http://lod.bco-dmo.org/id/dataset/881078
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
2022-09-26
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Single cell N2 fixation measurements from UCYN-A symbiosis in the Southern California Current System from 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.881078.1
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., Turk-Kubo, K. (2024) Single cell N2 fixation measurements from UCYN-A symbiosis in the Southern California Current System from May 2017 (SP1714) and October (SP1724) SCCS cruises. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-06-04 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.881078.1 [access date]
Single cell N2 fixation measurements Dataset Description: <p>These data were published in Turk-Kubo et al. (2021). Table 1, Figure 6, Table S6, Table S7.</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. Seawater was sampled directly from Niskin® bottles into acid-washed 1.2 l polycarbonate bottles through 210 µm Nitex® mesh (Wildco, Yulee, FL) to remove large grazers.</p>
<p>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
Latitude
Longitude
nearshore_offshore
Cell
ROI
PN
at_15N
individual_single_cell_N2_fixation_rate
at_15N2_mean
at_15N2_stdev
Cameca nanoSIMS 50L
theme
None, User defined
Cruise identfier
station
latitude
longitude
sample description
Nitrogen
nitrogen fixation rate
featureType
BCO-DMO Standard Parameters
Mass Spectrometer
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
-115.914
28.289
32.846
2024-06-24
California Current waters off the Southern California shelf
0
BCO-DMO catalogue of parameters from Single cell N2 fixation measurements from UCYN-A symbiosis in the Southern California Current System from 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/915993.rdf
Name: Cruise
Units: unitless
Description: <p>Cruise: SP1714 or SP1727</p>
http://lod.bco-dmo.org/id/dataset-parameter/915994.rdf
Name: Station
Units: unitless
Description: <p>Station number</p>
http://lod.bco-dmo.org/id/dataset-parameter/915995.rdf
Name: Latitude
Units: decimal degrees
Description: <p>Latitude of sampling, south is negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/915996.rdf
Name: Longitude
Units: decimal degrees
Description: <p>Longitude of sampling, west is negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/915997.rdf
Name: nearshore_offshore
Units: unitless
Description: <p>nearshore or offshore sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/915998.rdf
Name: Cell
Units: unitless
Description: <p>cell number</p>
http://lod.bco-dmo.org/id/dataset-parameter/915999.rdf
Name: ROI
Units: unitless
Description: <p>Region of interest: Host, UCYN-A1 or UCYN-A2</p>
http://lod.bco-dmo.org/id/dataset-parameter/916000.rdf
Name: PN
Units: Femtomole Nitrogen per cell (fmol N cell-1)
Description: <p>Particulate Nitrogen</p>
http://lod.bco-dmo.org/id/dataset-parameter/916001.rdf
Name: at_15N
Units: precentage (%)
Description: <p>Atom % (percentage) enrichment of the particulate nitrogen</p>
http://lod.bco-dmo.org/id/dataset-parameter/916002.rdf
Name: individual_single_cell_N2_fixation_rate
Units: Femtomole Nitrogen per cell per day (fmol N cell-1 d-1)
Description: <p>Individual single-cell N2 fixation rate</p>
http://lod.bco-dmo.org/id/dataset-parameter/916003.rdf
Name: at_15N2_mean
Units: precentage (%)
Description: <p>Atom % enrichment of the N2 pool - average</p>
http://lod.bco-dmo.org/id/dataset-parameter/916004.rdf
Name: at_15N2_stdev
Units: precentage (%)
Description: <p>Atom % enrichment of the N2 pool - standard deviation</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
5873
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/925ef363-ebbf-4c33-bd95-e98237e6325d/content
download
https://doi.org/10.26008/1912/bco-dmo.881078.1
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. Seawater was sampled directly from Niskin® bottles into acid-washed 1.2 l polycarbonate bottles through 210 µm Nitex® mesh (Wildco, Yulee, FL) to remove large grazers.</p>
<p>Methodology described in depth in Turk-Kubo et al. (2021)</p>
Specified by the Principal Investigator(s)
<p>Subsamples (95 ml) taken from the incubation bottles were fixed with sterile-filtered formaldehyde (MilliporeSigma) at a final concentration of 1.85% (v/v) for &gt;1 h at 4 °C, then concentrated with 0.6 µm pore-size polycarbonate filters (MilliporeSigma) under gentle vacuum, air-dried and stored at −80 °C. UCYN-A1 and UCYN-A2 symbioses were targeted using 5′-horseradish peroxidase-labeled oligonucleotide probes (Biomers, Inc., Ulm/Donau, Germany), using helper and competitor probes for both symbionts and hosts (Biomers). Protocols for CARD-FISH hybridizations followed procedures described in detail by Cabello et al. 2016.</p>
<p>Samples were visualized, transferred, and mapped to facilitate nanoSIMS analyses according to protocols detailed in Mills et al. 2020. Individual symbioses were analyzed on a Cameca nanoSIMS 50 L at the Stanford Nano Shared Facilities (Stanford, CA). Once targets were located using the charged-coupled device camera and the secondary electron image, image fields were rastered with a 16 keV Cesium primary ion beam (~5 pA) focused into ca. 120 nm spot diameter (256 × 256 pixels, dwell time 1 ms per pixel). Images of&nbsp;<sup>12</sup>C<sup>−</sup>,&nbsp;<sup>13</sup>C<sup>−</sup>,&nbsp;<sup>12</sup>C<sup>14</sup>N<sup>−</sup>and&nbsp;<sup>12</sup>C<sup>15</sup>N<sup>−</sup>&nbsp;were measured over 30–100 planes with a mass resolving power of ca. 8000. Regions of interest were defined around UCYN-A and host cells using Look@nanoSIMS. Isotope ratios of UCYN-A and haptophyte cells were calculated as described in Mills et al. 2020.</p>
<p>Methodology described in depth in Turk-Kubo et al. (2021)</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
Cameca nanoSIMS 50L
Cameca nanoSIMS 50L
PI Supplied Instrument Name: Cameca nanoSIMS 50L PI Supplied Instrument Description:Samples for single cell N2 fixation and CO2 fixation rates were analyzed using a Cameca nanoSIMS 50L (https://www.cameca.com/products/sims/nanosims) located at Stanford University’s nano shared facilities (SNSF, https://snsf.stanford.edu/equipment/xsa/nanosims.html). Instrument Name: Mass Spectrometer Instrument Short Name:Mass Spec Instrument Description: General term for instruments used to measure the mass-to-charge ratio of ions; generally used to find the composition of a sample by generating a mass spectrum representing the masses of sample components. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB16/
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