Accessing BCO-DMO data
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| Dataset Title: | [Growth rates of Line P diatoms in added Zn and Co incubation studies] - Growth rates NE Pacific and Atlantic diatom isolates under various Zn and Co additions in experiments with cultures collected from R/V Thomas G. Thompson cruise TN280, along Line P in the NE Pacific, in May of 2012. (US GEOTRACES PMT: Cobalt Biogeochemical Cycling and Connections to Metalloenzymes in the Pacific Ocean) 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_807316) |
| Information: | Summary
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Attributes {
s {
Culture {
String bcodmo_name "sample_descrip";
String description "Culture name (e.g. Line P Thalassiosira sp. UNC1203)";
String long_name "Culture";
String units "unitless";
}
Experiment_Type {
String bcodmo_name "exp_type";
String description "Experiment Type. One (simple) or both (matrix) metals added.";
String long_name "Experiment Type";
String units "unitless";
}
Added_Zn {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 100.0;
String bcodmo_name "trace_metal_conc";
String description "Total amount of added zinc (Zn) to incubation.";
String long_name "Added Zn";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P03/current/C035/";
String units "nanomoles per liter (nmol/L)";
}
Added_Co {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 100.0;
String bcodmo_name "trace_metal_conc";
String description "Total amount of added cobalt (Co) to incubation.";
String long_name "Added Co";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P03/current/C035/";
String units "nanomoles per liter (nmol/L)";
}
Total_Zn {
Float32 _FillValue NaN;
Float32 actual_range 0.9, 100.9;
String bcodmo_name "trace_metal_conc";
String description "Total zinc (Zn). Added Zn and background media Zn.";
String long_name "Total Zn";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P03/current/C035/";
String units "nanomoles per liter (nmol/L)";
}
Total_Co {
Float32 _FillValue NaN;
Float32 actual_range 0.1, 100.1;
String bcodmo_name "trace_metal_conc";
String description "Total cobalt (Co). Added Co and background media Co.";
String long_name "Total Co";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P03/current/C035/";
String units "nanomoles per liter (nmol/L)";
}
log_Zn2plus {
Float32 _FillValue NaN;
Float32 actual_range -13.04, -10.99;
String bcodmo_name "trace_metal_conc";
String description "Log of calculated free Zn2+ ion concentration in media. [Zn2+]";
String long_name "Log Zn2plus";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P03/current/C035/";
String units "moles per liter (mol/L)";
}
log_Co2plus {
Float32 _FillValue NaN;
Float32 actual_range -13.63, -10.63;
String bcodmo_name "growth";
String description "Log of calculated free Co2+ ion concentration in media. [Co2+]";
String long_name "Log Co2plus";
String units "moles per liter (mol/L)";
}
Growth_rate_replicate_A {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 0.96;
String bcodmo_name "growth";
String description "Growth rate of treatment replicate A";
String long_name "Growth Rate Replicate A";
String units "per day (d-1)";
}
Growth_rate_replicate_B {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 0.97;
String bcodmo_name "growth";
String description "Growth rate of treatment replicate B";
String long_name "Growth Rate Replicate B";
String units "per day (d-1)";
}
Growth_rate_average {
String bcodmo_name "growth";
String description "Average growth rate of replicates A and B";
String long_name "Growth Rate Average";
String units "per day (d-1)";
}
Maximum_RFU {
Float32 _FillValue NaN;
Float32 actual_range 1.8, 306.4;
String bcodmo_name "unknown";
String description "Maximum relative fluorescence";
String long_name "Maximum RFU";
String units "Relative Fluorescence Units (RFU)";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
String acquisition_description
"Location: Northeast Pacific Line P Transect 48.8167 N 128.667 W
Media and culturing techniques
Northwest Atlantic Thalassiosira pseudonana CCMP1335 cultures were
maintained in a 24\\u00b0C incubator under constant fluorescent lighting (65
\\u00b5mol quanta m-2 s-1 PAR). Northeast Atlantic Phaeodactylum tricornutum
CCMP632 cultures were maintained in an 18\\u00b0C incubator under constant
fluorescent lighting (90 \\u00b5mol quanta m-2 s-1 PAR). Both Pacific Pseudo-
nitzschia delicatissima UNC1205 and Pacific Thalassiosira sp. UNC1203 were
grown in an 18\\u00b0C incubator under constant fluorescent lighting (85
\\u00b5mol quanta m-2 s-1 PAR). All cultures were randomly repositioned each
day to avoid any effect of subtle variation in light intensity on growth. T.
pseudonana CCMP1335 and P. tricornutum CCMP632 (Bigelow Laboratory, East
Boothbay, ME) were obtained from the Mincer and Saito laboratory culture
collections at the Woods Hole Oceanographic Institution, respectively. Pacific
P. delicatissima UNC1205 and Thalassiosira sp. UNC1203 were obtained from the
Marchetti laboratory at the University of North Carolina. Both Pacific
isolates were collected at station P8 of Line P, a Northeast Pacific ocean
transect located off of Vancouver Island comprising 26 sampling stations and
ending at Ocean Station Papa at 50\\u00b0N 145\\u00b0W (Fig. 1a). All cultures
were axenic and maintained by sterile technique until needed.
Polycarbonate and plastic bottles were cleaned to remove trace metal
contaminants before use. This procedure involved, at minimum, a 72h soak in
<1% Citranox detergent, five rinses in mili-Q water, a 7d soak in 10% HCl, and
five rinses with dilute acid (HCl, pH 2). Cultures were grown in microwave
sterilized 28 mL polycarbonate centrifuge tubes, and all solutions were
pipetted only after a tip rinse procedure consisting of three rinses with 10%
HCl followed by three rinses with sterile dilute HCl (pH 2). All culture work
was conducted in a Class 100 clean room.
Culture media was prepared after that used by Sunda and Huntsman for trace
metal experimentation (Sunda and Huntsman 1992, 1995b). Microwave sterilized,
0.2\\u00b5m-filtered Pacific seawater from the North Pacific station
\\u201cAloha\\u201d (22\\u00b0 45'N, 158\\u00b0 00'W) was used as the media base.
Macronutrients were added to this sterile base to a final concentration of
88.2\\u00b5M NaNO3, 41.5\\u00b5M NaH2PO4, and 106\\u00b5M Na2SiO3 and were
chelexed before use. Added vitamins included 2 nM biotin, 0.37 nM B12 as
cyanocobalamin, and 300 nM thiamine and were also chelexed before use. Trace
metals were added to final media concentrations of 10-7 M FeCl3, 4.8 x 10-8 M
MnCl2, 4.0 x 10-8 M CuSO4, 10-7 M NiCl2, and 10-8 M Na2O3Se within a 10-4 M
ethylenediamine tetraacetic acid disodium salt (EDTA, Acros Organics,
C10H14N2Na2O8) metal ion buffer system. All media amendments were sterile
filtered through acid rinsed 0.2\\u00b5m filters before addition to final
media, and final media equilibrated for at least 12h before inoculation.
Established cultures of each diatom were first acclimated in low-metal media
containing 1 nM total Zn or less for at least three transfers. These
acclimated cultures were used to initially inoculate transfer 1 (T1) cultures
at 1% volume. For all diatoms, Zn or Co limitation experiments were first
performed using a range of Zn concentrations with Co omitted and vice versa.
We refer to experiments using media amended with Zn or Co (while omitting the
other) as \\u201csimple limitation\\u201d experiments. Experiments varying
concentrations of both Zn and Co were also conducted, allowing for three-
dimensional visualizations of growth rates as used previously (Saito et al.
2002; Saito and Goepfert 2008). We refer to experiments using media amended
with both Zn and Co as \\u201cmatrix\\u201d experiments. In vivo fluorescence
(Turner Instruments TD-700) of simple and matrix experiment cultures was
measured on a near-daily basis as a proxy for chlorophyll a and is reported as
relative fluorescence units (RFU). Growth rates were calculated from the
exponential portion of each culture\\u2019s growth curve. Computed ratios of
[Zn2+] and [Co2+] to total concentrations, whose values are 10-3.99 and
10-3.63 respectively, were used to convert added metal concentrations to free
ion concentrations and are the same as those used by Sunda and Huntsman (Sunda
and Huntsman 1995).
Isolation sources and locations:
* Pseudonitzschia delicatissima UNC1205 and Thalassiosira UNC1203 were
isolated from
station P8 of the Line P transect, 48.817\\u00b0N 128.666\\u00b0W
* Phaeodactylum tricornutum CCMP632 was ordered from Bigelow, the strains
original
location of isolation was 54\\u00b0N 4\\u00b0W
* Thalassiosira pseudonana CCMP1335 was also from Bigelow, original location
of
isolation was 40.756\\u00b0 N 72.82\\u00b0 W";
String awards_0_award_nid "646122";
String awards_0_award_number "GBMF3782";
String awards_0_data_url "https://www.moore.org/grant-detail?grantId=GBMF3782";
String awards_0_funder_name "Gordon and Betty Moore Foundation: Marine Microbiology Initiative";
String awards_0_funding_acronym "MMI";
String awards_0_funding_source_nid "385";
String awards_1_award_nid "785825";
String awards_1_award_number "OCE-1736599";
String awards_1_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1736599";
String awards_1_funder_name "NSF Division of Ocean Sciences";
String awards_1_funding_acronym "NSF OCE";
String awards_1_funding_source_nid "355";
String awards_1_program_manager "Henrietta N Edmonds";
String awards_1_program_manager_nid "51517";
String cdm_data_type "Other";
String comment
"Growth rates of Line P diatoms in added Zn and Co incubation studies
PI: Mak A. Saito
Data Version 1: 2020-03-31";
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 "2020-03-31T21:27:30Z";
String date_modified "2020-04-10T14:55:30Z";
String defaultDataQuery "&time<now";
String doi "10.26008/1912/bco-dmo.807316.1";
String history
"2024-11-05T10:49:46Z (local files)
2024-11-05T10:49:46Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_807316.html";
String infoUrl "https://www.bco-dmo.org/dataset/807316";
String institution "BCO-DMO";
String instruments_0_acronym "TD-700";
String instruments_0_dataset_instrument_description "Turner Instruments TD-700 Fluorometer calibrated to a solid standard.";
String instruments_0_dataset_instrument_nid "807326";
String instruments_0_description "The TD-700 Laboratory Fluorometer is a benchtop fluorometer designed to detect fluorescence over the UV to red range. The instrument can measure concentrations of a variety of compounds, including chlorophyll-a and fluorescent dyes, and is thus suitable for a range of applications, including chlorophyll, water quality monitoring and fluorescent tracer studies. Data can be output as concentrations or raw fluorescence measurements.";
String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L22/current/TOOL0510/";
String instruments_0_instrument_name "Turner Designs 700 Laboratory Fluorometer";
String instruments_0_instrument_nid "694";
String instruments_0_supplied_name "Turner Instruments TD-700 Fluorometer";
String keywords "added, Added_Co, Added_Zn, average, bco, bco-dmo, biological, chemical, co2plus, culture, data, dataset, dmo, erddap, experiment, Experiment_Type, growth, Growth_rate_average, Growth_rate_replicate_A, Growth_rate_replicate_B, log, log_Co2plus, log_Zn2plus, management, maximum, Maximum_RFU, oceanography, office, preliminary, rate, replicate, rfu, total, Total_Co, Total_Zn, type, zn2plus";
String license "https://www.bco-dmo.org/dataset/807316/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/807316";
String param_mapping "{'807316': {}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/807316/parameters";
String people_0_affiliation "Woods Hole Oceanographic Institution";
String people_0_affiliation_acronym "WHOI";
String people_0_person_name "Mak A. Saito";
String people_0_person_nid "50985";
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 "Amber York";
String people_1_person_nid "643627";
String people_1_role "BCO-DMO Data Manager";
String people_1_role_type "related";
String project "PMT Cobalt and Metalloenzymes,MM Saito";
String projects_0_acronym "PMT Cobalt and Metalloenzymes";
String projects_0_description
"NSF abstract:
Cobalt is important for many forms of marine life, yet it is one of the scarcest nutrients in the sea. Cobalt's oceanic abundance and distribution, along with other scarce nutrients, can influence the growth of microscopic plants (phytoplankton). This in turn can influence carbon cycles in the ocean and atmosphere. Therefore, knowledge of the controls on cobalt's abundance and chemical forms in seawater is a valuable component of our ability to understand the ocean's influence on global carbon cycling. Within phytoplankton and other marine microbes, metals such as cobalt, iron, nickel, and copper are used as critical components of enzymes responsible for key cellular reactions. Since these enzymes require metals to work, they are named metalloenzymes. Participating in a Pacific Ocean cruise from Alaska to Tahiti, this project will study the oceanic distributions of dissolved cobalt and the cellular content of a group of metalloenzymes known to influence biogeochemical cycles. The project will provide scientific impact by creating new knowledge about oceanic micronutrients in regions of economic interest with regard to fisheries and deep-sea mining. Measurement of proteins in the North Pacific will provide data of broad biological and chemical interest and will be made available through a new NSF-funded \"EarthCube Ocean Protein Portal\" data base. Educational impact will stem from participation of a graduate student and two young technicians, as well as the PI's development of a high school chemistry curriculum for use in two local high schools, thus allowing teachers to include real oceanic and environmental data at their first introduction to chemistry.
Cobalt has a complex biogeochemical cycle. Both its inorganic and organic forms are used by biology in the upper ocean and it is removed from solution by being scavenged in the intermediate and deep ocean. This scavenging removal results in cobalt having the smallest oceanic inventory of any biologically utilized element. Recent studies, however, have found that large dissolved cobalt plumes occur in major oxygen minimum zones due to a combination of less scavenging and additions from sedimentary and remineralization fluxes. The GP15 US GEOTRACES Pacific Meridional Transect (PMT) provides an opportunity to examine the influence of oxygen depletion on cobalt chemistry. Moreover, the study of the protein component of microbial communities using new proteomic techniques will provide evidence of how different major microorganisms respond to the chemical environment (e.g. through transporter production for specific nutrients and micronutrients) as well as the biochemical basis for metal requirements related to the use of specific metalloenzymes. Specifically, the PMT provides an opportunity to confirm that the Pacific oxygen minimum zones contain a large amount of cobalt and to test the hypotheses that simultaneous zinc scarcity could induce wide-scale biochemical substitution of cobalt for zinc in the North Pacific Ocean.";
String projects_0_end_date "2019-10";
String projects_0_geolocation "Laboratory Study and Cultures from Northeast Pacific Line P Transect 48.8167 N 128.667 W";
String projects_0_name "US GEOTRACES PMT: Cobalt Biogeochemical Cycling and Connections to Metalloenzymes in the Pacific Ocean";
String projects_0_project_nid "785826";
String projects_0_start_date "2017-11";
String projects_1_acronym "MM Saito";
String projects_1_description "In support of obtaining deeper knowledge of major biogeochemically relevant proteins to inform a mechanistic understanding of global marine biogeochemical cycles.";
String projects_1_end_date "2019-12";
String projects_1_name "Marine Microbial Investigator Award: Investigator Mak Saito";
String projects_1_project_nid "786672";
String projects_1_start_date "2013-05";
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 "Growth rates of two NE Pacific Line P diatom isolates and two Atlantic diatom isolates under various Zn and Co additions. Cultures were collected from the GeoMICS expedition on the R/V Thomas G. Thompson (cruise TN280), along Line P in the NE Pacific, in May of 2012.";
String title "[Growth rates of Line P diatoms in added Zn and Co incubation studies] - Growth rates NE Pacific and Atlantic diatom isolates under various Zn and Co additions in experiments with cultures collected from R/V Thomas G. Thompson cruise TN280, along Line P in the NE Pacific, in May of 2012. (US GEOTRACES PMT: Cobalt Biogeochemical Cycling and Connections to Metalloenzymes in the Pacific Ocean)";
String version "1";
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.