Accessing BCO-DMO data
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| Dataset Title: | [chlorophyll] - Extracted chlorophyll data from CTD rosette bottles from R/V Thomas G. Thompson and R/V Kilo Moana cruises TN277, KM1301, KM1312 in the Eastern North Pacific Ocean from 2012-2013 (POWOW project) (Seasonal and decadal changes in temperature drive Prochlorococcus ecotype distribution patterns) 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_3751) |
| Information: | Summary
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| FGDC
| ISO 19115
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Attributes {
s {
cruise_name {
String bcodmo_name "Cruise Name";
String description "Cruise identifier (POWOW1 = TN277 = R/V Thomas G. Thompson cruise 277; POWOW2 = KM1301 = R/V Kilo Moana cruise 1301).";
String long_name "Cruise Name";
String units "text";
}
cast {
String bcodmo_name "cast";
String description "Consecutive CTD cast number. CTD numbers are unique and sequential across stations.";
String long_name "Cast";
String units "unitless";
}
latitude {
String _CoordinateAxisType "Lat";
Float64 _FillValue NaN;
Float64 actual_range 21.3911, 46.6888;
String axis "Y";
String bcodmo_name "latitude";
Float64 colorBarMaximum 90.0;
Float64 colorBarMinimum -90.0;
String description "Latitude at start of CTD cast. Positive = North.";
String ioos_category "Location";
String long_name "Latitude";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/LATX/";
String standard_name "latitude";
String units "degrees_north";
}
longitude {
String _CoordinateAxisType "Lon";
Float64 _FillValue NaN;
Float64 actual_range -160.6166, -118.316;
String axis "X";
String bcodmo_name "longitude";
Float64 colorBarMaximum 180.0;
Float64 colorBarMinimum -180.0;
String description "Longitude at start of CTD cast. Positive = East.";
String ioos_category "Location";
String long_name "Longitude";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/LONX/";
String standard_name "longitude";
String units "degrees_east";
}
depth_w {
Int16 _FillValue 32767;
Int16 actual_range 349, 6055;
String bcodmo_name "depth_w";
Float64 colorBarMaximum 8000.0;
Float64 colorBarMinimum -8000.0;
String colorBarPalette "TopographyDepth";
String description "Depth of the water (bottom depth) at sampling station.";
String long_name "Depth";
String standard_name "depth";
String units "meters";
}
month_utc {
String bcodmo_name "month_utc";
String description "2-digit month of year, UTC.";
String long_name "Month Utc";
String units "mm (01 to 12)";
}
day_utc {
String bcodmo_name "day_utc";
String description "2-digit day of month, UTC.";
String long_name "Day Utc";
String units "dd (01 to 31)";
}
year {
Int16 _FillValue 32767;
Int16 actual_range 2012, 2013;
String bcodmo_name "year";
String description "4-digit year. in YYYY format";
String long_name "Year";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/YEARXXXX/";
String units "unitless";
}
time_utc {
String bcodmo_name "time_utc";
String description "Time (UTC) at start of sample collection, 24-hour clock.";
String long_name "Time Utc";
String units "HHMM.mm";
}
time {
String _CoordinateAxisType "Time";
Float64 actual_range 1.33060596e+9, 1.3749522e+9;
String axis "T";
String bcodmo_name "ISO_DateTime_UTC";
String description "Date/Time (UTC) ISO8601 formatted. T indicates start of time string; Z indicates UTC.";
String ioos_category "Time";
String long_name "ISO Date Time UTC";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/DTUT8601/";
String source_name "ISO_DateTime_UTC";
String standard_name "time";
String time_origin "01-JAN-1970 00:00:00";
String time_precision "1970-01-01T00:00:00.00Z";
String units "seconds since 1970-01-01T00:00:00Z";
}
depth {
String _CoordinateAxisType "Height";
String _CoordinateZisPositive "down";
Float64 _FillValue NaN;
Float64 actual_range 0.0, 200.0;
String axis "Z";
String bcodmo_name "depth";
Float64 colorBarMaximum 8000.0;
Float64 colorBarMinimum -8000.0;
String colorBarPalette "TopographyDepth";
String description "Sample depth.";
String ioos_category "Location";
String long_name "Depth";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/DEPH/";
String positive "down";
String standard_name "depth";
String units "m";
}
bot {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 0, 24;
String bcodmo_name "bot";
String description "Rosette position of the bottle.";
String long_name "Bot";
String units "unitless";
}
chl_tot {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 2.215;
String bcodmo_name "chlorophyll a";
String description
"Total chlorophyll concentration, in milligrams Chl-a per cubic meter.
Measured using polycarbonate filter with 0.22um pore size.";
String long_name "Chl Tot";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/CPHLHPP1/";
String units "mg/m^3";
}
chl_2um {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 0.278;
String bcodmo_name "unknown";
String description
"> 2um chlorophyll concentration, measured in milligrams Chl-a per cubic meter.
Measured on POWOW1 cruise only using polycarbonate filter with 2um pore size.";
String long_name "Chl 2um";
String units "mg/m^3";
}
chl_20um {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 0.07;
String bcodmo_name "chl_a_20u";
String description
"> 20um chlorophyll concentration, measured in milligrams Chl-a per cubic meter.
Measured on POWOW1 cruise only using polycarbonate filter with 20um pore size.";
String long_name "Chl 20um";
String units "mg/m^3";
}
chl_0d8um {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 1.913;
String bcodmo_name "unknown";
String description
"> 0.8 um chlorophyll concentration, measured in milligrams Chl-a per cubic meter.
Measured on POWOW2 cruise only using polycarbonate filter with 0.8um pore size.";
String long_name "Chl 0d8um";
String units "mg/m^3";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson,.odvTxt";
String acquisition_description
"Methods described in Johnson et al. 2010:
Chlorophyll concentrations were measured by filtering 100 mL of seawater
sample onto a polycarbonate filter (of pore size 0.22 um, 2 um or 20 um on
POWOW1; and of pore size 0.22 um or 0.8\\u00a0um on POWOW2) using gentle vacuum
(<100 mm Hg) and extracting in 100% MeOH at -20 degrees C in the dark for >24
h following (Holm-Hansen and Riemann, 1978). Fluorescence was measured using a
Turner Designs 10-AU fluorometer following Welschmeyer (1994) that was
calibrated against a standard chlorophyll solution (Ritchie, 2006).";
String awards_0_award_nid "55018";
String awards_0_award_number "OCE-1031064";
String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1031064";
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 "David L. Garrison";
String awards_0_program_manager_nid "50534";
String cdm_data_type "Other";
String comment
"Extracted Chlorophyll Concentrations
PI: Zackary Johnson (Duke University)
Version History:
Dataset updated: 16 July 2014 (current version)
Dataset updated: 13 May 2014
Original data: 25 Oct 2012
Note: chl_0d8um = >0.8 um chl.";
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 "2012-10-22T19:49:07Z";
String date_modified "2019-03-05T17:44:53Z";
String defaultDataQuery "&time<now";
String doi "10.1575/1912/bco-dmo.3751.3";
Float64 Easternmost_Easting -118.316;
Float64 geospatial_lat_max 46.6888;
Float64 geospatial_lat_min 21.3911;
String geospatial_lat_units "degrees_north";
Float64 geospatial_lon_max -118.316;
Float64 geospatial_lon_min -160.6166;
String geospatial_lon_units "degrees_east";
Float64 geospatial_vertical_max 200.0;
Float64 geospatial_vertical_min 0.0;
String geospatial_vertical_positive "down";
String geospatial_vertical_units "m";
String history
"2024-11-23T17:05:32Z (local files)
2024-11-23T17:05:32Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_3751.html";
String infoUrl "https://www.bco-dmo.org/dataset/3751";
String institution "BCO-DMO";
String instruments_0_acronym "Turner Fluorometer -10AU";
String instruments_0_dataset_instrument_description "Fluorescence was measured using a Turner Designs 10-AU fluorometer following Welschmeyer (1994) that was calibrated against a standard chlorophyll solution (Ritchie, 2006).";
String instruments_0_dataset_instrument_nid "5827";
String instruments_0_description "The Turner Designs 10-AU Field Fluorometer is used to measure Chlorophyll fluorescence. The 10AU Fluorometer can be set up for continuous-flow monitoring or discrete sample analyses. A variety of compounds can be measured using application-specific optical filters available from the manufacturer. (read more from Turner Designs, turnerdesigns.com, Sunnyvale, CA, USA)";
String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L22/current/TOOL0393/";
String instruments_0_instrument_name "Turner Designs Fluorometer -10-AU";
String instruments_0_instrument_nid "464";
String instruments_0_supplied_name "Turner Designs Fluorometer -10-AU";
String keywords "0d8um, 20um, 2um, bco, bco-dmo, biological, bot, cast, chemical, chl, chl_0d8um, chl_20um, chl_2um, chl_tot, chlorophyll, cruise, cruise_name, data, dataset, date, day, day_utc, depth, depth_w, dmo, erddap, iso, latitude, longitude, management, month, month_utc, name, oceanography, office, preliminary, time, time_utc, tot, year";
String license "https://www.bco-dmo.org/dataset/3751/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/3751";
Float64 Northernmost_Northing 46.6888;
String param_mapping "{'3751': {'lat': 'master - latitude', 'depth': 'flag - depth', 'lon': 'master - longitude', 'ISO_DateTime_UTC': 'flag - time'}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/3751/parameters";
String people_0_affiliation "Duke University";
String people_0_person_name "Zackary I. Johnson";
String people_0_person_nid "50749";
String people_0_role "Principal Investigator";
String people_0_role_type "originator";
String people_1_affiliation "Woods Hole Oceanographic Institution";
String people_1_affiliation_acronym "WHOI BCO-DMO";
String people_1_person_name "Shannon Rauch";
String people_1_person_nid "51498";
String people_1_role "BCO-DMO Data Manager";
String people_1_role_type "related";
String project "POWOW";
String projects_0_acronym "POWOW";
String projects_0_description
"Project also known as 'Prochlorococcus Of Warming Ocean Waters' (POWOW).
The two numerically-dominant ecotypes of the marine cyanobacterium Prochlorococcus partition the surface ocean niche latitudinally, with ecotype eMIT9312 dominant in the 30 degree N to 30 degree S region and eMED4 dominant at higher latitudes. These ecotypes may account for 25-50% of primary production in open ocean ecosystems, but this percentage is dependent on which ecotype dominates. The relative abundance of the two ecotypes follows a log-linear relationship with temperature, with the transition from eMIT9312 to eMED4 occurring at approx. 18 degrees C. From these descriptive data, it has been hypothesized that temperature is the primary driver of relative abundance. Their contribution to net primary production, however, appears to be independent of temperature, suggesting temperature regulates ecotype dominance through photosynthesis-independent mechanisms.
To test these hypotheses, the PIs are undertaking a series of field and lab studies to investigate the effect of temperature change on the distribution of these ecotypes. Two cruises in the North Pacific will trace the transitions from eMIT9312- to eMED4-dominated regions, with one cruise during the winter and the other during summer. They have hypothesized that the ratio of ecotype abundance will move latitudinally with the seasonal shift in temperature gradient: migration of the 18 degrees C isotherm northward in the summer will be matched by a similar migration of the 1:1 ecotype transition point. Multiple crossings of the 18 degrees C isotherm are proposed, and the summer cruise will also follow the isotherm to the Western US coast to gain insight on physical and geochemical influences. Environmental variables such as nutrient concentrations, light/mixing depths, and virus /grazing based mortality, which may impinge on the relationship between temperature and ecotype ratio, will be assessed through a series of multivariate analyses of the collected suite of physical, chemical and biological data. Seasonal comparisons will be complemented with on-deck incubations and lab competition assays (using existing and new isolates) that will establish, for the first time, how fitness coefficients of these ecotypes relate to temperature. As latitudinal shifts in temperature gradient and migration of ecotypes during seasonal warming likely share common features with high latitude warming as a consequence of climate change, the investigator's analyses will contribute important biological parameters (e.g., abundances, production rates, temperature change coefficients) for modeling biological and biogeochemical responses to climate change. This research will be integrated with that of committed collaborators, generating data sufficient for ecosystem-scale characterizations of the contributions of temperature (relative to other forcing factors) in constraining the range and seasonal migration of these numerically dominant marine phototrophs.
Publications produced as result of this research:
Rowe, J.M., DeBruyn, J.M., Poorvin, L., LeCleir, G.R., Johnson, Z.I., Zinser, E.R., and Wilhelm, S.W. 2012. Viral and bacterial abundance and production in the Western Pacific Ocean and the relation to other oceanic realms. FEMS Microbiology Ecology, 72, p. 359. DOI: 10.1111/j.1574-6941.2011.01223.x
Morris, J.J., Lenski, R.E. and E.R. Zinser. 2012. The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss. mBio, 3, p. e00036-12. DOI: 10.1128/mBio.00036-12
Morris, J.J., Johnson, Z.I., Szul, M.J., Keller, M., and Zinser, E.R. 2011. Dependence of the cyanobacterium Prochlorococcus on hydrogen peroxide scavenging microbes for growth at the ocean's surface. PLoS One, 6(2), p. 16805. DOI:10.1371/journal.pone.0016805
Ringuet, S., Sassano, L., and Johnson, Z.I. 2011. A suite of microplate reader-based colorimetric methods to quantify ammonium, nitrate, orthophosphate and silicate concentrations for aquatic nutrient monitoring. Journal of Environmental Monitoring. DOI:10.1039/C0EM00290A
Ritchie, A.E. and Johnson, Z.I. 2012. Abundance and genetic diversity of aerobic anoxygenic phototrophic bacteria of coastal regions of the Pacific Ocean. Applied and Environmental Microbiology, 78, p. 2858. DOI: 10.1128/AEM.06268-11";
String projects_0_end_date "2014-09";
String projects_0_geolocation "Eastern North Pacific Ocean";
String projects_0_name "Seasonal and decadal changes in temperature drive Prochlorococcus ecotype distribution patterns";
String projects_0_project_nid "2237";
String projects_0_project_website "http://oceanography.ml.duke.edu/johnson/research/powow/";
String projects_0_start_date "2010-10";
String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
String publisher_type "institution";
String sourceUrl "(local files)";
Float64 Southernmost_Northing 21.3911;
String standard_name_vocabulary "CF Standard Name Table v55";
String summary "Extracted chlorophyll concentrations from POWOW1 (TN277), POWOW2 (KM1301), and POWOW3 (KM1312) cruises. POWOW1 data include total chlorophyll (>0.22 um), >2 um, and >20 um. POWOW2 and POWOW3 data include total chlorophyll (>0.22 um) and >0.8 um.";
String time_coverage_end "2013-07-27T19:10:00.00Z";
String time_coverage_start "2012-03-01T12:46:00.00Z";
String title "[chlorophyll] - Extracted chlorophyll data from CTD rosette bottles from R/V Thomas G. Thompson and R/V Kilo Moana cruises TN277, KM1301, KM1312 in the Eastern North Pacific Ocean from 2012-2013 (POWOW project) (Seasonal and decadal changes in temperature drive Prochlorococcus ecotype distribution patterns)";
String version "3";
Float64 Westernmost_Easting -160.6166;
String xml_source "osprey2erddap.update_xml() v1.3";
}
}
Data Access Protocol (DAP) and its
selection constraints.
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.