http://lod.bco-dmo.org/id/dataset/564859
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
2015-08-28
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Phytoplankton clone library matches collected from the R/V Atlantic Explorer and R/V Oceanus cruises along the Bermuda Atlantic Time Series Station (BATS) from 2008-2010 (Plankton particle flux project)
2015-08-28
publication
2015-08-28
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2020-10-12
publication
https://doi.org/10.26008/1912/bco-dmo.564859.1
Susanne Neuer
Arizona 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: Neuer, S. (2020) Phytoplankton clone library matches collected from the R/V Atlantic Explorer and R/V Oceanus cruises along the Bermuda Atlantic Time Series Station (BATS) from 2008-2010 (Plankton particle flux project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2015-08-28 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.564859.1 [access date]
Phytoplankton clone library matches from BATS cruises 2008-2010 Dataset Description: <p>This dataset includes links to GenBank accession of&nbsp;18S rRNA gene clone library sequences with the closest sequence matches from the NCBI database. The samples are from&nbsp;the upper water column as well as from shallow drifting traps during regular BATS cruises from December 2008-April 2010.</p> Methods and Sampling: <p>Water column samples were collected at BATS during the 2009 and 2010 winter bloom periods from the upper 150 m in Niskin bottles attached to a sampling rosette. Particle interceptor traps (PITs) with both fixed (2% formalin final concentration, deployment time 72 hr) and unfixed (deployment time 24 hr) collection tubes were deployed at 150 m depth in close proximity to the station and during the same time period as the water column collection in order to collect sinking particles below the euphotic zone. Clone libraries were constructed from 2-L samples collected at two depths in the euphotic zone, one close to the surface (10 m) and one from either the bottom of the euphotic zone if the water column was well mixed (most stations sampled; around 120-130 m) or from the chlorophyll maximum if one was present (around 80 m; samples from March 24 and April 24, 2010). Libraries were also constructed from sinking particles collected in two tubes of the PITs from the trap array located at 150 m depth. Unfixed traps were selected unless the sample was unavailable or prior results using DGGE indicated that the fixed trap would be more suitable due to occurrence of fungi and metazoans in the unfixed traps. DNA was extracted from these samples and a region of the 18S ribosomal RNA gene was amplified by PCR using eukaryotic primers. Samples from selected dates and depths were cloned and sequenced and broad taxonomic groups were determined for each sequence using their closest similarity match from BLAST (Basic Local Alignment Search Tool, <a href="http://blast.ncbi.nlm.nih.gov/" target="_blank">http://blast.ncbi.nlm.nih.gov/</a>).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0752592 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0752592
completed
Susanne Neuer
Arizona State University
480-727-7254
College of Liberal Arts and Sciences School of Life Sciences 427 East Tyler Mall
Tempe
AZ
85287-4501
USA
susanne.neuer@asu.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
cruise_id
cruise_name
year
month
day
sample_type
depth
clone_id
accession_number
super_grp_1
phylogenetic_grp
acc_closest_match
closest_match_id
match_pcent
acc_cl_cult_match
closest_cultured_match
closest_match_cultur_pcent
CTD
Sediment Trap
theme
None, User defined
Cruise identfier
cruise name
year
month of year
day of month
sample type
depth
taxon
accession number
No BCO-DMO term
featureType
BCO-DMO Standard Parameters
CTD - profiler
Niskin bottle
Sediment Trap
instrument
BCO-DMO Standard Instruments
AE0901
AE0902
AE1001
AE1006
AE1009
OC449-10
service
Deployment Activity
Bermuda AtlanticTime Series Station (BATS)
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.
Ocean Carbon and Biogeochemistry
http://us-ocb.org/
Ocean Carbon and Biogeochemistry
The Ocean Carbon and Biogeochemistry (OCB) program focuses on the ocean's role as a component of the global Earth system, bringing together research in geochemistry, ocean physics, and ecology that inform on and advance our understanding of ocean biogeochemistry. The overall program goals are to promote, plan, and coordinate collaborative, multidisciplinary research opportunities within the U.S. research community and with international partners. Important OCB-related activities currently include: the Ocean Carbon and Climate Change (OCCC) and the North American Carbon Program (NACP); U.S. contributions to IMBER, SOLAS, CARBOOCEAN; and numerous U.S. single-investigator and medium-size research projects funded by U.S. federal agencies including NASA, NOAA, and NSF.
The scientific mission of OCB is to study the evolving role of the ocean in the global carbon cycle, in the face of environmental variability and change through studies of marine biogeochemical cycles and associated ecosystems.
The overarching OCB science themes include improved understanding and prediction of: 1) oceanic uptake and release of atmospheric CO2 and other greenhouse gases and 2) environmental sensitivities of biogeochemical cycles, marine ecosystems, and interactions between the two.
The OCB Research Priorities (updated January 2012) include: ocean acidification; terrestrial/coastal carbon fluxes and exchanges; climate sensitivities of and change in ecosystem structure and associated impacts on biogeochemical cycles; mesopelagic ecological and biogeochemical interactions; benthic-pelagic feedbacks on biogeochemical cycles; ocean carbon uptake and storage; and expanding low-oxygen conditions in the coastal and open oceans.
OCB
largerWorkCitation
program
Composition of the plankton community and its contribution to particle flux in the Sargasso Sea
https://osprey.bco-dmo.org/project/2245
Composition of the plankton community and its contribution to particle flux in the Sargasso Sea
<p>The overall objective of this proposal is to investigate linkages between the presence of different key groups of phytoplankton in the euphotic zone and their contribution to particle flux at the subtropical North Atlantic time-series station BATS (Bermuda Atlantic Time-series Study) by applying a range of traditional and novel molecular techniques.</p>
<p>The 'biological pump', the photosynthetically mediated transformation of dissolved inorganic carbon into particulate and dissolved organic carbon in surface ocean waters and its subsequent export to deep water, is a significant driver of the atmospheric carbon uptake by the oceans. But this "biologically pumped" production, inasmuch as it depends on the composition and activity of planktonic organisms, is susceptible to long-term climatic changes in surface ocean properties such as increased temperature and changes in nutrient supply, especially in subtropical gyres. The sub-tropical gyres and the transition zones at their boundaries play an important role in the global carbon cycle because of their vast size and generally high per area export production. As evidenced in recent studies, the biological mechanisms driving regional to basin scale variability in carbon export in these biomes is far from understood, thus limiting our ability to mechanistically explain the biological pump and to predict its possible responses in the face of environmental change. In an effort to improve this situation with an accurate assessment of the contribution of different plankton groups to overall fluxes, the investigators will test the following two specific hypotheses: 1. The long held notion that large cells and those with mineral tests are major contributors to downward particle flux needs to be re-evaluated. We hypothesize that pico and nanoplankton (also those without mineral tests) are generally important contributors to downward particle flux at BATS. Consequently, the diversity of taxonomic groups contributing to particle flux is greater than previously expected. 2. The relative contribution of taxonomic groups to downward particle flux is a function of physical forcing. We hypothesize that episodic events (e.g., winter storms and eddies) lead to a reduction in diversity of sedimenting phytoplankton (e.g., dominance by a single group such as diatoms) compared to periods marked by more stable conditions in the water column. The broader impacts include furthering knowledge of the diversity and biology of phytoplankton groups that have a significant impact on the carbon export in subtropical gyres, thereby advancing our understanding of regional to basin scale variability in the biogeochemistry of these biomes. The project provides new opportunities for undergraduate and graduate education, as well as offer research opportunities to local high school students and teachers as part of the "Ask-a-Biologist" initiative. The project also includes an international component through collaboration with a molecular ecology group in Barcelona, Spain.</p>
Plankton particle flux
largerWorkCitation
project
eng; USA
biota
oceans
Bermuda AtlanticTime Series Station (BATS)
-64.6504
-63.7119
31.1715
32.4006
2008-12-14
2010-04-24
BATS site: Bermuda Atlantic Time-Series Study: 31° 45’N, 64° 10’W
0
BCO-DMO catalogue of parameters from Phytoplankton clone library matches collected from the R/V Atlantic Explorer and R/V Oceanus cruises along the Bermuda Atlantic Time Series Station (BATS) from 2008-2010 (Plankton particle flux 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/564951.rdf
Name: cruise_id
Units: unitless
Description: <p>official rvdata cruise name</p>
http://lod.bco-dmo.org/id/dataset-parameter/564952.rdf
Name: cruise_name
Units: unitless
Description: <p>original cruise number</p>
http://lod.bco-dmo.org/id/dataset-parameter/564953.rdf
Name: year
Units: YYYY
Description: <p>year of sampling</p>
http://lod.bco-dmo.org/id/dataset-parameter/564954.rdf
Name: month
Units: MM
Description: <p>month of sampling</p>
http://lod.bco-dmo.org/id/dataset-parameter/564955.rdf
Name: day
Units: DD
Description: <p>day of sampling</p>
http://lod.bco-dmo.org/id/dataset-parameter/564956.rdf
Name: sample_type
Units: unitless
Description: <p>type of sample: from the water column (CTD) or from a sediment trap</p>
http://lod.bco-dmo.org/id/dataset-parameter/564957.rdf
Name: depth
Units: meters
Description: <p>sampling depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/564958.rdf
Name: clone_id
Units: unitless
Description: <p>clone identification</p>
http://lod.bco-dmo.org/id/dataset-parameter/564959.rdf
Name: accession_number
Units: unitless
Description: <p>GenBank accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/564960.rdf
Name: super_grp_1
Units: unitless
Description: <p>first rank super group</p>
http://lod.bco-dmo.org/id/dataset-parameter/564961.rdf
Name: phylogenetic_grp
Units: unitless
Description: <p>phylogenetic group</p>
http://lod.bco-dmo.org/id/dataset-parameter/564962.rdf
Name: acc_closest_match
Units: unitless
Description: <p>accession number of closest match</p>
http://lod.bco-dmo.org/id/dataset-parameter/564963.rdf
Name: closest_match_id
Units: unitless
Description: <p>closest match</p>
http://lod.bco-dmo.org/id/dataset-parameter/564964.rdf
Name: match_pcent
Units: percent
Description: <p>% match</p>
http://lod.bco-dmo.org/id/dataset-parameter/564965.rdf
Name: acc_cl_cult_match
Units: unitless
Description: <p>accession number of closest cultured match</p>
http://lod.bco-dmo.org/id/dataset-parameter/564966.rdf
Name: closest_cultured_match
Units: unitless
Description: <p>closest cultured match</p>
http://lod.bco-dmo.org/id/dataset-parameter/564967.rdf
Name: closest_match_cultur_pcent
Units: percent
Description: <p>% match closest cultured</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
618757
https://darchive.mblwhoilibrary.org/bitstream/1912/26306/1/dataset-564859_phytofluxbats-clone-library-2008-1010__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.564859.1
download
onLine
dataset
<p>Water column samples were collected at BATS during the 2009 and 2010 winter bloom periods from the upper 150 m in Niskin bottles attached to a sampling rosette. Particle interceptor traps (PITs) with both fixed (2% formalin final concentration, deployment time 72 hr) and unfixed (deployment time 24 hr) collection tubes were deployed at 150 m depth in close proximity to the station and during the same time period as the water column collection in order to collect sinking particles below the euphotic zone. Clone libraries were constructed from 2-L samples collected at two depths in the euphotic zone, one close to the surface (10 m) and one from either the bottom of the euphotic zone if the water column was well mixed (most stations sampled; around 120-130 m) or from the chlorophyll maximum if one was present (around 80 m; samples from March 24 and April 24, 2010). Libraries were also constructed from sinking particles collected in two tubes of the PITs from the trap array located at 150 m depth. Unfixed traps were selected unless the sample was unavailable or prior results using DGGE indicated that the fixed trap would be more suitable due to occurrence of fungi and metazoans in the unfixed traps. DNA was extracted from these samples and a region of the 18S ribosomal RNA gene was amplified by PCR using eukaryotic primers. Samples from selected dates and depths were cloned and sequenced and broad taxonomic groups were determined for each sequence using their closest similarity match from BLAST (Basic Local Alignment Search Tool, <a href="http://blast.ncbi.nlm.nih.gov/" target="_blank">http://blast.ncbi.nlm.nih.gov/</a>).</p>
Specified by the Principal Investigator(s)
<p>DNA was extracted from environmental samples, 18S rRNA amplified by PCR, cloned and sequenced. Sequences were assigned taxonomic groups using their closest match on NCBI BLAST.</p>
<p><strong>BCO-DMO Processing:</strong></p>
<p>- added conventional header with dataset name; PI name; version date<br />
- renamed parameters to BCO-DMO standard<br />
- sequences not served; see NCBI accession number links<br />
- added columns for cruise_id; cruise_name; year; month; day; sample_type; depth<br />
- added html links to accession numbers<br />
- removed trailing blanks and unprintable characters</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
CTD
CTD
PI Supplied Instrument Name: CTD Instrument Name: CTD - profiler Instrument Short Name: Instrument Description: The Conductivity, Temperature, Depth (CTD) unit is an integrated instrument package designed to measure the conductivity, temperature, and pressure (depth) of the water column. The instrument is lowered via cable through the water column. It permits scientists to observe the physical properties in real-time via a conducting cable, which is typically connected to a CTD to a deck unit and computer on a ship. The CTD is often configured with additional optional sensors including fluorometers, transmissometers and/or radiometers. It is often combined with a Rosette of water sampling bottles (e.g. Niskin, GO-FLO) for collecting discrete water samples during the cast.
This term applies to profiling CTDs. For fixed CTDs, see https://www.bco-dmo.org/instrument/869934. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/130/
PI Supplied Instrument Name: PI Supplied Instrument Description:Samples were collected using 10-Liter Niskin bottles attached to a CTD rosette. Instrument Name: Niskin bottle Instrument Short Name:Niskin bottle Instrument Description: A Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends. The bottles can be attached individually on a hydrowire or deployed in 12, 24, or 36 bottle Rosette systems mounted on a frame and combined with a CTD. Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/
Sediment Trap
Sediment Trap
PI Supplied Instrument Name: Sediment Trap Instrument Name: Sediment Trap Instrument Short Name:Sediment Trap Instrument Description: Sediment traps are specially designed containers deployed in the water column for periods of time to collect particles from the water column falling toward the sea floor. In general a sediment trap has a jar at the bottom to collect the sample and a broad funnel-shaped opening at the top with baffles to keep out very large objects and help prevent the funnel from clogging. This designation is used when the specific type of sediment trap was not specified by the contributing investigator. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/33/
Cruise: AE0901
AE0901
R/V Atlantic Explorer
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantic Explorer
vessel
AE0901
Anthony Knap
Bermuda Biological Station for Research
Cruise: AE0902
AE0902
R/V Atlantic Explorer
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantic Explorer
vessel
AE0902
Anthony Knap
Bermuda Biological Station for Research
Cruise: AE1001
AE1001
R/V Atlantic Explorer
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantic Explorer
vessel
AE1001
Anthony Knap
Bermuda Biological Station for Research
Cruise: AE1006
AE1006
R/V Atlantic Explorer
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantic Explorer
vessel
AE1006
Lilia Jackman
Bermuda Biological Station for Research
Cruise: AE1009
AE1009
R/V Atlantic Explorer
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantic Explorer
vessel
AE1009
Anthony Knap
Bermuda Biological Station for Research
Cruise: OC449-10
OC449-10
R/V Oceanus
Community Standard Description
International Council for the Exploration of the Sea
R/V Oceanus
vessel
OC449-10
Steven Bell
Bermuda Institute of Ocean Sciences
R/V Atlantic Explorer
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantic Explorer
vessel
R/V Oceanus
Community Standard Description
International Council for the Exploration of the Sea
R/V Oceanus
vessel