Bounding Coordinates South West [-47.5, 37.3], North East [-46.5, 38.5]

Taxonomic Coverage

microbial diversity

Kingdom Bacteria, Archaea, Eukaryota, Fungi

Temporal Coverage

Start Date / End Date 2012-04-25 / 2016-05-28

Project Data

Environmental metagenomic data generated from sequencing amplicon of in-shore, off-shore and plant-associated soil microbial communities of the sub-Antarctic Prince Edward and Marion Islands

Title FBIP: Survey of invertebrate and microbial diversity of the Prince Edward Islands system
Identifier FBIS150518118100
Funding Foundational Biodiversity Information Programme
Study Area Description Prince Edward and Marion Islands

The personnel involved in the project:

Rosemary Dorrington
  • Owner

Sampling Methods

- Soil/root samples were collected from various plants occuring on Marion Island, these samples were stored at -20oC and sent to the laboratory for analysis. Despite being frozen isolations were performed. - Surface seawater (taken from a depth of 5 m) and for the illumina samples (depth was approx 5m) was filtered through 100 µm mesh, followed by polyethersulfone membrane filters (0.22 µm) to collect bacteria. Filtered seawater and the filters were stored separately at -20ºC.

Study Extent Survey and metabarcoding of microorganism in Prince Edward and Marion Islands
Quality Control No

Method step description:

  1. Standard mycological culturing methods, used standard sequencing methods: - 16S rRNA genes using bacterial targeting and archaea targeting primers and 18S rRNA genes using universal eukaryote primers were amplified via polymerase chain reactions using genomic DNA extracted from biomass which was collected on the polyethersulfone membrane filters. Polymerase chain reaction products were sized on an agarose gel and extracted. The cleaned up extractions were then sequenced via pyrosequencing and Illumina sequencing. Sequence reads were curated using Mothur. - Extraction of genomic DNA from soil samples, followed by polymerase chain reaction (PCR) amplification of 16S rRNA and 18S rRNA gene for selected samples. PCR products were cut out from agarose gels to ensure the correct PCR product was obtain, each correct product was extracted from the gel and then purified, followed by sequencing on the Illumina platform. Raw sequence reads were curated using Mothur and classified according to the Silva v132 database. - Extraction of genomic DNA from root samples, followed by polymerase chain reaction (PCR) amplification of the ITS1 region. PCR products were cut out from agarose gels to ensure the correct PCR product was obtain, each correct product was extracted from the gel and then purified, followed by sequencing on the Illumina platform. - DNA was extracted from the isolated fungal endophytes, the ITS region was PCR amplified and amplicons were sent for sanger sequencing. When sequences were determined individual isolates were identified using BLAST on the NCBI website

Additional Metadata