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OAS accession Detail for 0292185
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| accessions_id: | 0292185 | archive |
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| Title: | 16S gene sequencing of microbial communities in South China Sea sediments from January to March 2014 (NCEI Accession 0292185) |
| Abstract: | This dataset contains data collected on R/V JOIDES Resolution during cruise IODP-349 in the South China Sea (Nan Hai) from 2014-01-30 to 2014-03-07. These data include depth and depth core. The instruments used to collect these data include Advanced Piston Corer, Automated DNA Sequencer, and Fluorometer. These data were collected by Andrew Thurber and Frederick Colwell of Oregon State University as part of the "Edginess in the subsurface: Microbial diversity of deep subseafloor ecotones (Edginess in the subsurface)" project and "Center for Dark Energy Biosphere Investigations (C-DEBI)" program. The Biological and Chemical Oceanography Data Management Office (BCO-DMO) submitted these data to NCEI on 2021-05-20. The following is the text of the dataset description provided by BCO-DMO: 16S gene sequencing of microbial communities from South China Sea sediments Dataset Description: Three locations in the SCS were cored during IODP Expedition 349 at sites U1431 (15° 22.5379’ N, 117° 00.0022’ E, 4240 meters below sea level (mbsl)), U1432 (18° 21.0831’ N, 116° 23.4504’ E, 3829 mbsl), and U1433 (12° 55.1380’ N, 115° 02.8345’ E, 4379 mbsl). Cores were split lengthwise onboard to reveal geological interfaces and the exposed sediment was aseptically scraped away prior to sampling. Samples were collected only from the center of the cores, avoiding the outside edges of the cores that may have contacted the core barrel. Samples were stored at -80°C until analysis. Down-core measurements of sediment methane concentrations, alkalinity, and pore water sulfate, ammonium, and phosphate were made onboard. Sediment ages were calculated based on paleomagnetic analysis and nanofossil characterization for each site. All samples described in this study were collected using an advanced piston core, a tool that minimizes core disturbance. In order to check whether contamination occurred, and consistent with other deep microbiology coring studies, we compared microbial communities present in fluids that drained from the core barrel (possibly from seawater intrusion during core retrieval) to those present in the center of the cores, a so-called fluid community tracer (FCT) approach. Samples of the drilling fluid from core U1433 were collected immediately when cores were brought onto the deck and were frozen at -80°C until analysis. To compare microbial communities in the drilling fluids to those in the cores, DNA from 10 FCT samples (235-790 mbsf) and a whole-round sample (13.5 mbsf) was extracted using a FastDNA Spin Kit for Soil (MP Biomedical, OH, USA). Pyrosequencing of the archaeal 16S rRNA gene of the FCT samples and the whole-round sample was conducted with a Roche 454 GS FLX+ Titanium platform (Roche 454 Life Sciences, CT, USA) at the Majorbio Bio-Pharm Technology Co., Ltd. (Shanghai, China). Primers used for amplification were Arch_344F (5′-ACGGGGCGCAGCAGGCGCGA-3′) and Arch_915R (5′-GTGCTCCCCCGCCAATTCCT-3′). Additional award numbers: Consortium for Ocean Leadership; award number: IUSSP410 C-DEBI; subaward number: 59209190 DCO/DLC; subaward number: 53587 Data are publicly accessible at NCBI under accession number PRJNA362622. |
| Date received: | 20210520 |
| Start date: | 20140130 |
| End date: | 20140307 |
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| West boundary: | 115.047 |
| East boundary: | 117 |
| North boundary: | 18.351 |
| South boundary: | 12.919 |
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| Submitting institution: | Biological and Chemical Oceanography Data Management Office |
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| Supplementary information: | Acquisition Description: DNA was extracted from 0.25 g of wet sediment using a MoBio PowerSoil DNA Isolation Kit. Extracted DNA was amplified in technical triplicate 25 uL reactions using universal 16S rRNA gene primers 515-fwd and 806-rev with Illumina sequencing adapters and barcodes. Triplicate PCR products were pooled, visualized on an agarose gel, and cleaned using a MoBio UltraClean PCR Clean-Up Kit. PCR products were quantified using a Qubit fluorometer and pooled prior to sequencing. Paired-end 250-bp sequencing was performed on an Illumina MiSeq at Oregon State University’s Center for Genome Research and Biocomputing. A sediment-free extraction was amplified and sequenced alongside sediment samples. |
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| Metadata version: | 1 |
| Keydate: | 2024-05-02 12:24:41+00 |
| Editdate: | 2024-05-02 12:25:39+00 |