http://lod.bco-dmo.org/id/dataset/756997
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2019-02-27
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Microbial community composition from 16s V4 region amplicon sequencing of the methane Seep at the Cinder Cones Cold Seep site, Nov 2016
2019-02-25
publication
2019-02-25
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2019-03-20
publication
https://doi.org/10.1575/1912/bco-dmo.756997.1
Andrew Thurber
Oregon State University
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Thurber, A. (2019) Microbial community composition from 16s V4 region amplicon sequencing of the methane Seep at the Cinder Cones Cold Seep site, Nov 2016. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2019-02-25 [if applicable, indicate subset used]. doi:10.1575/1912/bco-dmo.756997.1 [access date]
Microbial community composition of the Cinder Cones Cold Seep Dataset Description: <p>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 [<a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA387720" target="_blank">https://www.ncbi.nlm.nih.gov/bioproject/PRJNA387720</a>] with a subset of the data from that archive originating from this project.</p> Methods and Sampling: <p>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.&nbsp; Sediments&nbsp;were placed in whirlpack bags and kept at -80 until DNA was extracted.</p>
<p>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).&nbsp; 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.&nbsp; Controls and all samples were run on a gel to check for contamination.&nbsp; DNA was cleaned up using the MoBio UltraClean PCR Clean-Up Kit, samples were pooled into equal molar concentrations and submitted for sequencing.</p>
<p>Data were de-multiplexed and primers trimmed. No other data manipulation has been performed.</p>
Funding provided by NSF Office of Polar Programs (formerly NSF PLR) (NSF OPP) Award Number: OPP-1642570 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1642570
completed
Andrew Thurber
Oregon State University
541-737-4500
athurber@ucsb.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
accession
sample_name
organism
host
collection_date
geo_loc_name
lat
lon
Replicate
Sediment_Depth_cm
Habitat
theme
None, User defined
accession number
sample identification
sample description
sample type
date
site description
latitude
longitude
replicate
depth core
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Thermal Cycler
instrument
BCO-DMO Standard Instruments
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
EAGER: Elucidating the Antarctic Methane Cycle at the Cinder Cones Reducing Habitat
https://osprey.bco-dmo.org/project/709615
EAGER: Elucidating the Antarctic Methane Cycle at the Cinder Cones Reducing Habitat
<p>NSF abstract:</p>
<p>Methane is a potent greenhouse gas that is naturally emitted into the oceans by geologic seeps and microbial production. Based on studies of persistent deep-sea seeps at mid- and northern latitudes, researchers have learned that bacteria and archaea can create a "sediment filter" that oxidizes methane prior to its release. Antarctica is thought to contain large reservoirs of organic carbon buried beneath its ice which could a quantity of methane equivalent to all of the permafrost in the Arctic and yet we know almost nothing about the methane oxidizing microbes in this region. How these microbial communities develop and potentially respond to fluctuations in methane levels is an under-explored avenue of research. A bacterial mat was recently discovered at 78 degrees south, suggesting the possible presence of a methane seep, and associated microbial communities. This project will explore this environment in detail to assess the levels and origin of methane, and the nature of the microbial ecosystem present.</p>
<p>An expansive bacterial mat appeared and/or was discovered at 78 degrees south in 2011. This site, near McMurdo Station Antarctica, has been visited since the mid-1960s, but this mat was not observed until 2011. The finding of this site provides an unusual opportunity to study an Antarctic marine benthic habitat with active methane cycling and to examine the dynamics of recruitment and community succession of seep fauna including bacteria, archaea, protists and metazoans. This project will collect the necessary baseline data to facilitate further studies of Antarctic methane cycling. The concentration and source of methane will be determined at this site and at potentially analogous sites in McMurdo Sound. In addition to biogeochemical characterization of the sites, molecular analysis of the microbial community will quantify the time scales on which bacteria and archaea respond to methane input and provide information on rates of community development and succession in the Southern Ocean. Project activities will facilitate the training of at least one graduate student and results will be shared at both local and international levels. A female graduate student will be mentored as part of this project and data collected will form part of her dissertation. Lectures will be given in K-12 classrooms in Oregon to excite students about polar science. National and international audiences will be reached through blogs and presentations at a scientific conference. The PI's previous blogs have been used by K-12 classrooms as part of their lesson plans and followed in over 65 countries.</p>
Cinder Cone Seep
largerWorkCitation
project
eng; USA
biota
oceans
166.666
166.666
-77.8
-77.8
2016-11-03
2016-11-15
Ross Sea, Antarctica (78 S, 166 E)
0
BCO-DMO catalogue of parameters from Microbial community composition from 16s V4 region amplicon sequencing of the methane Seep at the Cinder Cones Cold Seep site, Nov 2016
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/757004.rdf
Name: accession
Units: unitless
Description: <p>NCBI accession number for the archive</p>
http://lod.bco-dmo.org/id/dataset-parameter/757005.rdf
Name: sample_name
Units: unitless
Description: <p>reference file name used in NCBI</p>
http://lod.bco-dmo.org/id/dataset-parameter/757006.rdf
Name: organism
Units: unitless
Description: <p>type of organism analyzed: all are marine sediment whose microbial community has been extracted</p>
http://lod.bco-dmo.org/id/dataset-parameter/757007.rdf
Name: host
Units: unitless
Description: <p>host type: these are environmental samples rather than from individual organisms</p>
http://lod.bco-dmo.org/id/dataset-parameter/757008.rdf
Name: collection_date
Units: unitless
Description: <p>Date sample was collected formatted as yyyy-mm-dd</p>
http://lod.bco-dmo.org/id/dataset-parameter/757009.rdf
Name: geo_loc_name
Units: unitless
Description: <p>location sampled</p>
http://lod.bco-dmo.org/id/dataset-parameter/757010.rdf
Name: lat
Units: decimal degrees
Description: <p>latitude; north is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/757011.rdf
Name: lon
Units: decimal degrees
Description: <p>longitude; east is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/757012.rdf
Name: Replicate
Units: unitless
Description: <p>Individual identifier for the core</p>
http://lod.bco-dmo.org/id/dataset-parameter/757013.rdf
Name: Sediment_Depth_cm
Units: centimeters
Description: <p>depth range from which microbial community was analyzed</p>
http://lod.bco-dmo.org/id/dataset-parameter/757014.rdf
Name: Habitat
Units: unitless
Description: <p>Whether the sample was from an area of active methane seepage or sampled as a control for this habitat.</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
24723
https://darchive.mblwhoilibrary.org/bitstream/1912/23875/1/dataset-756997_microbial-community-composition-cinder-cones-cold-seep__v1.tsv
download
https://doi.org/10.1575/1912/bco-dmo.756997.1
download
onLine
dataset
<p>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.&nbsp; Sediments&nbsp;were placed in whirlpack bags and kept at -80 until DNA was extracted.</p>
<p>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).&nbsp; 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.&nbsp; Controls and all samples were run on a gel to check for contamination.&nbsp; DNA was cleaned up using the MoBio UltraClean PCR Clean-Up Kit, samples were pooled into equal molar concentrations and submitted for sequencing.</p>
<p>Data were de-multiplexed and primers trimmed. No other data manipulation has been performed.</p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Processing Notes:</strong><br />
- added conventional header with dataset name, PI name, version date<br />
- modified parameter names to conform with BCO-DMO naming conventions<br />
- re-formatted date from m/d/yyyy to yyyy-mm-dd<br />
- split lat and lon into separate columns; converted lat to negative degrees</p>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
PI Supplied Instrument Name: Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
PI Supplied Instrument Name: Instrument Name: Thermal Cycler Instrument Short Name:Thermal Cycler Instrument 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)