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Dataset Title:  Fatty acid profiles of M. menidia females and their unfertilized eggs.   RSS
Institution:  BCO-DMO   (Dataset ID: bcodmo_dataset_719379)
Range: longitude = -72.02 to -72.02°E, latitude = 41.32 to 41.32°N
Information:  Summary ? | License ? | ISO 19115 | Metadata | Background (external link) | Subset | Data Access Form | Files
 
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The Dataset Attribute Structure (.das) for this Dataset

Attributes {
 s {
  Species {
    String description "Atlantic silverside; Menidia menidia";
    String ioos_category "Taxonomy";
    String long_name "Species";
    String units "unitless";
  }
  Collection_site {
    String description "Mumford Cove Connecticut USA";
    String ioos_category "Unknown";
    String long_name "Collection Site";
    String units "unitless";
  }
  latitude {
    String _CoordinateAxisType "Lat";
    Float64 _FillValue NaN;
    Float64 actual_range 41.32, 41.32;
    String axis "Y";
    Float64 colorBarMaximum 90.0;
    Float64 colorBarMinimum -90.0;
    String description "Latitude of field collection site";
    String ioos_category "Location";
    String long_name "Latitude";
    String standard_name "latitude";
    String units "degrees_north";
  }
  longitude {
    String _CoordinateAxisType "Lon";
    Float64 _FillValue NaN;
    Float64 actual_range -72.02, -72.02;
    String axis "X";
    Float64 colorBarMaximum 180.0;
    Float64 colorBarMinimum -180.0;
    String description "Longitude of field collection site";
    String ioos_category "Location";
    String long_name "Longitude";
    String standard_name "longitude";
    String units "degrees_east";
  }
  Collection_date {
    String description "Date of field collection for the spawners used in the experiment; YYYY/MM/DD";
    String ioos_category "Time";
    String long_name "Collection Date";
    String source_name "Collection_date";
    String units "unitless";
  }
  Fatty_acid {
    String description "Individual fatty acid nomenclature";
    String ioos_category "Unknown";
    String long_name "Fatty Acid";
    String units "unitless";
  }
  Female {
    String description "Five females denoted by letter A B C D E";
    String ioos_category "Unknown";
    String long_name "Female";
    String units "unitless";
  }
  Absolute_concentration_spawning_adult {
    Float32 _FillValue NaN;
    Float32 actual_range 0.0, 20.4;
    String description "Absolute fatty acid concentration in mg per g of dry weight";
    String ioos_category "Unknown";
    String long_name "Absolute Concentration Spawning Adult";
    String units "milligram per gram";
  }
  Absolute_concentration_eggs {
    Float32 _FillValue NaN;
    Float32 actual_range 0.0, 47.6;
    String description "Absolute fatty acid concentration in mg per g of dry weight";
    String ioos_category "Biology";
    String long_name "Absolute Concentration Eggs";
    String units "milligram per gram";
  }
  Relative_concentration_spawning_adult {
    Float32 _FillValue NaN;
    Float32 actual_range 0.0, 36.4;
    String description "Relative fatty acid concentration in percent of total fatty concentration";
    String ioos_category "Unknown";
    String long_name "Relative Concentration Spawning Adult";
    String units "percent";
  }
  Relative_concentration_eggs {
    Float32 _FillValue NaN;
    Float32 actual_range 0.0, 29.8;
    String description "Relative fatty acid concentration in percent of total fatty concentration";
    String ioos_category "Biology";
    String long_name "Relative Concentration Eggs";
    String units "percent";
  }
 }
  NC_GLOBAL {
    String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson";
    String acquisition_description 
"Methodology from\\u00a0Snyder, J.T.*, Murray, C.S.*, and Baumann, H. (2017)
Potential for maternal effects on offspring CO2-sensitivities in a coastal
marine fish. Journal of Experimental Marine Biology and Ecology (in press).
 
Five randomly selected females were strip-spawned onto cutout sections of
window screen (1-mm mesh) that were placed into separate seawater-filled
spawning dishes (Murray et al., 2014). To ensure full fertilization success
and randomize potential paternal effects, eggs were fertilized with a mixture
of milt from 22 males, thus producing full-sib and maternal half-sib embryos
from each female. Adults were measured for total length (TL; mean TLmale =
9.14 cm, mean TLfemale = 10.4 cm) and frozen for later analysis of FA. Mesh
screens with attached embryos were subsequently cut into smaller sections to
allow precise enumeration, and within 2-hr post-fertilization 100 embryos were
placed into each of three replicate rearing containers (20 L) per female and
CO2 treatment (i.e., 600 embryos for each of five females, 3 \\u00d7 100 in
ambient and 3 \\u00d7 100 in acidified treatments). Rearing containers were
filled with 1-um filtered, UV-sterilized seawater (~30 psu) from Long Island
Sound and placed in temperature-controlled water baths set to 24 deg C, the
known thermal optimum for survival and growth in this species (Middaugh et
al., 1987). Offspring were reared for 24 d post fertilization under a 15h
light:9h dark lighting regime. After hatch, larvae were fed ad libitum rations
of newly hatched brine shrimp nauplii Artemia salina (brineshrimpdirect.com),
and 50% of water was replaced every 5 d to ensure safe ammonia levels (< 0.25
ppm). Hatched larvae were counted and subsampled (n = 10 per replicate) at 1 d
post hatch (dph) by gently scooping them into identical 20 L containers, and
final samples were taken at 16 dph. All samples were preserved in 5% buffered
formalin for later measurements of larval standard length (SL, 0.01 mm) via
calibrated digital images (ImagePro Premier, MediaCybernetics). The experiment
thus quantified three related survival and three size traits for each
replicate, female, and CO2 treatment: embryo survival (fertilization to 1
dph), larval survival (1 to 16 dph), overall survival (fertilization to 16
dph), size (SL) at hatch (1 dph), SL at 16 dph, and larval growth rate (GR =
(SL16dph \\u2013 SL1dph)/15).
 
CO2 regime:\\u00a0
 
Offspring were reared at ambient (~ 400 uatm, pHNBS = 8.18) and acidified CO2
conditions (~2,300 uatm, pHNBS = 7.50). The higher value was set to a level
commonly used in OA research (consistent with projections of future pCO2
values for open oceans over in the next 200 yr (IPCC, 2007)) and represents
current conditions experienced during seasonal extremes by this species in
nature (Murray et al., 2014). Ambient conditions were achieved by bubbling
partially CO2-stripped air into each rearing container, thereby offsetting
metabolic CO2 accumulation. Acidified conditions were achieved via gas
proportioners (Cole Parmer\\u00ae) that mixed CO2 stripped air with 100% bone-
dry CO2 delivered to the bottom of each rearing container via air stones.
Target pH and temperature were monitored daily via a handheld pH probe
(Hach\\u00ae HQ40d portable meter with a PHC201 standard pH-probe) calibrated
regularly via two-point National Bureau of Standards (NBS) pH buffers
(electronic supplementary material, Fig.S1). To characterize actual pCO2
levels and related water chemistry parameters, water was sampled from four
randomly chosen rearing containers per treatment three times over the course
of the experiment and immediately measured for total alkalinity (AT) via
endpoint titration (Mettler Toledo\\u2122 G20 Potentiometric Titrator). The
instrument has previously been shown to quantify AT in Dr. Andrew
Dickson\\u2019s reference material (batch 147, AT= 2231.39 umol kg seawater-1)
with an average error of 0.6%. Actual levels of total dissolved inorganic
carbon (CT), partial pressure of CO2 (pCO2), fugacity of CO2 (fCO2), and
carbonate ion concentration were calculated in CO2SYS
([http://cdiac.ornl.gov/ftp/co2sys](\\\\\"http://cdiac.ornl.gov/ftp/co2sys\\\\\"))
based on measured AT, pH (NBS), temperature, and salinity using K1 and K2
constants from Mehrbach et al. (1973) refit by Dickson and Millero (1987) and
Dickson (1990) for KHSO4 (Table 1).
 
Fatty acid analysis:\\u00a0
 
Gas chromatography was used to quantify the absolute (mg g dry weight-1) and
relative concentrations (% of total) of 27 FAs for each of the 5 females
(whole individual) and their unfertilized eggs (~ 1 ml) following the methods
of Faulk and Holt (2005) as recently used for this species in Murray et al.
(2016). Briefly, frozen samples were shipped on dry ice to the Fisheries and
Mariculture Laboratory (University of Texas, Marine Science Institute), where
they were first dried and then homogenized in a solution of chloroform-
methanol (2:1 v/v) and tricosanoic acid (23:0) as an internal standard for
quantification of mg g\\u22121 dry mass of fatty acids. Lipids were cold-
extracted from approximately 50 mg of dry mass. Fatty-acid methyl esters were
prepared by saponification in potassium hydroxide, followed by
transesterification with 14% boron trifluoride in methanol. A Shimadzu GC-2014
gas chromatograph set with a Phenomenex ZB-WAX plus capillary column (30 m
long; 0.53 mm ID; 1.0 um thick) was used to quantify FAs, and individual FAs
were identified by comparison to commercial standards (Supelco, Inc). Two FAs,
12:0 and 15:1, were below detection limit or invariant across egg batches and
were therefore excluded from subsequent analyses.";
    String awards_0_award_nid "650183";
    String awards_0_award_number "OCE-1536336";
    String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1536336";
    String awards_0_funder_name "NSF Division of Ocean Sciences";
    String awards_0_funding_acronym "NSF OCE";
    String awards_0_funding_source_nid "355";
    String awards_0_program_manager "Dr Michael E. Sieracki";
    String awards_0_program_manager_nid "50446";
    String cdm_data_type "Other";
    String comment 
"Fatty Acid Profiles 
  H. Baumann and J. Nye, PIs 
  Version November 14th 2017";
    String Conventions "COARDS, CF-1.6, ACDD-1.3";
    String creator_email "info@bco-dmo.org";
    String creator_name "BCO-DMO";
    String creator_type "institution";
    String creator_url "https://www.bco-dmo.org/";
    String data_source "extract_data_as_tsv.pl v1.0";
    String date_created "2017-11-15T18:26:06Z";
    String date_modified "2017-11-15T22:42:11Z";
    String defaultDataQuery "&time";
    String doi "10.1575/1912/bco-dmo.719454";
    Float64 Easternmost_Easting -72.02;
    Float64 geospatial_lat_max 41.32;
    Float64 geospatial_lat_min 41.32;
    String geospatial_lat_units "degrees_north";
    Float64 geospatial_lon_max -72.02;
    Float64 geospatial_lon_min -72.02;
    String geospatial_lon_units "degrees_east";
    String history 
"2019-06-16T03:18:25Z (local files)
2019-06-16T03:18:25Z https://erddap.bco-dmo.org/tabledap/bcodmo_dataset_719379.das";
    String infoUrl "https://www.bco-dmo.org/dataset/719379";
    String institution "BCO-DMO";
    String instruments_0_acronym "Gas Chromatograph";
    String instruments_0_dataset_instrument_description "Used to quantify fatty acids";
    String instruments_0_dataset_instrument_nid "719394";
    String instruments_0_description "Instrument separating gases, volatile substances, or substances dissolved in a volatile solvent by transporting an inert gas through a column packed with a sorbent to a detector for assay. (from SeaDataNet, BODC)";
    String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB02/";
    String instruments_0_instrument_name "Gas Chromatograph";
    String instruments_0_instrument_nid "661";
    String instruments_0_supplied_name "Shimadzu GC-2014 gas chromatograph set with a Phenomenex ZB-WAX plus capillary column";
    String instruments_1_acronym "pH Sensor";
    String instruments_1_dataset_instrument_description "handheld pH probe";
    String instruments_1_dataset_instrument_nid "719388";
    String instruments_1_description "General term for an instrument that measures the pH or how acidic or basic a solution is.";
    String instruments_1_instrument_name "pH Sensor";
    String instruments_1_instrument_nid "674";
    String instruments_1_supplied_name "Hach� HQ40d portable meter with a PHC201 standard pH-probe";
    String instruments_2_acronym "Automatic titrator";
    String instruments_2_dataset_instrument_description "Used to measure total alkalinity";
    String instruments_2_dataset_instrument_nid "719393";
    String instruments_2_description "Instruments that incrementally add quantified aliquots of a reagent to a sample until the end-point of a chemical reaction is reached.";
    String instruments_2_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB12/";
    String instruments_2_instrument_name "Automatic titrator";
    String instruments_2_instrument_nid "682";
    String instruments_2_supplied_name "Mettler Toledo™�G20 Potentiometric Titrator";
    String keywords "absolute, Absolute_concentration_eggs, Absolute_concentration_spawning_adult, acid, adult, bco, bco-dmo, biological, biology, chemical, collection, Collection_site, concentration, data, dataset, date, dmo, eggs, erddap, fatty, Fatty_acid, female, latitude, longitude, management, oceanography, office, preliminary, relative, Relative_concentration_eggs, Relative_concentration_spawning_adult, site, spawning, species, taxonomy, time";
    String license 
"The data may be used and redistributed for free but is not intended
for legal use, since it may contain inaccuracies. Neither the data
Contributor, ERD, NOAA, nor the United States Government, nor any
of their employees or contractors, makes any warranty, express or
implied, including warranties of merchantability and fitness for a
particular purpose, or assumes any legal liability for the accuracy,
completeness, or usefulness, of this information.";
    String metadata_source "https://www.bco-dmo.org/api/dataset/719379";
    Float64 Northernmost_Northing 41.32;
    String param_mapping "{'719379': {'Lat': 'master - latitude', 'Lon': 'master - longitude'}}";
    String parameter_source "https://www.bco-dmo.org/mapserver/dataset/719379/parameters";
    String people_0_affiliation "University of Connecticut";
    String people_0_affiliation_acronym "UConn";
    String people_0_person_name "Hannes Baumann";
    String people_0_person_nid "528586";
    String people_0_role "Principal Investigator";
    String people_0_role_type "originator";
    String people_1_affiliation "Stony Brook University - SoMAS";
    String people_1_affiliation_acronym "SUNY-SB SoMAS";
    String people_1_person_name "Janet Nye";
    String people_1_person_nid "650186";
    String people_1_role "Co-Principal Investigator";
    String people_1_role_type "originator";
    String people_2_affiliation "University of Connecticut";
    String people_2_affiliation_acronym "UConn";
    String people_2_person_name "Hannes Baumann";
    String people_2_person_nid "528586";
    String people_2_role "Contact";
    String people_2_role_type "related";
    String people_3_affiliation "Woods Hole Oceanographic Institution";
    String people_3_affiliation_acronym "WHOI BCO-DMO";
    String people_3_person_name "Hannah Ake";
    String people_3_person_nid "650173";
    String people_3_role "BCO-DMO Data Manager";
    String people_3_role_type "related";
    String project "Collaborative research: Understanding the effects of acidification and hypoxia within and across generations in a coastal marine fish";
    String projects_0_acronym "HYPOA";
    String projects_0_description 
"Description from NSF award abstract:
Coastal marine ecosystems provide a number of important services and resources for humans, and at the same time, coastal waters are subject to environmental stressors such as increases in ocean acidification and reductions in dissolved oxygen. The effects of these stressors on coastal marine organisms remain poorly understood because most research to date has examined the sensitivity of species to one factor, but not to more than one in combination. This project will determine how a model fish species, the Atlantic silverside, will respond to observed and predicted levels of dissolved carbon dioxide (CO2) and oxygen (O2). Shorter-term experiments will measure embryo and larval survival, growth, and metabolism, and determine whether parents experiencing stressful conditions produce more robust offspring. Longer-term experiments will study the consequences of ocean acidification over the entire life span by quantifying the effects of high-CO2 conditions on the ratio of males to females, lifetime growth, and reproductive investment. These studies will provide a more comprehensive view of how multiple stressors may impact populations of Atlantic silversides and potentially other important forage fish species. This collaborative project will support and train three graduate students at the University of Connecticut and the Stony Brook University (NY), two institutions that attract students from minority groups. It will also provide a variety of opportunities for undergraduates to participate in research and the public to learn about the study, through summer research projects, incorporation in the \"Women in Science and Engineering\" program, and interactive displays of environmental data from monitoring buoys. The two early-career investigators are committed to increasing ocean literacy and awareness of NSF-funded research through public talks and presentations.
This project responds to the recognized need for multi-stressor assessments of species sensitivities to anthropogenic environmental change. It will combine environmental monitoring with advanced experimental approaches to characterize early and whole life consequences of acidification and hypoxia in the Atlantic silverside (Menidia menidia), a valued model species and important forage fish along most of the US east coast. Experiments will employ a newly constructed, computer-controlled fish rearing system to allow independent and combined manipulation of seawater pCO2 and dissolved oxygen (DO) content and the application of static and fluctuating pCO2 and DO levels that were chosen to represent contemporary and potential future scenarios in productive coastal habitats. First CO2, DO, and CO2 � DO dependent reaction norms will be quantified for fitness-relevant early life history (ELH) traits including pre- and post-hatch survival, time to hatch, post-hatch growth, by rearing offspring collected from wild adults from fertilization to 20 days post hatch (dph) using a full factorial design of 3 CO2 � 3 DO levels. Second, the effects of tidal and diel CO2 � DO fluctuations of different amplitudes on silverside ELH traits will be quantified. To address knowledge gaps regarding the CO2-sensitivity in this species, laboratory manipulations of adult spawner environments and reciprocal offspring exposure experiments will elucidate the role of transgenerational plasticity as a potential short-term mechanism to cope with changing environments. To better understand the mechanisms of fish early life CO2-sensitivity, the effects of temperature � CO2 on pre- and post-hatch metabolism will be robustly quantified. The final objective is to rear silversides from fertilization to maturity under different CO2 levels and assess potential CO2-effects on sex ratio and whole life growth and fecundity.
Related references:
Gobler, C.J. and Baumann, H. (2016) Hypoxia and acidification in ocean ecosystems: Coupled dynamics and effects on marine life. Biology Letters 12:20150976. doi:10.1098/rsbl.2015.0976
Baumann, H. (2016) Combined effects of ocean acidification, warming, and hypoxia on marine organisms. Limnology and Oceanography e-Lectures 6:1-43. doi:10.1002/loe2.10002
Depasquale, E., Baumann, H., and Gobler, C.J. (2015) Variation in early life stage vulnerability among Northwest Atlantic estuarine forage fish to ocean acidification and low oxygen Marine Ecology Progress Series 523: 145–156.doi:10.3354/meps11142";
    String projects_0_end_date "2018-11";
    String projects_0_geolocation "Eastern Long Island Sound, CT, USA";
    String projects_0_name "Collaborative research: Understanding the effects of acidification and hypoxia within and across generations in a coastal marine fish";
    String projects_0_project_nid "650184";
    String projects_0_start_date "2015-12";
    String publisher_name "Hannah Ake";
    String publisher_role "BCO-DMO Data Manager(s)";
    String sourceUrl "(local files)";
    Float64 Southernmost_Northing 41.32;
    String standard_name_vocabulary "CF Standard Name Table v29";
    String subsetVariables "Species, Collection_site, latitude, longitude";
    String summary 
"Gas chromatography was used to quantify the absolute (mg g dry weight-1) and
relative concentrations (% of total) of 27 FAs for each of 5 females (whole
individual) and their unfertilized eggs (~ 1 ml). Samples were first dried and
then homogenized in a solution of chloroform-methanol (2:1 v/v) and
tricosanoic acid (23:0) as an internal standard for quantification of mg
g\\u22121\\u00a0dry mass of fatty acids. Lipids were cold-extracted from
approximately 50 mg of dry mass. A Shimadzu GC-2014 gas chromatograph set with
a Phenomenex ZB-WAX plus capillary column (30\\u00a0m long; 0.53 mm ID; 1.0 um
thick) was used to quantify FAs, and individual FAs were identified by
comparison to commercial standards (Supelco, Inc).\\u00a0
 
These data are\\u00a0associated with the corresponding paper:
 
[Snyder, J.T.*, Murray, C.S.*, and Baumann, H. (2017) Potential for maternal
effects on offspring CO2-sensitivities in a coastal marine fish. Journal of
Experimental Marine Biology and Ecology (in
press).](\\\\https://doi.org/10.1016/j.jembe.2017.11.002\\\\)
 
Other datasets related to this paper:
 
[Survival, length, and growth responses of M. menidia offspring from different
females exposed to contrasting CO2 environments.](\\\\https://www.bco-
dmo.org/dataset/719420\\\\)";
    String title "Fatty acid profiles of M. menidia females and their unfertilized eggs.";
    String version "1";
    Float64 Westernmost_Easting -72.02;
    String xml_source "osprey2erddap.update_xml() v1.0-alpha";
  }
}

 

Using tabledap to Request Data and Graphs from Tabular Datasets

tabledap lets you request a data subset, a graph, or a map from a tabular dataset (for example, buoy data), via a specially formed URL. tabledap uses the OPeNDAP (external link) Data Access Protocol (DAP) (external link) and its selection constraints (external link).

The URL specifies what you want: the dataset, a description of the graph or the subset of the data, and the file type for the response.

Tabledap request URLs must be in the form
https://coastwatch.pfeg.noaa.gov/erddap/tabledap/datasetID.fileType{?query}
For example,
https://coastwatch.pfeg.noaa.gov/erddap/tabledap/pmelTaoDySst.htmlTable?longitude,latitude,time,station,wmo_platform_code,T_25&time>=2015-05-23T12:00:00Z&time<=2015-05-31T12:00:00Z
Thus, the query is often a comma-separated list of desired variable names, followed by a collection of constraints (e.g., variable<value), each preceded by '&' (which is interpreted as "AND").

For details, see the tabledap Documentation.


 
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