http://lod.bco-dmo.org/id/dataset/962330
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
2025-05-21
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Pelagic primary production and respiration in the York River Estuary sampled in 2018-2021.
2025-09-23
publication
2025-09-23
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2025-09-23
publication
https://doi.org/10.26008/1912/bco-dmo.962330.1
Iris C. Anderson
Virginia Institute of Marine Science
principalInvestigator
Mark J. Brush
Virginia Institute of Marine Science
principalInvestigator
Kimberly S. Reece
Virginia Institute of Marine Science
principalInvestigator
Bongkeun Song
Virginia Institute of Marine Science
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: Brush, M. J., Anderson, I. C., Reece, K. S., Song, B. (2025) Pelagic primary production and respiration in the York River Estuary sampled in 2018-2021. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-09-23 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.962330.1 [access date]
York River Estuary - Primary production & Respiration Dataset Description: Methods and Sampling: <!--[if gte mso 9]><xml>
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<p>Data were collected on several single-day cruises on small privateers out of the Virginia Institute of Marine Science, Gloucester Point, VA.&nbsp;Dissolved oxygen concentrations were measured with a Hach HQ40d portable oxygen meter and LDO101 luminescent dissolved oxygen sensors.&nbsp; Sensors were calibrated in water-saturated air prior to each incubation, and re-checked post-incubation. &nbsp;Salinity and turbidity were measured with a YSI 6600V2 connected to a ship-board Dataflow system and calibrated using YSI calibration solutions. &nbsp;Chlorophyll-a concentrations were measured on a 10 AU Turner Designs fluorometer periodically calibrated to a stock solution of known concentration and checked before each run with a solid standard from Turner Designs.</p>
<p>During 2018-19, surface water was collected bimonthly from five fixed channel stations along the axis of the YRE. During 2020 and 2021, surface water was collected approximately weekly at stations inside and outside of bloom patches (n=3 each) in late summer in the lower YRE; station locations followed individual bloom patches which varied cruise to cruise. Water was held in blackened bottles at <em>in situ</em> temperatures until being returned to the lab.&nbsp;</p>
<p>Metabolic incubations followed the methods of Giordano et al. (2012, <em>Mar Ecol Prog Ser</em> 458: 21–38) and Lake et al. (2013, <em>Mar Ecol Prog Ser</em> 492:21–39). Unfiltered water was placed into 60 ml light and dark biological oxygen demand (BOD) bottles and incubated in the dark (n=4 bottles per station) and light (10 irradiance values, 1 bottle each per station) at <em>in situ</em> temperatures in a light gradient box with illumination provided by a metal halide lamp. Irradiance levels varied from approximately 30 to over 2,000 uE/m2/s photosynthetically active radiation. Light bottles were typically incubated for 1-3 hours while dark bottles were incubated overnight to obtain a measurable change in oxygen. Salinity and turbidity of the water samples were obtained from the associated Dataflow record on each cruise (measured with a YSI 6600V2 datasonde). Triplicate samples for chlorophyll-a determination at each station were filtered through 0.7 um glass fiber filters which were frozen prior to analysis following Arar and Collins (1997, EPA Method 445.0). Samples were extracted in the dark for 24 h in 8 ml of a 45:45:10 dimethyl sulfoxide : acetone: distilled water solution with 1% diethylamine (Shoaf and Lium 1976, <em>Limnol Oceanogr</em> 21: 926−928), and read on a 10 AU Turner Designs fluorometer before and after acidification to compute active chlorophyll-a.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1737258 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1737258
completed
Iris C. Anderson
Virginia Institute of Marine Science
757-876-9436
P.O Box 1346
Gloucester Point
VA
23062
USA
iris@vims.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
Kimberly S. Reece
Virginia Institute of Marine Science
804-684-7407
P.O Box 1346
Gloucester Point
VA
23062
USA
kreece@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
asNeeded
Dataset Version: 1
Unknown
Date
Station
Lat
Long
Cruise
Type
Turbidity
Chla
Salinity
Calc_Kd
PsB
aB
bB
RB
R2adjB
GPP
Resp
Hach LDO101
Hach HQ40d portable oxygen meter
10 AU Turner Designs
YSI 6600V2
theme
None, User defined
date
station
latitude
longitude
cruise type
sample type
turbidity
chlorophyll a
salinity
irradiance
photosynthetic rate
respiration rate
correlation coefficient
primary production
featureType
BCO-DMO Standard Parameters
Oxygen Sensor
Oxygen Sensor
Turner Designs Fluorometer 10-AU
YSI Sonde 6-Series
instrument
BCO-DMO Standard Instruments
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.
Alteration of carbon fluxes by intense phytoplankton blooms in a microtidal estuary
https://osprey.bco-dmo.org/project/747588
Alteration of carbon fluxes by intense phytoplankton blooms in a microtidal estuary
<p><em>NSF Award Abstract:</em><br />
Estuaries, coastal water bodies where rivers mix with ocean water, are hotspots for the processing of carbon and nutrients moving from land to the coastal ocean. Within estuaries land-based nutrient inputs can cause intense blooms of single-celled algae called phytoplankton, which can have significant impacts on the ecosystem. As blooms move down-estuary some of the phytoplankton material is buried on the bottom, and some is decomposed, resulting in low oxygen conditions (hypoxia), harmful to marine life, and production of carbon dioxide (CO2), the major greenhouse gas, which can exchange with the atmosphere. The remaining phytoplankton material can be exported to the ocean. The type and amount of carbon exported from the estuary depend both on its biological activity and physical factors such as fresh water discharge, temperature, and light availability. If phytoplankton production is greater than decomposition, the estuary will take up atmospheric CO2 and export phytoplankton carbon to the coastal ocean. On the other hand, if decomposition is greater than production the estuary will be a source of CO2 to the atmosphere and dissolved CO2 to the coastal ocean. The investigators expect that intense phytoplankton blooms will greatly amplify carbon exchanges with the atmosphere, coastal ocean, and bottom sediments. As intense phytoplankton blooms increase in the future due to increased nutrient inputs and temperature, low oxygen events may become more frequent with potential negative impacts on fisheries and increased export of carbon to the coastal ocean and atmosphere. This study will fill critical gaps identified by the Coastal Carbon Synthesis Program in knowledge of how microtidal estuaries transform and export C to the atmosphere, benthos, and coastal ocean. In addition, there will be a strong teaching and training component to this project, with support for graduate and undergraduate students. The graduate student will be partnered with secondary teachers to gain teaching experience and enrich the middle school educational programs. Summer undergraduate interns will be recruited for a summer program from Hampton University, a historically Black college. There will be public outreach through participation in existing programs at VIMS.</p>
<p>Estuaries serve as critical hotspots for the processing of carbon (C) as it transits from land to the coastal ocean. Recent attempts to synthesize what is known about sources and fates of C in estuaries have noted large data gaps; thus, the role of estuaries, especially those that are microtidal, as important sources of carbon dioxide (CO2) to the atmosphere and total organic carbon (TOC) and dissolved inorganic carbon (DIC) to the coastal ocean, or as a C sink in bottom sediments, remains uncertain. Intensive phytoplankton blooms are becoming increasingly frequent in many estuaries and are likely to have important and yet unknown impacts on the C cycle. The trophic status of an estuary will determine in large part the species of C exported to the atmosphere, bottom sediments, and coastal ocean. The overarching objective of this project is to identify the impacts of intense phytoplankton blooms on C speciation, net C fluxes and exchanges in the Lower York River Estuary (LYRE), a representative mesotrophic, microtidal mid-Atlantic estuary. Metabolic processes are hypothesized to be spatially and temporally dynamic, driving the speciation, abundance, and fates of C in the LYRE. High spatiotemporal resolution sampling in the LYRE will capture rates of C cycling under both baseline conditions throughout most of the year, and during periods when the estuary is perturbed by widespread and intense, but patchy, late summer phytoplankton blooms. The short-term effects of physical drivers (wind, temperature, salinity, fresh water discharge, nutrient and organic carbon loads) and biological drivers (metabolic rates, bacterial and phytoplankton abundances and composition) on C transformations, speciation, and exchanges will be assessed. Expected longer term variations in the C cycle due to anthropogenic and natural disturbances will be predicted through use of modeling. In addition, laboratory manipulations will examine the impacts of specific organisms dominating intensive phytoplankton blooms on benthic metabolism, processing of organic C by the microbial community, and C fluxes to the water column.</p>
LYRE
largerWorkCitation
project
eng; USA
oceans
-76.7519
-76.3863
37.2238
37.4841
2018-02-07
2021-09-07
York River Estuary, Virginia
0
BCO-DMO catalogue of parameters from Pelagic primary production and respiration in the York River Estuary sampled in 2018-2021.
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/962385.rdf
Name: Date
Units: unitless
Description: <p>Cruise date</p>
http://lod.bco-dmo.org/id/dataset-parameter/962386.rdf
Name: Station
Units: unitless
Description: <p>Station number (fixed locations for bimonthly cruises; variable locations for intensive cruises).</p>
http://lod.bco-dmo.org/id/dataset-parameter/962387.rdf
Name: Lat
Units: decimal degrees
Description: <p>Latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/962388.rdf
Name: Long
Units: decimal degrees
Description: <p>Longitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/962389.rdf
Name: Cruise
Units: unitless
Description: <p>Type of cruise. Bimonthly cruises characterized the entire estuary; intensive cruises were focused on the lower estuary.</p>
http://lod.bco-dmo.org/id/dataset-parameter/962390.rdf
Name: Type
Units: unitless
Description: <p>Type of station for intensive cruises. "bloom" stations were inside of intense bloom patches; "non-bloom" stations were outside these patches. Not applicable for bimonthly cruises.</p>
http://lod.bco-dmo.org/id/dataset-parameter/962391.rdf
Name: Turbidity
Units: (NTU or FNU depending on the instrument used)
Description: <p>Water turbidity measured by a YSI</p>
http://lod.bco-dmo.org/id/dataset-parameter/962392.rdf
Name: Chla
Units: micrograms per liter (ug/l)
Description: <p>Extracted active chlorophyll-a (ug/l)</p>
http://lod.bco-dmo.org/id/dataset-parameter/962393.rdf
Name: Salinity
Units: unitless
Description: <p>Salinity measured by a YSI</p>
http://lod.bco-dmo.org/id/dataset-parameter/962394.rdf
Name: Calc_Kd
Units: m-1
Description: <p>Vertical attenuation coefficient for irradiance</p>
http://lod.bco-dmo.org/id/dataset-parameter/962395.rdf
Name: PsB
Units: mgO2/mgChl-a/h
Description: <p>Biomass-specific gross photosynthetic rate in the absence of photoinhibition</p>
http://lod.bco-dmo.org/id/dataset-parameter/962396.rdf
Name: aB
Units: mgO2/mgChl-a/h (uE/m2/s)-1
Description: <p>Initial slope of the biomass-specific photosynthesis-irradiance curve</p>
http://lod.bco-dmo.org/id/dataset-parameter/962397.rdf
Name: bB
Units: mgO2/mgChl-a/h (uE/m2/s)-1
Description: <p>Negative slope characterizing photoinhibition</p>
http://lod.bco-dmo.org/id/dataset-parameter/962398.rdf
Name: RB
Units: mgO2/mgChl-a/h
Description: <p>Biomass-specific respiration rate</p>
http://lod.bco-dmo.org/id/dataset-parameter/962399.rdf
Name: R2adjB
Units: unitless
Description: <p>Adjusted R-squared value from fitting the biomass-specific photosynthesis-irradiance curve</p>
http://lod.bco-dmo.org/id/dataset-parameter/962400.rdf
Name: GPP
Units: gO2/m2/d
Description: <p>Gross primary production</p>
http://lod.bco-dmo.org/id/dataset-parameter/962401.rdf
Name: Resp
Units: gO2/m2/d
Description: <p>Respiration</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
10411
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/c55ee3de-1876-4581-a977-c652193cb0e0/content
download
https://doi.org/10.26008/1912/bco-dmo.962330.1
download
onLine
dataset
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<p>Data were collected on several single-day cruises on small privateers out of the Virginia Institute of Marine Science, Gloucester Point, VA.&nbsp;Dissolved oxygen concentrations were measured with a Hach HQ40d portable oxygen meter and LDO101 luminescent dissolved oxygen sensors.&nbsp; Sensors were calibrated in water-saturated air prior to each incubation, and re-checked post-incubation. &nbsp;Salinity and turbidity were measured with a YSI 6600V2 connected to a ship-board Dataflow system and calibrated using YSI calibration solutions. &nbsp;Chlorophyll-a concentrations were measured on a 10 AU Turner Designs fluorometer periodically calibrated to a stock solution of known concentration and checked before each run with a solid standard from Turner Designs.</p>
<p>During 2018-19, surface water was collected bimonthly from five fixed channel stations along the axis of the YRE. During 2020 and 2021, surface water was collected approximately weekly at stations inside and outside of bloom patches (n=3 each) in late summer in the lower YRE; station locations followed individual bloom patches which varied cruise to cruise. Water was held in blackened bottles at <em>in situ</em> temperatures until being returned to the lab.&nbsp;</p>
<p>Metabolic incubations followed the methods of Giordano et al. (2012, <em>Mar Ecol Prog Ser</em> 458: 21–38) and Lake et al. (2013, <em>Mar Ecol Prog Ser</em> 492:21–39). Unfiltered water was placed into 60 ml light and dark biological oxygen demand (BOD) bottles and incubated in the dark (n=4 bottles per station) and light (10 irradiance values, 1 bottle each per station) at <em>in situ</em> temperatures in a light gradient box with illumination provided by a metal halide lamp. Irradiance levels varied from approximately 30 to over 2,000 uE/m2/s photosynthetically active radiation. Light bottles were typically incubated for 1-3 hours while dark bottles were incubated overnight to obtain a measurable change in oxygen. Salinity and turbidity of the water samples were obtained from the associated Dataflow record on each cruise (measured with a YSI 6600V2 datasonde). Triplicate samples for chlorophyll-a determination at each station were filtered through 0.7 um glass fiber filters which were frozen prior to analysis following Arar and Collins (1997, EPA Method 445.0). Samples were extracted in the dark for 24 h in 8 ml of a 45:45:10 dimethyl sulfoxide : acetone: distilled water solution with 1% diethylamine (Shoaf and Lium 1976, <em>Limnol Oceanogr</em> 21: 926−928), and read on a 10 AU Turner Designs fluorometer before and after acidification to compute active chlorophyll-a.</p>
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<p>Metabolic rates were computed as the change in dissolved oxygen over the course of the incubations (final minus initial) and expressed both as mgO2/l/h and normalized to chlorophyll-a (mgO2/mgChl-a/h). Photosynthesis-irradiance (P-I) curves were then statistically fit to the chlorophyll-a normalized data from each station using the Platt et al. (1980, <em>J Mar Res</em> 38: 687−701) function including photoinhibition:</p>
<p>P<sub>B</sub> = P<sub>sB</sub>*(1-EXP(-a<sub>B</sub>*PAR/P<sub>sB</sub>))*EXP(-b<sub>B</sub>*PAR/P<sub>sB</sub>)+R<sub>B</sub></p>
<p>where P<sub>B</sub> is the net photosynthetic rate (mgO2/mgChl-a/h), P<sub>sB</sub> is the gross photosynthetic rate in the absence of photoinhibition (mgO2/mgChl-a/h), a<sub>B</sub> is the initial slope of the P-I curve (mgO2/mgChl-a/h (uE/m2/s)<sup>-1</sup>), PAR is photosynthetically active radiation (uE/m2/s), b<sub>B</sub> is the negative slope characterizing photoinhibition (mgO2/mgChl-a/h (uE/m2/s)<sup>-1</sup>), R<sub>B</sub> is the rate of respiration (mgO2/mgChl-a/h), and the subscript B denotes that all parameters are normalized to chlorophyll-a biomass.</p>
<p>These P-I curves were then combined with hourly surface irradiance, light attenuation, and estuarine bathymetry to compute photosynthesis and respiration in 10 cm depth intervals each hour of the day, which were then vertically integrated and summed to obtain daily rates. Hourly PAR data were obtained from the Taskinas Creek meteorological station of the Chesapeake Bay National Estuarine Research Reserve in Virginia. To obtain representative rates and avoid biasing the data due to sampling on a particularly cloudy day, average hourly PAR was computed for each sampling date using the values from two weeks before and after the date; hourly values were converted to instantaneous PAR (uE/m2/s) to correspond to the units used in the P-I curves. Vertical attenuation coefficient for irradiance (m<sup>-1</sup>) was computed from turbidity, chlorophyll-a, and salinity using the multiple linear regressions in Lake et al. (2015, <em>Estuaries and Coasts</em> 38: 2149-2171) developed for the York River. Vertically-integrated, daily rates were area-weighted to account for variations in estuarine bathymetry. For bimonthly cruises, stations were evenly spaced in five boxes along the axis of the estuary; bathymetry within each box was used to area-weight the rates. For intensive cruises, area-weighting was based on the bathymetry of the lower YRE.</p>
<p>Calculation of vertically-integrated, daily rates assumed respiration was constant over each 24-hour period at the rate measured in the dark, and that chlorophyll-a concentrations were constant over depth for bimonthly cruises as well as at stations outside of bloom patches during intensive cruises. &nbsp;The two dinoflagellates that bloomed during intensive cruises are known to vertically migrate and aggregate near the surface at midday, so assumptions had to be made regarding the vertical distribution of chlorophyll-a at stations inside bloom patches during intensive cruises. &nbsp;We assumed that the observed chlorophyll-a at those stations occurred in the upper 1 m of the water column from 10 a.m. to 2 p.m. only based on vertical profiling.&nbsp; Below 1 m during the same four hours, chlorophyll-a was set at an average of the concentrations measured at stations outside of bloom patches.&nbsp; For the rest of the day when these species migrate to depth, surface chlorophyll-a (above 1 m) was set at the average of the non-bloom stations, and the high chlorophyll-a concentration measured at the surface was evenly distributed below 1 m.</p>
Specified by the Principal Investigator(s)
* Converted Date column to ISO format (YYYY-MM-DD)
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Specified by BCO-DMO Data Managers
asNeeded
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Hach LDO101
Hach LDO101
PI Supplied Instrument Name: Hach LDO101 PI Supplied Instrument Description:Dissolved oxygen concentrations were measured with Hach LDO101 luminescent dissolved oxygen sensors. Instrument Name: Oxygen Sensor Instrument Short Name:Dissolved Oxygen Sensor Instrument Description: An electronic device that measures the proportion of oxygen (O2) in the gas or liquid being analyzed
Hach HQ40d portable oxygen meter
Hach HQ40d portable oxygen meter
PI Supplied Instrument Name: Hach HQ40d portable oxygen meter PI Supplied Instrument Description:Dissolved oxygen concentrations were measured with a Hach HQ40d portable oxygen meter. Instrument Name: Oxygen Sensor Instrument Short Name:Dissolved Oxygen Sensor Instrument Description: An electronic device that measures the proportion of oxygen (O2) in the gas or liquid being analyzed
10 AU Turner Designs
10 AU Turner Designs
PI Supplied Instrument Name: 10 AU Turner Designs PI Supplied Instrument Description: Chlorophyll-a concentrations were measured on a 10 AU Turner Designs fluorometer periodically calibrated to a stock solution of known concentration and checked before each run with a solid standard from Turner Designs. Instrument Name: Turner Designs Fluorometer 10-AU Instrument Short Name:Turner Fluorometer 10-AU Instrument Description: The Turner Designs 10-AU Field Fluorometer is used to measure Chlorophyll fluorescence. The 10AU Fluorometer can be set up for continuous-flow monitoring or discrete sample analyses. A variety of compounds can be measured using application-specific optical filters available from the manufacturer (read more from Turner Designs, turnerdesigns.com, Sunnyvale, CA, USA). Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0393/
YSI 6600V2
YSI 6600V2
PI Supplied Instrument Name: YSI 6600V2 PI Supplied Instrument Description:Salinity and turbidity were measured with a YSI 6600V2 connected to a ship-board Dataflow system and calibrated using YSI calibration solutions. Instrument Name: YSI Sonde 6-Series Instrument Short Name:YSI Sonde 6-Series Instrument Description: YSI 6-Series water quality sondes and sensors are instruments for environmental monitoring and long-term deployments. YSI datasondes accept multiple water quality sensors (i.e., they are multiparameter sondes). Sondes can measure temperature, conductivity, dissolved oxygen, depth, turbidity, and other water quality parameters. The 6-Series includes several models. More from YSI. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0737/