http://lod.bco-dmo.org/id/dataset/3373
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
2010-10-13
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Links to accessions for 18S rDNA, chloroplast and metagenomics (picoeukaryote) data from multiple cruises from the Sargasso Sea and CalCOFI line 67 from 2001-2009 (PHYTO_GENOME project)
2011-01-18
publication
2011-01-18
revision
BCO-DMO Linked Data URI
2011-01-18
creation
http://lod.bco-dmo.org/id/dataset/3373
Dr Alexandra Z. Worden
Monterey Bay Aquarium Research Institute
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: Worden, A. Z. (2011) Links to accessions for 18S rDNA, chloroplast and metagenomics (picoeukaryote) data from multiple cruises from the Sargasso Sea and CalCOFI line 67 from 2001-2009 (PHYTO_GENOME project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 18 January 2011) Version Date 2011-01-18 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/3373 [access date]
Links to Accessions for 18S rDNA , chloroplast and metagenomics data Dataset Description: <p>Accessions for 18S rDNA , chloroplast and metagenomics data<br />
<br />
Biliphyte sequences from this study have been deposited in GenBank under Accession No. EU368003-EU368039<br />
<br />
Cuvelier ML, Ortiz A, Kim E, Moehlig H, Richardson DE, Heidelberg JF, Archibald JM, Worden AZ (2008).<br />
Widespread distribution of a unique marine protistan lineage. Environmental Microbiology. Vol. 10:1621-1634.<br />
<br />
Prymnesiophyte sequences from this study have been deposited in GenBank under Accession Nos.<br />
HM581528-HM581638 and HM565909-HM565914. Other scaffolds with predicted genes from this Whole<br />
Genome Shotgun/454 project have been deposited at DNA Data Bank of Japan/European Molecular Biology<br />
Laboratory/GenBank under the accession no. AEAR00000000. The version described in this paper is<br />
the first version, AEAR01000000.<br />
<br />
Cuvelier ML, Allen* AE, Monier* A, McCrow JP, Messie M, Tringe SG, Woyke T, Welsh RM, Ishoey T,<br />
Lee JH, Binder BJ, DuPont CL, Latasa M, Guigand C, Buck KR, Hilton J, Thiagarajan M, Caler E,<br />
Read B, Lasken RS, Chavez FP &amp; AZ Worden (2010). Targeted metagenomics and ecology of globally<br />
important uncultured eukaryotic phytoplankton. Proceedings of the National Academy of Sciences USA.<br />
<br />
Alveolate sequences from this study have been deposited in GenBank under:<br />
EU818567-EU818691, EU836584-EU836597, EU818578-EU818566, EU817966-EU818077,<br />
EU836613-EU836615; EU817882-EU817965; EU836616-EU816617<br />
<br />
Guillou L, Viprey M, Chambouvet A, Welsh RM, Kirkham AR, Massana R, Scanlan DJ and&nbsp;AZ Worden (2008).<br />
Widespread occurrence and genetic diversity of marine parasitoids belonging to Syndiniales (Alveolata).<br />
Environmental Microbiology. DOI: 10.1111/j.1462-2920.2008.01731.x</p> Methods and Sampling: <p>Samples were typically taken at the surface and deep chlorophyll maximum using a niskin rosette, all contextual data available (typically temperature and salinity) was deposited with the GenBank Submission for each sequence.<br />
<br />
<u>Field sites and sample collection</u><br />
Five cruises were conducted, two transects from coastal New England to the BATS site (R/V Endeavor cruise EN351 and R/V Oceanus cruise OC413) and three transects across the Florida Straits (R/V Walton Smith cruises WS0503, WS0518, WS0528) with characteristics as in Table 1. Samples were collected in surface and DCM waters using a Sea-Bird Niskin Rosette equipped with standard CTD and PAR detectors (see also below). For DNA extraction samples, 1 l of seawater was gravity filtered through 2 um pore size filters (GE Osmonics, Minnetonka, MN, USA) and then onto a 0.45 um pore size (2001) or 0.2 um pore size (2005) Supor filter (Pall Gelman, Ann Arbor, MI, USA) using vacuum. For FISH samples whole seawater (no size fractionation) was preserved with 1% paraformaldahyde (final concentration) for at least 1 h in the dark at 4&deg;C. For each replicate, volumes of 180 ml or more of seawater were gently filtered onto a 25 mm, 0.2 um Anodisc filter (Whatman, Maidstone, England). The filters were then subjected to an ethanol dehydration series at 50%, 80%, 100% (diluted in sterile, 18.2 &deg; H2O) for 3 min each and stored at -80&deg;C. Flow cytometry samples were preserved with 0.25% (final concentration) fresh electron microscopy grade glutaraldehyde (Tousimis, Rockville, MD, USA), flash frozen in liquid nitrogen and moved to -80&deg;C for long-term storage.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0623928 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0623928
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0836721 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0836721
completed
Dr Alexandra Z. Worden
Monterey Bay Aquarium Research Institute
831-775-2122
Monterey Bay Aquarium Research Institute (MBARI) 7700 Sandholdt Rd.
Moss Landing
CA
95039
USA
azworden@mbari.org
pointOfContact
asNeeded
Dataset Version: 18 January 2011
Unknown
Sequence
Accession_Number_Series
Accession_Number_Link
CTD Sea-Bird
Niskin bottle
Photosynthetically Available Radiation Sensor
theme
None, User defined
No BCO-DMO term
accession number
featureType
BCO-DMO Standard Parameters
CTD Sea-Bird
Niskin bottle
Photosynthetically Available Radiation Sensor
instrument
BCO-DMO Standard Instruments
EN351
EN360
OC374
OC413
WS0503
WS0518
WS0528
WS0705
CN207
service
Deployment Activity
32N 64W, Sargasso Sea, Vicinity of BATS
Approx 25N 75W, Florida Straits
Approx 25N 75W, Florida Straits
eastern North Pacific (CalCOFI line 67)
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.
Unveiling the contributions and regulation of picoeukaryotic phytoplankton in oceanic environments
http://www.mbari.org/phyto-genome/research.htm
Unveiling the contributions and regulation of picoeukaryotic phytoplankton in oceanic environments
<p>The growth rates and fate of primary producers in the oceans are key factors<br />
regulating carbon flux in the biosphere. While resource limitation is known to<br />
play a major regulatory role, the specific factors controlling growth and mortality<br />
of picophytoplankton (<2 microm diameter) are poorly understood. In particular,<br />
due to the small size and low sinking quotient of these dominant primary producers,<br />
determinants of their fate and transport in the water column are critical to the<br />
development of predictive models of carbon flux and its likely perturbation due to<br />
climate change. Picophytoplankton is composed of cyanobacteria, (Prochlorococcus<br />
and Synechococcus) and small eukaryotes. While the picocyanobacteria have received<br />
much attention, little is known about the distribution and dynamics of picophytoeukaryotes,<br />
particularly in oceanic settings. The few comparative measurements made to date indicate<br />
that the productivity of picophytoeukaryotes can rival that of picocyanobacteria. Hence,<br />
knowledge regarding the role of picophytoeukaryotes in open ocean environments is urgently<br />
needed. However, this knowledge is only valuable when put in the context of the total<br />
picophytoplankton community and, therefore, quantification of picocyanobacteria must also<br />
be included.</p>
<p>The overall goal is to develop a method for determining underlying physiological controls<br />
of picophytoeukaryotes. A targeted approach will be used, combining flow sorting, cDNA<br />
libraries and Expressed Sequence Tags (EST), allowing real-time expressional responses to<br />
be identified. This knowledge will highlight key physiological constraints and information<br />
on molecular underpinnings of picoeukaryotic population dynamics as well as aiding future<br />
efforts to isolate open-ocean picoeukaryotes. This is an important additional benefit from<br />
the work since environmental clone library data has demonstrated that such picoeukaryotes<br />
are poorly represented in culture collections. Long-term, the environmental genomic approach<br />
developed will also provide a high throughput mechanism for profiling expressional responses<br />
(mRNA) in the field. In the proposed work, expressional responses will be evaluated in two<br />
ocean basins, the equatorial Atlantic and the South Pacific.</p>
<p>
PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH<br />
Cuvelier et al. "Widespread distribution of a unique marine protistan lineage.," Environmental Microbiology, 2008.</p>
<p><strong>Note:</strong><br />
All contextual data available (typically temperature and salinity) was deposited with the GenBank Submission for each sequence.</p>
PHYTO_GENOME
largerWorkCitation
project
eng; USA
oceans
32N 64W, Sargasso Sea, Vicinity of BATS; Approx 25N 75W, Florida Straits; Approx 25N 75W, Florida Straits; eastern North Pacific (CalCOFI line 67)
2011-01-18
Sargasso Sea, Gulf Stream, Florida Straits and eastern North Pacific (CalCOFI line 67)
0
BCO-DMO catalogue of parameters from Links to accessions for 18S rDNA, chloroplast and metagenomics (picoeukaryote) data from multiple cruises from the Sargasso Sea and CalCOFI line 67 from 2001-2009 (PHYTO_GENOME 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/23221.rdf
Name: Sequence
Units: text
Description: <p>Environmental DNA sequencing type</p>
http://lod.bco-dmo.org/id/dataset-parameter/23222.rdf
Name: Accession_Number_Series
Units: text
Description: <p>GenBank Start-End accession numbers of sequence</p>
http://lod.bco-dmo.org/id/dataset-parameter/23223.rdf
Name: Accession_Number_Link
Units: text
Description: <p>Link to accession number at GenBank</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
59395
https://datadocs.bco-dmo.org/file/6YYMwEVuy9D3zx/Accessions.csv
Accessions.csv
Primary data file for dataset ID 3373
download
https://osprey.bco-dmo.org/dataset/3373/data/download
download
onLine
dataset
<p>Samples were typically taken at the surface and deep chlorophyll maximum using a niskin rosette, all contextual data available (typically temperature and salinity) was deposited with the GenBank Submission for each sequence.<br />
<br />
<u>Field sites and sample collection</u><br />
Five cruises were conducted, two transects from coastal New England to the BATS site (R/V Endeavor cruise EN351 and R/V Oceanus cruise OC413) and three transects across the Florida Straits (R/V Walton Smith cruises WS0503, WS0518, WS0528) with characteristics as in Table 1. Samples were collected in surface and DCM waters using a Sea-Bird Niskin Rosette equipped with standard CTD and PAR detectors (see also below). For DNA extraction samples, 1 l of seawater was gravity filtered through 2 um pore size filters (GE Osmonics, Minnetonka, MN, USA) and then onto a 0.45 um pore size (2001) or 0.2 um pore size (2005) Supor filter (Pall Gelman, Ann Arbor, MI, USA) using vacuum. For FISH samples whole seawater (no size fractionation) was preserved with 1% paraformaldahyde (final concentration) for at least 1 h in the dark at 4&deg;C. For each replicate, volumes of 180 ml or more of seawater were gently filtered onto a 25 mm, 0.2 um Anodisc filter (Whatman, Maidstone, England). The filters were then subjected to an ethanol dehydration series at 50%, 80%, 100% (diluted in sterile, 18.2 &deg; H2O) for 3 min each and stored at -80&deg;C. Flow cytometry samples were preserved with 0.25% (final concentration) fresh electron microscopy grade glutaraldehyde (Tousimis, Rockville, MD, USA), flash frozen in liquid nitrogen and moved to -80&deg;C for long-term storage.</p>
Specified by the Principal Investigator(s)
<p>PCR, cloning and Sanger sequencing for all 18S rDNA<br />
sequences; metagenomic data was produced by multiple<br />
displacement amplification of flow cytometrically sorted<br />
cells with subsequent Sanger and 454-FLX sequencing. See<br />
Cuvelier et al. 2008 and Cuvelier et al. 2010 for greater<br />
detail if desired.</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 Sea-Bird
CTD Sea-Bird
PI Supplied Instrument Name: CTD Sea-Bird Instrument Name: CTD Sea-Bird Instrument Short Name:CTD Sea-Bird Instrument Description: A Conductivity, Temperature, Depth (CTD) sensor package from SeaBird Electronics. This instrument designation is used when specific make and model are not known or when a more specific term is not available in the BCO-DMO vocabulary. Refer to the dataset-specific metadata for more information about the specific CTD used. More information from: http://www.seabird.com/ Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/130/
Niskin bottle
Niskin bottle
PI Supplied Instrument Name: Niskin bottle 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/
Photosynthetically Available Radiation Sensor
Photosynthetically Available Radiation Sensor
PI Supplied Instrument Name: Photosynthetically Available Radiation Sensor Instrument Name: Photosynthetically Available Radiation Sensor Instrument Short Name:PAR sensor Instrument Description: A PAR sensor measures photosynthetically available (or active) radiation. The sensor measures photon flux density (photons per second per square meter) within the visible wavelength range (typically 400 to 700 nanometers). PAR gives an indication of the total energy available to plants for photosynthesis. This instrument name is used when specific type, make and model are not known. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/122/
Cruise: EN351
EN351
R/V Endeavor
Community Standard Description
International Council for the Exploration of the Sea
R/V Endeavor
vessel
EN351
Dr Brian Binder
University of Georgia
Cruise: EN360
EN360
R/V Endeavor
Community Standard Description
International Council for the Exploration of the Sea
R/V Endeavor
vessel
EN360
Dr Brian Binder
University of Georgia
Cruise: OC374
OC374
R/V Oceanus
Community Standard Description
International Council for the Exploration of the Sea
R/V Oceanus
vessel
OC374
Dr Brian Binder
University of Georgia
Cruise: OC413
OC413
R/V Oceanus
Community Standard Description
International Council for the Exploration of the Sea
R/V Oceanus
vessel
OC413
Dr Brian Binder
University of Georgia
Cruise: WS0503
WS0503
R/V F.G. Walton Smith
Community Standard Description
International Council for the Exploration of the Sea
R/V F.G. Walton Smith
vessel
Cruise: WS0518
WS0518
R/V F.G. Walton Smith
Community Standard Description
International Council for the Exploration of the Sea
R/V F.G. Walton Smith
vessel
Cruise: WS0528
WS0528
R/V F.G. Walton Smith
Community Standard Description
International Council for the Exploration of the Sea
R/V F.G. Walton Smith
vessel
Cruise: WS0705
WS0705
R/V F.G. Walton Smith
Community Standard Description
International Council for the Exploration of the Sea
R/V F.G. Walton Smith
vessel
WS0705
Dr Alexandra Z. Worden
Monterey Bay Aquarium Research Institute
Cruise: CN207
CN207
R/V C_N
vessel
R/V Endeavor
Community Standard Description
International Council for the Exploration of the Sea
R/V Endeavor
vessel
R/V Oceanus
Community Standard Description
International Council for the Exploration of the Sea
R/V Oceanus
vessel
R/V F.G. Walton Smith
Community Standard Description
International Council for the Exploration of the Sea
R/V F.G. Walton Smith
vessel
R/V C_N
vessel