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| Dataset Title: | [TP sediments with pretreatment] - Total phosphorus concentrations in NMR sediment pretreatment extracts from samples collected during R/V JOIDES Resolution cruise JRES-336 (IODP336, North Pond) to the western flank of the mid-Atlantic Ridge in November of 2011 (Potential phosphorus uptake mechanisms of the deep sedimentary biosphere) 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_816576) |
| Information: | Summary
| License
| ISO 19115
| Metadata
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Attributes {
s {
Extract {
String bcodmo_name "sample_descrip";
String description "Extract solution";
String long_name "Extract";
String units "unitless";
}
Step {
String bcodmo_name "sample_descrip";
String description "Step in the sequential extraction scheme (1-4)";
String long_name "Step";
String units "unitless";
}
Dilution {
String bcodmo_name "sample_descrip";
String description "Sample dilution";
String long_name "Dilution";
String units "unitless";
}
Sample_ID {
String bcodmo_name "sample";
String description "Sample ID, unique sample identifier";
String long_name "Sample ID";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
String units "unitless";
}
Date {
String bcodmo_name "date";
String description "Date the samples were analyzed in ISO 8601 format yyyy-mm-dd";
String long_name "Date";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/ADATAA01/";
String source_name "Date";
String time_precision "1970-01-01";
String units "nd";
}
Analyte_Name {
String bcodmo_name "sample_descrip";
String description "Element analyzed";
String long_name "Analyte Name";
String units "unitless";
}
Int_Corr {
Float64 _FillValue NaN;
Float64 actual_range -8736.84, 3.163645165e+7;
String bcodmo_name "unknown";
String description "Intensity (corrected)";
String long_name "Int Corr";
String units "unitless";
}
RSD_Corr_Int {
Float32 _FillValue NaN;
Float32 actual_range 0.14, 1383.25;
String bcodmo_name "unknown";
String description "Relative standard deviation (RSD) of corrected intensity";
String long_name "RSD Corr Int";
String units "unitless";
}
Conc_Calib {
Float32 _FillValue NaN;
Float32 actual_range -0.2, 122.54;
String bcodmo_name "P";
String description "Calibrated concentration of total phosphorous";
String long_name "Conc Calib";
String units "parts per million (ppm)";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
String acquisition_description
"Location:\\u00a0North Atlantic, western flank of the mid-Atlantic
Ridge\\u00a022.75589 N 46.08125 W
Methodology:
Prior to the extraction, we freeze-dried, ground and sieved sediment samples
to less than 125 \\u03bcm (Ruttenberg 1992). For a given sample, we weighed
four sample replicates (2 g) and placed each in 250 mL HDPE bottles. Sodium
dithionite (F.W. 147.12 g/mol; 7.4 g) was added to each sample split, followed
by 200 mL of citrate-bicarbonate solution (pH 7.6). This step produces
effervescence, so the solution should be added slowly to the sample. We shook
samples for 8 h and then centrifuged them at 3,700 rpm for 15 min. We filtered
the supernatants with a 0.4 \\u03bcm polycarbonate filter. We took 20 mL
aliquots from the filtrate for each sample split for MRP and total P analyses,
and kept them refrigerated until analysis within 24 h. We added 200 mL of
ultrapure water to the solid residue for each sample split as a wash step
after the above reductive step, shook samples for 2 h, and then centrifuged
them at 3,700 rpm for 15 min. We filtered the supernatants with 0.4 \\u03bcm
polycarbonate filters and set aside 20 mL of filtrate from each sample split
for MRP and total P analyses. We then extracted the solid sample residues in
200 mL of sodium acetate buffer (pH 4.0) for 6 h. At the end of this
extraction step, we centrifuged the bottles at 3,700 rpm for 15 min, filtered
the supernatants with 0.4 \\u03bcm polycarbonate filters and took a 20 mL
aliquot of filtrate from each sample split for MRP and total P analyses. We
added 200 mL of ultrapure water to the solid residue for each sample split as
a wash step, shook samples for 2 h, and then centrifuged them at 3,700 rpm for
15 min.\\u00a0 We filtered the supernatants with 0.4 \\u03bcm polycarbonate
filters and set aside 20 mL of filtrate from each sample split for MRP and
total P analyses. We repeated the water rinse step, and collected aliquots for
MRP and total P analyses as in the previous steps. The concentrations of\\u00a0
TP were determined as described below.
Solid sediment sample residues following the pretreatment described above were
transferred to two 50 mL centrifuge tubes (2 sample replicates combined per
tube). We added 20 mL of 0.25 M NaOH + 0.05 M Na2EDTA solution to each tube,
vortexed until all sediment was resuspended and then shook samples for 6 h at
room temperature (Cade-Menun et al. 2005). We used a solid to solution ratio
of 1:5 for this step to minimize the amount of freeze-dried material that will
need to be dissolved for the 31P NMR experiments. Large amounts of salts from
the NaOH-EDTA concentrated in NMR samples lead to higher viscosity and
increase line broadening on NMR spectra (Cade-Menun and Liu 2014). We chose an
extraction time of 6 h to improve total P recovery while limiting the
degradation of natural P compounds in the sample. At the end of the
extraction, samples were centrifuged at 3,700 rpm for 15 min and supernatants
decanted into 50 mL centrifuge tubes. We collected a 500 \\u03bcL aliquot from
each sample, which we diluted with 4.5 mL of ultrapure water. These were
refrigerated until analysis for total P content on the ICP-OES. The sample
residues and supernatants were frozen on a slant to maximize the exposed
surface area during the lyophilization step; this was done immediately after
the removal of the 500 \\u03bcL aliquot. Once completely frozen, the uncapped
tubes containing supernatants and residues were freeze-dried over the course
of 48 h. Each tube was covered with parafilm with small holes from a tack to
minimize contamination. Freeze-dried supernatants from identical sample splits
were combined and dissolved in 500 \\u03bcL each of ultrapure water, D2O, NaOH-
EDTA and 10 M NaOH prior to 31P NMR analysis.\\u00a0 The D2O is required as
signal lock in the spectrometer (Cade-Menun and Liu 2014). Sample pH was
maintained at a pH > 12 to optimize peak separation (Cade-Menun 2005; Cade-
Menun and Liu 2014). Sample pH was assessed with a glass electrode, and
verified with pH paper to account for the alkaline error caused by the high
salt content of our samples (Covington 1985).
Freeze-dried sample residues were ashed in crucibles at 550oC for 2 h and then
extracted in 25 mL of 0.5 M sulfuric acid for 16 h (Olsen and Sommers 1982;
Cade-Menun and Lavkulich 1997). We centrifuged samples at 3,700 rpm for 15
min, filtered supernatants with 0.4 \\u03bcm polycarbonate filters, and
measured P content on an ICP-OES.\\u00a0
Total P concentrations in sediment extracts were measured using inductively
coupled plasma optical emission spectroscopy (ICP-OES). Standards were
prepared with the same solutions as those used for the extraction procedure in
order to minimize matrix effects on P measurements. Sediment extracts and
standards (0 \\u03bcM, 3.2 \\u03bcM, 32 \\u03bcM and 320 \\u03bcM) were diluted to
lower salt content to prevent salt buildup on the nebulizer (1:20 dilution for
step 1, 1:10 for steps 2 \\u2013 4). Concentration data from both wavelengths
(213 nm and 214 nm) were averaged to obtain extract concentrations for each
sample. The detection limit for P on this instrument for both wavelengths is
0.4 \\u03bcM. The MRP concentrations were measured on a QuikChem 8000 automated
ion analyzer. Standards were prepared with the same solutions used for the
extraction step to minimize matrix effects on P measurements. Sediment
extracts and standards (0 \\u2013 30 \\u03bcM PO4) were diluted ten-fold to
prevent matrix interference with color development. The detection limit for P
on this instrument is 0.2 \\u03bcM. We derived MUP concentrations by
subtracting MRP from total P concentrations.";
String awards_0_award_nid "554980";
String awards_0_award_number "OCE-0939564";
String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward?AWD_ID=0939564";
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
"Iodp336-tp-sed-pre
PI: Adina Paytan
Data Version 1: 2020-06-23";
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 dataset_current_state "Final and no updates";
String date_created "2020-06-23T18:47:07Z";
String date_modified "2020-06-30T18:11:16Z";
String defaultDataQuery "&time<now";
String doi "10.26008/1912/bco-dmo.816576.1";
String history
"2024-11-23T17:02:55Z (local files)
2024-11-23T17:02:55Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_816576.html";
String infoUrl "https://www.bco-dmo.org/dataset/816576";
String institution "BCO-DMO";
String instruments_0_acronym "ICP-OES";
String instruments_0_dataset_instrument_nid "816583";
String instruments_0_description "Also referred to as an Inductively coupled plasma atomic emission spectroscope (ICP-AES). These instruments pass nebulised samples into an inductively-coupled gas plasma (8-10000 K) where they are atomised and excited. The de-excitation optical emissions at characteristic wavelengths are spectroscopically analysed. It is often used in the detection of trace metals.";
String instruments_0_instrument_name "Inductively Coupled Plasma Optical Emission Spectrometer";
String instruments_0_instrument_nid "639924";
String instruments_0_supplied_name "ICP-OES";
String keywords "analyte, Analyte_Name, bco, bco-dmo, biological, calib, chemical, conc, Conc_Calib, corr, data, dataset, date, dilution, dmo, erddap, extract, int, Int_Corr, management, name, oceanography, office, preliminary, rsd, RSD_Corr_Int, sample, Sample_ID, step, time";
String license "https://www.bco-dmo.org/dataset/816576/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/816576";
String param_mapping "{'816576': {}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/816576/parameters";
String people_0_affiliation "University of California-Santa Cruz";
String people_0_affiliation_acronym "UC Santa Cruz";
String people_0_person_name "Adina Paytan";
String people_0_person_nid "50821";
String people_0_role "Principal Investigator";
String people_0_role_type "originator";
String people_1_affiliation "University of California-Santa Cruz";
String people_1_affiliation_acronym "UC Santa Cruz";
String people_1_person_name "Dr Delphine Defforey";
String people_1_person_nid "664058";
String people_1_role "Co-Principal Investigator";
String people_1_role_type "originator";
String people_2_affiliation "Woods Hole Oceanographic Institution";
String people_2_affiliation_acronym "WHOI BCO-DMO";
String people_2_person_name "Amber D. York";
String people_2_person_nid "643627";
String people_2_role "BCO-DMO Data Manager";
String people_2_role_type "related";
String project "Deep sea sediments";
String projects_0_acronym "Deep sea sediments";
String projects_0_description
"The goal of this project is to explore potential microbial P uptake mechanisms in marine sediments beneath the North Atlantic Gyre and their effects on the relative distribution of organic P compounds as a function of burial depth and changing redox conditions. We use a combination of metagenomic analyses and solution 31P nuclear magnetic resonance spectroscopy (31P NMR) to investigate (1) the presence of microbial functional genes pertaining to P uptake and metabolism and (2) the possible P substrates for the deep biosphere in these oligotrophic sediments.
NSF C-DEBI Award #156246 to Dr. Adina Paytan
NSF C-DEBI Award #157598 to Dr. Delphine Defforey";
String projects_0_end_date "2015-04";
String projects_0_geolocation "Mid-Atlantic Ridge flank";
String projects_0_name "Potential phosphorus uptake mechanisms of the deep sedimentary biosphere";
String projects_0_project_nid "664073";
String projects_0_start_date "2015-03";
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 "Total phosphorus concentrations in nuclear magnetic resonance (NMR) sediment pretreatment extracts from samples collected during R/V JOIDES Resolution cruise JRES-336 (IODP336, North Pond) to the western flank of the mid-Atlantic Ridge in November of 2011. Samples were analyzed in 2016.";
String title "[TP sediments with pretreatment] - Total phosphorus concentrations in NMR sediment pretreatment extracts from samples collected during R/V JOIDES Resolution cruise JRES-336 (IODP336, North Pond) to the western flank of the mid-Atlantic Ridge in November of 2011 (Potential phosphorus uptake mechanisms of the deep sedimentary biosphere)";
String version "1";
String xml_source "osprey2erddap.update_xml() v1.5";
}
}
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.