Sediment cores were collected using a Furor Hydraulic Piston Corer following the Integrated Ocean Drilling Program (IODP) guidelines for obtaining high quality microbiology cores.
URL | https://www.bco-dmo.org/dataset/746718 |
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Download URL | https://www.bco-dmo.org/dataset/746718/data/download |
Media Type | text/tab-separated-values |
Created | September 26, 2018 |
Modified | September 26, 2018 |
State | Final no updates expected |
Acquisition Description
In summary, sediment cores were collected using a Furor Hydraulic Piston Corer following the Integrated Ocean Drilling Program (IODP) guidelines for obtaining high quality microbiology cores. Aboard ship, whole round cores were subcored by paring the outer two cm of sediment with an alcohol and flame sterilized chisel. The sub-cores were placed into sterile Whirl Pak Bags and stored at -80C. DNA was extracted from 10g of sediment using a PowerMax Soil DNA extraction kit. DNA was amplified using 27F and 1492R (bacterial) or 4F and 1492R (archaeal) universal primers. 150ng of bacterial and 50ng of archaeal amplicons were hybridized to the PhyloChip array.
Processing Description
Data processing can be found in Briggs et al. (2013).
BCO-DMO Processing:
- added conventional header with dataset name, PI name, version date
- modified parameter names to conform with BCO-DMO naming conventions
- adjusted the duplicate column header HY03682 to HY03682_A
- appended latitude and longitude fields for mapping.
Instruments
Parameters
In biology, kingdom is the second highest taxonomic rank, just below domain (also called super-kingdom: Bacteria, Archaea, Eukarya). Kingdoms are divided into smaller groups called phyla. Various classification systems divide life into 5 to 8 kingdoms.
phylum, organism taxonomic level. May include super-phylum and sub-phylum
phylum, organism taxonomic level. May include super-phylum and sub-phylum
order, organism taxonomic level; may include super-order and sub-order
Family. One of the levels in the taxonomic system of classification; typically ends in 'ae'. . May include super-family and sub-family.
Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details
Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details
Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details
Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details
Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details
Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details
Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details
Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details
Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details
Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details
Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details
Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details
Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details
Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details
Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details
Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details
Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details
Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details
Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details
Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details
Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details
Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details
Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details
Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details
Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details
Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details
Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details
Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details
Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details
Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details
Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details
Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details
Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details
Longitude in decimal degrees east.
longitude, in decimal degrees, East is positive, negative denotes West; Reported in some datsets as degrees, minutes
Dataset Maintainers
Name | Affiliation | Contact |
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Brandon R. Briggs | Oregon State University (OSU) | ✓ |
Frederick S. Colwell | Oregon State University (OSU) | ✓ |
Mathew Biddle | Oregon State University (OSU) | |
Woods Hole Oceanographic Institution (WHOI BCO-DMO) |
BCO-DMO Project Info
Project Title | The Effect of Methane on Microbial Community Distributions in the Ulleung Basin |
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Acronym | Methane_Microbes |
URL | https://www.bco-dmo.org/project/738552 |
Created | June 14, 2018 |
Modified | June 14, 2018 |
Project Description
The DEBI/C-DEBI research exchange gave me the opportunity to travel to Lawrence Berkeley National Laboratory (LBNL) to work with Dr. Eoin Brodie. While at LBNL, I was able to learn and adopt a new microarray technology for subseafloor microbial ecology investigations. The PhyloChip is a microarray that contains probes for Bacterial and Archaeal 16s rRNA genes and uses parallel hybridization to minimizes the influence of dominant organisms; therefore, it is highly sensitive to rare microbes. In addition, to this data the research exchange provided necessary funding for me to finish my dissertation. The research exchange funds allowed two sites in the Ulleung Basin to be fully analyzed and incorporated into my dissertation “Geomicrobiology of sediment containing methane”. This collaboration also introduced me to how research is conducted at a national laboratory. This information is valuable in deciding my future career path. Whatever that path may be the collaboration and techniques that I learned will continue beyond graduate school, as we are planning future studies using the PhyloChip. For more on this method, see Briggs, Pohlman, Torres, Reidel, Brodie and Colwell’s 2011 AEM paper Macroscopic biofilms in fracture-dominated sediment that anaerobically oxidize methane.
Data Project Maintainers
Name | Affiliation | Role |
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Brandon R. Briggs | Oregon State University (OSU) | Principal Investigator |