Accessing BCO-DMO data
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BCO-DMO ERDDAP
Accessing BCO-DMO data |
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| Dataset Title: | Pore water and solid phase iron geochemical data from a coastal Maine intertidal mudflat from November 2015 to November 2016 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_737962) |
| Information: | Summary
| License
| ISO 19115
| Metadata
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Attributes {
s {
site {
String bcodmo_name "site";
String description "Name of sampling site";
String long_name "Site";
String units "unitless";
}
latitude {
String _CoordinateAxisType "Lat";
Float64 _FillValue NaN;
Float64 actual_range 43.994827, 43.994827;
String axis "Y";
String bcodmo_name "latitude";
Float64 colorBarMaximum 90.0;
Float64 colorBarMinimum -90.0;
String description "Latitude of sampling site";
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 -69.648632, -69.648632;
String axis "X";
String bcodmo_name "longitude";
Float64 colorBarMaximum 180.0;
Float64 colorBarMinimum -180.0;
String description "Longitude of sampling site";
String ioos_category "Location";
String long_name "Longitude";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/LONX/";
String source_name "long";
String standard_name "longitude";
String units "degrees_east";
}
date {
Int32 _FillValue 2147483647;
Int32 actual_range 20151118, 20161109;
String bcodmo_name "date";
String description "Date of sampling; formatted as yyyymmdd";
String long_name "Date";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/ADATAA01/";
String units "unitless";
}
depth {
String _CoordinateAxisType "Height";
String _CoordinateZisPositive "down";
Float64 _FillValue NaN;
Float64 actual_range 0.5, 9.5;
String axis "Z";
String bcodmo_name "depth";
Float64 colorBarMaximum 8000.0;
Float64 colorBarMinimum -8000.0;
String colorBarPalette "TopographyDepth";
String description "Sampling 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";
}
sed_temp {
Float32 _FillValue NaN;
Float32 actual_range 0.5, 21.0;
String bcodmo_name "temperature";
String description "Sediment temperature";
String long_name "Sed Temp";
String units "degrees Celsius";
}
salinity {
Float32 _FillValue NaN;
Float32 actual_range 19.5, 37.0;
String bcodmo_name "sal";
Float64 colorBarMaximum 37.0;
Float64 colorBarMinimum 32.0;
String description "Low tide surface water salinity";
String long_name "Sea Water Practical Salinity";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/PSALST01/";
String units "practical salinity units";
}
ferrous_iron {
Int16 _FillValue 32767;
Int16 actual_range 0, 272;
String bcodmo_name "Fe";
String description "Dissolved pore water ferrous iron";
String long_name "Ferrous Iron";
String units "micromoles per liter (umol/L)";
}
poorly_crystalline_iron_oxide {
Int16 _FillValue 32767;
Int16 actual_range 41, 380;
String bcodmo_name "Fe";
String description "Sedimentary poorly-crystalline iron oxide Fe";
String long_name "Poorly Crystalline Iron Oxide";
String units "micromoles per gram dry sediment (umol/g)";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson";
String acquisition_description
"Sediment cores were retrieved from bioturbated, intertidal sediments at low
tide with a 7.5 cm (inner diameter) clear Plexiglas liner by pushing it
directly into the sediment with minimum pressure as not to artificially force
the sediment horizons together. The end of the core (i.e., the deepest
horizon) was plugged with a rubber stopper and the sediment core was placed on
ice. Typical transport back to the laboratory for pore water extraction was
0.5 hours. Sediment temperature and bottom water salinity were recorded at the
time of sampling with an alcohol thermometer and refractometer, respectively.
Once back to the laboratory, the cores were removed from ice and 5 cm Rhizons
(0.16-0.19 um pore size) were inserted into pre-drilled 7 mm holes at 1 cm
depth intervals to a depth of 10 cm. Pore waters were extracted by pulling
negative pressure on the Rhizon with a 10 mL sterile syringe and holding the
syringe plunger in place with a small wooden block placed between the syringe
body and the plunger. Once pore water was extracted in the syringe, it was
removed from the Rhizon, dispensed into a 15 mL centrifuge tube, and 250 uL of
pore water was immediately transferred to 250 uL of Ferrozine buffer (10 mM in
50 mM HEPES buffer) and read on a MultiSkan MCC plate reader at 562 nm
absorbance. The sediment core was then extruded and sliced into 1 cm intervals
and dried in an oven at 70-80 degrees C for 24 hours, and then poorly-
crystalline iron oxides (i.e., ferrihydrite and lepidocrocite) were extracted
with 1 M hydroxylamine HCl in 25 % acetic acid (v/v) for 48 hours on a
rotating shaker at 200 rpm. The extractions were allowed to settle for a few
hours, then 10 uL was diluted into 990 uL (1:100 dilution) of distilled water
containing 100 uL of Ferrozine buffer. The samples were read as above at 562
nm on the Multiskan MCC plate reader.
Note: data were not collected for months of August and October .";
String awards_0_award_nid "544591";
String awards_0_award_number "OCE-1459600";
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_1_award_nid "626092";
String awards_1_award_number "OCE-1459252";
String awards_1_data_url "http://www.nsf.gov/awardsearch/showAward?AWD_ID=1459252";
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 "David L. Garrison";
String awards_1_program_manager_nid "50534";
String cdm_data_type "Other";
String comment
"Seasonal iron biogeochemistry
PI: David Emerson (Bigelow Laboratory for Ocean Sciences)
Co-PI: Peter Girguis (Harvard University)
Contact: Jacob Beam (Bigelow Laboratory for Ocean Sciences)
Version date: 01 June 2018";
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 "2018-06-01T19:12:56Z";
String date_modified "2019-03-15T18:25:03Z";
String defaultDataQuery "&time<now";
String doi "10.1575/1912/bco-dmo.737962.1";
Float64 Easternmost_Easting -69.648632;
Float64 geospatial_lat_max 43.994827;
Float64 geospatial_lat_min 43.994827;
String geospatial_lat_units "degrees_north";
Float64 geospatial_lon_max -69.648632;
Float64 geospatial_lon_min -69.648632;
String geospatial_lon_units "degrees_east";
Float64 geospatial_vertical_max 9.5;
Float64 geospatial_vertical_min 0.5;
String geospatial_vertical_positive "down";
String geospatial_vertical_units "m";
String history
"2024-04-25T15:37:57Z (local files)
2024-04-25T15:37:57Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_737962.html";
String infoUrl "https://www.bco-dmo.org/dataset/737962";
String institution "BCO-DMO";
String instruments_0_acronym "Refractometer";
String instruments_0_dataset_instrument_nid "737976";
String instruments_0_description
"A refractometer is a laboratory or field device for the measurement of an index of refraction (refractometry). The index of refraction is calculated from Snell's law and can be calculated from the composition of the material using the Gladstone-Dale relation.
In optics the refractive index (or index of refraction) n of a substance (optical medium) is a dimensionless number that describes how light, or any other radiation, propagates through that medium.";
String instruments_0_instrument_name "Refractometer";
String instruments_0_instrument_nid "679";
String instruments_0_supplied_name "Handheld salinity refractometer with temperature compensation (Marine Depot)";
String instruments_1_dataset_instrument_nid "737977";
String instruments_1_description "Plate readers (also known as microplate readers) are laboratory instruments designed to detect biological, chemical or physical events of samples in microtiter plates. They are widely used in research, drug discovery, bioassay validation, quality control and manufacturing processes in the pharmaceutical and biotechnological industry and academic organizations. Sample reactions can be assayed in 6-1536 well format microtiter plates. The most common microplate format used in academic research laboratories or clinical diagnostic laboratories is 96-well (8 by 12 matrix) with a typical reaction volume between 100 and 200 uL per well. Higher density microplates (384- or 1536-well microplates) are typically used for screening applications, when throughput (number of samples per day processed) and assay cost per sample become critical parameters, with a typical assay volume between 5 and 50 µL per well. Common detection modes for microplate assays are absorbance, fluorescence intensity, luminescence, time-resolved fluorescence, and fluorescence polarization. From: https://en.wikipedia.org/wiki/Plate_reader, 2014-09-0-23.";
String instruments_1_instrument_name "plate reader";
String instruments_1_instrument_nid "528693";
String instruments_1_supplied_name "MultiSkan MCC plate reader";
String instruments_2_dataset_instrument_nid "737974";
String instruments_2_description
"Capable of being performed in numerous environments, push coring is just as it sounds. Push coring is simply pushing the core barrel (often an aluminum or polycarbonate tube) into the sediment by hand. A push core is useful in that it causes very little disturbance to the more delicate upper layers of a sub-aqueous sediment.
Description obtained from: http://web.whoi.edu/coastal-group/about/how-we-work/field-methods/coring/";
String instruments_2_instrument_name "Push Corer";
String instruments_2_instrument_nid "628287";
String instruments_3_dataset_instrument_nid "737975";
String instruments_3_instrument_name "Thermometer";
String instruments_3_instrument_nid "725867";
String keywords "bco, bco-dmo, biological, chemical, crystalline, data, dataset, date, density, depth, dmo, earth, Earth Science > Oceans > Salinity/Density > Salinity, erddap, ferrous, ferrous_iron, iron, latitude, longitude, management, ocean, oceanography, oceans, office, oxide, poorly, poorly_crystalline_iron_oxide, practical, preliminary, salinity, science, sea, sea_water_practical_salinity, seawater, sed, sed_temp, site, temperature, water";
String keywords_vocabulary "GCMD Science Keywords";
String license "https://www.bco-dmo.org/dataset/737962/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/737962";
Float64 Northernmost_Northing 43.994827;
String param_mapping "{'737962': {'lat': 'flag - latitude', 'depth': 'flag - depth', 'long': 'flag - longitude'}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/737962/parameters";
String people_0_affiliation "Bigelow Laboratory for Ocean Sciences";
String people_0_person_name "David Emerson";
String people_0_person_nid "544585";
String people_0_role "Principal Investigator";
String people_0_role_type "originator";
String people_1_affiliation "Harvard University";
String people_1_person_name "Peter Girguis";
String people_1_person_nid "544586";
String people_1_role "Co-Principal Investigator";
String people_1_role_type "originator";
String people_2_affiliation "Bigelow Laboratory for Ocean Sciences";
String people_2_person_name "Jacob Beam";
String people_2_person_nid "737970";
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 "Shannon Rauch";
String people_3_person_nid "51498";
String people_3_role "BCO-DMO Data Manager";
String people_3_role_type "related";
String project "SedimentaryIronCycle";
String projects_0_acronym "SedimentaryIronCycle";
String projects_0_description
"Iron is a critical element for life that serves as an essential trace element for eukaryotic organisms. It is also able to support the growth of a cohort of microbes that can either gain energy for growth via oxidation of ferrous (Fe(II)) to ferric (Fe(III)) iron, or by utilizing Fe(III) for anaerobic respiration coupled to oxidation of simple organic matter or H2. This coupled process is referred to as the microbial iron cycle. One of the primary sources of iron to the ocean comes from dissolved iron (dFe) that is produced through oxidation and reduction processes in the sediment where iron is abundant. The dFe is transported into the overlaying water where it is an essential nutrient for phytoplankton responsible for primary production in the world’s oceans. In fact, iron limitation significantly impacts production in as much as a third of the world’s open oceans. The basic geochemistry of this process is understood; however important gaps exist in our knowledge about the details of how the iron cycle works, and how critical a role bacteria play in it.
Intellectual Merit. Conventional wisdom holds that most of the iron oxidation in sediments is abiological, as a result of the rapid kinetics of chemical iron oxidation in the presence of oxygen. This proposal aims to question this conventional view and enhance our understanding of the microbes involved in the sedimentary iron cycle, with an emphasis on the bacteria that catalyze the oxidation of iron. These Fe-oxidizing bacteria (FeOB) utilize iron as a sole energy source for growth, and are autotrophic. They were only discovered in the ocean about forty-five years ago, and are now known to be abundant at hydrothermal vents that emanate ferrous-rich fluids. More recently, the first evidence was published that they could inhabit coastal sediments, albeit at reduced numbers, and even be abundant in some continental shelf sediments. These habitats are far removed from hydrothermal vents, and reveal the sediments may be an important habitat for FeOB that live on ferrous iron generated in the sediment. This begs the question: are FeOB playing an important role in the oxidative part of the sedimentary Fe-cycle? One important attribute of FeOB is their ability to grow at very low levels of O2, an essential strategy for them to outcompete chemical iron oxidation. How low a level of O2 can sustain them, and how this might affect their distribution in sediments is unknown. In part, this is due to the technical challenges of measuring O2 concentrations and dynamics at very low levels; yet these concentrations could be where FeOB flourish. The central hypothesis of this proposal is that FeOB are more common in marine sedimentary environments than previously recognized, and play a substantive role in governing the iron flux from the sediments into the water column by constraining the release of dFe from sediments. A set of experimental objectives are proposed to test this. A survey of near shore regions in the Gulf of Maine, and a transect along the Monterey Canyon off the coast of California will obtain cores of sedimentary muds and look at the vertical distribution of FeOB and putative Fe-reducing bacteria using sensitive techniques to detect their presence and relative abundance. Some of these same sediments will be used in a novel reactor system that will allow for precise control of O2 levels and iron concentration to measure the dynamics of the iron cycle under different oxygen regimens. Finally pure cultures of FeOB with different O2 affinities will be tested in a bioreactor coupled to a highly sensitive mass spectrometer to determine the lower limits of O2 utilization for different FeOB growing on iron, thus providing mechanistic insight into their activity and distribution in low oxygen environments.
Broader Impacts. An important impact of climate change on marine environments is a predicted increase in low O2 or hypoxic zones in the ocean. Hypoxia in association with marine sediments will have a profound influence on the sedimentary iron cycle, and is likely to lead to greater inputs of dFe into the ocean. In the longer term, this increase in dFe flux could alleviate iron-limitation in some regions of the ocean, thereby enhancing the rate of CO2-fixation and draw down of CO2 from the atmosphere. This is one important reason for developing a better understanding of microbial control of sedimentary iron cycle. This project will also provide training to a postdoctoral scientist, graduate students and undergraduates. This project will contribute to a student initiated exhibit, entitled ‘Iron and the evolution of life on Earth’ at the Harvard Museum of Natural History providing a unique opportunity for undergraduate training and outreach.";
String projects_0_geolocation "Intertidal coastal river and coastal shelf sediments, mid-coast, Maine, USA; Monteray Bay Canyon, sediments, CA, USA";
String projects_0_name "Collaborative Research: The Role of Iron-oxidizing Bacteria in the Sedimentary Iron Cycle: Ecological, Physiological and Biogeochemical Implications";
String projects_0_project_nid "544584";
String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
String publisher_type "institution";
String sourceUrl "(local files)";
Float64 Southernmost_Northing 43.994827;
String standard_name_vocabulary "CF Standard Name Table v55";
String subsetVariables "site,latitude,longitude";
String summary "Pore water and solid phase iron geochemical data from a coastal Maine intertidal mudflat from November 2015 to November 2016.";
String title "Pore water and solid phase iron geochemical data from a coastal Maine intertidal mudflat from November 2015 to November 2016";
String version "1";
Float64 Westernmost_Easting -69.648632;
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.