http://lod.bco-dmo.org/id/dataset/659109
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
2016-09-19
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Net calcification of L. pertusa specimens exposed to different pH treatments collected on R/V Ronald Brown in Florida from October to November 2010 (Lophelia OA project)
2016-09-19
publication
2016-09-19
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2019-05-13
publication
https://doi.org/10.1575/1912/bco-dmo.659109.1
Erik E. Cordes
Temple 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: Cordes, E. (2016) Net calcification of L. pertusa specimens exposed to different pH treatments collected on R/V Ronald Brown in Florida from October to November 2010 (Lophelia OA project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2016-09-19 [if applicable, indicate subset used]. doi:10.1575/1912/bco-dmo.659109.1 [access date]
Net calcification of L. pertusa exposed to different pH treatments. Dataset Description: <p>Net calcification data (percent total weight per day) for <em>Lophelia pertusa</em> exposed to different pH treatments. Specimens used in this experiment were collected on RB-10-07: NOAA Ship Ronald H. Brown, from October-November 2010.</p> Methods and Sampling: <p>All methods are fully described in:</p>
<p>Lunden et al. 2014 Frontiers in Marine Science “Acute survivorship of the deep-sea coral <em>Lophelia pertusa</em> from the Gulf of Mexico under acidification, warming, and deoxygenation”</p>
<p><strong>From the Paper:</strong></p>
<p>Forty-one nubbins of <em>L. pertusa</em> used in the experiments were collected in November 2010 on the NOAA Ship Ronald H. Brown with ROV Jason II as part of the “Lophelia II” project jointly sponsored by the Bureau of Ocean Energy Management and the NOAA Office of Ocean Exploration and Research in the Gulf of Mexico (GoM). Permits for the collection of corals were obtained from the U.S. Department of the Interior prior to any collection activities. Spatially discrete coral branches were collected with the ROV and placed in temperature-insulated bioboxes (volume = 20 l) at depth. Upon return to the surface, corals were kept alive in 20 l aquaria in the ship’s constant-temperature room. Partial water changes were made regularly while at sea. Upon return to port, corals were immediately transported overnight to the laboratory on wet ice.</p>
<p>In the laboratory, corals were maintained in one of two 570 liter recirculating aquaria systems at temperature 8 degrees celsius and salinity 35 ppt (Lunden et al., 2014). Regular partial water changes (15–20%) were performed with seawater made using Instant Ocean&nbsp;sea salt. Submersible power heads were placed in each holding tank to ensure water movement and turbulence sufficient to cause swaying of coral polyps. Corals were fed three times weekly using a combination of MarineSnow&nbsp;PlanktonDiet (Two Little Fishies, Miami Gardens, FL) and freshly hatched Artemia nauplii.</p>
<p>Survivorship was assessed by daily observations of polyp tissue presence and behavior. Final survivorship counts were taken 3 to 4 days following the end of each treatment after transfer to the maintenance tank. Survivorship is reported as percent cumulative mortality.</p>
<p>Net calcification was measured using the buoyant weight technique (Davies, 1989). Coral nubbins were buoyantly weighed at the start and end of each experimental period (days eight and fifteen) using a Denver Instruments SI-64 analytical balance (d = 0.1mg, Fisher Scientific, Waltham, MA). A weighing chamber was constructed using 1/2” plexiglass to prevent disturbances from air movement during weighing. Each coral nubbin was transported individually from its respective aquarium to the weighing chamber in a four-liter Pyrex&nbsp;beaker and suspended from the balance. The buoyant weight was recorded after the coral nubbin stabilized, typically 2 min. Each coral nubbin was weighed three times to determine measurement precision (2–3 mg). Seawater density was determined in each aquarium by buoyantly weighing a 2.5 cm^2 aluminum block with known density (2.7 g/cm^−3). Coral weight in air (i.e., dry weight) was calculated by the following equation:&nbsp;</p>
<p>Wa = Ww / (1− (Dw/SD))&nbsp;</p>
<p>Where<br />
Wa = coral weight in air (dry weight)&nbsp;<br />
Ww = coral weight in water (buoyant weight)&nbsp;<br />
Dw = density of seawater&nbsp;<br />
SD = coral skeletal density (= 2.82 g/cm^−3, Lunden et al., 2013).&nbsp;</p>
<p>Coral growth rate is reported as percent growth per day (%/d−1), which was calculated by the equation:</p>
<p>Gt = 100 × (Mt2 − Mt1)/(Mt1(T2 −T1))</p>
<p>Where<br />
Gt =growth rate as %/d^−1&nbsp;<br />
Mt2 = mass (mg, dry weight) at time 2 (end of experimental period, day 15)&nbsp;<br />
Mt1= mass (mg, dry weight) at time 1 (start of experimental period, day 8)<br />
T2 = time 2 (end of experimental period, day 15)&nbsp;<br />
T1= time 1 (start of experimental period, day 8)</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1220478 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1220478
completed
Erik E. Cordes
Temple University
215-204-8876
Temple University Biology-Life Sciences 315
Philadelphia
PA
19122
USA
ecordes@temple.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
pH_treatment
group
individual
temperature
salinity
TA
pH_total
omega_Ar
dry_weight_start
dry_weight_end
net_calcification
percent_survivorship
Aquarium
Denver Instruments SI-64 Analytical Balance
Temperature sensor
theme
None, User defined
treatment
sample identification
individual
temperature of sample or a generic measurement (not in-situ water temp)
salinity
total alkalinity (TA)
pH
Aragonite Saturation State
dry_wgt_globec
growth
No BCO-DMO term
featureType
BCO-DMO Standard Parameters
Aquarium
scale or balance
Water Temperature Sensor
instrument
BCO-DMO Standard Instruments
RB1007
service
Deployment Activity
Florida
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.
Science, Engineering and Education for Sustainability NSF-Wide Investment (SEES): Ocean Acidification (formerly CRI-OA)
https://www.nsf.gov/funding/pgm_summ.jsp?pims_id=503477
Science, Engineering and Education for Sustainability NSF-Wide Investment (SEES): Ocean Acidification (formerly CRI-OA)
NSF Climate Research Investment (CRI) activities that were initiated in 2010 are now included under Science, Engineering and Education for Sustainability NSF-Wide Investment (SEES). SEES is a portfolio of activities that highlights NSF's unique role in helping society address the challenge(s) of achieving sustainability. Detailed information about the SEES program is available from NSF (https://www.nsf.gov/funding/pgm_summ.jsp?pims_id=504707).
In recognition of the need for basic research concerning the nature, extent and impact of ocean acidification on oceanic environments in the past, present and future, the goal of the SEES: OA program is to understand (a) the chemistry and physical chemistry of ocean acidification; (b) how ocean acidification interacts with processes at the organismal level; and (c) how the earth system history informs our understanding of the effects of ocean acidification on the present day and future ocean.
Solicitations issued under this program:
NSF 10-530, FY 2010-FY2011
NSF 12-500, FY 2012
NSF 12-600, FY 2013
NSF 13-586, FY 2014
NSF 13-586 was the final solicitation that will be released for this program.
PI Meetings:
1st U.S. Ocean Acidification PI Meeting(March 22-24, 2011, Woods Hole, MA)
2nd U.S. Ocean Acidification PI Meeting(Sept. 18-20, 2013, Washington, DC)
3rd U.S. Ocean Acidification PI Meeting (June 9-11, 2015, Woods Hole, MA – Tentative)
NSF media releases for the Ocean Acidification Program:
Press Release 10-186 NSF Awards Grants to Study Effects of Ocean Acidification
Discovery Blue Mussels "Hang On" Along Rocky Shores: For How Long?
Discovery nsf.gov - National Science Foundation (NSF) Discoveries - Trouble in Paradise: Ocean Acidification This Way Comes - US National Science Foundation (NSF)
Press Release 12-179 nsf.gov - National Science Foundation (NSF) News - Ocean Acidification: Finding New Answers Through National Science Foundation Research Grants - US National Science Foundation (NSF)
Press Release 13-102 World Oceans Month Brings Mixed News for Oysters
Press Release 13-108 nsf.gov - National Science Foundation (NSF) News - Natural Underwater Springs Show How Coral Reefs Respond to Ocean Acidification - US National Science Foundation (NSF)
Press Release 13-148 Ocean acidification: Making new discoveries through National Science Foundation research grants
Press Release 13-148 - Video nsf.gov - News - Video - NSF Ocean Sciences Division Director David Conover answers questions about ocean acidification. - US National Science Foundation (NSF)
Press Release 14-010 nsf.gov - National Science Foundation (NSF) News - Palau's coral reefs surprisingly resistant to ocean acidification - US National Science Foundation (NSF)
Press Release 14-116 nsf.gov - National Science Foundation (NSF) News - Ocean Acidification: NSF awards $11.4 million in new grants to study effects on marine ecosystems - US National Science Foundation (NSF)
SEES-OA
largerWorkCitation
program
Physiological and genetic responses of the deep-water coral, Lophelia pertusa, to ongoing ocean acidification in the Gulf of Mexico
https://osprey.bco-dmo.org/project/2224
Physiological and genetic responses of the deep-water coral, Lophelia pertusa, to ongoing ocean acidification in the Gulf of Mexico
<p>The Gulf of Mexico deep water ecosystems are threatened by the persistent threat of ocean acidification. Deep-water corals will be among the first to feel the effects of this process, in particular the deep-water scleractinians that form their skeleton from aragonite. The continued shoaling of the aragonite saturation horizon (the depth below which aragonite is undersaturated) will place many of the known, and as yet undiscovered, deep-water corals at risk in the very near future. The most common deep-water framework-forming scleractinian in the world's oceans is <em>Lophelia pertusa</em>. This coral is most abundant in the North Atlantic, where aragonite saturation states are relatively high, but it also creates extensive reef structures between 300 and 600 m depth in the Gulf of Mexico where aragonite saturation states were previously unknown. Preliminary data indicate that pH at this depth range is between 7.85 and 8.03, and the aragonite saturation state is typically between 1.28 and 1.69. These are the first measurements of aragonite saturation state for the deep Gulf of Mexico, and are among the lowest Aragonite saturation state yet recorded for framework-forming corals in any body of water, at any depth.</p>
<p>This project will examine the effects of ocean acidification on<em> L. pertusa</em>, combining laboratory experiments, rigorous oceanographic measurements, the latest genome and transcriptome sequencing platforms, and quantitative PCR and enzyme assays to examine changes in coral gene expression and enzyme activity related to differences in carbonate chemistry. Short-term and long-term laboratory experiments will be performed at Aragonite saturation state of 1.45 and 0.75 and the organismal (e.g., survivorship and calcification rate) and genetic (e.g., transcript abundance) responses of the coral will be monitored. Genomic DNA and RNA will be extracted, total mRNA purified, and comprehensive and quantitative profiles of the transcriptome generated using a combination of 454 and Illumina sequencing technologies. Key genes in the calcification pathways as well as other differentially expressed genes will be targeted for specific qPCR assays to verify the Illumina sequencing results. On a research cruise,<em> L. pertusa</em> will be sampled (preserved at depth) along a natural gradient in carbonate chemistry, and included in the Illumina sequencing and qPCR assays. Water samples will be obtained by submersible-deployed niskin bottles adjacent to the coral collections as well as CTD casts of the water column overlying the sites. Water samples will be analyzed for pH, alkalinity, nitrates and soluble reactive phosphorus. These will be used in combination with historical data in a model to hindcast Aragonite saturation state.</p>
<p>This project will provide new physiological and genetic data on an ecologically-significant and anthropogenically-threatened deepwater coral in the Gulf of Mexico. An experimental system, already developed by the PIs, offers controlled conditions to test the effect of Aragonite saturation state on calcification rates in scleractinians and, subsequently, to identify candidate genes and pathways involved in the response to reduced pH and Aragonite saturation state. Both long-term and population sampling experiments will provide additional transcriptomic data and specifically investigate the expression of the candidate genes. These results will contribute to our understanding of the means by which scleractinians may acclimate and acclimatize to low pH, alkalinity, and Aragonite saturation state. Furthermore, the investigators will continue a time series of oceanographic measurements of the carbonate system in the Gulf of Mexico, which will allow the inclusion of this significant body of water in models of past and future ocean acidification scenarios.</p>
Lophelia OA
largerWorkCitation
project
eng; USA
oceans
Florida
2016-09-19
Northern Gulf of Mexico
0
BCO-DMO catalogue of parameters from Net calcification of L. pertusa specimens exposed to different pH treatments collected on R/V Ronald Brown in Florida from October to November 2010 (Lophelia OA 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/659118.rdf
Name: pH_treatment
Units: unitless
Description: <p>pH treatment; ambient, low, or very low</p>
http://lod.bco-dmo.org/id/dataset-parameter/659119.rdf
Name: group
Units: unitless
Description: <p>Specimen group</p>
http://lod.bco-dmo.org/id/dataset-parameter/659120.rdf
Name: individual
Units: unitless
Description: <p>Specimen ID number</p>
http://lod.bco-dmo.org/id/dataset-parameter/659121.rdf
Name: temperature
Units: celsius
Description: <p>Water temperature</p>
http://lod.bco-dmo.org/id/dataset-parameter/659122.rdf
Name: salinity
Units: PPT
Description: <p>Salinity of water</p>
http://lod.bco-dmo.org/id/dataset-parameter/659123.rdf
Name: TA
Units: micromoles per kilogram (umol/kg -1)
Description: <p>Total alkalinity of water</p>
http://lod.bco-dmo.org/id/dataset-parameter/659124.rdf
Name: pH_total
Units: unitless
Description: <p>pH measured on the total hydrogen scale</p>
http://lod.bco-dmo.org/id/dataset-parameter/659125.rdf
Name: omega_Ar
Units: unitless
Description: <p>Saturation state of aragonite</p>
http://lod.bco-dmo.org/id/dataset-parameter/659126.rdf
Name: dry_weight_start
Units: grams
Description: <p>Dry weight at start of experiment</p>
http://lod.bco-dmo.org/id/dataset-parameter/659127.rdf
Name: dry_weight_end
Units: grams
Description: <p>Dry weight at end of experiment</p>
http://lod.bco-dmo.org/id/dataset-parameter/659128.rdf
Name: net_calcification
Units: percent per day (%/d -1)
Description: <p>Percent growth of coral colony per day</p>
http://lod.bco-dmo.org/id/dataset-parameter/659129.rdf
Name: percent_survivorship
Units: percent
Description: <p>Percent survivorship</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
3647
https://darchive.mblwhoilibrary.org/bitstream/1912/24122/1/dataset-659109_lophelia-pertusa-experiments-calcification-and-ph__v1.tsv
download
https://doi.org/10.1575/1912/bco-dmo.659109.1
download
onLine
dataset
<p>All methods are fully described in:</p>
<p>Lunden et al. 2014 Frontiers in Marine Science “Acute survivorship of the deep-sea coral <em>Lophelia pertusa</em> from the Gulf of Mexico under acidification, warming, and deoxygenation”</p>
<p><strong>From the Paper:</strong></p>
<p>Forty-one nubbins of <em>L. pertusa</em> used in the experiments were collected in November 2010 on the NOAA Ship Ronald H. Brown with ROV Jason II as part of the “Lophelia II” project jointly sponsored by the Bureau of Ocean Energy Management and the NOAA Office of Ocean Exploration and Research in the Gulf of Mexico (GoM). Permits for the collection of corals were obtained from the U.S. Department of the Interior prior to any collection activities. Spatially discrete coral branches were collected with the ROV and placed in temperature-insulated bioboxes (volume = 20 l) at depth. Upon return to the surface, corals were kept alive in 20 l aquaria in the ship’s constant-temperature room. Partial water changes were made regularly while at sea. Upon return to port, corals were immediately transported overnight to the laboratory on wet ice.</p>
<p>In the laboratory, corals were maintained in one of two 570 liter recirculating aquaria systems at temperature 8 degrees celsius and salinity 35 ppt (Lunden et al., 2014). Regular partial water changes (15–20%) were performed with seawater made using Instant Ocean&nbsp;sea salt. Submersible power heads were placed in each holding tank to ensure water movement and turbulence sufficient to cause swaying of coral polyps. Corals were fed three times weekly using a combination of MarineSnow&nbsp;PlanktonDiet (Two Little Fishies, Miami Gardens, FL) and freshly hatched Artemia nauplii.</p>
<p>Survivorship was assessed by daily observations of polyp tissue presence and behavior. Final survivorship counts were taken 3 to 4 days following the end of each treatment after transfer to the maintenance tank. Survivorship is reported as percent cumulative mortality.</p>
<p>Net calcification was measured using the buoyant weight technique (Davies, 1989). Coral nubbins were buoyantly weighed at the start and end of each experimental period (days eight and fifteen) using a Denver Instruments SI-64 analytical balance (d = 0.1mg, Fisher Scientific, Waltham, MA). A weighing chamber was constructed using 1/2” plexiglass to prevent disturbances from air movement during weighing. Each coral nubbin was transported individually from its respective aquarium to the weighing chamber in a four-liter Pyrex&nbsp;beaker and suspended from the balance. The buoyant weight was recorded after the coral nubbin stabilized, typically 2 min. Each coral nubbin was weighed three times to determine measurement precision (2–3 mg). Seawater density was determined in each aquarium by buoyantly weighing a 2.5 cm^2 aluminum block with known density (2.7 g/cm^−3). Coral weight in air (i.e., dry weight) was calculated by the following equation:&nbsp;</p>
<p>Wa = Ww / (1− (Dw/SD))&nbsp;</p>
<p>Where<br />
Wa = coral weight in air (dry weight)&nbsp;<br />
Ww = coral weight in water (buoyant weight)&nbsp;<br />
Dw = density of seawater&nbsp;<br />
SD = coral skeletal density (= 2.82 g/cm^−3, Lunden et al., 2013).&nbsp;</p>
<p>Coral growth rate is reported as percent growth per day (%/d−1), which was calculated by the equation:</p>
<p>Gt = 100 × (Mt2 − Mt1)/(Mt1(T2 −T1))</p>
<p>Where<br />
Gt =growth rate as %/d^−1&nbsp;<br />
Mt2 = mass (mg, dry weight) at time 2 (end of experimental period, day 15)&nbsp;<br />
Mt1= mass (mg, dry weight) at time 1 (start of experimental period, day 8)<br />
T2 = time 2 (end of experimental period, day 15)&nbsp;<br />
T1= time 1 (start of experimental period, day 8)</p>
Specified by the Principal Investigator(s)
<p><strong>Data Management Office Notes:</strong></p>
<p>-Separate tabs in the&nbsp;original file have been served as separate&nbsp;datasets.<br />
-Re-formatted column names to comply with BCO-DMO naming standards.&nbsp;</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
Aquarium
Aquarium
PI Supplied Instrument Name: Aquarium PI Supplied Instrument Description:20 L aquaria were used on the ship and 570 L recirculating aquaria systems were used in the lab Instrument Name: Aquarium Instrument Short Name:Aquarium Instrument Description: Aquarium - a vivarium consisting of at least one transparent side in which water-dwelling plants or animals are kept
Denver Instruments SI-64 Analytical Balance
Denver Instruments SI-64 Analytical Balance
PI Supplied Instrument Name: Denver Instruments SI-64 Analytical Balance PI Supplied Instrument Description:Used for buoyant weights; d = 0.1mg, Fisher Scientific Instrument Name: scale or balance Instrument Short Name: Instrument Description: Devices that determine the mass or weight of a sample. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB13/
Temperature sensor
Temperature sensor
PI Supplied Instrument Name: Temperature sensor PI Supplied Instrument Description:Indicates water temperature Instrument Name: Water Temperature Sensor Instrument Short Name:Water Temp Sensor Instrument Description: General term for an instrument that measures the temperature of the water with which it is in contact (thermometer). Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/134/
Cruise: RB1007
RB1007
Community Standard Description
International Council for the Exploration of the Sea
NOAA Ship Ronald H. Brown
vessel
RB1007
Erik E. Cordes
Temple University
Community Standard Description
International Council for the Exploration of the Sea
NOAA Ship Ronald H. Brown
vessel