http://lod.bco-dmo.org/id/dataset/704359
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
2017-06-06
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Change in denitrification due to oyster reefs from the coast of North Carolina in 2010
2017-06-06
publication
2017-06-06
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2019-03-28
publication
https://doi.org/10.1575/1912/bco-dmo.704359.1
Michael F. Piehler
University of North Carolina at Chapel Hill
principalInvestigator
Mark J. Brush
Virginia Institute of Marine Science
principalInvestigator
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: Piehler, M., Brush, M., Song, B., Tobias, C. (2017) Change in denitrification due to oyster reefs from the coast of North Carolina in 2010. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2017-06-06 [if applicable, indicate subset used]. doi:10.1575/1912/bco-dmo.704359.1 [access date]
Change in denitrification (N2 Flux) due to the oyster reef. Dataset Description: <p>Nutrient flux data from several landscapes in coastal North Carolina.</p> Methods and Sampling: <p><span style="font-family:inherit; font-size:14px">Methodology from&nbsp;</span><strong><span style="font-family:open sans,arial,helvetica,lucida sans unicode,sans-serif; font-size:inherit">Smyth, A. R., Piehler, M. F. and Grabowski, J. H. (2015), Habitat context influences nitrogen removal by restored oyster reefs. J Appl Ecol, 52: 716–725. doi:<a href="http://onlinelibrary.wiley.com/doi/10.1111/1365-2664.12435/abstract" style="color: rgb(0, 102, 153); margin: 0px; padding: 0px; border: 0px; font-style: inherit; font-variant: inherit; font-weight: inherit; font-stretch: inherit; font-size: inherit; line-height: inherit; font-family: inherit; vertical-align: baseline; text-decoration-line: none;" target="_blank">10.1111/1365-2664.12435</a></span></strong></p>
<p>Within 4&nbsp;h of collection, sediment cores were set up in a continuous flow core incubation system to measure steady-state nutrient and dissolved gas fluxes, described in Piehler &amp; Smyth (2011). Briefly, cores were sealed with gas-tight lids, which had an inflow and outflow port. Water from a reservoir was pulled over the cores at a flow rate of 1&nbsp;mL min−1. Triplicate dissolved gases and duplicate dissolved inorganic nitrogen samples were collected from the outflow and inflow periodically over the next 24&nbsp;h. To examine how sediments from different habitat contexts responded to nitrate pulses, nitrate concentration in the reservoir water was elevated with NaNO3&nbsp;(~800&nbsp;μm) after 48&nbsp;h of sampling. Dissolved gas and inorganic nitrogen samples were then collected for an additional 48&nbsp;h. Incubations were conducted in the dark and at ambient temperature (30&nbsp;°C).</p>
<p>Water samples from laboratory experiments were&nbsp;analysed&nbsp;immediately upon collection for dissolved gasses (N2,&nbsp;O2&nbsp;and Ar) with membrane inlet mass spectrometry (MIMS). Concentrations of dissolved N2&nbsp;and O2&nbsp;were determined using the ratio with Ar (Kana&nbsp;et&nbsp;al.&nbsp;1994). Coefficients of variation for N2/Ar were 0·05% and 0·04% for O2/Ar. Water samples from laboratory experiments for dissolved nutrient determination were filtered through Whatman GF/F glass&nbsp;fibre&nbsp;filters (25&nbsp;mm diameter, 0·7&nbsp;μm nominal pore size) and frozen until analysis. Dissolved inorganic nutrients were analysed with a Lachat Quick-Chem 8000 automated ion analyser for&nbsp; [math formula] + [math formula] &nbsp;(reported as NOx) and&nbsp; [math formula] &nbsp;concentrations using standard protocols (Lachat Instruments, Milwaukee, WI, USA:&nbsp; [math formula] / [math formula] &nbsp;method 31-107-04-1-A,&nbsp; [math formula] &nbsp;method 31-107-06-1-A; detection limits: 0·04&nbsp;μm&nbsp;NOx, 0·18&nbsp;μm&nbsp; [math formula] ; CV(%): 0·9% NOx&nbsp;and 2·6%&nbsp; [math formula] ).</p>
<p>Upon completion of the incubations, the upper 2&nbsp;cm of sediment in each core was sampled for organic matter content by mass difference from dried sediments before ignition (105&nbsp;°C for 6&nbsp;h) and after ignition (525&nbsp;°C for 3&nbsp;h).</p>
<p><strong>Water Quality Data:</strong></p>
<p><img alt="" src="https://datadocs.bco-dmo.org/d3/data_docs/OysterReef_N2O_Emission/WaterQualityData.png" style="height:283px; width:500px" /></p>
<p>&nbsp;</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
completed
Michael F. Piehler
University of North Carolina at Chapel Hill
252-726-6841 x160
Institute of Marine Science 3431 Arendell St.
Morehead City
North Carolina
28557
U.S.A.
mpiehler@email.unc.edu
pointOfContact
Mark J. Brush
Virginia Institute of Marine Science
804-684-7402
P.O Box 1346
Gloucester Point
VA
23062
USA
brush@vims.edu
pointOfContact
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: 1
Unknown
date
area
location
lat
lon
nutrients
dN2
IRMS
Lachat Quick-Chem 8000 automated ion analyzer
YSI 600 Series Sonde and Model 650 data logger
theme
None, User defined
date
site
latitude
longitude
treatment
No BCO-DMO term
featureType
BCO-DMO Standard Parameters
Isotope-ratio Mass Spectrometer
Nutrient Autoanalyzer
Temperature Logger
instrument
BCO-DMO Standard Instruments
Cheerystone_Inlet
service
Deployment Activity
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
-76.626
-76.6081
34.6804
34.6951
2010-06-28
2010-06-28
0
BCO-DMO catalogue of parameters from Change in denitrification due to oyster reefs from the coast of North Carolina in 2010
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/704617.rdf
Name: date
Units: unitless
Description: <p>Date of collection; YYYY/MM/DD</p>
http://lod.bco-dmo.org/id/dataset-parameter/704618.rdf
Name: area
Units: unitless
Description: <p>Type of substrate where oysters were measured</p>
http://lod.bco-dmo.org/id/dataset-parameter/704619.rdf
Name: location
Units: unitless
Description: <p>PI issued location IDs that correspond to specific coordinates and experimental treatments</p>
http://lod.bco-dmo.org/id/dataset-parameter/704620.rdf
Name: lat
Units: decimal degrees
Description: <p>Latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/704621.rdf
Name: lon
Units: decimal degrees
Description: <p>Longitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/704622.rdf
Name: nutrients
Units: unitless
Description: <p>Indication of whether or not experimental levels of nutrients were used</p>
http://lod.bco-dmo.org/id/dataset-parameter/704623.rdf
Name: dN2
Units: umol N m-2 hr-1
Description: <p>Change in denitrification (N2 flux) due to the oyster reef. Calculated by difference from reef and control in each location.</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
1181
https://darchive.mblwhoilibrary.org/bitstream/1912/23940/1/dataset-704359_change-denitrification-n2-flux__v1.tsv
download
https://doi.org/10.1575/1912/bco-dmo.704359.1
download
onLine
dataset
<p><span style="font-family:inherit; font-size:14px">Methodology from&nbsp;</span><strong><span style="font-family:open sans,arial,helvetica,lucida sans unicode,sans-serif; font-size:inherit">Smyth, A. R., Piehler, M. F. and Grabowski, J. H. (2015), Habitat context influences nitrogen removal by restored oyster reefs. J Appl Ecol, 52: 716–725. doi:<a href="http://onlinelibrary.wiley.com/doi/10.1111/1365-2664.12435/abstract" style="color: rgb(0, 102, 153); margin: 0px; padding: 0px; border: 0px; font-style: inherit; font-variant: inherit; font-weight: inherit; font-stretch: inherit; font-size: inherit; line-height: inherit; font-family: inherit; vertical-align: baseline; text-decoration-line: none;" target="_blank">10.1111/1365-2664.12435</a></span></strong></p>
<p>Within 4&nbsp;h of collection, sediment cores were set up in a continuous flow core incubation system to measure steady-state nutrient and dissolved gas fluxes, described in Piehler &amp; Smyth (2011). Briefly, cores were sealed with gas-tight lids, which had an inflow and outflow port. Water from a reservoir was pulled over the cores at a flow rate of 1&nbsp;mL min−1. Triplicate dissolved gases and duplicate dissolved inorganic nitrogen samples were collected from the outflow and inflow periodically over the next 24&nbsp;h. To examine how sediments from different habitat contexts responded to nitrate pulses, nitrate concentration in the reservoir water was elevated with NaNO3&nbsp;(~800&nbsp;μm) after 48&nbsp;h of sampling. Dissolved gas and inorganic nitrogen samples were then collected for an additional 48&nbsp;h. Incubations were conducted in the dark and at ambient temperature (30&nbsp;°C).</p>
<p>Water samples from laboratory experiments were&nbsp;analysed&nbsp;immediately upon collection for dissolved gasses (N2,&nbsp;O2&nbsp;and Ar) with membrane inlet mass spectrometry (MIMS). Concentrations of dissolved N2&nbsp;and O2&nbsp;were determined using the ratio with Ar (Kana&nbsp;et&nbsp;al.&nbsp;1994). Coefficients of variation for N2/Ar were 0·05% and 0·04% for O2/Ar. Water samples from laboratory experiments for dissolved nutrient determination were filtered through Whatman GF/F glass&nbsp;fibre&nbsp;filters (25&nbsp;mm diameter, 0·7&nbsp;μm nominal pore size) and frozen until analysis. Dissolved inorganic nutrients were analysed with a Lachat Quick-Chem 8000 automated ion analyser for&nbsp; [math formula] + [math formula] &nbsp;(reported as NOx) and&nbsp; [math formula] &nbsp;concentrations using standard protocols (Lachat Instruments, Milwaukee, WI, USA:&nbsp; [math formula] / [math formula] &nbsp;method 31-107-04-1-A,&nbsp; [math formula] &nbsp;method 31-107-06-1-A; detection limits: 0·04&nbsp;μm&nbsp;NOx, 0·18&nbsp;μm&nbsp; [math formula] ; CV(%): 0·9% NOx&nbsp;and 2·6%&nbsp; [math formula] ).</p>
<p>Upon completion of the incubations, the upper 2&nbsp;cm of sediment in each core was sampled for organic matter content by mass difference from dried sediments before ignition (105&nbsp;°C for 6&nbsp;h) and after ignition (525&nbsp;°C for 3&nbsp;h).</p>
<p><strong>Water Quality Data:</strong></p>
<p><img alt="" src="https://datadocs.bco-dmo.org/d3/data_docs/OysterReef_N2O_Emission/WaterQualityData.png" style="height:283px; width:500px" /></p>
<p>&nbsp;</p>
Specified by the Principal Investigator(s)
<p><span style="font-family:inherit; font-size:14px">Methodology from&nbsp;</span><strong><span style="font-family:open sans,arial,helvetica,lucida sans unicode,sans-serif; font-size:inherit">Smyth, A. R., Piehler, M. F. and Grabowski, J. H. (2015), Habitat context influences nitrogen removal by restored oyster reefs. J Appl Ecol, 52: 716–725. doi:<a href="http://onlinelibrary.wiley.com/doi/10.1111/1365-2664.12435/abstract" style="margin: 0px; padding: 0px; border: 0px; font-style: inherit; font-variant: inherit; font-weight: inherit; font-stretch: inherit; font-size: inherit; line-height: inherit; font-family: inherit; vertical-align: baseline; text-decoration-line: none; color: rgb(0, 102, 153);" target="_blank">10.1111/1365-2664.12435</a></span></strong></p>
<p><span style="font-family:inherit; font-size:14px"><span style="font-family:open sans,arial,helvetica,lucida sans unicode,sans-serif; font-size:inherit">Fluxes across the sediment–water interface were calculated as (Co−Ci)&nbsp;×&nbsp;f/a, where&nbsp;Co&nbsp;is the outflow concentration (μmol L−1),&nbsp;Ci&nbsp;is the inflow concentration,&nbsp;f&nbsp;is the flow rate (0·06&nbsp;L h−1), and&nbsp;a&nbsp;is the sediment surface area (0·0032&nbsp;m2). Successive measurements from each core (triplicates for dissolved gas and duplicates for dissolved inorganic nutrients) were averaged to give core-specific values. This results in a net N2flux (gross denitrification – gross nitrogen fixation) and does not distinguish between the sources of N2. Consequently, denitrification refers to net N2&nbsp;production. Oxygen fluxes were calculated using the concentrations of O2&nbsp;obtained from the MIMS, presented as sediment oxygen demand (SOD), and serve as an indicator of organic matter quality, such that more labile organic matter is associated with higher SOD (Ferguson, Eyre &amp; Gay&nbsp;2003). To determine the influence of oyster reefs on sediment N2&nbsp;fluxes, the change in denitrification between the control and reef habitat pair in each zone was calculated (Kellogg&nbsp;et&nbsp;al.&nbsp;2014). Denitrification efficiency was computed as the percentage of the dissolved inorganic nitrogen efflux that was N2&nbsp;(Piehler &amp; Smyth&nbsp;2011).</span></span></p>
<p><span style="font-family:inherit; font-size:14px"><span style="font-family:open sans,arial,helvetica,lucida sans unicode,sans-serif; font-size:inherit">Statistical analyses were performed using&nbsp;r&nbsp;2.13.1 (R Foundation for Statistical Computing&nbsp;2011). Linear mixed-effects models (lme&nbsp;in&nbsp;R nlme&nbsp;package), where habitat nested in sampling location was included as a random effect for the intercept, were used to investigate the effects of oyster reef presence, habitat context, nitrate concentration (ambient vs. elevated) and the interaction between these factors on response variables. Fluxes of N2, NOx&nbsp;( [math formula] &nbsp;+&nbsp; [math formula] )&nbsp; [math formula] , denitrification efficiency and SOD were analysed using all three fixed effects. For sediment organic matter, only habitat context and reef presence were included as fixed effects. The effects of ambient vs. elevated nitrate concentration and habitat context on oyster reef-mediated changes in denitrification were also analysed with a mixed-effects model (fixed effects: nitrate concentration&nbsp;×&nbsp;habitat context; random effects: habitat nested in location). Relationships between oyster density and habitat context were made using a mixed-effects model (fixed effects: habitat context; random effects: habitat nested in location). Comparisons were conducted using linear contrasts and judged against an alpha level of 0·05. Interactions were assessed using Tukey's HSD (lsmeans&nbsp;in&nbsp;R lsmeans&nbsp;package). Assumptions of homogeneity were tested using Levene's tests. Regression analyses were used to investigate the effect of oyster density on denitrification. Models with the lowest Akaike's information criterion corrected for small sample sizes (AICc) were chosen.</span></span></p>
<p><span style="font-family:inherit; font-size:14px"><strong>BCO-DMO Processing Notes:</strong></span></p>
<p><span style="font-family:inherit; font-size:14px">- column names reformatted to comply with BCO-DMO naming standards.<br />
- lat and lon&nbsp;columns added to correspond with locations.</span></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
IRMS
IRMS
PI Supplied Instrument Name: 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/
Lachat Quick-Chem 8000 automated ion analyzer
Lachat Quick-Chem 8000 automated ion analyzer
PI Supplied Instrument Name: Lachat Quick-Chem 8000 automated ion analyzer PI Supplied Instrument Description:Used to analyze dissolved inorganic nutrients Instrument Name: Nutrient Autoanalyzer Instrument Short Name:Nutrient Autoanalyzer Instrument Description: Nutrient Autoanalyzer is a generic term used when specific type, make and model were not specified. In general, a Nutrient Autoanalyzer is an automated flow-thru system for doing nutrient analysis (nitrate, ammonium, orthophosphate, and silicate) on seawater samples. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB04/
YSI 600 Series Sonde and Model 650 data logger
YSI 600 Series Sonde and Model 650 data logger
PI Supplied Instrument Name: YSI 600 Series Sonde and Model 650 data logger PI Supplied Instrument Description:Used to collect water quality data Instrument Name: Temperature Logger Instrument Short Name: Instrument Description: Records temperature data over a period of time.
Deployment: Cheerystone_Inlet
Cheerystone_Inlet
shoreside Virginia
shoreside
Cheerystone_Inlet
Bongkeun Song
Virginia Institute of Marine Science
shoreside Virginia
shoreside