http://lod.bco-dmo.org/id/dataset/615529
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
2015-10-07
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Elemental ratio data from Mass Spec analysis of newly settled oyster spat from Pamlico Sound, North Carolina from June to August of 2012 (EstuarineMetaDyn project)
2015-10-07
publication
2015-10-07
revision
BCO-DMO Linked Data URI
2015-10-07
creation
http://lod.bco-dmo.org/id/dataset/615529
F. Joel Fodrie
University of North Carolina at Chapel Hill
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: Fodrie, F. J. (2015) Elemental ratio data from Mass Spec analysis of newly settled oyster spat from Pamlico Sound, North Carolina from June to August of 2012 (EstuarineMetaDyn project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). Version Date 2015-10-07 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/615529 [access date]
Elemental ratio data from Mass Spec analysis of newly settled oyster spat Dataset Description: <p>Elemental ratio data (X:Ca) from laser ablation inductively coupled plasma mass spectrometer (LA ICP-MS) analysis of newly settled oyster spat collected from Pamlico Sound, NC.</p> Methods and Sampling: <p>Spat settlement collectors were constructed by affixing 2-3 wire strings, each containing 12 adult oyster shells, to private and public docks or stand-alone wooden pilings, throughout BBCPS study system. Settlement collectors were deployed on June 7<sup>th</sup> and 21<sup>st</sup> and again on August 1<sup>st</sup> and 16<sup>th</sup> of 2012 and retrieved approximately 2 weeks later as part of an ongoing settlement sampling program (Eggleston and Puckett, <em>unpubl.data</em>). Recovered settlement collectors were frozen until individual spat could be counted and removed from adult oyster shells with a tungsten probe. Spat were divided by collection site and collection period and refrozen at -23°C.</p>
<p>Spat from the field settlement collections were thawed and placed individually in 2 mL centrifuge tubes filled with 100 mL of 15% H<sub>2</sub>O<sub>2</sub> solution buffered in 0.05 N ultrapure NaOH. Samples were sonicated for 10 min to remove organic material. The H<sub>2</sub>O<sub>2</sub> solution was then removed and replaced with a 100 mL solution of 1% ultrapure HNO<sub>3 </sub>(OPTIMA grade; Fisher Scientific; Hampton, NJ). Samples were then sonicated for 5 additional min to dissolve any remaining tissue and surface impurities. Spat were then rinsed three times with ultrapure H<sub>2</sub>O and dried overnight in a laminar flow hood. After drying, spat were mounted in haphazard order onto a glass microscope slide with double-sided tape and stored until analysis.</p>
<p>Both larval and spat samples were analyzed using a Thermo-Fisher Element2 inductively coupled plasma mass spectrometer with a Teledyne ATLex 300si-x 193nm Excimer laser ablation unit (LA ICP-MS). To correct for mass bias and instrument drift, National Institute of Technology Standards-certified standards (Reference Material 612, 614, and 616) were run at the beginning and end of every 4 slide sequence (~140 burns). Concentrations of the following elements were quantified from laboratory larval samples: <sup>48</sup>Ca, <sup>55</sup>Mn, <sup>88</sup>Sr, <sup>138</sup>Ba, and <sup>208</sup>Pb; and from field-collected spat: <sup>26</sup>Mg, <sup>48</sup>Ca, <sup>55</sup>Mn, <sup>63</sup>Cu, <sup>88</sup>Sr, <sup>118</sup>Sn,<sup> 138</sup>Ba, and <sup>208</sup>Pb. These elements were all analyzed in low-resolution mode, and were chosen because of their previous use in uptake and tagging studies of fish otoliths and bivalve shells (Bath Martin &amp; Thorrold 2005; Strasser et al. 2008a,b; Fodrie et al. 2011).</p>
<p>To determine elemental signatures of the collection sites, the outermost (most recently formed) section of the settler shell was also ablated with a 150 μm transect with 40 μm spot size and 80% intensity. Elemental variability among the larval portion of settler shells was also examined to broadly explore potential larval sources. Larval shell of each spat sample was identified and sampled in a line transect of 110 μm with 40 μm spot size and 80% intensity. Isotope intensities were converted into elemental ratios (X:Ca) following Becker et al. (2007).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1155609 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1155609
completed
F. Joel Fodrie
University of North Carolina at Chapel Hill
252-726-6841
Institute of Marine Sciences & Department of Marine Sciences 3431 Arendell Street
Morehead City
NC
28557
USA
jfodrie@unc.edu
pointOfContact
asNeeded
Unknown
Burn_Number
Burn_Date
Mg26
Mn55
Co59
Cu63
Sr88
Cd112
Ba138
Sn118
La139
Ce140
Pb208
Spat_ID
Sample_Site
Sample_Site_2
Date_Collected
Month_Collected
Sample_Type
Sal
Temp
Site_Code
Lat
Lon
Teledyne ATLex 300si-x 193nm Excimer laser ablation unit
Thermo-Fisher Element2 inductively coupled plasma mass spectrometer
theme
None, User defined
sample description
date
element
sample identification
site
month of year
replicate
salinity
water temperature at measurement depth
latitude
longitude
featureType
BCO-DMO Standard Parameters
Laser
Mass Spectrometer
instrument
BCO-DMO Standard Instruments
Fodrie_SpatStrings
service
Deployment Activity
Pamlico Sound, North Carolina
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.
Interacting Effects of Local Demography and Larval Connectivity on Estuarine Metapopulation Dynamics
https://osprey.bco-dmo.org/project/559332
Interacting Effects of Local Demography and Larval Connectivity on Estuarine Metapopulation Dynamics
<p>Description from NSF award abstract:<br />
The PIs will use the eastern oyster (<em>Crassostrea virginica</em>) in Pamlico Sound, North Carolina, as a model system and will attempt to optimize the design of networks of no-take reserves as a strategy for maintaining metapopulations of this commercially harvested species. The project specifically recognizes that network persistence depends on (1) the potential for growth, survival, and reproduction within reserves, and (2) the potential to distribute offspring among reserves. Thus, demographic processes within reserves and settling areas play important roles, along with variability of physical transport. The PIs plan to:<br />
(1) test and refine 3D bio-physical models of connectivity due to oyster larval transport in a shallow, wind-dominated system;<br />
(2) test, refine, and apply technology to detect natal origins of larvae using geochemical tags in larval shell; and<br />
(3) integrate regional connectivity and demographic rates to model metapopulation dynamics.</p>
<p>This study will produce new tools and test and refine others used for studying larval connectivity, a fundamentally important process in the maintenance of natural populations, and thus in biological conservation and resource management. The tools include a hydrodynamic modeling tool coupled with an open-source particle tracking model that will be available on-line with computer code and user guide. The project will use integrated modeling approaches to evaluate the design of reserve networks: results will be directly useful to improving oyster and ecosystem-based management in Pamlico Sound, and the methods will inform approaches to network design in other locations.</p>
EstuarineMetaDyn
largerWorkCitation
project
eng; USA
biota
inlandWaters
Pamlico Sound, North Carolina
-76.7528
-75.4818
34.6562
35.8416
2012-06-13
2012-08-25
North Carolina Estuaries
0
BCO-DMO catalogue of parameters from Elemental ratio data from Mass Spec analysis of newly settled oyster spat from Pamlico Sound, North Carolina from June to August of 2012 (EstuarineMetaDyn 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/722643.rdf
Name: Burn_Number
Units: unitless
Description: <p>Number corresponding to the order in which the samples were burned (in a given sequence) during LA ICP-MS analysis</p>
http://lod.bco-dmo.org/id/dataset-parameter/722644.rdf
Name: Burn_Date
Units: unitless
Description: <p>date the sample was run through the mass spectometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/722645.rdf
Name: Mg26
Units: dimensionless
Description: <p>Elemental ratio (Mg:Ca). Mg26 isotope intensity in counts per second divided by the Ca48 concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/722646.rdf
Name: Mn55
Units: dimensionless
Description: <p>Elemental ratio (Mn:Ca). Mn55 isotope intensity in counts per second divided by the Ca48 concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/722647.rdf
Name: Co59
Units: dimensionless
Description: <p>Elemental ratio (Co:Ca). Co59 isotope intensity in counts per second divided by the Ca48 concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/722648.rdf
Name: Cu63
Units: dimensionless
Description: <p>Elemental ratio (Cu:Ca). Cu63 isotope intensity in counts per second divided by the Ca48 concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/722649.rdf
Name: Sr88
Units: dimensionless
Description: <p>Elemental ratio (Sr:Ca). Sr88 isotope intensity in counts per second divided by the Ca48 concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/722650.rdf
Name: Cd112
Units: dimensionless
Description: <p>Elemental ratio (Cd:Ca). Cd112 isotope intensity in counts per second divided by the Ca48 concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/722651.rdf
Name: Ba138
Units: dimensionless
Description: <p>Elemental ratio (Ba:Ca). Ba138 isotope intensity in counts per second divided by the Ca48 concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/722652.rdf
Name: Sn118
Units: dimensionless
Description: <p>Elemental ratio (Sn:Ca). Sn118 isotope intensity in counts per second divided by the Ca48 concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/722653.rdf
Name: La139
Units: dimensionless
Description: <p>Elemental ratio (La:Ca). La139 isotope intensity in counts per second divided by the Ca48 concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/722654.rdf
Name: Ce140
Units: dimensionless
Description: <p>Elemental ratio (Ce:Ca). Ce140 isotope intensity in counts per second divided by the Ca48 concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/722655.rdf
Name: Pb208
Units: dimensionless
Description: <p>Elemental ratio (Pb:Ca). Pb208 isotope intensity in counts per second divided by the Ca48 concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/722656.rdf
Name: Spat_ID
Units: unitless
Description: <p>Idenifier for oyster spat bag the sampled spat came from</p>
http://lod.bco-dmo.org/id/dataset-parameter/722657.rdf
Name: Sample_Site
Units: unitless
Description: <p>Geomorphological quadrants the data were grouped into for analysis</p>
http://lod.bco-dmo.org/id/dataset-parameter/722658.rdf
Name: Sample_Site_2
Units: unitless
Description: <p>Geomorphological quadrants the data were grouped into for analysis</p>
http://lod.bco-dmo.org/id/dataset-parameter/722659.rdf
Name: Date_Collected
Units: unitless
Description: <p>Date of spat collection in format yyyymmdd</p>
http://lod.bco-dmo.org/id/dataset-parameter/722660.rdf
Name: Month_Collected
Units: unitless
Description: <p>Month of spat collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/722661.rdf
Name: Sample_Type
Units: unitless
Description: <p>Identifier for replicate burn performed on each shell (S1 or S2).</p>
http://lod.bco-dmo.org/id/dataset-parameter/722662.rdf
Name: Sal
Units: PSU
Description: <p>Average salinity at sample site during length of experiment (June to August of 2012)</p>
http://lod.bco-dmo.org/id/dataset-parameter/722663.rdf
Name: Temp
Units: degrees centigrade
Description: <p>Average temperature at sample site during length of experiment (June to August of 2012)</p>
http://lod.bco-dmo.org/id/dataset-parameter/722664.rdf
Name: Site_Code
Units: untiless
Description: <p>Site identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/722665.rdf
Name: Lat
Units: decimal degrees
Description: <p>Latitude of site</p>
http://lod.bco-dmo.org/id/dataset-parameter/722666.rdf
Name: Lon
Units: decimal degrees
Description: <p>Longitude of site</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
178814
https://datadocs.bco-dmo.org/file/xooy0QVsQ5vV96/spatdata.csv
spatdata.csv
Primary data file for dataset ID 615529
download
https://osprey.bco-dmo.org/dataset/615529/data/download
download
onLine
dataset
<p>Spat settlement collectors were constructed by affixing 2-3 wire strings, each containing 12 adult oyster shells, to private and public docks or stand-alone wooden pilings, throughout BBCPS study system. Settlement collectors were deployed on June 7<sup>th</sup> and 21<sup>st</sup> and again on August 1<sup>st</sup> and 16<sup>th</sup> of 2012 and retrieved approximately 2 weeks later as part of an ongoing settlement sampling program (Eggleston and Puckett, <em>unpubl.data</em>). Recovered settlement collectors were frozen until individual spat could be counted and removed from adult oyster shells with a tungsten probe. Spat were divided by collection site and collection period and refrozen at -23°C.</p>
<p>Spat from the field settlement collections were thawed and placed individually in 2 mL centrifuge tubes filled with 100 mL of 15% H<sub>2</sub>O<sub>2</sub> solution buffered in 0.05 N ultrapure NaOH. Samples were sonicated for 10 min to remove organic material. The H<sub>2</sub>O<sub>2</sub> solution was then removed and replaced with a 100 mL solution of 1% ultrapure HNO<sub>3 </sub>(OPTIMA grade; Fisher Scientific; Hampton, NJ). Samples were then sonicated for 5 additional min to dissolve any remaining tissue and surface impurities. Spat were then rinsed three times with ultrapure H<sub>2</sub>O and dried overnight in a laminar flow hood. After drying, spat were mounted in haphazard order onto a glass microscope slide with double-sided tape and stored until analysis.</p>
<p>Both larval and spat samples were analyzed using a Thermo-Fisher Element2 inductively coupled plasma mass spectrometer with a Teledyne ATLex 300si-x 193nm Excimer laser ablation unit (LA ICP-MS). To correct for mass bias and instrument drift, National Institute of Technology Standards-certified standards (Reference Material 612, 614, and 616) were run at the beginning and end of every 4 slide sequence (~140 burns). Concentrations of the following elements were quantified from laboratory larval samples: <sup>48</sup>Ca, <sup>55</sup>Mn, <sup>88</sup>Sr, <sup>138</sup>Ba, and <sup>208</sup>Pb; and from field-collected spat: <sup>26</sup>Mg, <sup>48</sup>Ca, <sup>55</sup>Mn, <sup>63</sup>Cu, <sup>88</sup>Sr, <sup>118</sup>Sn,<sup> 138</sup>Ba, and <sup>208</sup>Pb. These elements were all analyzed in low-resolution mode, and were chosen because of their previous use in uptake and tagging studies of fish otoliths and bivalve shells (Bath Martin &amp; Thorrold 2005; Strasser et al. 2008a,b; Fodrie et al. 2011).</p>
<p>To determine elemental signatures of the collection sites, the outermost (most recently formed) section of the settler shell was also ablated with a 150 μm transect with 40 μm spot size and 80% intensity. Elemental variability among the larval portion of settler shells was also examined to broadly explore potential larval sources. Larval shell of each spat sample was identified and sampled in a line transect of 110 μm with 40 μm spot size and 80% intensity. Isotope intensities were converted into elemental ratios (X:Ca) following Becker et al. (2007).</p>
Specified by the Principal Investigator(s)
<p>Means and standard errors for field-collected larval and settlement shell Sr:Ca and Ba:Ca ratios were calculated and plotted by site to assess spatial variation in geochemical signatures among collection sites. Signatures from larval shells were used to examine possible temperature and salinity gradients present among natal sites. Additionally, contour plots were used to explore how settler shell elemental concentrations of Mn, Sr, Ba, and Pb varied with temperature and salinity. Contour plots were created using the <em>graphics</em> package in R (version 3.0.3). Multiple regression models were then used to quantitatively assess the relationship between salinity, temperature and shell signatures in a natural environment. Because some collection sites did not produce any spat over a given collection period, spat were grouped only by site to increase the sample size and statistical power of our results. A logarithmic transformation of elemental ratio was used as the response variable.</p>
<p>Linear Discriminate Function Analysis (DFA) was used to examine spatial variability in settler shell geochemistry and to determine the viability of using geochmical fingerprints to assess connectivity in oyster populations. All 23 sites were used in preliminary DFAs, however the classification success was low, directing us toward independent examination of PS sites from the BBCS sites. Because adjacent sites often experienced similar temperature/salinity gradients, PS sites were then grouped by geographic quadrant within PS: Northwest (NW; WC, EH, StP), Northeast (NE; RD, HT), Southeast (SE; OK, CI, WB), and Southwest (SW; OR, SoP, SQ). BBCS sites were similarly broken up into 5 groups based on geomorphology and site location: Bay (JB, WM), Creek (WH, TC), Newport (NeU, NeM, NeL), North (NoU, NoM, NoL), and Sound (BoS, BaS). Jack-knifed classification matrices, without sample replacement, were compared to expected classification matrices, based on random chance, to assess classification success. Sites were additionally grouped based on similar temperature and salinity profiles, however classification success did not improve significantly over geomorphological quadrants so analysis did not continue with these groupings. Because natal origins are unknown and modeled dispersal pathways for the area (e.g. Haase et al. 2012) have not been empirically validated, no DFA was performed on larval signatures.</p>
<p>&nbsp;</p>
<p>BCO-DMO Data Manager Processing Notes:<br />
* added a conventional header with dataset name, PI name, version date<br />
* modified parameter names to conform with BCO-DMO naming conventions<br />
* rounded LR params to 5 decimal places<br />
* replaced parameter name \s with _<br />
* removed parameter name chars (LR) as data submitter indicated it is irrelevant and part of post-processing.<br />
* removed #DIV/0! values<br />
* removed "Name" column as data submitter indicated it is irrelevant and part of post-processing.<br />
* Added Site Code, Lat, and Lon from site info dataset</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
Teledyne ATLex 300si-x 193nm Excimer laser ablation unit
Teledyne ATLex 300si-x 193nm Excimer laser ablation unit
PI Supplied Instrument Name: Teledyne ATLex 300si-x 193nm Excimer laser ablation unit PI Supplied Instrument Description:http://www.cetac.com/product_dashboard/laser-ablation.htm Instrument Name: Laser Instrument Short Name: Instrument Description: A device that generates an intense beam of coherent monochromatic light (or other electromagnetic radiation) by stimulated emission of photons from excited atoms or molecules.
Thermo-Fisher Element2 inductively coupled plasma mass spectrometer
Thermo-Fisher Element2 inductively coupled plasma mass spectrometer
PI Supplied Instrument Name: Thermo-Fisher Element2 inductively coupled plasma mass spectrometer PI Supplied Instrument Description:Both larval and spat samples were analyzed using a Thermo-Fisher Element2 inductively coupled plasma mass spectrometer with a Teledyne ATLex 300si-x 193nm Excimer laser ablation unit (LA ICP-MS). To correct for mass bias and instrument drift, National Institute of Technology Standards-certified standards (Reference Material 612, 614, and 616) were run at the beginning and end of every 4 slide sequence (~140 burns). 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/
Deployment: Fodrie_SpatStrings
Fodrie_SpatStrings
shoreside Pamlico-Oysters
shoreside
shoreside Pamlico-Oysters
shoreside