Accessing BCO-DMO data
log in    
Brought to you by BCO-DMO    

ERDDAP > info > bcodmo_dataset_659379

Title Sum-
Institution Dataset ID
     data   graph     files  public Calcification rates from pH experiments on Lophelia pertusa specimens collected from the
Norwegian Skagerrak and the Gulf of Mexico (Lophelia OA project)
   ?     I   M   background (external link) RSS Subscribe BCO-DMO bcodmo_dataset_659379

The Dataset's Variables and Attributes

Row Type Variable Name Attribute Name Data Type Value
attribute NC_GLOBAL access_formats String .htmlTable,.csv,.json,.mat,.nc,.tsv
attribute NC_GLOBAL acquisition_description String Acquisition Description for Tisler\u00a0Reef Data:

Net calcification was measured using the total alkalinity anomaly (Smith & Key
1975; Ohde & Hossain 2004). Corals were individually placed in closed glass
chambers (220 ml) in a water bath that maintained temperature to +/-0.2
degrees C during all trials. To avoid hypoxia or the severe reductions of pH
during incubations, ambient air was continuously bubbled into the chambers at
a slow rate (1-2 bubbles s-1). This also provided adequate circulation within
the chamber. A 60 ml water sample was collected by syringe before and after
the incubation period, and measured for total alkalinity in duplicate. The
respiration rate of each colony was measured as oxygen consumption in
a\u00a0400 ml closed acrylic chamber during hour-long incubations. Dissolved
oxygen concentrations were measured in\u00a0umol\u00a0L-1\u00a0using a
Strathkelvin 782 dual oxygen meter and SI130\u00a0microcathode\u00a0electrode.
The feeding rate of each colony was measured as the capture rate of
adult\u00a0Artemia salina\u00a0during a one-hour period in 0.8 L incubation
chambers containing a starting prey density of 125\u00a0Artemia\u00a0L-1.

Acquisition Description for Gulf of Mexico Data:

The buoyant weight of each colony was obtained at the start and end of the
two-week experimental period by weighing fragments submerged in seawater and
attached by a hook to an analytical balance (Denver
Instrument,\u00a0precision\u00a0of 0.1 mg). The respiration rate of each
colony was measured as oxygen consumption in an 800 ml closed acrylic chamber
during hour-long incubations. Dissolved oxygen concentrations were measured
in\u00a0umol\u00a0L-1\u00a0using a Strathkelvin 782 dual oxygen meter and
SI130\u00a0microcathode\u00a0electrode. The feeding rate of each colony was
measured as the capture rate of adult\u00a0Artemia salina\u00a0during a one-
hour period in 0.8 L incubation chambers containing a starting prey density of
attribute NC_GLOBAL awards_0_award_nid String 54992
attribute NC_GLOBAL awards_0_award_number String OCE-1220478
attribute NC_GLOBAL awards_0_data_url String http://www.nsf.gov/awardsearch/showAward?AWD_ID=1220478 (external link)
attribute NC_GLOBAL awards_0_funder_name String NSF Division of Ocean Sciences
attribute NC_GLOBAL awards_0_funding_acronym String NSF OCE
attribute NC_GLOBAL awards_0_funding_source_nid String 355
attribute NC_GLOBAL awards_0_program_manager String David L. Garrison
attribute NC_GLOBAL awards_0_program_manager_nid String 50534
attribute NC_GLOBAL cdm_data_type String Other
attribute NC_GLOBAL comment String Physiology - Calcification
E. Cordes & R. Kulalthinal, PIs
Version 16 September 2016
attribute NC_GLOBAL Conventions String COARDS, CF-1.6, ACDD-1.3
attribute NC_GLOBAL creator_email String info at bco-dmo.org
attribute NC_GLOBAL creator_name String BCO-DMO
attribute NC_GLOBAL creator_type String institution
attribute NC_GLOBAL creator_url String https://www.bco-dmo.org/ (external link)
attribute NC_GLOBAL data_source String extract_data_as_tsv version 2.3 19 Dec 2019
attribute NC_GLOBAL date_created String 2016-09-20T21:06:24Z
attribute NC_GLOBAL date_modified String 2019-05-10T17:09:03Z
attribute NC_GLOBAL defaultDataQuery String &time<now
attribute NC_GLOBAL doi String 10.1575/1912/bco-dmo.659379.1
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/659379 (external link)
attribute NC_GLOBAL institution String BCO-DMO
attribute NC_GLOBAL instruments_0_acronym String O2 microsensor
attribute NC_GLOBAL instruments_0_dataset_instrument_description String Measured dissolved oxygen concentrations
attribute NC_GLOBAL instruments_0_dataset_instrument_nid String 659388
attribute NC_GLOBAL instruments_0_description String A miniaturized Clark-type dissolved oxygen instrument, including glass micro-sensors with minute tips (diameters ranging from 1 to 800 um). A gold or platinum sensing cathode is polarized against an internal reference and, driven by external partial pressure, oxygen from the environment penetrates through the sensor tip membrane and is reduced at the sensing cathode surface. A picoammeter converts the resulting reduction current to a signal. The size of the signal generated by the electrode is proportional to the flux of oxygen molecules to the cathode.The sensor also includes a polarized guard cathode, which scavenges oxygen in the electrolyte, thus minimizing zero-current and pre-polarization time.With the addition of a meter and a sample chamber, the respiration of a small specimen can be measured. Example: Strathkelvin Inst. http://www.strathkelvin.com
attribute NC_GLOBAL instruments_0_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L05/current/351/ (external link)
attribute NC_GLOBAL instruments_0_instrument_name String Oxygen Microelectrode Sensor
attribute NC_GLOBAL instruments_0_instrument_nid String 701
attribute NC_GLOBAL instruments_0_supplied_name String SI130 microcathode electrode
attribute NC_GLOBAL instruments_1_acronym String Dissolved Oxygen Sensor
attribute NC_GLOBAL instruments_1_dataset_instrument_description String Measured dissolved oxygen concentrations
attribute NC_GLOBAL instruments_1_dataset_instrument_nid String 659389
attribute NC_GLOBAL instruments_1_description String An electronic device that measures the proportion of oxygen (O2) in the gas or liquid being analyzed
attribute NC_GLOBAL instruments_1_instrument_name String Dissolved Oxygen Sensor
attribute NC_GLOBAL instruments_1_instrument_nid String 705
attribute NC_GLOBAL instruments_1_supplied_name String Strathkelvin 782 dual oxygen meter
attribute NC_GLOBAL instruments_2_acronym String Scale
attribute NC_GLOBAL instruments_2_dataset_instrument_description String Used to weigh specimens
attribute NC_GLOBAL instruments_2_dataset_instrument_nid String 659597
attribute NC_GLOBAL instruments_2_description String An instrument used to measure weight or mass.
attribute NC_GLOBAL instruments_2_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L05/current/LAB13/ (external link)
attribute NC_GLOBAL instruments_2_instrument_name String Scale
attribute NC_GLOBAL instruments_2_instrument_nid String 714
attribute NC_GLOBAL instruments_2_supplied_name String Scale
attribute NC_GLOBAL keywords String afdm, alkalinity, bco, bco-dmo, biological, bouyant, bouyant_weight, calcification, change, chemical, data, dataset, day, dmo, dry, dry_weight, erddap, fragment, fragment_num, management, net, net_calcification, num, oceanography, office, pH_treatment, polyps, polyps_num, preliminary, starting, starting_DW, tank, treatment, ttl, ttl_alkalinity_change, weight
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/659379/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/659379 (external link)
attribute NC_GLOBAL param_mapping String {'659379': {}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/659379/parameters (external link)
attribute NC_GLOBAL people_0_affiliation String Temple University
attribute NC_GLOBAL people_0_affiliation_acronym String Temple
attribute NC_GLOBAL people_0_person_name String Erik E Cordes
attribute NC_GLOBAL people_0_person_nid String 51539
attribute NC_GLOBAL people_0_role String Principal Investigator
attribute NC_GLOBAL people_0_role_type String originator
attribute NC_GLOBAL people_1_affiliation String Temple University
attribute NC_GLOBAL people_1_affiliation_acronym String Temple
attribute NC_GLOBAL people_1_person_name String Dr Robert J. Kulathinal
attribute NC_GLOBAL people_1_person_nid String 51540
attribute NC_GLOBAL people_1_role String Co-Principal Investigator
attribute NC_GLOBAL people_1_role_type String originator
attribute NC_GLOBAL people_2_affiliation String Temple University
attribute NC_GLOBAL people_2_affiliation_acronym String Temple
attribute NC_GLOBAL people_2_person_name String Erik E Cordes
attribute NC_GLOBAL people_2_person_nid String 51539
attribute NC_GLOBAL people_2_role String Contact
attribute NC_GLOBAL people_2_role_type String related
attribute NC_GLOBAL people_3_affiliation String Woods Hole Oceanographic Institution
attribute NC_GLOBAL people_3_affiliation_acronym String WHOI BCO-DMO
attribute NC_GLOBAL people_3_person_name String Hannah Ake
attribute NC_GLOBAL people_3_person_nid String 650173
attribute NC_GLOBAL people_3_role String BCO-DMO Data Manager
attribute NC_GLOBAL people_3_role_type String related
attribute NC_GLOBAL project String Lophelia OA
attribute NC_GLOBAL projects_0_acronym String Lophelia OA
attribute NC_GLOBAL projects_0_description String 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 Lophelia pertusa. 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.
This project will examine the effects of ocean acidification on L. pertusa, 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, L. pertusa 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.
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.
attribute NC_GLOBAL projects_0_end_date String 2015-08
attribute NC_GLOBAL projects_0_geolocation String Northern Gulf of Mexico
attribute NC_GLOBAL projects_0_name String Physiological and genetic responses of the deep-water coral, Lophelia pertusa, to ongoing ocean acidification in the Gulf of Mexico
attribute NC_GLOBAL projects_0_project_nid String 2224
attribute NC_GLOBAL projects_0_start_date String 2012-09
attribute NC_GLOBAL publisher_name String Biological and Chemical Oceanographic Data Management Office (BCO-DMO)
attribute NC_GLOBAL publisher_type String institution
attribute NC_GLOBAL sourceUrl String (local files)
attribute NC_GLOBAL standard_name_vocabulary String CF Standard Name Table v55
attribute NC_GLOBAL summary String Calcification rates from pH experiments on Lophelia pertusa specimens collected from the Norwegian Skagerrak and the Gulf of Mexico (Lophelia OA project)
attribute NC_GLOBAL title String Calcification rates from pH experiments on Lophelia pertusa specimens collected from the Norwegian Skagerrak and the Gulf of Mexico (Lophelia OA project)
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.3
variable location   String  
attribute location bcodmo_name String site
attribute location description String Location where specimen was collected; Tisler Reef or the Gulf of Mexico
attribute location long_name String Location
attribute location units String unitless
variable pH_treatment   float  
attribute pH_treatment _FillValue float NaN
attribute pH_treatment actual_range float 7.6, 8.1
attribute pH_treatment bcodmo_name String treatment
attribute pH_treatment description String Level of pH treatment
attribute pH_treatment long_name String P H Treatment
attribute pH_treatment units String unitless
variable tank   String  
attribute tank bcodmo_name String tank
attribute tank description String Tank number
attribute tank long_name String Tank
attribute tank units String unitless
variable fragment_num   String  
attribute fragment_num bcodmo_name String sample
attribute fragment_num description String Fragment ID number
attribute fragment_num long_name String Fragment Num
attribute fragment_num nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/ACYC/ (external link)
attribute fragment_num units String unitless
variable polyps_num   byte  
attribute polyps_num _FillValue byte 127
attribute polyps_num actual_range byte 3, 15
attribute polyps_num bcodmo_name String count
attribute polyps_num description String Number of polyps on fragment
attribute polyps_num long_name String Polyps Num
attribute polyps_num units String count
variable starting_DW   float  
attribute starting_DW _FillValue float NaN
attribute starting_DW actual_range float 7.08, 79.74
attribute starting_DW bcodmo_name String dry_wgt
attribute starting_DW description String Starting dry weight
attribute starting_DW long_name String Starting DW
attribute starting_DW units String grams
variable AFDM   float  
attribute AFDM _FillValue float NaN
attribute AFDM actual_range float 0.25, 3.29
attribute AFDM bcodmo_name String dry_wgt
attribute AFDM description String Ash free dry mass
attribute AFDM long_name String AFDM
attribute AFDM units String grams
variable day   byte  
attribute day _FillValue byte 127
attribute day actual_range byte 0, 14
attribute day bcodmo_name String day
attribute day description String Day of measurement; 0 or 14
attribute day long_name String Day
attribute day nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/DAYXXXXX/ (external link)
attribute day units String day
variable ttl_alkalinity_change   float  
attribute ttl_alkalinity_change _FillValue float NaN
attribute ttl_alkalinity_change actual_range float 113.5, 1052.0
attribute ttl_alkalinity_change bcodmo_name String TALK
attribute ttl_alkalinity_change description String Total alkalinity change
attribute ttl_alkalinity_change long_name String Ttl Alkalinity Change
attribute ttl_alkalinity_change nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/MDMAP014/ (external link)
attribute ttl_alkalinity_change units String Unknown
variable net_calcification   float  
attribute net_calcification _FillValue float NaN
attribute net_calcification actual_range float -0.0149, 0.087
attribute net_calcification bcodmo_name String growth
attribute net_calcification description String Percent growth of coral colony per day
attribute net_calcification long_name String Net Calcification
attribute net_calcification units String percent per day (%/d -1)
variable bouyant_weight   float  
attribute bouyant_weight _FillValue float NaN
attribute bouyant_weight actual_range float 5.73, 50.87
attribute bouyant_weight bcodmo_name String weight
attribute bouyant_weight description String Bouyant weight of sample
attribute bouyant_weight long_name String Bouyant Weight
attribute bouyant_weight units String grams
variable dry_weight   float  
attribute dry_weight _FillValue float NaN
attribute dry_weight actual_range float 9.02, 79.85
attribute dry_weight bcodmo_name String dry_wgt
attribute dry_weight description String Dry weight of sample
attribute dry_weight long_name String Dry Weight
attribute dry_weight units String grams

The information in the table above is also available in other file formats (.csv, .htmlTable, .itx, .json, .jsonlCSV1, .jsonlCSV, .jsonlKVP, .mat, .nc, .nccsv, .tsv, .xhtml) via a RESTful web service.

ERDDAP, Version 2.02
Disclaimers | Privacy Policy | Contact