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Dataset Title:  pH measurements from laboratory water column experiments on the behavioral
effects of ocean acidification on Olympia oyster larvae (Ostrea lurida), July
2017
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Institution:  BCO-DMO   (Dataset ID: bcodmo_dataset_753080)
Information:  Summary ? | License ? | ISO 19115 | Metadata | Background (external link) | Data Access Form | Files
 
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Things You Can Do With Your Graphs

Well, you can do anything you want with your graphs, of course. But some things you might not have considered are:

The Dataset Attribute Structure (.das) for this Dataset

Attributes {
 s {
  trial {
    Byte _FillValue 127;
    Byte actual_range 1, 2;
    String bcodmo_name "exp_id";
    String description "Trial number";
    String long_name "Trial";
    String units "unitless";
  }
  date {
    String bcodmo_name "date_local";
    String description "Date of trial formatted as yyyy-mm-dd";
    String long_name "Date";
    String source_name "date";
    String time_precision "1970-01-01";
    String units "unitless";
  }
  column_name {
    String bcodmo_name "sample";
    String description "Identifies the experimental water column treatment and replicate #: AN-# = Acidic water at the top and Neutral water at the bottom ; NN-# = Neutral water at the top and Neutral water at the bottom; NA-# = Neutral water at the top and Acid water at the bottom";
    String long_name "Column Name";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
    String units "unitless";
  }
  column_depth_cat {
    Float64 _FillValue NaN;
    String bcodmo_name "depth";
    String description "Water column depth category where the pH sample was collected. top = 18-20 cm from bottom of water column; bottom = 1-2 cm from the bottom of the water column; transition point = middle of the water column where two treatment waters meet";
    String long_name "Column Depth Cat";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/DEPH/";
    String units "unitless";
  }
  column_depth_cm {
    String bcodmo_name "depth";
    String description "Water column depth in cm where the pH sample was collected.";
    String long_name "Column Depth Cm";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/DEPH/";
    String units "centimeters (cm)";
  }
  pH {
    Float32 _FillValue NaN;
    Float32 actual_range 7.43, 7.9;
    String bcodmo_name "pH";
    Float64 colorBarMaximum 9.0;
    Float64 colorBarMinimum 7.0;
    String description "pH of seawater in water column";
    String long_name "Sea Water Ph Reported On Total Scale";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/PHXXZZXX/";
    String units "standard pH units";
  }
 }
  NC_GLOBAL {
    String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
    String acquisition_description 
"Collection & Larval Rearing
 
We collected adult Olympia oysters (Ostrea lurida) from Fidalgo Bay in June
2017 and maintained them in a sea table with continuous flowing seawater
heated to 19-20\\u00b0C at the Shannon Point Marine Center. We fed adult
oysters were fed concentrated algae once a day (Shellfish Diet, Reed
Mariculture) and utilized banjo-style filters (60-m) attached to the outflow
pipes of the sea table to catch released O. lurida larvae. We then collected
and reared larvae at 12\\u00b0C in 3-L jars (2 individuals mL-1). Each jar of
larvae received a 50% water change with 0.35-m filtered sea water and were fed
Isochrysis galbana algae (50,000 cells mL-1) daily.
 
Experimental Design
 
To measure the effect of pH conditions on the vertical distribution of larvae
we established three experimental pycnocline treatments within clear
plexiglass water columns (2.5cm x 2.5cm x 30cm): (1) ambient water (400ppm) in
the top layer and acidic water in the bottom layer (1500ppm), (2) ambient
water (400ppm) in both top and bottom layers, and (3) acidic water (1500ppm)
in the top layer and ambient water (400ppm) in the bottom layer. Each water
layer was 60-mL of water and filled the column 10-cm high, so when each
experimental treatment was established it filled the column to 20-cm. We
established the experimental treatments by increasing the density of seawater
in the bottom layer by 0.003-0.005 g ml-1 using dialyzed Percoll (Mills 1984;
Podolskey & Emlet 1993). Experimental treatment water was kept at 12\\u00b0C
and pre-equilibrated to the desired pCO2 level and density. We also included
blue food coloring (1 drop per 100-mL) to the dense bottom layer to more
easily visualize the density layers while establishing experimental
treatments. We set-up four replicate columns for each experimental treatment
making twelve columns total per experiment.
 
On the day of each experiment, we incubated the experimental treatment columns
in clear plexiglass water baths connected to a Fisher Scientific Isotemp
recirculating water bath to maintain treatment temperature at 12\\u00b0C
throughout the experiment. We carefully injected 150 larvae by syringe into
the bottom 2-cm of each column with no more than 2-mL of their culture water.
Olympia oyster larvae are highly phototactic (personal observations), so we
gave the larvae 10 minutes to acclimate in darkness and then recorded their
vertical position in the water columns under infrared light. We video recorded
the larvae\\u2019s vertical position in each column using an infrared uEye
camera equipped with Edmund Optics VIS-NIR Lens mounted on a motorized stand.
We later counted by eye the number of larvae per centimeter area of each
column from the videos.
 
Sampling and analytical procedures:
 
Carefully collected water with a syringe and pipet from the top 1-3cm of the
column, the bottom 1-3cm of the water column and right at the transition layer
where the top and bottom layers of water met and was visible by the blue dye
in the bottom layer of water. The water from the syringe was carefully
transferred to a clean 2 ml microcentrifuge tube and pH was measured directly
using a pH probe (Micro PerpHect Ross Ross\\u00ae Combination pH electrode) and
read with a Thermo Scientific Orion Star pH meter.";
    String awards_0_award_nid "684166";
    String awards_0_award_number "OCE-1538626";
    String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1538626";
    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 
"pH measurements 
   Ostrea behavior lab expts, July 2017 
   S. Arellano, B. Olson, S. Yang (WWU) 
   version: 2019-01-14";
    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 "2019-01-17T14:28:24Z";
    String date_modified "2019-09-25T19:58:11Z";
    String defaultDataQuery "&time<now";
    String doi "10.1575/1912/bco-dmo.753080.1";
    String history 
"2020-12-03T10:04:36Z (local files)
2020-12-03T10:04:36Z https://erddap.bco-dmo.org/tabledap/bcodmo_dataset_753080.das";
    String infoUrl "https://www.bco-dmo.org/dataset/753080";
    String institution "BCO-DMO";
    String instruments_0_acronym "in-situ incubator";
    String instruments_0_dataset_instrument_description "Used to maintain treatment temperature during experiment";
    String instruments_0_dataset_instrument_nid "753087";
    String instruments_0_description "A device on shipboard or in the laboratory that holds water samples under controlled conditions of temperature and possibly illumination.";
    String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/82/";
    String instruments_0_instrument_name "In-situ incubator";
    String instruments_0_instrument_nid "494";
    String instruments_0_supplied_name "Fisher Scientific Isotemp Circulating Water Bath";
    String instruments_1_acronym "Benchtop pH Meter";
    String instruments_1_dataset_instrument_description "The pH electrode was prepared before each set of measurements following instructions in the ROSS® Electrode User Guide (Thermo Fisher Scientific Inc.) and calibrated with a three-buffer calibration using Thermo ScientificTM OrionTM pH Buffer Individual Use Pouches.";
    String instruments_1_dataset_instrument_nid "753090";
    String instruments_1_description 
"An instrument consisting of an electronic voltmeter and pH-responsive electrode that gives a direct conversion of voltage differences to differences of pH at the measurement temperature.  (McGraw-Hill Dictionary of Scientific and Technical Terms) 
This instrument does not map to the NERC instrument vocabulary term for 'pH Sensor' which measures values in the water column.  Benchtop models are typically employed for stationary lab applications.";
    String instruments_1_instrument_name "Benchtop pH Meter";
    String instruments_1_instrument_nid "681";
    String instruments_1_supplied_name "Thermo Scientific Orion Star A214 pH/ISE meter with a Micro PerpHect Ross® Combination pH electrode";
    String keywords "bco, bco-dmo, biological, cat, chemical, chemistry, column, column_depth_cat, column_depth_cm, column_name, data, dataset, date, depth, dmo, earth, Earth Science > Oceans > Ocean Chemistry > pH, erddap, management, name, ocean, oceanography, oceans, office, preliminary, reported, scale, science, sea, sea_water_ph_reported_on_total_scale, seawater, time, total, trial, water";
    String keywords_vocabulary "GCMD Science Keywords";
    String license "https://www.bco-dmo.org/dataset/753080/license";
    String metadata_source "https://www.bco-dmo.org/api/dataset/753080";
    String param_mapping "{'753080': {'column_depth_cat': 'master - depth'}}";
    String parameter_source "https://www.bco-dmo.org/mapserver/dataset/753080/parameters";
    String people_0_affiliation "Western Washington University";
    String people_0_affiliation_acronym "WWU";
    String people_0_person_name "Shawn M Arellano";
    String people_0_person_nid "684169";
    String people_0_role "Principal Investigator";
    String people_0_role_type "originator";
    String people_1_affiliation "Western Washington University";
    String people_1_affiliation_acronym "WWU";
    String people_1_person_name "Dr Brady  M. Olson";
    String people_1_person_nid "51528";
    String people_1_role "Co-Principal Investigator";
    String people_1_role_type "originator";
    String people_2_affiliation "Western Washington University";
    String people_2_affiliation_acronym "WWU";
    String people_2_person_name "Dr Sylvia Yang";
    String people_2_person_nid "684172";
    String people_2_role "Co-Principal Investigator";
    String people_2_role_type "originator";
    String people_3_affiliation "Woods Hole Oceanographic Institution";
    String people_3_affiliation_acronym "WHOI BCO-DMO";
    String people_3_person_name "Nancy Copley";
    String people_3_person_nid "50396";
    String people_3_role "BCO-DMO Data Manager";
    String people_3_role_type "related";
    String project "Climate stressors on larvae";
    String projects_0_acronym "Climate stressors on larvae";
    String projects_0_description 
"In the face of climate change, future distribution of animals will depend not only on whether they adjust to new conditions in their current habitat, but also on whether a species can spread to suitable locations in a changing habitat landscape. In the ocean, where most species have tiny drifting larval stages, dispersal between habitats is impacted by more than just ocean currents alone; the swimming behavior of larvae, the flow environment the larvae encounter, and the length of time the larvae spend in the water column all interact to impact the distance and direction of larval dispersal. The effects of climate change, especially ocean acidification, are already evident in shellfish species along the Pacific coast, where hatchery managers have noticed shellfish cultures with 'lazy larvae syndrome.' Under conditions of increased acidification, these 'lazy larvae' simply stop swimming; yet, larval swimming behavior is rarely incorporated into studies of ocean acidification. Furthermore, how ocean warming interacts with the effects of acidification on larvae and their swimming behaviors remains unexplored; indeed, warming could reverse 'lazy larvae syndrome.' This project uses a combination of manipulative laboratory experiments, computer modeling, and a real case study to examine whether the impacts of ocean warming and acidification on individual larvae may affect the distribution and restoration of populations of native oysters in the Salish Sea. The project will tightly couple research with undergraduate education at Western Washington University, a primarily undergraduate university, by employing student researchers, incorporating materials into undergraduate courses, and pairing marine science student interns with art student interns to develop art projects aimed at communicating the effects of climate change to public audiences
As studies of the effects of climate stress in the marine environment progress, impacts on individual-level performance must be placed in a larger ecological context. While future climate-induced circulation changes certainly will affect larval dispersal, the effects of climate-change stressors on individual larval traits alone may have equally important impacts, significantly altering larval transport and, ultimately, species distribution. This study will experimentally examine the relationship between combined climate stressors (warming and acidification) on planktonic larval duration, morphology, and swimming behavior; create models to generate testable hypotheses about the effects of these factors on larval dispersal that can be applied across systems; and, finally, use a bio-physically coupled larval transport model to examine whether climate-impacted larvae may affect the distribution and restoration of populations of native oysters in the Salish Sea.";
    String projects_0_end_date "2018-08";
    String projects_0_geolocation "Coastal Pacific, USA";
    String projects_0_name "RUI: Will climate change cause 'lazy larvae'? Effects of climate stressors on larval behavior and dispersal";
    String projects_0_project_nid "684167";
    String projects_0_start_date "2015-09";
    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 summary "This dataset contains pH measurements collected from a laboratory water column experiments to investigate the behavioral effects of ocean acidification on Olympia oyster larvae (Ostrea lurida).";
    String title "pH measurements from laboratory water column experiments on the behavioral effects of ocean acidification on Olympia oyster larvae (Ostrea lurida), July 2017";
    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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