URLhttps://www.bco-dmo.org/dataset/746718
Download URLhttps://www.bco-dmo.org/dataset/746718/data/download
Media Typetext/tab-separated-values
CreatedSeptember 26, 2018
ModifiedSeptember 26, 2018
StateFinal 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

Furor Hydraulic Piston Corer [Piston Corer]
Details
Instance Description (Furor Hydraulic Piston Corer)

Sediment cores were collected using a Furor Hydraulic Piston Corer following the Integrated Ocean Drilling Program (IODP) guidelines for obtaining high quality microbiology cores.

The piston corer is a type of bottom sediment sampling device. A long, heavy tube is plunged into the seafloor to extract samples of mud sediment. A piston corer uses a "free fall" of the coring rig to achieve a greater initial force on impact than gravity coring. A sliding piston inside the core barrel reduces inside wall friction with the sediment and helps to evacuate displaced water from the top of the corer. A piston corer is capable of extracting core samples up to 90 feet in length.

Parameters

Domain [kingdom]
Details
Domain
Domain level phylogenetic classification

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 [phylum]
Details
Phylum
Phylum level phylogenetic classification

phylum, organism taxonomic level. May include super-phylum and sub-phylum

Subphylum [phylum]
Details
Subphylum
Subphylum level phylogenetic classification

phylum, organism taxonomic level. May include super-phylum and sub-phylum

Class [class]
Details
Class
Class level phylogenetic classification
Class. Taxonomic class of organism. May include super-class and sub-class.
Order [order]
Details
Order
Order level phylogenetic classification

order, organism taxonomic level; may include super-order and sub-order

Family [family]
Details
Family
Familty level phylgenetic classification

Family. One of the levels in the taxonomic system of classification; typically ends in 'ae'. . May include super-family and sub-family.

BSR03691 [flag]
Details
BSR03691
Presence (1) Absence (0) in sample BSR03691

Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details

BSR03692 [flag]
Details
BSR03692
Presence (1) Absence (0) in sample BSR03692

Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details

BSR36165_A [flag]
Details
BSR36165_A
Presence (1) Absence (0) in sample BSR36165_A

Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details

HY03682 [flag]
Details
HY03682
Presence (1) Absence (0) in sample HY03682

Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details

HY03684 [flag]
Details
HY03684
Presence (1) Absence (0) in sample HY03684

Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details

HY03685 [flag]
Details
HY03685
Presence (1) Absence (0) in sample HY03685

Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details

HY03687 [flag]
Details
HY03687
Presence (1) Absence (0) in sample HY03687

Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details

HY03689 [flag]
Details
HY03689
Presence (1) Absence (0) in sample HY03689

Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details

HY03690 [flag]
Details
HY03690
Presence (1) Absence (0) in sample HY03690

Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details

HY03672 [flag]
Details
HY03672
Presence (1) Absence (0) in sample HY03672

Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details

HY03673 [flag]
Details
HY03673
Presence (1) Absence (0) in sample HY03673

Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details

HY03675 [flag]
Details
HY03675
Presence (1) Absence (0) in sample HY03675

Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details

HY03676 [flag]
Details
HY03676
Presence (1) Absence (0) in sample HY03676

Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details

HY03682_A [flag]
Details
HY03682_A
Presence (1) Absence (0) in sample HY03682_A

Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details

HY36145_A [flag]
Details
HY36145_A
Presence (1) Absence (0) in sample HY36145_A

Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details

HY36146_A [flag]
Details
HY36146_A
Presence (1) Absence (0) in sample HY36146_A

Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details

HY36147_A [flag]
Details
HY36147_A
Presence (1) Absence (0) in sample HY36147_A

Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details

HY36148_A [flag]
Details
HY36148_A
Presence (1) Absence (0) in sample HY36148_A

Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details

HY36149 [flag]
Details
HY36149
Presence (1) Absence (0) in sample HY36149

Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details

HY36150_A [flag]
Details
HY36150_A
Presence (1) Absence (0) in sample HY36150_A

Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details

HY36153_A [flag]
Details
HY36153_A
Presence (1) Absence (0) in sample HY36153_A

Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details

HY36154_A [flag]
Details
HY36154_A
Presence (1) Absence (0) in sample HY36154_A

Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details

HY36151_A [flag]
Details
HY36151_A
Presence (1) Absence (0) in sample HY36151_A

Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details

HY36152_A [flag]
Details
HY36152_A
Presence (1) Absence (0) in sample HY36152_A

Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details

SMI03648 [flag]
Details
SMI03648
Presence (1) Absence (0) in sample SMI03648

Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details

SMI36123_A [flag]
Details
SMI36123_A
Presence (1) Absence (0) in sample SMI36123_A

Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details

SMI36124_A [flag]
Details
SMI36124_A
Presence (1) Absence (0) in sample SMI36124_A

Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details

SMI03647 [flag]
Details
SMI03647
Presence (1) Absence (0) in sample SMI03647

Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details

SMI36126_A [flag]
Details
SMI36126_A
Presence (1) Absence (0) in sample SMI36126_A

Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details

SMI36127_A [flag]
Details
SMI36127_A
Presence (1) Absence (0) in sample SMI36127_A

Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details

SMI36128_A [flag]
Details
SMI36128_A
Presence (1) Absence (0) in sample SMI36128_A

Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details

SMI03649 [flag]
Details
SMI03649
Presence (1) Absence (0) in sample SMI03649

Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details

SMI03650 [flag]
Details
SMI03650
Presence (1) Absence (0) in sample SMI03650

Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurance or success, depth indicator. See dataset documentation for specific details

lon [longitude]
Details
lon

Longitude in decimal degrees east.

longitude, in decimal degrees, East is positive, negative denotes West; Reported in some datsets as degrees, minutes

lat [latitude]
Details
lat

Latitude in decimal degrees north.

latitude, in decimal degrees, North is positive, negative denotes South; Reported in some datasets as degrees, minutes

Dataset Maintainers

NameAffiliationContact
Brandon R. BriggsOregon State University (OSU)
Frederick S. ColwellOregon State University (OSU)
Mathew BiddleWoods Hole Oceanographic Institution (WHOI BCO-DMO)

BCO-DMO Project Info

Project TitleThe Effect of Methane on Microbial Community Distributions in the Ulleung Basin
AcronymMethane_Microbes
URLhttps://www.bco-dmo.org/project/738552
CreatedJune 14, 2018
ModifiedJune 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.

Project Maintainers
NameAffiliationRoleContact
Brandon R. BriggsOregon State University (OSU)Principal Investigator
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