http://lod.bco-dmo.org/id/dataset/881028
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
2022-09-23
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Hydrological, biogeochemcial and N2-fixer qPCR-derived abundance data for May 2017 (SP1714) and October (SP1724) SCCS cruises.
2024-06-24
publication
2024-06-24
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2024-06-24
publication
https://doi.org/10.26008/1912/bco-dmo.881028.1
Jonathan P. Zehr
University of California-Santa Cruz
principalInvestigator
Kevin R. Arrigo
Stanford 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: Zehr, J. P., Arrigo, K. R., Turbo-Kirk, K. (2024) Hydrological, biogeochemcial and N2-fixer qPCR-derived abundance data for May 2017 (SP1714) and October (SP1724) SCCS cruises. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-06-24 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.881028.1 [access date]
qPCR abundance data Dataset Description: <p>These data were published in Turk-Kubo et al. (2021).&nbsp;Table 1, Figure 3, Table S1, Table S2</p>
<p>&nbsp;</p>
<p>Meaning different No Data values:</p>
<p>UD = undetected<br />
na = not applicable<br />
- - = parameter&nbsp;not measured<br />
DNQ = detected, not quantified<br />
Empty cells = means that the value reported in the average nifH L-1 column is quantified.&nbsp;</p> Methods and Sampling: <p>Samples were collected using standard oceanographic techniques. A CTD Rosette with 24 10L Niskin bottles was lowered to the maximum sampling depth and then brought back to the surface. Methodology described in depth in Turk-Kubo et al. (2021)</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1559165 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1559165
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1559152 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1559152
completed
Jonathan P. Zehr
University of California-Santa Cruz
831-459 4009
E&MS A438, Ocean Sciences Department 1156 High Street
Santa Cruz
CA
95064
USA
zehrj@ucsc.edu
pointOfContact
Kevin R. Arrigo
Stanford University
650-723-3599
Department of Earth System Science/ Y2E2 Building Room 141
Stanford
CA
94305
USA
arrigo@stanford.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Cruise
Station
Depth
latitude
longitude
Sample_Date
bottom_depth
mix_layer_depth
temperature
salinity
oxygen
fluorescence
PAR
potential_density
Nitrate
Phosphate
P
chla_ave
chla_stdev
UCYN_A1_ave
UCYN_A1_stdev
UCYN_A1_DNQ
UCYN_A2_ave
UCYN_A2_stdev
UCYN_A2_DNQ
UCYN_B_ave
UCYN_B_stdev
UCYN_B_DNQ
Tricho_ave
Tricho_stdev
Tricho_DNQ
Het_2_ave
Het_2_stdev
Het_2_DNQ
g_24774A11_ave
g_24774A11_stdev
g_24774A11_DNQ
Lachat QuikChem 8000 Flow Injection Analyzer
Turner Fluorometer TD-700
theme
None, User defined
Cruise identfier
station
depth
latitude
longitude
date
depth_bottom
mixed layer depth
water temperature at measurement depth
salinity
dissolved Oxygen
fluorescence
PAR
sigma-theta
Nitrate
phosphate
Phosphorus
chlorophyll a
genetic material concentration
sample description
featureType
BCO-DMO Standard Parameters
Flow Injection Analyzer
Turner Designs 700 Laboratory Fluorometer
instrument
BCO-DMO Standard Instruments
SP1714
SP1727
service
Deployment Activity
California Current waters off the coast of Southern California and Baja California
Southern California Current waters
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.
Collaborative Research: Biogeochemical significance of the abundant, uncultivated symbiotic cyanobacteria UCYN-A
https://osprey.bco-dmo.org/project/699979
Collaborative Research: Biogeochemical significance of the abundant, uncultivated symbiotic cyanobacteria UCYN-A
<p><em>NSF Award Abstract:</em><br />
Nitrogen is a nutrient whose availability limits growth and productivity of ecosystems. Nitrogen is extremely abundant in the atmosphere in the inert form of gaseous N2, but most organisms cannot reduce N2 into a biologically available form. In all environments, including agricultural soils, there are microorganisms that can make available the N from gaseous N2 by reducing it to the biologically available form, ammonium. In the vast expanses of the open ocean, few organisms are known to have this ability, and recently a unique symbiosis between a single-celled cyanobacterium and a single-celled algae was discovered, which appears to be very widely distributed and likely of global biogeochemical significance. The cyanobacterium in this symbiotic partnership has very unusual metabolism and genomic streamlining. Little is known of the symbiosis because it is not detectable except by modern molecular biological techniques. Recent work has shown this symbiosis to be very widely spread through the oceans, and that there is previously unrecognized diversity in both the cyanobacterial and algal hosts. This research will examine the environmental distributions and the biogeochemical significance of this diversity in coastal US waters. The investigators will engage the public in ocean sciences through internship programs at local high schools and for undergraduate students at Stanford, and by documenting their field research in a 'virtual cruise' blog.</p>
<p>In the marine environment, the contribution of N2 fixation to the fixed nitrogen (N) pool is poorly quantified, in part due to an incomplete understanding on the abundance, activity, and physiology of diazotrophs. The symbiotic unicellular cyanobacteria (UCYN-A) is a poorly characterized, yet globally important, group of marine diazotrophs. UCYN-A is widely distributed in the marine environment, and lives symbiotically with a picoeukaryotic prymnesiophyte alga. We now know that there are multiple ecotypes of UCYN-A, which may be adapted to specific locations in the water-column and different oceanic provinces. Typically N2 fixation was considered unimportant in coastally influenced and non-tropical waters, however recent data shows that multiple subclades of UCYN-A are present. The distribution and rate of N2 fixation by UCYN-A subclades in coastal/nearshore environments is a major unknown in the oceanic N cycle. Its presence in nearshore waters may change the paradigm of the balance between basin N sources (N2 fixation) and sinks (denitrification). Likewise, significant N2 fixation by UCYN-A will need to be considered when determining estimates of new production in coastally influenced waters. This project aims to quantify the significance of different UCYN-A subclades to coastal/nearshore N budgets. It tackles the issue of determining N2 fixation rates by different UCYN-A subclades in coastal waters through rigorous fieldwork off the west coast of North America. The temporal and spatial distribution of UCYN-A subclades, as well as the rates of N2 fixation, will be determined by coupling N2 fixation measurements of bulk communities and individual cells (nanoSIMS) with molecular assays to study these widespread, but dilute, diazotrophic symbionts and their hosts. Additionally the investigators will conduct experiments aimed at constraining the effects of light and nutrient ratios (N/P) on UCYN-A N2 fixation rates, and the prymnesiophyte host's rate of carbon fixation. They will conduct this work through seasonal sampling of a coastal site in the Southern California Bight (Scripps Pier) and on two process cruises in the coastal waters between central California and the Baja Peninsula. The cruise work will provide an opportunity to understand the temporal dynamics of the UCYN-A/prymnesiophyte associations over larger spatial scales. Finally, evidence suggests that unidentified UCYN-A subclades and hosts exist and the investigators have developed a strategy to identify and quantify their temporal and spatial distributions as well as their N2 fixation activities. Data on the coastal distribution, ecology and activity of UCYN-A is critical for obtaining a better understanding of their contribution to fixed N to the marine environment. The group-specific and bulk rates of N2 fixation measured in this study of coastally influenced waters, will provide data for future modeling efforts, which will make an important contribution to constraining oceanic N2 fixation inputs.</p>
BSUCS
largerWorkCitation
project
eng; USA
oceans
California Current waters off the coast of Southern California and Baja California; Southern California Current waters
-120.249
-114.931
28.288
33.825
2017-05-03
2017-10-11
California Current waters off the Southern California shelf
0
BCO-DMO catalogue of parameters from Hydrological, biogeochemcial and N2-fixer qPCR-derived abundance data for May 2017 (SP1714) and October (SP1724) SCCS cruises.
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/915923.rdf
Name: Cruise
Units: unitless
Description: <p>Cruise ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/915924.rdf
Name: Station
Units: unitless
Description: <p>Station number</p>
http://lod.bco-dmo.org/id/dataset-parameter/915925.rdf
Name: Depth
Units: meters (m)
Description: <p>Sampling depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/915926.rdf
Name: latitude
Units: decimal degrees
Description: <p>sampling latittude, south is negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/915927.rdf
Name: longitude
Units: decimal degrees
Description: <p>sampling longitude, west is negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/915928.rdf
Name: Sample_Date
Units: unitless
Description: <p>sampling date</p>
http://lod.bco-dmo.org/id/dataset-parameter/915929.rdf
Name: bottom_depth
Units: meters (m)
Description: <p>bottom depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/915930.rdf
Name: mix_layer_depth
Units: meters (m)
Description: <p>mixed layer depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/915931.rdf
Name: temperature
Units: Degrees Celcius (°C)
Description: <p>temperature</p>
http://lod.bco-dmo.org/id/dataset-parameter/915932.rdf
Name: salinity
Units: psu
Description: <p>salinity</p>
http://lod.bco-dmo.org/id/dataset-parameter/915933.rdf
Name: oxygen
Units: milliliters per liter (mL L-1)
Description: <p>oxygen</p>
http://lod.bco-dmo.org/id/dataset-parameter/915934.rdf
Name: fluorescence
Units: milligrams per cubic meters (mg m-3)
Description: <p>fluoresence</p>
http://lod.bco-dmo.org/id/dataset-parameter/915935.rdf
Name: PAR
Units: unitless
Description: <p>Photosynthetically active radiation</p>
http://lod.bco-dmo.org/id/dataset-parameter/915936.rdf
Name: potential_density
Units: kilograms per cubic meters (kg m-3)
Description: <p>potential density. σθ</p>
http://lod.bco-dmo.org/id/dataset-parameter/915937.rdf
Name: Nitrate
Units: micromoles (µM)
Description: <p>nitrate</p>
http://lod.bco-dmo.org/id/dataset-parameter/915938.rdf
Name: Phosphate
Units: micromoles (µM)
Description: <p>phosphate (PO43- )</p>
http://lod.bco-dmo.org/id/dataset-parameter/915939.rdf
Name: P
Units: unitless
Description: <p>P* is the amount of dissolved PO43− in the environment relative to what is expected if N and P uptake and remineralization proceed according to Redfield proportions. P* = PO43− − (NO3− + NO2−)/16</p>
http://lod.bco-dmo.org/id/dataset-parameter/915940.rdf
Name: chla_ave
Units: micrograms per liter (µg L-1)
Description: <p>Average chlorophyll a</p>
http://lod.bco-dmo.org/id/dataset-parameter/915941.rdf
Name: chla_stdev
Units: micrograms per liter (µg L-1)
Description: <p>Standard deviation chlorophyll a</p>
http://lod.bco-dmo.org/id/dataset-parameter/915942.rdf
Name: UCYN_A1_ave
Units: nitrogenase gene per liter (nifH L-1)
Description: <p>Average of UCYN-A1 gene expression</p>
http://lod.bco-dmo.org/id/dataset-parameter/915943.rdf
Name: UCYN_A1_stdev
Units: nitrogenase gene per liter (nifH L-1)
Description: <p>Standard deviation of UCYN-A1 gene expression</p>
http://lod.bco-dmo.org/id/dataset-parameter/915944.rdf
Name: UCYN_A1_DNQ
Units: unitless
Description: <p>UCYN-A1 gene expression detected, not quantified</p>
http://lod.bco-dmo.org/id/dataset-parameter/915945.rdf
Name: UCYN_A2_ave
Units: nitrogenase gene per liter (nifH L-1)
Description: <p>Average of UCYN-A2 gene expression</p>
http://lod.bco-dmo.org/id/dataset-parameter/915946.rdf
Name: UCYN_A2_stdev
Units: nitrogenase gene per liter (nifH L-1)
Description: <p>Standard deviation of UCYN-A2 gene expression</p>
http://lod.bco-dmo.org/id/dataset-parameter/915947.rdf
Name: UCYN_A2_DNQ
Units: unitless
Description: <p>UCYN-A2 gene expression detected, not quantified</p>
http://lod.bco-dmo.org/id/dataset-parameter/915948.rdf
Name: UCYN_B_ave
Units: nitrogenase gene per liter (nifH L-1)
Description: <p>Average of UCYN-B gene expression</p>
http://lod.bco-dmo.org/id/dataset-parameter/915949.rdf
Name: UCYN_B_stdev
Units: nitrogenase gene per liter (nifH L-1)
Description: <p>Standard deviation of UCYN-B gene expression</p>
http://lod.bco-dmo.org/id/dataset-parameter/915950.rdf
Name: UCYN_B_DNQ
Units: unitless
Description: <p>UCYN-B gene expression detected, not quantified</p>
http://lod.bco-dmo.org/id/dataset-parameter/915951.rdf
Name: Tricho_ave
Units: nitrogenase gene per liter (nifH L-1)
Description: <p>Average of UCYN-A1 gene expression</p>
http://lod.bco-dmo.org/id/dataset-parameter/915952.rdf
Name: Tricho_stdev
Units: nitrogenase gene per liter (nifH L-1)
Description: <p>Standard deviation of UCYN-A1 gene expression</p>
http://lod.bco-dmo.org/id/dataset-parameter/915953.rdf
Name: Tricho_DNQ
Units: unitless
Description: <p>UCYN-A1 gene expression detected, not quantified</p>
http://lod.bco-dmo.org/id/dataset-parameter/915954.rdf
Name: Het_2_ave
Units: nitrogenase gene per liter (nifH L-1)
Description: <p>Average of UCYN-A1 gene expression</p>
http://lod.bco-dmo.org/id/dataset-parameter/915955.rdf
Name: Het_2_stdev
Units: nitrogenase gene per liter (nifH L-1)
Description: <p>Standard deviation of UCYN-A1 gene expression</p>
http://lod.bco-dmo.org/id/dataset-parameter/915956.rdf
Name: Het_2_DNQ
Units: unitless
Description: <p>UCYN-A1 gene expression detected, not quantified</p>
http://lod.bco-dmo.org/id/dataset-parameter/915957.rdf
Name: g_24774A11_ave
Units: nitrogenase gene per liter (nifH L-1)
Description: <p>Average of γ-24774A11 gene expression</p>
http://lod.bco-dmo.org/id/dataset-parameter/915958.rdf
Name: g_24774A11_stdev
Units: nitrogenase gene per liter (nifH L-1)
Description: <p>Standard deviation of γ-24774A11 gene expression</p>
http://lod.bco-dmo.org/id/dataset-parameter/915959.rdf
Name: g_24774A11_DNQ
Units: unitless
Description: <p>γ-24774A11 gene expression detected, not quantified</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
32084
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/22ead044-66a6-4619-be3c-6eae2c72472e/content
download
https://doi.org/10.26008/1912/bco-dmo.881028.1
download
onLine
dataset
<p>Samples were collected using standard oceanographic techniques. A CTD Rosette with 24 10L Niskin bottles was lowered to the maximum sampling depth and then brought back to the surface. Methodology described in depth in Turk-Kubo et al. (2021)</p>
Specified by the Principal Investigator(s)
<p>Samples for the measurement of nitrate plus nitrite and phosphate (PO<sub>4</sub><sup>3−</sup>)&nbsp;concentrations were filtered through precombusted GF/F filters and analyzed using standard techniques on a Lachat QuikChem 8000 Flow Injection Analyzer. Chl&nbsp;<em>a</em>&nbsp;samples from each depth were filtered onto GF/F filters, extracted in the dark at 3 °C in 90% acetone for 24 h and measured fluorometrically using a Turner Fluorometer TD-700 as described in Welschmeyer et al.</p>
<p>For DNA collection and extraction, seawater was filtered through Sterivex<sup>TM</sup>&nbsp;filters using gentle peristaltic pumping and flash-frozen in liquid N<sub>2</sub>. DNA was extracted using the DNeasy Plant Kit (Qiagen, Germantown, MD) using modifications to the manufacturer’s guidelines described in detail in Moisander et al. 2007. On-column steps were automated using a QIACube (Qiagen). DNA was quantified using the Picogreen® dsDNA Quantitation kit (Molecular Probes, Eugene, OR).</p>
<p>Gene-based abundance estimates of UCYN-A1, UCYN-A2,&nbsp;<em>Crocosphaera</em>&nbsp;(UCYN-B),&nbsp;<em>Trichodesmium</em>,&nbsp;<em>Richelia</em>&nbsp;associated with&nbsp;<em>Hemiaulus</em>&nbsp;(Het-2), and gamma&nbsp;A (γ-24774A11) were determined using Taqman® qPCR assays. Protocols used for all aspects of qPCR analysis, including reaction conditions, the use of linearized plasmids and inhibition reactions, and calculation of unknowns follow those described in detail by Goebel et al. 2010, apart from a 64 °C annealing temperature for the UCYN-A2 assay. The LOD and LOQ for all assays ranged between 25-31 and 200-250&nbsp;<em>nifH</em>&nbsp;copies l<sup>−1</sup>, respectively. Targets with&nbsp;<em>nifH</em>&nbsp;copies &gt;LOD and &lt;LOQ are detected not quantified (DNQ).</p>
<p>Methodology described in depth in Turk-Kubo et al. (2021).&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
Lachat QuikChem 8000 Flow Injection Analyzer
Lachat QuikChem 8000 Flow Injection Analyzer
PI Supplied Instrument Name: Lachat QuikChem 8000 Flow Injection Analyzer PI Supplied Instrument Description:Nutrients were measured on a Lachat QuikChem 8000 Flow Injection Analyzer. Instrument Name: Flow Injection Analyzer Instrument Short Name:FIA Instrument Description: An instrument that performs flow injection analysis. Flow injection analysis (FIA) is an approach to chemical analysis that is accomplished by injecting a plug of sample into a flowing carrier stream. FIA is an automated method in which a sample is injected into a continuous flow of a carrier solution that mixes with other continuously flowing solutions before reaching a detector. Precision is dramatically increased when FIA is used instead of manual injections and as a result very specific FIA systems have been developed for a wide array of analytical techniques. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB36/
Turner Fluorometer TD-700
Turner Fluorometer TD-700
PI Supplied Instrument Name: Turner Fluorometer TD-700 PI Supplied Instrument Description:Fluorometric analysis of Chl a was measured using a Turner Fluorometer TD-700 (Turner Designs, Inc., San Jose, CA). Instrument Name: Turner Designs 700 Laboratory Fluorometer Instrument Short Name:TD-700 Instrument Description: The TD-700 Laboratory Fluorometer is a benchtop fluorometer designed to detect fluorescence over the UV to red range. The instrument can measure concentrations of a variety of compounds, including chlorophyll-a and fluorescent dyes, and is thus suitable for a range of applications, including chlorophyll, water quality monitoring and fluorescent tracer studies. Data can be output as concentrations or raw fluorescence measurements. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0510/
Cruise: SP1714
SP1714
R/V Robert Gordon Sproul
Community Standard Description
International Council for the Exploration of the Sea
R/V Robert Gordon Sproul
vessel
SP1714
Matthew M. Mills
Stanford University
Cruise: SP1727
SP1727
R/V Robert Gordon Sproul
Community Standard Description
International Council for the Exploration of the Sea
R/V Robert Gordon Sproul
vessel
SP1727
Matthew M. Mills
Stanford University
R/V Robert Gordon Sproul
Community Standard Description
International Council for the Exploration of the Sea
R/V Robert Gordon Sproul
vessel