http://lod.bco-dmo.org/id/dataset/3627
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
2012-02-29
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Q-PCR counts of Synechococcus clades from R/V Knorr, R/V Kilo Moana, R/V Seward Johnson KN192-05, KM0701, SJ0609 in the S. Atlantic subtropical gyre and Benguela upwelling region from 2006-2007 (Fe_Synechococcus project)
2012-02-29
publication
2012-02-29
revision
BCO-DMO Linked Data URI
2012-02-29
creation
http://lod.bco-dmo.org/id/dataset/3627
Eric A. Webb
Woods Hole Oceanographic Institution
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: Webb, E. A. (2012) Q-PCR counts of Synechococcus clades from R/V Knorr, R/V Kilo Moana, R/V Seward Johnson KN192-05, KM0701, SJ0609 in the S. Atlantic subtropical gyre and Benguela upwelling region from 2006-2007 (Fe_Synechococcus project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). Version Date 2012-02-29 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/3627 [access date]
Q-PCR counts of Synechococcus clades Dataset Description: <p>Synechococcus is one of the most abundant phytoplankton on earth and contributes significantly to marine primary production, thus an understanding of the distribution and diversity of this genus is important.&nbsp; This quantitative PCR enumeration of nine marine Synechococcus clades found in multiple oceanic regimes is the most comprehensive study to date.&nbsp; This work builds on the research of Zwirglmaier et al (2007 and 2008) and Tai and Palenik (2010), confirming patterns seen previously and extending observations into new areas, but it also provides new information on previously unstudied clades, the environmental niches of different clades, and defining the dominant oligotrophic clade.</p> Methods and Sampling: <p>Samples were collected on open ocean research cruises and coastal research cruises in locations throughout the Pacific and Atlantic oceans: The tropical North Atlantic (R/V Seward Johnson, SJ0609, in June 2006), the tropical South Atlantic and Benguela Upwelling system (CoFeMUG, R/V Knorr, KN192-05 Nov 2007), a transect through the North and South Pacific&nbsp; (R/V Kilo Moana, KM0701 Feb 2007), the San Pedro Channel off Southern California (R/V Seawatch). The SPOT0509 cruise on R/V Seawatch was a single day cruise in May 2009 to the San Pedro Ocean Time Series station (33.55, -118.4).</p>
<p>Pacific: Transect from Hawaii to Brisbane, Australia<br />
North Atlantic:&nbsp; From Cape Verde to Barbados<br />
South Atlantic: Brazil to Namibia<br />
North Pacific from Hawaii to Bering Sea<br />
Costa Rica Upwelling dome</p>
<p>Samples for all cruises, except the tropical North Atlantic and the South Pacific (from New Caledonia to Australia), were collected by taking a 100 ml sample from a Niskin bottle on the CTD rosette, filtered through a 0.4 um polycarbonate filter, and frozen at -20 &deg;C until DNA extraction. In the North Atlantic and South Pacific, larger volumes (1-2 L with the volume always determined) were filtered onto 0.2 um polyethersulfone filters and frozen in liquid nitrogen.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0825922 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0825922
completed
Eric A. Webb
Woods Hole Oceanographic Institution
213-740-7954
Department of Biological Sciences, Marine and Environmental Biology Section; Dornsife College of Letters, Arts, and Sciences 3616 Trousdale Parkway AHF 331
Los Angeles
CA
90089-0371
USA
eawebb@usc.edu
pointOfContact
asNeeded
Unknown
cruise_id
cruise_synonym
month_start
day_start
year_start
month_end
day_end
year_end
region
lat
lon
lon_360
depth
temp
sal
NO3_NO2
NO3
NO2
PO4
clade
abundance
Niskin bottle
theme
None, User defined
Cruise identfier
month_start
day_start
year_start
month_end
day_end
year_end
region
latitude
longitude
longitude from 0 to 360 degrees
depth
water temperature at measurement depth
salinity
nitrate plus nitrite
Nitrate
Nitrite
reactive phosphorus (PO4)
No BCO-DMO term
synechococcus abundance
featureType
BCO-DMO Standard Parameters
Niskin bottle
instrument
BCO-DMO Standard Instruments
KN192-05
KM0701
SJ0609
service
Deployment Activity
South Atlantic subtropical gyre and Benguela upwelling region
SP1/South Pacific
Tropical North Atlantic
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.
The role of iron (Fe) in controlling in situ distributions and activities of marine Synechococcus
https://osprey.bco-dmo.org/project/2202
The role of iron (Fe) in controlling in situ distributions and activities of marine Synechococcus
<p>The unicellular cyanobacterium Synechococcus is one of the most abundant primary producers in the marine environment. It is also extremely widespread; Synechococcus has been found in open ocean, coastal and even polar environments. Unlike its close relative, Prochlorococcus, Synechococcus has the ability to use NO3 and has been shown to respond in the field to NO3 inputs, suggesting that this organism may play a key role in global carbon cycling and especially new production. To date, 16 potential clades have been identified, and it is thought that this high diversity allows for the radiation of Synechococcus into many different environmental conditions. However, despite the ubiquity and abundance of Synechococcus, there are few studies characterizing the physiology and niche adaptations of each clade. Iron (Fe) shows great potential as a defining factor for niche adaptations, as its concentration varies over the geographic range of Synechococcus, as well as annually at specific locations, and has been shown to limit primary production in both open ocean and coastal settings. In addition, culture work indicates that Synechococcus strains have different abilities to grow on low concentrations of Fe. A comparison of the available genomes of marine Synechococcus shows great diversity in the presence or absence of known genes related to Fe stress, suggesting that Fe could have played a key role in the diversification and niche adaptation of Synechococcus. This project will study the effects of Fe on growth and carbon fixation in 11 different clades of Synechococcus (using at least 2 strains from each clade whenever possible) and the role of Fe limitation in determining the distribution of Synechococcus clades on temporal and spatial scales. This project will produce a comprehensive and systematic data set on the impact of Fe-specific niche differentiation in Synechococcus, offer new insight into the factors that control clade distribution, and provide understanding of the biogeochemical consequences of Synechococcus diversity.</p>
Fe_Synechococcus
largerWorkCitation
project
eng; USA
oceans
South Atlantic subtropical gyre and Benguela upwelling region; SP1/South Pacific; Tropical North Atlantic
2012-02-29
Pacific: Transect from Hawaii to Brisbane, Australia; North Atlantic: from Cape Verde to Barbados; South Atlantic: Brazil to Namibia
0
BCO-DMO catalogue of parameters from Q-PCR counts of Synechococcus clades from R/V Knorr, R/V Kilo Moana, R/V Seward Johnson KN192-05, KM0701, SJ0609 in the S. Atlantic subtropical gyre and Benguela upwelling region from 2006-2007 (Fe_Synechococcus 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/30126.rdf
Name: cruise_id
Units: text
Description: <p>Cruise identifier.</p>
http://lod.bco-dmo.org/id/dataset-parameter/30127.rdf
Name: cruise_synonym
Units: text
Description: <p>Alternate identifier of the cruise.</p>
http://lod.bco-dmo.org/id/dataset-parameter/30128.rdf
Name: month_start
Units: mm (01 to 12)
Description: <p>Month the cruise began (2-digits).</p>
http://lod.bco-dmo.org/id/dataset-parameter/30129.rdf
Name: day_start
Units: dd (01 to 31)
Description: <p>Day the cruise began (2-digits).</p>
http://lod.bco-dmo.org/id/dataset-parameter/30130.rdf
Name: year_start
Units: YYYY
Description: <p>Year the cruise began (4-digits).</p>
http://lod.bco-dmo.org/id/dataset-parameter/30131.rdf
Name: month_end
Units: mm (01 to 12)
Description: <p>Month the cruise ended (2-digits).</p>
http://lod.bco-dmo.org/id/dataset-parameter/30132.rdf
Name: day_end
Units: dd (01 to 31)
Description: <p>Day the cruise ended (2-digits).</p>
http://lod.bco-dmo.org/id/dataset-parameter/30133.rdf
Name: year_end
Units: YYYY
Description: <p>Year the cruise ended (4-digits).</p>
http://lod.bco-dmo.org/id/dataset-parameter/30134.rdf
Name: region
Units: text
Description: <p>Description of the geographic sampling area.</p>
http://lod.bco-dmo.org/id/dataset-parameter/30135.rdf
Name: lat
Units: decimal degrees
Description: <p>Latitude in decimal degrees. Positive = North.</p>
http://lod.bco-dmo.org/id/dataset-parameter/30136.rdf
Name: lon
Units: decimal degrees
Description: <p>Longitude in decimal degrees. Positive = East. Calculated from the original lon_360 provided by PI.</p>
http://lod.bco-dmo.org/id/dataset-parameter/30137.rdf
Name: lon_360
Units: decimal degrees
Description: <p>Longitude ranging from 0 to 360 degrees.</p>
http://lod.bco-dmo.org/id/dataset-parameter/30138.rdf
Name: depth
Units: meters
Description: <p>Sample depth.</p>
http://lod.bco-dmo.org/id/dataset-parameter/30139.rdf
Name: temp
Units: unknown
Description: <p>Temperature.</p>
http://lod.bco-dmo.org/id/dataset-parameter/30140.rdf
Name: sal
Units: dimensionless
Description: <p>Salinity.</p>
http://lod.bco-dmo.org/id/dataset-parameter/30141.rdf
Name: NO3_NO2
Units: uM
Description: <p>Nitrate and Nitrite, micromolar.</p>
http://lod.bco-dmo.org/id/dataset-parameter/30142.rdf
Name: NO3
Units: uM
Description: <p>Nitrate, micromolar.</p>
http://lod.bco-dmo.org/id/dataset-parameter/30143.rdf
Name: NO2
Units: uM
Description: <p>Nitrite, micromolar.</p>
http://lod.bco-dmo.org/id/dataset-parameter/30144.rdf
Name: PO4
Units: uM
Description: <p>Orthophosphate, (phosphate, reactive phosphorus), micromolar.</p>
http://lod.bco-dmo.org/id/dataset-parameter/30419.rdf
Name: clade
Units: text
Description: <p>Clade.</p>
http://lod.bco-dmo.org/id/dataset-parameter/30420.rdf
Name: abundance
Units: cells/mL
Description: <p>Number of cells per milliliter.</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
119681
https://datadocs.bco-dmo.org/file/8XXgy5jSwDGxDx/Synechococcus_QPCR.csv
Synechococcus_QPCR.csv
Primary data file for dataset ID 3627
download
https://osprey.bco-dmo.org/dataset/3627/data/download
download
onLine
dataset
<p>Samples were collected on open ocean research cruises and coastal research cruises in locations throughout the Pacific and Atlantic oceans: The tropical North Atlantic (R/V Seward Johnson, SJ0609, in June 2006), the tropical South Atlantic and Benguela Upwelling system (CoFeMUG, R/V Knorr, KN192-05 Nov 2007), a transect through the North and South Pacific&nbsp; (R/V Kilo Moana, KM0701 Feb 2007), the San Pedro Channel off Southern California (R/V Seawatch). The SPOT0509 cruise on R/V Seawatch was a single day cruise in May 2009 to the San Pedro Ocean Time Series station (33.55, -118.4).</p>
<p>Pacific: Transect from Hawaii to Brisbane, Australia<br />
North Atlantic:&nbsp; From Cape Verde to Barbados<br />
South Atlantic: Brazil to Namibia<br />
North Pacific from Hawaii to Bering Sea<br />
Costa Rica Upwelling dome</p>
<p>Samples for all cruises, except the tropical North Atlantic and the South Pacific (from New Caledonia to Australia), were collected by taking a 100 ml sample from a Niskin bottle on the CTD rosette, filtered through a 0.4 um polycarbonate filter, and frozen at -20 &deg;C until DNA extraction. In the North Atlantic and South Pacific, larger volumes (1-2 L with the volume always determined) were filtered onto 0.2 um polyethersulfone filters and frozen in liquid nitrogen.</p>
Specified by the Principal Investigator(s)
<p>BCO-DMO calculated lon from the lon_360 column provided by the PI. Parameter names were changed to conform to BCO-DMO convention.</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
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/
Cruise: KN192-05
KN192-05
R/V Knorr
Community Standard Description
International Council for the Exploration of the Sea
R/V Knorr
vessel
KN192-05
Mak A. Saito
Woods Hole Oceanographic Institution
http://bcodata.whoi.edu/CoFeMUG/CruiseReport_KN192-5.pdf
Report describing KN192-05
Cruise: KM0701
KM0701
R/V Kilo Moana
Community Standard Description
International Council for the Exploration of the Sea
R/V Kilo Moana
vessel
KM0701
Zackary I. Johnson
University of Hawai'i
http://bcodata.whoi.edu/WP2/wp2_cruise_report.pdf
Report describing KM0701
Cruise: SJ0609
SJ0609
Community Standard Description
International Council for the Exploration of the Sea
R/V Seward Johnson
vessel
SJ0609
Jonathan P. Zehr
University of California-Santa Cruz
R/V Knorr
Community Standard Description
International Council for the Exploration of the Sea
R/V Knorr
vessel
R/V Kilo Moana
Community Standard Description
International Council for the Exploration of the Sea
R/V Kilo Moana
vessel
Community Standard Description
International Council for the Exploration of the Sea
R/V Seward Johnson
vessel