FBIP: Survey of invertebrate and microbial diversity of the Prince Edward Islands system
Citation
Dorrington R (2021). FBIP: Survey of invertebrate and microbial diversity of the Prince Edward Islands system. South African National Biodiversity Institute. Occurrence dataset https://doi.org/10.15468/r3rf47 accessed via GBIF.org on 2024-01-26.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 IslandsSampling Description
Study Extent
Survey and metabarcoding of microorganism in Prince Edward and Marion IslandsSampling
- 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.Quality Control
NoMethod steps
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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
Taxonomic Coverages
microbial diversity
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Bacteriarank: kingdom
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Archaearank: kingdom
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Eukaryotarank: kingdom
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Fungirank: kingdom
Geographic Coverages
Prince Edward and Marion Islands
Bibliographic Citations
Contacts
Rosemary Dorringtonoriginator
position: Professor
Rhodes University
Room 515, Biological Sciences Building, Prince Alfred Road
Grahamstown
6140
Eastern Cape
ZA
Telephone: +27 46 6038442
email: r.dorrington@ru.ac.za
Rosemary Dorrington
metadata author
position: Professor
Rhodes University
Room 515, Biological Sciences Building, Prince Alfred Road
Grahamstown
6140
Eastern Cape
ZA
Telephone: +27 46 6038442
email: r.dorrington@ru.ac.za
Mahlatse Kgatla
distributor
position: Data Quality Specialist
SANBI
2 Cussonia Avenue
Pretoria
0184
Gauteng
ZA
Telephone: 0128435196
email: m.kgatla@sanbi.org.za
Rosemary Dorrington
administrative point of contact
position: Professor
Rhodes University
Room 515, Biological Sciences Building, Prince Alfred Road
Grahamstown
6140
Eastern Cape
ZA
Telephone: +27 46 6038442
email: r.dorrington@ru.ac.za