http://lod.bco-dmo.org/id/dataset/662996
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
2016-10-26
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Metadata associated with genomic and genetic data collected from organisms obtained on BOWLs landers, R/V Oceanus June 22-27, 2014 (BOWLS project)
2016-10-26
publication
2016-10-26
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2023-03-09
publication
https://doi.org/10.26008/1912/bco-dmo.662996.1
Craig R. Smith
University of Hawaiʻi at Mānoa
principalInvestigator
Kenneth M. Halanych
Auburn 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: Smith, C. R., Halanych, K. M. (2021) Metadata associated with genomic and genetic data collected from organisms obtained on BOWLs landers, R/V Oceanus June 22-27, 2014 (BOWLS project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2016-10-26 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.662996.1 [access date]
Sample log for specimens collected for genomics analyses Dataset Description: Methods and Sampling: <p>The investigators deployed four free-vehicle Bone-Wood Landers (BOWLs) as moorings that (1) sink autonomously to the deep-sea floor, (2) expose 9 controlled experimental substrates of whale bone, wood, or inert materials at the seafloor for months to years, and (3) upon acoustic command, enclose each experimental substrate in a sealed 500-micrometer mesh bag and returns to the ocean surface. This new BOWL technology allows controlled quantitative study of biotic colonization, biodiversity, ecosystem function and connectivity for bone, wood and other experimental substrates in the deep sea at relatively low fabrication and ship-time costs.</p>
<p><strong>Genomic methods:</strong><br />
RAD_seq&nbsp; = This is 2b-RAD Single Nucleotide Polymorphism (SNP) data collected with the Wang et al. 2012 protocol. The raw reads will be deposited in NCBI Small Read Archive. The data is Illumina SE 50bp data.</p>
<p>mt_genome = This is Illumina PE 150bp data derive from total genomic DNA extracted from the organisms listed in the spreadsheet. The raw reads will be deposited in NCBI Small Read Archive and the assembled mitochondrial genome will be submitted to NCBI GenBank.</p>
<p>Endosymbiont_genome = This is Illumina PE 150bp data derive from total genomic DNA extracted from the organisms listed in the spreadsheet. The raw reads will be deposited in NCBI Small Read Archive and the assembled endosymbiont genome will be submitted to NCBI GenBank.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1155188 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1155188
completed
Craig R. Smith
University of Hawaiʻi at Mānoa
808-956-7776
Department of Oceanography 1000 Pope Road
Honolulu
HI
96822
USA
craigsmi@hawaii.edu
pointOfContact
Kenneth M. Halanych
Auburn University
334-844-3222
101 Life Sciences Building Department of Biological Sciences, Auburn University
Auburn
AL
36849
USA
ken@auburn.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
genomic_method
taxon
species
lander
lab_identifier
block_bone
individuals
lat
lon
depth
Illumina SE
Illumina PE
theme
None, User defined
sampling_method
taxon
species
instrument
sample identification
count
latitude
longitude
depth
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Automated DNA Sequencer
instrument
BCO-DMO Standard Instruments
OC1406B
service
Deployment Activity
Coast of Oregon
place
Locations
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.
Biodiversity, connectivity and ecosystem function in organic-rich whale-bone and wood-fall habitats in the deep sea
http://craigrsmithlab.com/bowls-project/
Biodiversity, connectivity and ecosystem function in organic-rich whale-bone and wood-fall habitats in the deep sea
<p><em>Description from NSF award abstract:</em><br />
Organic-rich habitat islands support specialized communities throughout natural ecosystems and often play fundamental roles in maintaining alpha and beta diversity, thus facilitating adaptive radiation and evolutionary novelty. Whale-bone and wood falls occur widely in the deep-sea and contribute fundamentally to biodiversity and evolutionary novelty; nonetheless, large-scale patterns of biodiversity, connectivity, and ecosystem function in these organic-rich metacommunity systems remain essentially unexplored.</p>
<p>The PIs propose a novel comparative experimental approach to evaluate bathymetric, regional, and inter-basin variations in biodiversity and connectivity, as well as interactions between biodiversity and ecosystem function, in whale-bone and wood-fall habitats at the deep-sea floor. Their experiments will use bottom landers to carry and hold samples of bone and wood and a control substrate (basalt) at two depths (1500 and 3000 m), 250-500 km apart, in the NE Pacific and SW Atlantic basins, with quantitative recovery of the colonizing assemblages 15 month later. Each depth will have three replicates. Their experiments will test fundamental hypotheses concerning biodiversity (genetic and taxonomic) and biogeography of macrofaunal and microbial organisms exploiting these resource-rich habitats in energy limited deep-sea environments, and will explore the utility of whale-bone and wood falls as model experimental systems to address patterns of connectivity and decomposer function in the deep sea.</p>
BOWLS
largerWorkCitation
project
eng; USA
biota
oceans
Coast of Oregon
-127.59288
-63.16567
43.9087
65.09983
2014-06-22
2014-06-22
Off the Oregon and Washington State coast; roughly 43.833N, 127.5W to 47.3N, 127.4W
0
BCO-DMO catalogue of parameters from Metadata associated with genomic and genetic data collected from organisms obtained on BOWLs landers, R/V Oceanus June 22-27, 2014 (BOWLS 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/663000.rdf
Name: genomic_method
Units: unitless
Description: <p>The genomic method used to analyze specimen:<br />
RAD_seq = restriction site-associated DNA sequencing (RADSeq);<br />
mt_genome = mitochondrial genome sequencing;<br />
Endosymbiont_genome = Endosymbiont genome was sequenced</p>
http://lod.bco-dmo.org/id/dataset-parameter/663001.rdf
Name: taxon
Units: unitless
Description: <p>broad taxonomic group</p>
http://lod.bco-dmo.org/id/dataset-parameter/663002.rdf
Name: species
Units: unitless
Description: <p>genus and species name</p>
http://lod.bco-dmo.org/id/dataset-parameter/663003.rdf
Name: lander
Units: unitless
Description: <p>BOWLS lander identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/663004.rdf
Name: lab_identifier
Units: unitless
Description: <p>specimen identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/663005.rdf
Name: block_bone
Units: unitless
Description: <p>substrate identifier; NA=not applicable</p>
http://lod.bco-dmo.org/id/dataset-parameter/663006.rdf
Name: individuals
Units: individuals
Description: <p>number of individuals found in colonized substrate; NA=not applicable</p>
http://lod.bco-dmo.org/id/dataset-parameter/663007.rdf
Name: lat
Units: decimal degrees
Description: <p>latitude; north is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/663008.rdf
Name: lon
Units: decimal degrees
Description: <p>longitude; east is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/663009.rdf
Name: depth
Units: meteres
Description: <p>sample depth</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
2161
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/77011d35-2333-5f2c-adcb-04bf3e2b9ee1/content
download
https://doi.org/10.26008/1912/bco-dmo.662996.1
download
onLine
dataset
<p>The investigators deployed four free-vehicle Bone-Wood Landers (BOWLs) as moorings that (1) sink autonomously to the deep-sea floor, (2) expose 9 controlled experimental substrates of whale bone, wood, or inert materials at the seafloor for months to years, and (3) upon acoustic command, enclose each experimental substrate in a sealed 500-micrometer mesh bag and returns to the ocean surface. This new BOWL technology allows controlled quantitative study of biotic colonization, biodiversity, ecosystem function and connectivity for bone, wood and other experimental substrates in the deep sea at relatively low fabrication and ship-time costs.</p>
<p><strong>Genomic methods:</strong><br />
RAD_seq&nbsp; = This is 2b-RAD Single Nucleotide Polymorphism (SNP) data collected with the Wang et al. 2012 protocol. The raw reads will be deposited in NCBI Small Read Archive. The data is Illumina SE 50bp data.</p>
<p>mt_genome = This is Illumina PE 150bp data derive from total genomic DNA extracted from the organisms listed in the spreadsheet. The raw reads will be deposited in NCBI Small Read Archive and the assembled mitochondrial genome will be submitted to NCBI GenBank.</p>
<p>Endosymbiont_genome = This is Illumina PE 150bp data derive from total genomic DNA extracted from the organisms listed in the spreadsheet. The raw reads will be deposited in NCBI Small Read Archive and the assembled endosymbiont genome will be submitted to NCBI GenBank.</p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Processing:</strong><br />
- added conventional header with dataset name, PI name, version date<br />
- column names reformatted to comply with BCO-DMO standards<br />
- removed 'm' from depth column entries<br />
- converted lat and lon from degrees and decimal minutes to decimal degrees"<br />
- replaced spaces with underscores</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
Illumina SE
Illumina SE
PI Supplied Instrument Name: Illumina SE PI Supplied Instrument Description:Used for the RADSeq 50 bp data 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.
Illumina PE
Illumina PE
PI Supplied Instrument Name: Illumina PE PI Supplied Instrument Description:Used for the mitochondrial and endosymbiont genome 150bp data 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.
Cruise: OC1406B
OC1406B
R/V Oceanus
Community Standard Description
International Council for the Exploration of the Sea
R/V Oceanus
vessel
OC1406B
Craig R. Smith
University of Hawaiʻi at Mānoa
R/V Oceanus
Community Standard Description
International Council for the Exploration of the Sea
R/V Oceanus
vessel