http://lod.bco-dmo.org/id/dataset/716443
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
2017-10-09
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
McMurdo Spiophanes beds 16s V4 region community composition from sediment cores at McMurdo Station, Antarctia on Sept 9th, 2012 (McMurdo Benthos project)
2017-10-10
publication
2017-10-10
revision
BCO-DMO Linked Data URI
2017-10-10
creation
http://lod.bco-dmo.org/id/dataset/716443
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. (2017) McMurdo Spiophanes beds 16s V4 region community composition from sediment cores at McMurdo Station, Antarctia on Sept 9th, 2012 (McMurdo Benthos project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). Version Date 2017-10-10 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/716443 [access date]
McMurdo Spiophanes beds 16s V4 region community composition Dataset Description: <p>This dataset includes accession numbers for raw genetic sequence reads&nbsp;from sediment cores of McMurdo Station Spiophanes beds to investigate 16s V4 region community composition.</p>
<p>The accession numbers in this dataset are part of the BioProject&nbsp;titled&nbsp; <a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA387720" target="_blank">16S Amplicon Data from an Antarctic Cold Seep (PRJNA387720)</a> at the National Center for Biotechnology Information (NCBI).&nbsp;&nbsp;</p>
<p>Sediment cores at McMurdo Station were taken&nbsp;at ”The Jetty”, Hutt Point, Ross Sea, Antarctica&nbsp;at a depth of 20m.</p> Methods and Sampling: <p><strong>Methodology: </strong></p>
<p>Sediment cores were collected from the Spiophanes beds at the “Jetty” dive location and vertically sectioned into cm intervals with the exterior of the cores discarded to avoid vertical smearing.&nbsp; Sediment were placed in whirlpack bags and kept at -80 until DNA was extracted.&nbsp;<br />
&nbsp;<br />
<strong>Sampling and analytical procedures:</strong></p>
<p>&nbsp;Between 0.25 and 0.5 grams of frozen sediment had DNA extracted using the MoBio (now Qiagen) PowerSoil kits. rimers and amplification follows 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.&nbsp; 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.&nbsp;</p>
<p>Sequencing was performed on the Illumina MiSeq platform using the V.2 chemistry at the Center for Genome Research and Biocomputing at Oregon State University.&nbsp;&nbsp;</p>
Funding provided by NSF Office of Polar Programs (formerly NSF PLR) (NSF OPP) Award Number: OPP-1103428 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1103428
completed
Andrew Thurber
Oregon State University
541-737-4500
athurber@ucsb.edu
pointOfContact
asNeeded
Unknown
accession
sample_name
organism
host
collection_date
geo_loc_name
lat_lon
lat
lon
Replicate
Sediment_Depth
accession_link
theme
None, User defined
accession number
sample identification
sample description
date
site description
latitude
longitude
replicate
depth below seafloor
featureType
BCO-DMO Standard Parameters
Thurber_Hutt_Point_2012
service
Deployment Activity
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.
Microbe - Metazoan Interactions in an Antarctic Infaunal Community
https://osprey.bco-dmo.org/project/716214
Microbe - Metazoan Interactions in an Antarctic Infaunal Community
<p>The biota of the world's seafloor is fueled by bursts of seasonal primary production. For food-limited sediment communities to persist, a balance must exist between metazoan consumption of and competition with bacteria, a balance which likely changes through the seasons. Polar marine ecosystems are ideal places to study such complex interactions due to stark seasonal shifts between heterotrophic and autotrophic communities, and temperatures that may limit microbial processing of organic matter. The research will test the following hypotheses: 1) heterotrophic bacteria compete with macrofauna for food; 2) as phytoplankton populations decline macrofauna increasingly consume microbial biomass to sustain their populations; and 3) in the absence of seasonal photosynthetic inputs, macrofaunal biodiversity will decrease unless supplied with microbially derived nutrition. Observational and empirical studies will test these hypotheses at McMurdo Station, Antarctica, where a high-abundance macro-infaunal community is adapted to this boom-and-bust cycle of productivity. The investigator will mentor undergraduates from a predominantly minority-serving institution, in the fields of invertebrate taxonomy and biogeochemistry. The general public and young scientists will be engaged through lectures at local K-12 venues and launch of an interactive website. The results will better inform scientists and managers about the effects of climate change on polar ecosystems and the mechanisms of changing productivity patterns on global biodiversity.</p>
McMurdo Benthos
largerWorkCitation
project
eng; USA
oceans
166.639
166.639
-77.846
-77.846
2012-09-09
2012-09-09
Ross Sea, 78 S 167 E
0
BCO-DMO catalogue of parameters from McMurdo Spiophanes beds 16s V4 region community composition from sediment cores at McMurdo Station, Antarctia on Sept 9th, 2012 (McMurdo Benthos 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
http://lod.bco-dmo.org/id/dataset-parameter/716517.rdf
Name: accession
Units: unitless
Description: <p>BioSample (a description of the biological source material) accession number at the National Center for Biotechnology Information (NCBI). An associated raw genetic accession in the Sequence Read Archive (SRA) is associated with this BioSample and can be fount at NCBI</p>
http://lod.bco-dmo.org/id/dataset-parameter/716518.rdf
Name: sample_name
Units: unitless
Description: <p>reference file name used in NCBI</p>
http://lod.bco-dmo.org/id/dataset-parameter/716519.rdf
Name: organism
Units: unitless
Description: <p>All are marine sediment whose microbial community has been extracted</p>
http://lod.bco-dmo.org/id/dataset-parameter/716520.rdf
Name: host
Units: unitless
Description: <p>These are environmental samples; not from individual organisms.</p>
http://lod.bco-dmo.org/id/dataset-parameter/716521.rdf
Name: collection_date
Units: unitless
Description: <p>Date sample was collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/716522.rdf
Name: geo_loc_name
Units: unitless
Description: <p>location sampled</p>
http://lod.bco-dmo.org/id/dataset-parameter/716523.rdf
Name: lat_lon
Units: Latitude and longitude in format decimal degrees with cardinal direction
Description: <p>specific location of collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/716524.rdf
Name: lat
Units: decimal degrees
Description: <p>Latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/716525.rdf
Name: lon
Units: decimal degrees
Description: <p>Longitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/716526.rdf
Name: Replicate
Units: unitless
Description: <p>Individual identifier for the core (all 1s are from one core; 2 from another; etc).</p>
http://lod.bco-dmo.org/id/dataset-parameter/716527.rdf
Name: Sediment_Depth
Units: centimeters
Description: <p>Sediment depth range below seafloor from which microbial community was analyzed.</p>
http://lod.bco-dmo.org/id/dataset-parameter/716528.rdf
Name: accession_link
Units: unitless
Description: <p>Link to the BioSample (a description of the biological source material) accession page at the National Center for Biotechnology Information (NCBI). An associated raw genetic accession in the Sequence Read Archive (SRA) is associated with this BioSample and can be fount at NCBI</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
3631
https://datadocs.bco-dmo.org/file/R88XmOBtvWKyW0/Spiophanes_Microbial.csv
Spiophanes_Microbial.csv
Primary data file for dataset ID 716443
download
https://osprey.bco-dmo.org/dataset/716443/data/download
download
onLine
dataset
<p><strong>Methodology: </strong></p>
<p>Sediment cores were collected from the Spiophanes beds at the “Jetty” dive location and vertically sectioned into cm intervals with the exterior of the cores discarded to avoid vertical smearing.&nbsp; Sediment were placed in whirlpack bags and kept at -80 until DNA was extracted.&nbsp;<br />
&nbsp;<br />
<strong>Sampling and analytical procedures:</strong></p>
<p>&nbsp;Between 0.25 and 0.5 grams of frozen sediment had DNA extracted using the MoBio (now Qiagen) PowerSoil kits. rimers and amplification follows 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.&nbsp; 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.&nbsp;</p>
<p>Sequencing was performed on the Illumina MiSeq platform using the V.2 chemistry at the Center for Genome Research and Biocomputing at Oregon State University.&nbsp;&nbsp;</p>
Specified by the Principal Investigator(s)
<p>Data processing: Data were de-multiplexed and primers trimmed. No other data manipulation has been performed.</p>
<p>BCO-DMO Data Manager Processing Notes:<br />
* added a conventional header with dataset name, PI name, version date<br />
* modified parameter names to conform with BCO-DMO naming conventions<br />
* blank values replaced with no data value 'nd' for "no data" so they are recognized in our system<br />
* Latitude and Longitude converted to decimal degrees<br />
* added ISO Date format generated from Date and Time values<br />
* changed date format to yyyy-mm-dd<br />
* updated coordinates in data for hutt&nbsp;point sample site based on correspondence with data contributor.</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
Deployment: Thurber_Hutt_Point_2012
Thurber_Hutt_Point_2012
Ross Island
island
Thurber_Hutt_Point_2012
Andrew Thurber
Oregon State University
Ross Island
island