http://lod.bco-dmo.org/id/dataset/709621
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
2017-07-25
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Trichodesmium data from R/V Atlantic Explorer cruise AE1409 in the Western Tropical North Atlantic from May 2014 (P Processing by Tricho project)
2017-07-20
publication
2017-07-20
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2021-05-24
publication
https://doi.org/10.26008/1912/bco-dmo.709621.1
Benjamin A.S. Van Mooy
Woods Hole Oceanographic Institution
principalInvestigator
Sonya T. Dyhrman
Lamont-Doherty Earth Observatory
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: Van Mooy, B. A., Dyhrman, S. T. (2021) Trichodesmium data from R/V Atlantic Explorer cruise AE1409 in the Western Tropical North Atlantic from May 2014 (P Processing by Tricho project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2017-07-20 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.709621.1 [access date]
Trichodesmium data from cruise AE1409 Dataset Description: <p>Trichodesmium, nitrogen fixation rates, and P uptake&nbsp;data from cruise AE1409.</p> Methods and Sampling: <p>All data collected as described in Van Mooy et al (2015).</p>
<p>Sampling - Trichodesmium colonies were collected with surface water net tows along a cruise transect in the western North Atlantic aboard the R/V Atlantic Explorer (AE1409) during May 2014. Sampling occurred at the same time each day (~7:30-8:30 am) using nets with a mesh size of 130 um. Nets were deployed and hauled through the surface water column 6 times before recovery. Individual Trichodesmium colonies were isolated and washed three times by successive transfer through fresh 0.2 um sterile-filtered local surface seawater. A pooled sample of colonies was isolated and processed from each station. For each sample, an average of ~30 cleaned colonies were transferred onto 47 mm 5 um pore size polycarbonate filters, gently vacuum filtered to remove excess liquid, flash frozen and stored in liquid nitrogen until extraction and sequencing. There were no discernable changes in average colony size from one station to another across the transect. In order to broadly assess the microbiome composition of the North Atlantic Trichodesmium populations, colony composition was sampled to reflect the distribution of Trichodesmium colony morphology found in net tows. At all stations raft type colonies were much more abundant than puff or bowtie variants with approximately 30 rafts to 2 puff/bowtie colonies. As such, the data largely reflect the dominant raft morphology.</p>
<p>Nitrogen Fixation Rates - N2 fixation was measured using the acetylene reduction technique as previously described (Capone, 1993; Paerl, 1994). Briefly, approximately 20 Trichodesmium colonies were placed in a 60 mL polycarbonate bottle containing 60 mL of filtered seawater. A 1 mL aliquot of acetylene was injected into the bottle through a septum cap, the bottle was gently inverted, and allowed to incubate in an on-deck incubator at ambient temperature and light. The headspace of the bottle was analyzed for ethylene approximately every 30 minutes and the rate of ethylene production through acetylene reduction was determined by linear regression. All incubations were conducted in triplicate between approximately local noon and 2 PM.</p>
<p>Phosphate uptake rates - The incubation bottles were carried to a laboratory van that was designated solely for work with radioactive isotopes. Each incubation bottle was spiked with approximately 1.5 uCi of 33P-phosphoric acid. The final concentration of 33P-phosphate in the incubations was approximately 6 pmol L-1, which was likely approximately two orders of magnitude smaller than ambient phosphate concentrations. The bottles were capped and mixed by gently inverting. At each station, three incubations were dedicated to measuring 33P-phosphate uptake and three incubations were dedicated to measuring the chemical reduction of 33P-phosphate to P(III) compounds. The bottles were placed in a flow-through on-deck incubator that was maintained at surface seawater temperatures by continually flushing with the surface seawater from the ship’s pumping system. Temperature in the incubators was occasionally monitored with a waterproof temperature logger (Onset), and found to be within 1C of surface water temperature. The incubators used a combination of neutral density screening and blue transparent film to achieve a light intensity of mimicking PAR at roughly 20m, as confirmed using an underwater spherical quantum sensor (Li-Cor). At three occasions during the cruise (Stations 2, 4, and 9), an additional set of triplicate incubations for each measurement were terminated immediately (i.e. prior to incubation) and processed identically to the experimental incubations; data from these incubations were used to quantify background 33P signals in all of our measurements (i.e. analytical blanks). Background 33P was consistent at all three stations, and was averaged and then subtracted from all of the experimental results; the standard deviation of the background was propagated as analytical error. In all cases the 33P radioactivity recovered from the experimental incubations was three times greater than the background 33P radioactivity. Incubations proceeded for an average of 3.25 h before being terminated by vacuum (approximately 200 mbar) filtration on 25 mm diameter polycarbonate membranes (Millipore); a poresize of 0.2 um was used for whole community incubations and a poresize of 5.0 um was used for the Trichodesmium incubations. The membranes were quickly rinsed three times with freshly filtered (0.2 um poresize polycarbonate membrane) surface seawater. The membranes were then immediately placed in a liquid scintillation vial containing 10 mL of UltimaGold liquid (Perkin Elmer) scintillation cocktail, which was then shaken vigorously. After resting for a few hours, the 33P-radioacitivity in the vials was determined using a liquid scintillation counter (Perkin Elmer). A steady-state phosphate turnover rate was calculated by dividing the total 33P radioactivity retained on the membranes by the total 33P radioactivity added to the incubations and the incubation time. Turnover times (reciprocal of turnover rates) varied from between 15 and 50 hours (not shown), which is much longer than the incubation time and validates the steady-state calculation.</p>
<p>Phosphate concentrations - Phosphate in seawaters samples and incubations was quantified using MAGnesium Induced Coprecipitation (MAGIC) as described by Karl and Tien (1992).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1332898 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1332898
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1332912 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1332912
completed
Benjamin A.S. Van Mooy
Woods Hole Oceanographic Institution
(508) 289 2322
Department of Marine Chemistry and Geochemistry, MS #4, Fye 117 Woods Hole Oceanographic Institution
Woods Hole
MA
02543
USA
bvanmooy@whoi.edu
pointOfContact
Sonya T. Dyhrman
Lamont-Doherty Earth Observatory
845-365-8465
102E Geoscience 61 Route 9W, PO Box 1000
Palisades
NY
10964
USA
dyhrman@ldeo.columbia.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Station
N2_fix_avg
N2_fix_std_dev
MAGIC_PO4
Alk_phos_avg
Alk_phos_std_dev
PO4_uptake_avg
PO4_uptake_std_dev
Lat
Long
Date
on-deck incubator
underwater spherical quantum sensor (Li-Cor)
liquid scintillation counter (Perkin Elmer)
net
temperature logger (Onset)
theme
None, User defined
station number
nitrogen fixation rate
reactive phosphorus (PO4)
No BCO-DMO term
radiotracer phosphate uptake
latitude
longitude
date
featureType
BCO-DMO Standard Parameters
In-situ incubator
LI-COR Biospherical PAR Sensor
Liquid Scintillation Counter
Plankton Net
Water Temperature Sensor
instrument
BCO-DMO Standard Instruments
AE1409
service
Deployment Activity
Western 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.
Dissolved Phosphorus Processing by Trichodesmium Consortia: Quantitative Partitioning, Role of Microbial Coordination, and Impact on Nitrogen Fixation
https://osprey.bco-dmo.org/project/565176
Dissolved Phosphorus Processing by Trichodesmium Consortia: Quantitative Partitioning, Role of Microbial Coordination, and Impact on Nitrogen Fixation
<p><em>Description from NSF award abstract:</em><br />
Colonies of the cyanbacterium <em>Trichodesmium</em> are responsible for a large fraction of N2 fixation in nutrient-poor, open-ocean ecosystems, ultimately fueling primary production in both <em>Trichodesmium</em> and in the broader planktonic community. However, in some parts of the ocean, the scarcity of dissolved phosphorus limits rates of <em>Trichodesmium </em>N2 fixation. <em>Trichodesmium</em> colonies employ an arsenal of strategies to mitigate the effects of phosphorus limitation, and the consortia of epibiotic bacteria in the colonies may play a significant role in phosphorus acquisition.</p>
<p>In this study, researchers from Woods Hole Oceanographic Institution and Columbia University will use metagenomic and metatranscriptomic sequencing to investigate how phosphorus metabolism is coordinated in <em>Trichodesmium </em>consortia, and to discern the role of quorum sensing in phosphorus acquisition and partitioning. Results from this study are expected to expand understanding of <em>Trichodesmium</em> from a monospecific colony whose primary function is fixing CO2 and N2 toward a unique planktonic consortium with a diverse, complex, and highly coordinated overall metabolism that exerts profound control over the cycling of inorganic and organic nutrients in the oligotrophic upper ocean.</p>
P Processing by Tricho
largerWorkCitation
project
eng; USA
oceans
Western Tropical North Atlantic
-64.9907
-53.2711
9.8155
27.8657
2014-05-10
2014-05-25
Western Tropical North Atlantic
0
BCO-DMO catalogue of parameters from Trichodesmium data from R/V Atlantic Explorer cruise AE1409 in the Western Tropical North Atlantic from May 2014 (P Processing by Tricho 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/709648.rdf
Name: Station
Units: unitless
Description: <p>Numeric identifier for the station where the data was collected.</p>
http://lod.bco-dmo.org/id/dataset-parameter/709649.rdf
Name: N2_fix_avg
Units: Picomole of nitrogen per colony hour (pmol N/(colony h))
Description: <p>Average nitrogen fixation rate.</p>
http://lod.bco-dmo.org/id/dataset-parameter/709650.rdf
Name: N2_fix_std_dev
Units: Picomole of nitrogen per colony hour (pmol N/(colony h))
Description: <p>Standard deviation of nitrogen fixation rate.</p>
http://lod.bco-dmo.org/id/dataset-parameter/709651.rdf
Name: MAGIC_PO4
Units: Nanomole per liter (nmol/L)
Description: <p>Phosphate measured using magnesium-induced co-precipitation.</p>
http://lod.bco-dmo.org/id/dataset-parameter/709652.rdf
Name: Alk_phos_avg
Units: Picomole Phosphorus per colony hour (pmol P/(colony h))
Description: <p>Average alkaline phosphatase rates.</p>
http://lod.bco-dmo.org/id/dataset-parameter/709653.rdf
Name: Alk_phos_std_dev
Units: Picomole Phosphorus per colony hour (pmol P/(colony h))
Description: <p>Standard deviation of alkaline phosphatase rates.</p>
http://lod.bco-dmo.org/id/dataset-parameter/709654.rdf
Name: PO4_uptake_avg
Units: Picomole Phosphorus per colony hour (pmol P/(colony h))
Description: <p>Average phosphate uptake rate.</p>
http://lod.bco-dmo.org/id/dataset-parameter/709655.rdf
Name: PO4_uptake_std_dev
Units: Picomole Phosphorus per colony hour (pmol P/(colony h))
Description: <p>Standard deviation of phosphate uptake rate.</p>
http://lod.bco-dmo.org/id/dataset-parameter/709656.rdf
Name: Lat
Units: Decimal Degrees
Description: <p>Latitude of sampling. Positive values indicate North.</p>
http://lod.bco-dmo.org/id/dataset-parameter/709657.rdf
Name: Long
Units: Decimal Degrees
Description: <p>Longitude of sampling. Negative values indicate West.</p>
http://lod.bco-dmo.org/id/dataset-parameter/709658.rdf
Name: Date
Units: YYYYMMDD
Description: <p>Sampling date formatted as YYYYMMDD.</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
956
https://darchive.mblwhoilibrary.org/bitstream/1912/27169/1/dataset-709621_trichodesmiumae1409__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.709621.1
download
onLine
dataset
<p>All data collected as described in Van Mooy et al (2015).</p>
<p>Sampling - Trichodesmium colonies were collected with surface water net tows along a cruise transect in the western North Atlantic aboard the R/V Atlantic Explorer (AE1409) during May 2014. Sampling occurred at the same time each day (~7:30-8:30 am) using nets with a mesh size of 130 um. Nets were deployed and hauled through the surface water column 6 times before recovery. Individual Trichodesmium colonies were isolated and washed three times by successive transfer through fresh 0.2 um sterile-filtered local surface seawater. A pooled sample of colonies was isolated and processed from each station. For each sample, an average of ~30 cleaned colonies were transferred onto 47 mm 5 um pore size polycarbonate filters, gently vacuum filtered to remove excess liquid, flash frozen and stored in liquid nitrogen until extraction and sequencing. There were no discernable changes in average colony size from one station to another across the transect. In order to broadly assess the microbiome composition of the North Atlantic Trichodesmium populations, colony composition was sampled to reflect the distribution of Trichodesmium colony morphology found in net tows. At all stations raft type colonies were much more abundant than puff or bowtie variants with approximately 30 rafts to 2 puff/bowtie colonies. As such, the data largely reflect the dominant raft morphology.</p>
<p>Nitrogen Fixation Rates - N2 fixation was measured using the acetylene reduction technique as previously described (Capone, 1993; Paerl, 1994). Briefly, approximately 20 Trichodesmium colonies were placed in a 60 mL polycarbonate bottle containing 60 mL of filtered seawater. A 1 mL aliquot of acetylene was injected into the bottle through a septum cap, the bottle was gently inverted, and allowed to incubate in an on-deck incubator at ambient temperature and light. The headspace of the bottle was analyzed for ethylene approximately every 30 minutes and the rate of ethylene production through acetylene reduction was determined by linear regression. All incubations were conducted in triplicate between approximately local noon and 2 PM.</p>
<p>Phosphate uptake rates - The incubation bottles were carried to a laboratory van that was designated solely for work with radioactive isotopes. Each incubation bottle was spiked with approximately 1.5 uCi of 33P-phosphoric acid. The final concentration of 33P-phosphate in the incubations was approximately 6 pmol L-1, which was likely approximately two orders of magnitude smaller than ambient phosphate concentrations. The bottles were capped and mixed by gently inverting. At each station, three incubations were dedicated to measuring 33P-phosphate uptake and three incubations were dedicated to measuring the chemical reduction of 33P-phosphate to P(III) compounds. The bottles were placed in a flow-through on-deck incubator that was maintained at surface seawater temperatures by continually flushing with the surface seawater from the ship’s pumping system. Temperature in the incubators was occasionally monitored with a waterproof temperature logger (Onset), and found to be within 1C of surface water temperature. The incubators used a combination of neutral density screening and blue transparent film to achieve a light intensity of mimicking PAR at roughly 20m, as confirmed using an underwater spherical quantum sensor (Li-Cor). At three occasions during the cruise (Stations 2, 4, and 9), an additional set of triplicate incubations for each measurement were terminated immediately (i.e. prior to incubation) and processed identically to the experimental incubations; data from these incubations were used to quantify background 33P signals in all of our measurements (i.e. analytical blanks). Background 33P was consistent at all three stations, and was averaged and then subtracted from all of the experimental results; the standard deviation of the background was propagated as analytical error. In all cases the 33P radioactivity recovered from the experimental incubations was three times greater than the background 33P radioactivity. Incubations proceeded for an average of 3.25 h before being terminated by vacuum (approximately 200 mbar) filtration on 25 mm diameter polycarbonate membranes (Millipore); a poresize of 0.2 um was used for whole community incubations and a poresize of 5.0 um was used for the Trichodesmium incubations. The membranes were quickly rinsed three times with freshly filtered (0.2 um poresize polycarbonate membrane) surface seawater. The membranes were then immediately placed in a liquid scintillation vial containing 10 mL of UltimaGold liquid (Perkin Elmer) scintillation cocktail, which was then shaken vigorously. After resting for a few hours, the 33P-radioacitivity in the vials was determined using a liquid scintillation counter (Perkin Elmer). A steady-state phosphate turnover rate was calculated by dividing the total 33P radioactivity retained on the membranes by the total 33P radioactivity added to the incubations and the incubation time. Turnover times (reciprocal of turnover rates) varied from between 15 and 50 hours (not shown), which is much longer than the incubation time and validates the steady-state calculation.</p>
<p>Phosphate concentrations - Phosphate in seawaters samples and incubations was quantified using MAGnesium Induced Coprecipitation (MAGIC) as described by Karl and Tien (1992).</p>
Specified by the Principal Investigator(s)
<p>BCO-DMO Processing:<br />
Added conventional header with dataset name, PI name, version date.<br />
Modified parameter names to conform with BCO-DMO naming conventions.<br />
Re-formatted date from m/dd/yyyy to yyyymmdd.<br />
Replaced spaces and / with underscores.<br />
Added coordinate information to the data from the station list provided by the PI.&nbsp;</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
on-deck incubator
on-deck incubator
PI Supplied Instrument Name: on-deck incubator PI Supplied Instrument Description:A 1 mL aliquot of acetylene was injected into the bottle through a septum cap, the bottle was gently inverted, and allowed to incubate in an on-deck incubator at ambient temperature and light. Instrument Name: In-situ incubator Instrument Short Name:in-situ incubator Instrument Description: A device on a ship or in the laboratory that holds water samples under controlled conditions of temperature and possibly illumination. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/82/
underwater spherical quantum sensor (Li-Cor)
underwater spherical quantum sensor (Li-Cor)
PI Supplied Instrument Name: underwater spherical quantum sensor (Li-Cor) PI Supplied Instrument Description:The incubators used a combination of neutral density screening and blue transparent film to achieve a light intensity of mimicking PAR at roughly 20m, as confirmed using an underwater spherical quantum sensor (Li-Cor). Instrument Name: LI-COR Biospherical PAR Sensor Instrument Short Name:LI-COR Biospherical PAR Instrument Description: The LI-COR Biospherical PAR Sensor is used to measure Photosynthetically Available Radiation (PAR) in the water column. This instrument designation is used when specific make and model are not known. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0074/
liquid scintillation counter (Perkin Elmer)
liquid scintillation counter (Perkin Elmer)
PI Supplied Instrument Name: liquid scintillation counter (Perkin Elmer) PI Supplied Instrument Description:After resting for a few hours, the 33P-radioacitivity in the vials was determined using a liquid scintillation counter (Perkin Elmer). Instrument Name: Liquid Scintillation Counter Instrument Short Name:LSC Instrument Description: Liquid scintillation counting is an analytical technique which is defined by the incorporation of the radiolabeled analyte into uniform distribution with a liquid chemical medium capable of converting the kinetic energy of nuclear emissions into light energy. Although the liquid scintillation counter is a sophisticated laboratory counting system used to quantify the activity of particulate emitting (ß and a) radioactive samples, it can also detect the auger electrons emitted from 51Cr and 125I samples.
Liquid scintillation counters are instruments assaying alpha and beta radiation by quantitative detection of visible light produced by the passage of rays or particles through a suitable scintillant incorporated into the sample. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB21/
net
net
PI Supplied Instrument Name: net PI Supplied Instrument Description:Trichodesmium colonies were collected with surface water net tows along a cruise transect in the western North Atlantic aboard the R/V Atlantic Explorer (AE1409) during May 2014. Sampling occurred at the same time each day (~7:30-8:30 am) using nets with a mesh size of 130 μm. Nets were deployed and hauled through the surface water column 6 times before recovery. Instrument Name: Plankton Net Instrument Short Name:Plankton Net Instrument Description: A Plankton Net is a generic term for a sampling net that is used to collect plankton. It is used only when detailed instrument documentation is not available. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/22/
temperature logger (Onset)
temperature logger (Onset)
PI Supplied Instrument Name: temperature logger (Onset) PI Supplied Instrument Description:Temperature in the incubators was occasionally monitored with a waterproof temperature logger (Onset). Instrument Name: Water Temperature Sensor Instrument Short Name:Water Temp Sensor Instrument Description: General term for an instrument that measures the temperature of the water with which it is in contact (thermometer). Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/134/
Cruise: AE1409
AE1409
R/V Atlantic Explorer
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantic Explorer
vessel
AE1409
Benjamin A.S. Van Mooy
Woods Hole Oceanographic Institution
R/V Atlantic Explorer
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantic Explorer
vessel