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Dataset Title:  Otolith microstructure of young-of-year Atlantic silversides (Menidia menidia)
from Mumford Cove during 2015
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Institution:  BCO-DMO   (Dataset ID: bcodmo_dataset_782247)
Information:  Summary ? | License ? | ISO 19115 | Metadata | Background (external link) | Subset | Files | Make a graph
 
Variable ?   Optional
Constraint #1 ?
Optional
Constraint #2 ?
   Minimum ?
   or a List of Values ?
   Maximum ?
 
 Species (unitless) ?      
   - +  ?
 Collection_Date (unitless) ?          "2015-10-23"    "2015-12-18"
 Individual_number (unitless) ?          2    335
 Total_length (centimeters (cm)) ?          4.4    12.6
 Total_length_class (centimeters (cm)) ?          4.0    12.0
 Total_length_group (unitless) ?          1    2
 Sex (unitless) ?          0    1
 Age (days post hatch) ?          100    148
 Hatch_Date (unitless) ?          "2015-05-28"    "NaN"
 Biweekly_hatch_interval (unitless) ?          1    4
 Hatch_check_radius (micrometer (um)) ?          6.1    19.3
 Otolith_size (micrometer (um)) ?          365.7    727.0
 Hatch_check_flag (unitless) ?          1    4
 Otolith_flag (unitless) ?          1    4
 Scaling_factor (unitless) ?          0.224    2.906
 Increment_formation_date (unitless) ?          "2015-05-29"    "NaN"
 Temperature (degrees Celsius) ?          10.9    26.62
 Increment (Number) ?          1    147
 Increment_width (micrometer (um)) ?          0.76    13.06
 Length_at_age (millimeter (mm)) ?          5.22    110.93
 Growth_rate (millimeter per day (mm/d)) ?          0.09    1.8
 
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The Dataset Attribute Structure (.das) for this Dataset

Attributes {
 s {
  Species {
    String bcodmo_name "species";
    String description "Study species, Atlantic silverside young-of-year 2015, Menidia menidia";
    String long_name "Species";
    String units "unitless";
  }
  Collection_Date {
    String bcodmo_name "date";
    String description "Sampling date 2015: 23 October, 20 November, 18 December. Format: yyyy-mm-dd";
    String long_name "Collection Date";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/ADATAA01/";
    String source_name "Collection_Date";
    String time_precision "1970-01-01";
    String units "unitless";
  }
  Individual_number {
    Int16 _FillValue 32767;
    Int16 actual_range 2, 335;
    String bcodmo_name "count";
    Float64 colorBarMaximum 100.0;
    Float64 colorBarMinimum 0.0;
    String description "Running number of analyzed specimens";
    String long_name "Individual Number";
    String units "unitless";
  }
  Total_length {
    Float32 _FillValue NaN;
    Float32 actual_range 4.4, 12.6;
    String bcodmo_name "length";
    String description "Total length of specimen";
    String long_name "Total Length";
    String units "centimeters (cm)";
  }
  Total_length_class {
    Float32 _FillValue NaN;
    Float32 actual_range 4.0, 12.0;
    String bcodmo_name "length";
    String description "1 cm total length class of analyzed specimen";
    String long_name "Total Length Class";
    String units "centimeters (cm)";
  }
  Total_length_group {
    Byte _FillValue 127;
    Byte actual_range 1, 2;
    String bcodmo_name "length";
    String description "Separating the bimodal total length distribution in small (1) versus large (2) young-of-year silverside specimens - October/November collections 1:";
    String long_name "Total Length Group";
    String units "unitless";
  }
  Sex {
    Byte _FillValue 127;
    Byte actual_range 0, 1;
    String bcodmo_name "sex";
    String description "Sex of analyzed specimen; 0 = female, 1 = male";
    String long_name "Sex";
    String units "unitless";
  }
  Age {
    Int16 _FillValue 32767;
    Int16 actual_range 100, 148;
    String bcodmo_name "age";
    String description "Age of specimen (October collection only)";
    String long_name "Age";
    Int16 missing_value 99;
    String units "days post hatch";
  }
  Hatch_Date {
    String bcodmo_name "date";
    String description "Back-calculated date of hatch (October collection only). Format: yyyy-mm-dd";
    String long_name "Hatch Date";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/ADATAA01/";
    String units "unitless";
  }
  Biweekly_hatch_interval {
    Byte _FillValue 127;
    Byte actual_range 1, 4;
    String bcodmo_name "unknown";
    String description "14 day interval of back-calculated hatch day from 1 (earliest) to 4 (latest) - October collection only - see methods of corresponding publication for actual dates.";
    String long_name "Biweekly Hatch Interval";
    String units "unitless";
  }
  Hatch_check_radius {
    Float32 _FillValue NaN;
    Float32 actual_range 6.1, 19.3;
    String bcodmo_name "length";
    String description "Distance between the otolith core and the hatch check, i.e., the beginning of daily increment formation";
    String long_name "Hatch Check Radius";
    String units "micrometer (um)";
  }
  Otolith_size {
    Float32 _FillValue NaN;
    Float32 actual_range 365.7, 727.0;
    String bcodmo_name "width";
    String description "Cumulative width of the hatch check radius and all measured increments";
    String long_name "Otolith Size";
    String units "micrometer (um)";
  }
  Hatch_check_flag {
    Byte _FillValue 127;
    Byte actual_range 1, 4;
    String bcodmo_name "q_flag";
    Float64 colorBarMaximum 150.0;
    Float64 colorBarMinimum 0.0;
    String description "Quality flag of the clarity of the hatch check from 1 (best) to 4 (worst)";
    String long_name "Hatch Check Flag";
    String units "unitless";
  }
  Otolith_flag {
    Byte _FillValue 127;
    Byte actual_range 1, 4;
    String bcodmo_name "q_flag";
    Float64 colorBarMaximum 150.0;
    Float64 colorBarMinimum 0.0;
    String description "Quality flag of otolith microstructure interpretability from 1 (best) to 4 (worst)";
    String long_name "Otolith Flag";
    String units "unitless";
  }
  Scaling_factor {
    Float32 _FillValue NaN;
    Float32 actual_range 0.224, 2.906;
    String bcodmo_name "unknown";
    String description "Scaling factor representing the proportion of specimens per 1cm Total length class in the otolith sample relative to the population sample in the beach seine collection, please see methods in corresponding publication for details";
    String long_name "Scaling Factor";
    String units "unitless";
  }
  Increment_formation_date {
    String bcodmo_name "date";
    String description "Date in 2015 when the corresponding otolith increment was formed. Format: yyyy-mm-dd";
    String long_name "Increment Formation Date";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/ADATAA01/";
    String units "unitless";
  }
  Temperature {
    Float32 _FillValue NaN;
    Float32 actual_range 10.9, 26.62;
    String bcodmo_name "temperature";
    String description "Average water temperature in Mumford Cove on the corresponding date of increment formation, obtained from monitoring probe";
    String long_name "Temperature";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/TEMPP901/";
    String units "degrees Celsius";
  }
  Increment {
    Int16 _FillValue 32767;
    Int16 actual_range 1, 147;
    String bcodmo_name "unknown";
    String description "Running number of increment from hatch to the edge of the otolith (October collection only) or the first 60 days post hatch (November and December collections)";
    String long_name "Increment";
    String units "Number";
  }
  Increment_width {
    Float32 _FillValue NaN;
    Float32 actual_range 0.76, 13.06;
    String bcodmo_name "width";
    String description "Width of increment formed at given age/date post hatch";
    String long_name "Increment Width";
    String units "micrometer (um)";
  }
  Length_at_age {
    Float32 _FillValue NaN;
    Float32 actual_range 5.22, 110.93;
    String bcodmo_name "length";
    String description "Back-calculated total length at age (days post hatch) - October collection only";
    String long_name "Length At Age";
    String units "millimeter (mm)";
  }
  Growth_rate {
    Float32 _FillValue NaN;
    Float32 actual_range 0.09, 1.8;
    String bcodmo_name "growth";
    String description "Back-calculated growth rate on the day of increment formation - October collection only";
    String long_name "Growth Rate";
    String units "millimeter per day (mm/d)";
  }
 }
  NC_GLOBAL {
    String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
    String acquisition_description 
"Young-of-year (YoY) Atlantic silversides were collected from Mumford Cove
(41.32N, 72.02W), a small, salt-marsh dominated embayment in eastern Long
Island Sound (Connecticut USA, 0.5 km\\u00b2, 1-3 m depth). From a biweekly
beach seine survey (30\\u00d72m seine with 3mm mesh), three samples on 23
October, 20 November, and 18 December 2015 were used. On each date, samples
were pooled from two independent seine casts. All silversides were euthanized,
enumerated, measured for total length (TL) to the lower 5 mm and preserved
frozen (-20\\u00b0C). From each collection, ~100 individuals were selected for
otolith microstructure analysis using a TL-stratified random sampling design.
For each individual, we again measured TL (nearest 0.1 mm) and determined its
sex via visual inspection of gonads, before extracting both sagittal otoliths.
Sagittae were mounted on microscope slides using CrystalBond 509 thermoplastic
cement. If equally suitable, the left or right sagitta was randomly chosen for
analysis. Otoliths were hand-polished using 9 \\u00b5m then 3 \\u00b5m lapping
films (3M) until daily increments along the entire reading axis were clearly
visible under 400x magnification (Nikon Eclipse E400 compound microscope).
Otoliths were measured and read across the sagittal plane from the nucleus to
the dorsal or ventral otolith edge, because the more conventional core to
post-rostrum axis proved to be too curved to be reliably interpretable.
Increments were enumerated and measured using Image Pro Premier (V9.1)
connected to a Luminera Infinity2-2 digital camera. For each otolith section,
multiple focal planes were captured and merged into multi-layer images to aid
the reader interpreting the otolith microstructure. The radius of the hatch-
check (\\u00b5m) was measured. The last growth increment was presumed to be
incomplete and thus excluded from growth analyses. Increment number was
assumed to correspond to an individuals\\u2019 age in days post hatch (dph).
Hatch date was calculated by subtracting age from the date of collection,
while the formation date of each increment was calculated by adding the
increment number to the hatch date.
 
To estimate the thermal history of October YoY we used continuous temperature
data recorded by a Manta Sub2 probe (Eureka\\u00a9 Water Probes) at our study
site. Three small gaps in the record (<8 days) were linearly interpolated.
Daily temperatures during a larger data gap (34 days, 18 June - 22 July) were
estimated via linear regression between the Mumford Cove dataset and
temperatures in nearby Niantic Bay (2015-2016) that were strongly correlated
(TMumford= 1.07*TNiantic \\u2013 0.54 r\\u00b2= 0.92, F = 6024.9, p < 0.001).
Average daily temperatures were then linked to the corresponding day of
increment formation for each individual. To quantify the thermal dependency of
larval growth in October YoY, we calculated the mean experienced temperature
during the first 30 dph for each individual and correlated it to its mean
daily growth rate over the first 30dph (GR30) and its back-calculated TL at
day 30 post hatch (TL30, a proxy for the end of the larval stage).";
    String awards_0_award_nid "650191";
    String awards_0_award_number "OCE-1536165";
    String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1536165";
    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 "Michael E. Sieracki";
    String awards_0_program_manager_nid "50446";
    String cdm_data_type "Other";
    String comment 
"Otolith microstructure of YoY Atlantic silversides 
   from Mumford Cove, 2015 
  PI: Hannes Baumann (UConn) 
  Version date: 20-Nov-2019";
    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 version 2.3  19 Dec 2019";
    String date_created "2019-11-20T17:09:13Z";
    String date_modified "2019-11-20T20:15:01Z";
    String defaultDataQuery "&amp;time&lt;now";
    String doi "10.1575/1912/bco-dmo.782247.1";
    String history 
"2022-08-20T02:14:23Z (local files)
2022-08-20T02:14:23Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_782247.html";
    String infoUrl "https://www.bco-dmo.org/dataset/782247";
    String institution "BCO-DMO";
    String instruments_0_acronym "camera";
    String instruments_0_dataset_instrument_description "Luminera® Infinity2-2 digital camera, Image Pro® Premier (V9.1)";
    String instruments_0_dataset_instrument_nid "782257";
    String instruments_0_description "All types of photographic equipment including stills, video, film and digital systems.";
    String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/311/";
    String instruments_0_instrument_name "Camera";
    String instruments_0_instrument_nid "520";
    String instruments_0_supplied_name "Luminera® Infinity2-2 digital camera";
    String instruments_1_acronym "Water Quality Multiprobe";
    String instruments_1_dataset_instrument_description "Eureka Manta Sub2 monitoring probe, deployed 0.5m above bottom in Mumford Cove, CT";
    String instruments_1_dataset_instrument_nid "782258";
    String instruments_1_description "An instrument which measures multiple water quality parameters based on the sensor configuration.";
    String instruments_1_instrument_name "Water Quality Multiprobe";
    String instruments_1_instrument_nid "678";
    String instruments_1_supplied_name "Eureka Manta Sub2 monitoring probe";
    String instruments_2_dataset_instrument_description "Nikon Eclipse E400 compound microscope, 400x magnification";
    String instruments_2_dataset_instrument_nid "782256";
    String instruments_2_description "Instruments that generate enlarged images of samples using the phenomena of reflection and absorption of visible light. Includes conventional and inverted instruments. Also called a \"light microscope\".";
    String instruments_2_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB05/";
    String instruments_2_instrument_name "Microscope-Optical";
    String instruments_2_instrument_nid "708";
    String instruments_2_supplied_name "Nikon Eclipse E400 compound microscope";
    String keywords "age, array, array-data, bco, bco-dmo, biological, biweekly, Biweekly_hatch_interval, check, chemical, class, collection, comprehensive, data, dataset, date, dmo, erddap, factor, flag, formation, group, growth, Growth_rate, hatch, Hatch_check_flag, Hatch_check_radius, Hatch_Date, increment, Increment_formation_date, Increment_width, individual, Individual_number, interval, large, length, Length_at_age, management, number, oceanography, office, otolith, Otolith_flag, Otolith_size, preliminary, radius, rate, scaling, Scaling_factor, sex, size, species, stewardship, system, temperature, time, total, Total_length, Total_length_class, Total_length_group, width";
    String license "https://www.bco-dmo.org/dataset/782247/license";
    String metadata_source "https://www.bco-dmo.org/api/dataset/782247";
    String param_mapping "{'782247': {}}";
    String parameter_source "https://www.bco-dmo.org/mapserver/dataset/782247/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 "University of Connecticut";
    String people_1_affiliation_acronym "UConn";
    String people_1_person_name "Julie W. Pringle";
    String people_1_person_nid "782289";
    String people_1_role "Student";
    String people_1_role_type "related";
    String people_2_affiliation "Woods Hole Oceanographic Institution";
    String people_2_affiliation_acronym "WHOI BCO-DMO";
    String people_2_person_name "Shannon Rauch";
    String people_2_person_nid "51498";
    String people_2_role "BCO-DMO Data Manager";
    String people_2_role_type "related";
    String project "HYPOA";
    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 "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
    String publisher_type "institution";
    String sourceUrl "(local files)";
    String standard_name_vocabulary "CF Standard Name Table v55";
    String subsetVariables "Species";
    String summary "Back-calculated age, hatch date, length-at-age, growth rate, and experienced temperature of young-of-year Atlantic silversides (Menidia menidia) collected during 3 successive collections in Mumford Cove, CT in fall 2015.";
    String title "Otolith microstructure of young-of-year Atlantic silversides (Menidia menidia) from Mumford Cove during 2015";
    String version "1";
    String xml_source "osprey2erddap.update_xml() v1.3";
  }
}

 

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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