http://lod.bco-dmo.org/id/dataset/661581
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
2016-10-14
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Sets of sediment cores taken for isotope pairing and other nitrogen cycle parameters seasonally since November 2013 from two oyster farm and control sites in Rhode Island and New York
2016-10-14
publication
2016-10-14
revision
BCO-DMO Linked Data URI
2016-10-14
creation
http://lod.bco-dmo.org/id/dataset/661581
Bongkeun Song
Virginia Institute of Marine Science
principalInvestigator
Craig Tobias
University of Connecticut
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: Song, B., Tobias, C. (2016) Sets of sediment cores taken for isotope pairing and other nitrogen cycle parameters seasonally since November 2013 from two oyster farm and control sites in Rhode Island and New York. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 14 October 2016) Version Date 2016-10-14 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/661581 [access date]
Sets of sediment cores taken for isotope pairing and other nitrogen cycle parameters seasonally since November 2013 Dataset Description: <p>Sets of sediment cores taken for isotope pairing and other nitrogen cycle parameters seasonally since November 2013&nbsp;from two oyster farm and control sites.&nbsp;</p>
<p><strong>Status:&nbsp;</strong>Data are restricted from public access until 08 November 2017. Please contact the PI for prior access.</p> Methods and Sampling: <p>Samples were collected at coastal oyster farms in Rhode Island (41&nbsp;22'&nbsp;45"&nbsp;N, 71&nbsp;38'&nbsp;43"&nbsp;W) and New York (41&nbsp;16'&nbsp;9"&nbsp;N, 71&nbsp;59'&nbsp;29"&nbsp;W). At both locations, the approximate depth is 2 meters.</p>
<p>Coupled direct denitrification (DNF), direct DNF, and dissimilatory nitrate reduction to ammonium (DNRA) are measured in sediments collected from each site in areas that are influenced by oysters and areas that are not. Seasonally five intact sediment cores are taken from directly underneath oyster growth and from control sites in both farms. Cores are incubated at in situ temperature with no air headspace and <sup>15</sup>N-NO<sub>3</sub><sup>-</sup> tracer added to the overlying water.&nbsp;Each core is sacrificed and slurried as a single time point.&nbsp;Water column dissolved inorganic nitrogen (DIN) samples are analyzed colorimetrically for concentration (WestCo SmartChem).&nbsp;N<sub>2</sub> isotopologues are measured on the membrane inlet mass spectrometer (MIMS) and are used to calculate rates of both coupled and direct DNF via the isotope pairing method (IPT, Steingruber et al. 2001).&nbsp;Sediment bound <sup>15</sup>N-NH4<sup>+ </sup>enrichment is measured using the azide hypobromide method (Zhang et al. 2007) and are run on the isotope ratio mass spectrometer (IRMS).&nbsp;<sup>15</sup>N-NH4<sup>+ </sup>enrichment is then used to calculate rates of DNRA.&nbsp;Additionally, sediment sub-samples are run on an elemental analyzer (EA) coupled to IRMS for sediment C:N, <sup>15</sup>N, and&nbsp;<sup>13</sup>C.&nbsp;Finally, in order to constrain the overall <sup>15</sup>N mass balance intermediate pools such as NO<sub>2</sub> and N<sub>2</sub>O are also analyzed.</p>
<p><em>Related references:</em><br />
Steingruber, S. M., Friedrich, J., Gächter, R., &amp; Wehrli, B. 2001. Measurement of denitrification in sediments with the 15N isotope pairing technique. Applied and Environmental Microbiology, 67(9), 3771-3778. doi:<a href="http://dx.doi.org/10.1128/AEM.67.9.3771-3778.2001" target="_blank">10.1128/AEM.67.9.3771-3778.2001</a></p>
<p>Zhang, L., M. A. Altabet, T. Wu, O. Hadas.&nbsp;2007. Sensitive measurement of NH<sub>4</sub><sup>+</sup> <sup>15</sup>N/<sup>14</sup>N (<sup>15</sup>NH<sub>4</sub><sup>+</sup>) at natural abundance levels in fresh and salt waters. Analytical Chemistry 79:5297-5303. doi:<a href="http://dx.doi.org/10.1021/ac070106d" target="_blank">10.1021/ac070106d</a></p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1233372 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1233372
onGoing
Bongkeun Song
Virginia Institute of Marine Science
804-684-7411
P.O Box 1346
Gloucester Point
VA
23692
USA
songb@vims.edu
pointOfContact
Craig Tobias
University of Connecticut
860-405-9140
1080 Shennecossett Rd.
Groton
CT
06340
USA
craig.tobias@uconn.edu
pointOfContact
asNeeded
Dataset Version: 14 October 2016
Unknown
date
season
location
state
lat
lon
site
N2O_flux
NO2_flux
NO3_flux
sediment_15N
pcnt_OM
gC_per _gsed
d13C
d15N
mgN_per_gsed
C_to_N
WestCo SmartChem
isotope ratio mass spectrometer
membrane inlet mass spectrometer
theme
None, User defined
date
season
site
latitude
longitude
No BCO-DMO term
d13C
Carbon to Nitrogen ratio (C:N)
featureType
BCO-DMO Standard Parameters
Discrete Analyzer
Isotope-ratio Mass Spectrometer
Membrane Inlet Mass Spectrometer
instrument
BCO-DMO Standard Instruments
UConn_Tobias_2013-14
service
Deployment Activity
Coastal oyster farms in Rhode Island and New York
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.
Microbial Regulation of Greenhouse Gas N2O Emission from Intertidal Oyster Reefs
https://osprey.bco-dmo.org/project/527289
Microbial Regulation of Greenhouse Gas N2O Emission from Intertidal Oyster Reefs
<p><em>Extracted from the NSF award abstract:</em></p>
<p>Oyster reefs are biogeochemical hot spots and prominent estuarine habitats that provide disproportionate ecological function. Suspension-feeding eastern oysters, Crassostrea virginica, are capable of improving water quality and diminishing eutrophication by filtering nutrients and particles from the water and depositing them in the sediments. Remineralization of these deposits may enhance sedimentary denitrification that facilitates nitrogen removal in tidal estuaries. However, the scientific underpinning of oyster reef function has been challenged in various studies. In addition, recent studies of filter feeding invertebrates reported the production of nitrous oxide (N2O), a greenhouse gas, as an end product of incomplete denitrification by gut microbes. C. virginica could be another source of N2O flux from intertidal habitats. Preliminary work indicated substantial N2O production from individual oysters. The estimated N2O production from high density oyster reefs may exceed the N2O flux measured from some estuaries. With the new discovery of N2O emission and uncertainty regarding eutrophication control, the ecological value of oyster reef restoration may become equivocal.</p>
<p>This project will quantify N2O fluxes to understand the factors controlling N2O emission from oyster reefs. Sedimentary N processes will be examined to develop an oyster reef N model to estimate N2O emission from tidal creek estuaries relative to other N cycling processes. The PIs hypothesize that intertidal oyster reefs are a substantial source of N2O emission from estuarine ecosystems and the magnitude of emission may be linked to water quality. If substantial N2O flux from oyster reefs is validated, ecological benefits of oyster reef restoration should be reevaluated. This interdisciplinary research team includes a microbial ecologist, a biogeochemist, an ecologist and an ecosystem modeler. They will utilize stable isotope and molecular microbiological techniques to quantify oyster N2O production, elucidate microbial sources of N2O emission from oysters and sediments, and estimate seasonal variation of N2O fluxes from oyster reefs. Measurements from this study will be integrated into a coupled oyster bioenergetics-sediment biogeochemistry model to compare system level rates of N cycling on oyster reefs as a function of oyster density and water quality. Modeling results will be used to assess the relative trade-offs of oyster restoration associated with N cycling. They expect to deliver the following end products:1) estimation of annual N2O flux from oyster reefs as an additional source of greenhouse gases from estuaries, 2) a better understanding of the environmental and microbial factors influencing N2O and N2 fluxes in tidal estuaries, 3) transformative knowledge for the effect of oyster restoration on water quality enhancement and ecosystem function, 4) direct guidance for oyster restoration projects whose goals include water quality enhancement, and 5) a modeling tool for use in research and restoration planning.</p>
Oyster Reef N2O Emission
largerWorkCitation
project
eng; USA
oceans
Coastal oyster farms in Rhode Island and New York
2016-10-14
0
BCO-DMO catalogue of parameters from Sets of sediment cores taken for isotope pairing and other nitrogen cycle parameters seasonally since November 2013 from two oyster farm and control sites in Rhode Island and New York
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/680908.rdf
Name: date
Units: unitless
Description: <p>Date of sampling formatted as yyyy-mm-dd</p>
http://lod.bco-dmo.org/id/dataset-parameter/680909.rdf
Name: season
Units: unitless
Description: <p>Season of sampling</p>
http://lod.bco-dmo.org/id/dataset-parameter/680910.rdf
Name: location
Units: unitless
Description: <p>Sampling location name</p>
http://lod.bco-dmo.org/id/dataset-parameter/680911.rdf
Name: state
Units: unitless
Description: <p>State of sampling location (NY or RI)</p>
http://lod.bco-dmo.org/id/dataset-parameter/680912.rdf
Name: lat
Units: decimal degrees
Description: <p>Latitude of sampling location</p>
http://lod.bco-dmo.org/id/dataset-parameter/680913.rdf
Name: lon
Units: decimal degrees
Description: <p>Longitude of sampling location</p>
http://lod.bco-dmo.org/id/dataset-parameter/680914.rdf
Name: site
Units: unitless
Description: <p>Site (Oyster or Control)</p>
http://lod.bco-dmo.org/id/dataset-parameter/680915.rdf
Name: N2O_flux
Units: micromoles per square meter per hour (umol m-2 h-1)
Description: <p>N2O flux</p>
http://lod.bco-dmo.org/id/dataset-parameter/680916.rdf
Name: NO2_flux
Units: micromoles per square meter per hour (umol m-2 h-1)
Description: <p>NO2 flux</p>
http://lod.bco-dmo.org/id/dataset-parameter/680917.rdf
Name: NO3_flux
Units: micromoles per square meter per hour (umol m-2 h-1)
Description: <p>NO3 flux</p>
http://lod.bco-dmo.org/id/dataset-parameter/680918.rdf
Name: sediment_15N
Units: micromoles (umol)
Description: <p>Sediment 15N</p>
http://lod.bco-dmo.org/id/dataset-parameter/680919.rdf
Name: pcnt_OM
Units: percent (%)
Description: <p>Percent organic matter</p>
http://lod.bco-dmo.org/id/dataset-parameter/680920.rdf
Name: gC_per _gsed
Units: g C / g sediment
Description: <p>grams of Carbon per grams of sediment</p>
http://lod.bco-dmo.org/id/dataset-parameter/680921.rdf
Name: d13C
Units: per mil
Description: <p>d13C</p>
http://lod.bco-dmo.org/id/dataset-parameter/680922.rdf
Name: d15N
Units: per mil
Description: <p>d15N</p>
http://lod.bco-dmo.org/id/dataset-parameter/680923.rdf
Name: mgN_per_gsed
Units: mg N / g sediment
Description: <p>milligrams of Nitrogen per grams of sediment</p>
http://lod.bco-dmo.org/id/dataset-parameter/680924.rdf
Name: C_to_N
Units: dimensionless (ratio)
Description: <p>C:N</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
https://osprey.bco-dmo.org/dataset/661581/data/download
download
onLine
dataset
<p>Samples were collected at coastal oyster farms in Rhode Island (41&nbsp;22'&nbsp;45"&nbsp;N, 71&nbsp;38'&nbsp;43"&nbsp;W) and New York (41&nbsp;16'&nbsp;9"&nbsp;N, 71&nbsp;59'&nbsp;29"&nbsp;W). At both locations, the approximate depth is 2 meters.</p>
<p>Coupled direct denitrification (DNF), direct DNF, and dissimilatory nitrate reduction to ammonium (DNRA) are measured in sediments collected from each site in areas that are influenced by oysters and areas that are not. Seasonally five intact sediment cores are taken from directly underneath oyster growth and from control sites in both farms. Cores are incubated at in situ temperature with no air headspace and <sup>15</sup>N-NO<sub>3</sub><sup>-</sup> tracer added to the overlying water.&nbsp;Each core is sacrificed and slurried as a single time point.&nbsp;Water column dissolved inorganic nitrogen (DIN) samples are analyzed colorimetrically for concentration (WestCo SmartChem).&nbsp;N<sub>2</sub> isotopologues are measured on the membrane inlet mass spectrometer (MIMS) and are used to calculate rates of both coupled and direct DNF via the isotope pairing method (IPT, Steingruber et al. 2001).&nbsp;Sediment bound <sup>15</sup>N-NH4<sup>+ </sup>enrichment is measured using the azide hypobromide method (Zhang et al. 2007) and are run on the isotope ratio mass spectrometer (IRMS).&nbsp;<sup>15</sup>N-NH4<sup>+ </sup>enrichment is then used to calculate rates of DNRA.&nbsp;Additionally, sediment sub-samples are run on an elemental analyzer (EA) coupled to IRMS for sediment C:N, <sup>15</sup>N, and&nbsp;<sup>13</sup>C.&nbsp;Finally, in order to constrain the overall <sup>15</sup>N mass balance intermediate pools such as NO<sub>2</sub> and N<sub>2</sub>O are also analyzed.</p>
<p><em>Related references:</em><br />
Steingruber, S. M., Friedrich, J., Gächter, R., &amp; Wehrli, B. 2001. Measurement of denitrification in sediments with the 15N isotope pairing technique. Applied and Environmental Microbiology, 67(9), 3771-3778. doi:<a href="http://dx.doi.org/10.1128/AEM.67.9.3771-3778.2001" target="_blank">10.1128/AEM.67.9.3771-3778.2001</a></p>
<p>Zhang, L., M. A. Altabet, T. Wu, O. Hadas.&nbsp;2007. Sensitive measurement of NH<sub>4</sub><sup>+</sup> <sup>15</sup>N/<sup>14</sup>N (<sup>15</sup>NH<sub>4</sub><sup>+</sup>) at natural abundance levels in fresh and salt waters. Analytical Chemistry 79:5297-5303. doi:<a href="http://dx.doi.org/10.1021/ac070106d" target="_blank">10.1021/ac070106d</a></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
WestCo SmartChem
WestCo SmartChem
PI Supplied Instrument Name: WestCo SmartChem PI Supplied Instrument Description:Water column DIN samples are analyzed colorilmetrically for concentration (WestCo SmartChem). Instrument Name: Discrete Analyzer Instrument Short Name:Discrete Analyzer Instrument Description: Discrete analyzers utilize discrete reaction wells to mix and develop the colorimetric reaction, allowing for a wide variety of assays to be performed from one sample. These instruments are ideal for drinking water, wastewater, soil testing, environmental and university or research applications where multiple assays and high throughput are required.
isotope ratio mass spectrometer
isotope ratio mass spectrometer
PI Supplied Instrument Name: isotope ratio mass spectrometer PI Supplied Instrument Description:Sediment bound 15N-NH4+ enrichment is measured using the azide hypobromide method (Zhang et al. 2007) and are run on the isotope ratio mass spectrometer (IRMS). Instrument Name: Isotope-ratio Mass Spectrometer Instrument Short Name:IR Mass Spec; IRMS Instrument Description: The Isotope-ratio Mass Spectrometer is a particular type of mass spectrometer used to measure the relative abundance of isotopes in a given sample (e.g. VG Prism II Isotope Ratio Mass-Spectrometer). Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB16/
membrane inlet mass spectrometer
membrane inlet mass spectrometer
PI Supplied Instrument Name: membrane inlet mass spectrometer PI Supplied Instrument Description:N2 isotopologues are measured on the membrane inlet mass spectrometer (MIMS) and are used to calculate rates of both coupled and direct DNF via the isotope pairing method (IPT, Steingruber et al. 2001). Instrument Name: Membrane Inlet Mass Spectrometer Instrument Short Name:MIMS Instrument Description: Membrane-introduction mass spectrometry (MIMS) is a method of introducing analytes into the mass spectrometer's vacuum chamber via a semipermeable membrane.
Deployment: UConn_Tobias_2013-14
UConn_Tobias_2013-14
Univ_Connecticut
laboratory
UConn_Tobias_2013-14
Craig Tobias
University of Connecticut
Univ_Connecticut
laboratory