metabarcoding of eDNAbyss sediment samples
Citation
MGnify (2021). metabarcoding of eDNAbyss sediment samples. Sampling event dataset https://doi.org/10.15468/4ercfv accessed via GBIF.org on 2024-08-14.Description
Sediments were collected using multicore sampler, or simple cores when a submarine or a remote operated vehicle (ROV) were present. The cores were collected and sliced according to sediment depth and using a standardized scheme. Slices were preserved and treated individually. When hard substrate was collected, the gear ELFES designed on purpose to scratch and collect the surface of substrate, or bulk samples were retained after sieving communities. Nucleic acids (DNA or RNA) were extracted and submitted to a PCR-ligation protocols using 6 sets of primers pairs targeting metazoans (2 primer pairs targeting a fragment of Cytochrome Oxydase I and one of rDNA18S V1-V2), microeukaryotes (2 primer pairs targeting rDNA 18S V4 and V9) and prokaryotes (2 sets of primer pairs targeting rDNA16S V4-V5 respectively defined for prokaryotes in general, and archaebacterial in particular).Sampling Description
Sampling
Sediments were collected using multicore sampler, or simple cores when a submarine or a remote operated vehicle (ROV) were present. The cores were collected and sliced according to sediment depth and using a standardized scheme. Slices were preserved and treated individually. When hard substrate was collected, the gear ELFES designed on purpose to scratch and collect the surface of substrate, or bulk samples were retained after sieving communities. Nucleic acids (DNA or RNA) were extracted and submitted to a PCR-ligation protocols using 6 sets of primers pairs targeting metazoans (2 primer pairs targeting a fragment of Cytochrome Oxydase I and one of rDNA18S V1-V2), microeukaryotes (2 primer pairs targeting rDNA 18S V4 and V9) and prokaryotes (2 sets of primer pairs targeting rDNA16S V4-V5 respectively defined for prokaryotes in general, and archaebacterial in particular).Method steps
- Pipeline used: https://www.ebi.ac.uk/metagenomics/pipelines/5.0
Taxonomic Coverages
Geographic Coverages
Bibliographic Citations
- Trouche B, Brandt MI, Belser C, Orejas C, Pesant S, Poulain J, Wincker P, Auguet JC, Arnaud-Haond S, Maignien L. 2021. Diversity and Biogeography of Bathyal and Abyssal Seafloor Bacteria and Archaea Along a Mediterranean-Atlantic Gradient. Front Microbiol vol. 12 - DOI:10.3389/fmicb.2021.702016
- Schauberger C, Glud RN, Hausmann B, Trouche B, Maignien L, Poulain J, Wincker P, Arnaud-Haond S, Wenzhöfer F, Thamdrup B. 2021. Microbial community structure in hadal sediments: high similarity along trench axes and strong changes along redox gradients. ISME J vol. 15 - DOI:10.1038/s41396-021-01021-w
Contacts
originatorThe French National Sequencing Center (Genoscope)
Le Ponant Building D - 25 rue Leblanc
PARIS - RCS B 775 685 019
75015
FR
Telephone: +33 (0) 1 64 50 20 59
metadata author
The French National Sequencing Center (Genoscope)
Le Ponant Building D - 25 rue Leblanc
PARIS - RCS B 775 685 019
75015
FR
Telephone: +33 (0) 1 64 50 20 59
administrative point of contact
The French National Sequencing Center (Genoscope)
Le Ponant Building D - 25 rue Leblanc
PARIS - RCS B 775 685 019
75015
FR
Telephone: +33 (0) 1 64 50 20 59