Dataset: Microbial community composition of the Cinder Cones Cold Seep

Name: Microbial community composition from 16s V4 region amplicon sequencing of the methane Seep at the Cinder Cones Cold Seep site, Nov 2016
Published: 2019-02-25
Keywords: microbiome, sediment community, methane seep, methane, methanogen, methanotroph, biota, oceans

Cite This Dataset

DOI:10.1575/1912/bco-dmo.756997.1

Spatial Extent: N:-77.8 E:166.666 S:-77.8 W:166.666

Temporal Extent: 2016-11-03 - 2016-11-15

Project:

EAGER: Elucidating the Antarctic Methane Cycle at the Cinder Cones Reducing Habitat (Cinder Cone Seep)

Principal Investigator:

Andrew Thurber (Oregon State University, OSU-CEOAS)

BCO-DMO Data Manager:

Nancy Copley (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2019-02-25

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Microbial community composition from 16s V4 region amplicon sequencing of the methane Seep at the Cinder Cones Cold Seep site, Nov 2016

Abstract:

This dataset includes microbial community composition from 16s V4 region amplicon sequencing on 151 marine sediment community samples collected from the Cinder Cones Cold Seep site [-77.8, 166.666] in the Ross Sea region, Antarctica in November 2016. Data are uploaded to the NCBI Sequence Read Archive under submission SUB2655615 [https://www.ncbi.nlm.nih.gov/bioproject/PRJNA387720] with a subset of the data from that archive originating from this project.

Expand/Collapse All

Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2019-02-25	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.1575/1912/bco-dmo.756997.1	2019-03-20

Description

This dataset includes details on 151 marine sediment community samples collected from the Cinder Cones Cold Seep site [-77.8, 166.666] in the Ross Sea region, Antarctica in November 2016. Data are uploaded to the NCBI Sequence Read Archive under submission SUB2655615 [https://www.ncbi.nlm.nih.gov/bioproject/PRJNA387720] with a subset of the data from that archive originating from this project.

Methods & Sampling

Sediment cores were collected from the Cinder Cones site including a methane seep habitat and vertically sectioned into cm intervals with the exterior of the cores discarded to avoid vertical smearing. Sediments were placed in whirlpack bags and kept at -80 until DNA was extracted.

Between 0.25 and 0.5 grams of frozen sediment had DNA extracted using the MoBio (now Qiagen) PowerSoil kits. Primers and amplification procedures follow the Earth Microbiome Project Protocol (http://www.earthmicrobiome.org/protocols-and-standards/16s/) using the updated primers in Apprill et al (2015) following Caporaso et al. (2011). In short, triplicate PCRs were run using the 515FB and the 806RB primers that copy the V4 region if the 16s rRNA gene. These primers were barcoded allowing later in silico separation of pooled samples. Controls and all samples were run on a gel to check for contamination. DNA was cleaned up using the MoBio UltraClean PCR Clean-Up Kit, samples were pooled into equal molar concentrations and submitted for sequencing.

Data were de-multiplexed and primers trimmed. No other data manipulation has been performed.

Data Processing Description

BCO-DMO Processing Notes:
- added conventional header with dataset name, PI name, version date
- modified parameter names to conform with BCO-DMO naming conventions
- re-formatted date from m/d/yyyy to yyyy-mm-dd
- split lat and lon into separate columns; converted lat to negative degrees

Data Files

File
MethaneSeepData2016_MicrobialSampleIdentity.csv (Comma Separated Values (.csv), 24.14 KB) MD5:84b644f2c07befa77639c21b2933a9f6 Primary data file for dataset ID 756997

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Office of Polar Programs (formerly NSF PLR)	OPP-1642570

Deployments

None available yet

Instruments

Automated DNA Sequencer

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: Automated DNA Sequencer

Acronym: Automated Sequencer

Generic Description:

General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.

Thermal Cycler

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: Thermal Cycler

Generic Description:

A thermal cycler or "thermocycler" is a general term for a type of laboratory apparatus, commonly used for performing polymerase chain reaction (PCR), that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps. They can also be used to facilitate other temperature-sensitive reactions, including restriction enzyme digestion or rapid diagnostics.

(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
accession	NCBI accession number for the archive	unitless	accession_number
sample_name	reference file name used in NCBI	unitless	sample
organism	type of organism analyzed: all are marine sediment whose microbial community has been extracted	unitless	sample_descrip
host	host type: these are environmental samples rather than from individual organisms	unitless	sample_type
collection_date	Date sample was collected formatted as yyyy-mm-dd	unitless	date
geo_loc_name	location sampled	unitless	site_descrip
lat	latitude; north is positive	decimal degrees	lat
lon	longitude; east is positive	decimal degrees	lon
Replicate	Individual identifier for the core	unitless	replicate
Sediment_Depth_cm	depth range from which microbial community was analyzed	centimeters	depth_core
Habitat	Whether the sample was from an area of active methane seepage or sampled as a control for this habitat.	unitless	site_descrip