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Dataset Title:  Partitioning of iron and plutonium in exopolymeric substances and
intracellular biopolymers: a comparison study between the coccolithophore
Emiliania huxleyi and the diatom Skeletonema costatum
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Institution:  BCO-DMO   (Dataset ID: bcodmo_dataset_764480)
Information:  Summary ? | License ? | Metadata | Background (external link) | Files | Make a graph
 
Variable ?   Optional
Constraint #1 ?
Optional
Constraint #2 ?
   Minimum ?
 
   Maximum ?
 
 type (unitless) ?          "Coccosphere"    "Intracellular_biop..."
 Biopolymer_fraction (unitless) ?          "AEPS"    "Silica_frustule"
 Cell_type (unitless) ?          "E_Huxleyi"    "S_Costatum"
 Fe59_act_pcnt (unitless (%)) ?          "0.1+/-0.0"    "bdl"
 Pu238_act_pcnt (unitless (%)) ?          "0.1+/-0.0"    "bdl"
 Protein (microMole Carbon (uM-C)) ?          "115"    "na"
 TCHO (microMole Carbon (uM-C)) ?          1.0    38.2
 URA (microMole Carbon (uM-C)) ?          0.2    38.2
 Protein_C_TCHO_C (microMole Carbon (uM-C)) ?          0.0    7.8
 pcnt_URA_TCHO (microMole Carbon (uM-C)) ?          13    100
 
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The Dataset Attribute Structure (.das) for this Dataset

Attributes {
 s {
  type {
    String bcodmo_name "sample_descrip";
    String description "type";
    String long_name "Type";
    String units "unitless";
  }
  Biopolymer_fraction {
    String bcodmo_name "sample_descrip";
    String description "Biopolymer fraction type";
    String long_name "Biopolymer Fraction";
    String units "unitless";
  }
  Cell_type {
    String bcodmo_name "sample_descrip";
    String description "cell type";
    String long_name "Cell Type";
    String units "unitless";
  }
  Fe59_act_pcnt {
    String bcodmo_name "unknown";
    String description "Activity percentage";
    String long_name "Fe59 Act Pcnt";
    String units "unitless (%)";
  }
  Pu238_act_pcnt {
    String bcodmo_name "unknown";
    String description "Activity percentage";
    String long_name "Pu238 Act Pcnt";
    String units "unitless (%)";
  }
  Protein {
    String bcodmo_name "unknown";
    String description "amount of protein";
    String long_name "Protein";
    String units "microMole Carbon (uM-C)";
  }
  TCHO {
    Float32 _FillValue NaN;
    Float32 actual_range 1.0, 38.2;
    String bcodmo_name "unknown";
    String description "amount of TCHO-total carbohydrate";
    String long_name "TCHO";
    String units "microMole Carbon (uM-C)";
  }
  URA {
    Float32 _FillValue NaN;
    Float32 actual_range 0.2, 38.2;
    String bcodmo_name "unknown";
    String description "amount of URA-uronic acid";
    String long_name "URA";
    String units "microMole Carbon (uM-C)";
  }
  Protein_C_TCHO_C {
    Float32 _FillValue NaN;
    Float32 actual_range 0.0, 7.8;
    String bcodmo_name "unknown";
    String description "amount of protein to total carbohydrates";
    String long_name "Protein C TCHO C";
    String units "microMole Carbon (uM-C)";
  }
  pcnt_URA_TCHO {
    Byte _FillValue 127;
    Byte actual_range 13, 100;
    String bcodmo_name "unknown";
    String description "percent uronic acid to total carbohydrates";
    String long_name "Pcnt URA TCHO";
    String units "microMole Carbon (uM-C)";
  }
 }
  NC_GLOBAL {
    String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
    String acquisition_description 
"The seawater (< 1 kDa) was enriched with f/2 nutrients, trace metals and
vitamins, and autoclaved in pre-combusted and seawater-preconditioned clear
glassware. Known activity of 59Fe (gamma emitting radionuclide) and 238Pu
(alpha emitting radionuclide) were added into the seawater in pre-combusted
and seawater-preconditioned clear glassware.\\u00a0  
 After checking the pH of each radiolabeled medium to be 8.0, laboratory
axenic Skeletonema costatum (UTEX LB 2308) and Emiliania huxleyi (CCMP 371)
was added to 100 mL of media and incubated at a temperature of
19\\u00b11\\u00baC with a light:dark cycle of 14 h:10 h under an irradiation
condition of 100 \\u00b5mol-quanta/m2/s.  
 The sequential chemical extraction scheme for obtaining individual fractions
from S. costatum and E. huxleyi followed the procedures described in Chuang et
al. (2015) and Lin et al. (2017), with a few exceptions. For the extracellular
biopolymers excreted by the phytoplankton, non-attached exopolymeric
substances (NAEPS) in the surrounding seawater and attached EPS (AEPS)
associated with cellular surface, were harvested. Laboratory cultures were
centrifuged at 3000 x g for 30 min, followed by filtration of the supernatant
which was further concentrated and desalted with nanopure water (18.2 \\u03a9)
in 3 kDa Microsep centrifugal filter tubes (Milipore) to obtain the NAEPS
fraction, while the resultant pellet from the centrifugation was resuspended
by 50 mL 3% NaCl solution and stirred gently overnight at 4\\u00baC to extract
EPS from the cellular surface. The solution was also centrifuged, and the
supernatant containing the AEPS was then filtered to remove residual cells
before further desalting via the 3 kDa ultrafiltration centrifugation tubes.
The final volume of concentrated solution of each biopolymer fraction (>3 kDa)
was 2 mL.  
 For the S. costatum cultures, 10 mL of 100 mM EDTA (pH 8.0) solution was
added to the diatom cells from the previous AEPS extraction step. The diatom
cells were resuspended at 4\\u00baC overnight to extract the intracellular
material after diatom cell lysis and the supernatant was collected after
centrifugation to obtain the EDTA-extractable intracellular biopolymers. Then,
the resultant pellet was further resuspended in 10 mL of 1% SDS/10 mM Tris (pH
6.8) solution and heated at 95\\u00baC for 1 hr. The centrifuged supernatant
was also collected and defined as SDS-extractable biopolymer in S. costatum
cells.\\u00a0  
 To access the diatom frustule-associated biopolymers, 5 mL of 52% HF was
then added to the frustules and incubated on ice for 1 hr. After the
separation of HF-insoluble pellet, the HF-soluble fraction was evaporated
under N2 stream and neutralized, followed by the 3 kDa centrifugal filtration
to collect the digested frustule silica fraction (<3 kDa) and HF-soluble
frustule-associated biopolymer (>3 kDa). Lastly, the residue biopolymer in the
HF-insoluble pellet was collected with the resuspension in a 2 mL of 100 mM
ammonium acetate solution and sonication. Similar to NAEPS and AEPS, all the
S. costatum cellular biopolymers were concentrated and desalted with nanopure
water in 3 kDa Microsep centrifugal filter tubes (Milipore).  
 The coccosphere of the E. huxleyi cells was first dissolved before the
extraction of intracellular biopolymers. In brief, the pellet from the
previous AEPS extraction step was digested in 0.44 M acetic acid (HAc) (weak
acidity and non-oxidizing nature to avoid the breakage of cells) plus 0.1 M
NaCl solution at 4\\u00baC for 8 hr. After the digestion, the mixed solution
was centrifuged and filtered, followed by ultrafiltration of the supernatant
with 3 kDa Microsep centrifugal filter tubes. The retentate (>3 kDa) was
defined as coccosphere-associated biopolymers, and the permeate fraction (<3
kDa) was also collected to obtain the fraction of digested biogenic calcite.  
 The E. huxleyi cells after the removal of shells were further heated in 20
mL of 1% SDS/10 mM Tris mixed solution (pH 6.8) at 95 \\u00baC for 1 hr. The
supernatant was also collected through centrifugation and filtration, followed
by desalting with 3 kDa Microsep centrifugal filter tubes. Subsequently, the
remaining pellet was further digested by 0.04 M NH2OH\\u2022HCl/4.35 M HAc
mixture at 96 \\u00baC for 6 hr to obtain the intracellular metabolitic
biopolymer. The sum of these two fractions represents the intracellular
biopolymers in E. huxleyi cells.  
 All the solutions from the different extraction steps, including the >3 kDa
biopolymer fractions and the permeate (< 3 kDa, i.e., frustule and
coccosphere), were counted to determine the activity of 59Fe and 238Pu. 59Fe
activity was directly obtained from a Canberra ultrahigh purity germanium well
gamma detector at the decay energies of 1099 kev. All the solutions for the
gamma counting had the same volume and geometry to avoid geometry corrections,
and all the data were decay corrected.\\u00a0  
 238Pu activities were determined by alpha-spectroscopy (Xu et al., 2016).
Briefly, a known activity of 242Pu was spiked to trace the yield of 238Pu
during the extraction steps. The samples were oven-dried, then heated at 600
\\u00baC overnight in a ceramic crucible. The resulting ash fraction was then
digested in Teflon tubes overnight in concentrated HNO3 and HCl (1:1) at
85\\u00baC. The remaining solid residual fraction was collected by
centrifugation and discarded, and the supernatant was further evaporated to
incipient dryness. To convert all Pu ions to Pu(IV), a FeSO4\\u20227H2O (0.2
g/mL) solution, followed by 0.25 g of NaNO2, were added to each sample to
achieve a final volume of 3 mL for each sample. Samples were then passed
through an UTEVA column (Cat. # UT-C50-A, Eichrom, USA) to separate Pu from
other alpha-emitting radionuclides (e.g., 238U, 241Am). After washing the
column with an 8 M HNO3 solution, the Pu was eluted using freshly-prepared
0.02 M NH2OH\\u2022HCl/0.02 M ascorbic acid in 2 M HNO3. The Pu-containing
eluent was evaporated and re-constituted in 0.4 M (NH4)2SO4 (pH~2.6) for
electroplating onto a stainless steel planchet at 0.6 Amps current for 2 hr.
Sample-bearing planchets were then analyzed via alpha spectroscopy for at
least one week to obtain counting errors (1 sigma) lower than 5%.
 
Subsamples were taken from the concentrated biopolymers for the analysis of
protein, total carbohydrate (TCHO) and uronic acid (URA), respectively. In
brief, the protein abundance was measured through a modified Lowry protein
assay, using bovine serum albumin (BSA) as the standard. For the
concentrations of TCHO, samples were hydrolyzed by 0.09 M HCl (final
concentration) at 150\\u00baC for 1 h. After neutralization with NaOH solution,
the hydrolysate was measured by the 2,4,6-tripyridyl-triazine (TPTZ) method
(Hung et al., 2001), with glucose as the standard. URA concentrations were
determined by the metahydroxyphenyl method using glucuronic acid as the
standard (Hung and Santschi, 2001).\\u00a0";
    String awards_0_award_nid "735995";
    String awards_0_award_number "OCE-1356453";
    String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1356453";
    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 "Henrietta N Edmonds";
    String awards_0_program_manager_nid "51517";
    String cdm_data_type "Other";
    String comment 
"Partitioning of iron and plutonium in exopolymeric substances and intracellular biopolymers: a comparison study between the coccolithophore Emiliania huxleyi and the diatom Skeletonema costatum 
  PI: Peter H. Santschi 
  Version: 2019-04-08";
    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 "2019-04-08T17:02:21Z";
    String date_modified "2019-04-08T19:26:10Z";
    String defaultDataQuery "&amp;time&lt;now";
    String doi "10.1575/1912/bco-dmo.764480.1";
    String history 
"2021-11-29T05:06:22Z (local files)
2021-11-29T05:06:22Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_764480.html";
    String infoUrl "https://www.bco-dmo.org/dataset/764480";
    String institution "BCO-DMO";
    String instruments_0_acronym "Spectrometer";
    String instruments_0_dataset_instrument_description "Sample-bearing planchets were then analyzed via alpha spectroscopy for at least one week to obtain counting errors (1 sigma) lower than 5%.";
    String instruments_0_dataset_instrument_nid "764489";
    String instruments_0_description "A spectrometer is an optical instrument used to measure properties of light over a specific portion of the electromagnetic spectrum.";
    String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L22/current/TOOL0460/";
    String instruments_0_instrument_name "Spectrometer";
    String instruments_0_instrument_nid "667";
    String instruments_0_supplied_name "Canberra Quad Alpha Spectrometer Model 7404";
    String instruments_1_acronym "Spectrometer";
    String instruments_1_dataset_instrument_description "UV-Visible spectrometer, BioTek Instruments Inc Model EPOCH";
    String instruments_1_dataset_instrument_nid "764490";
    String instruments_1_description "A spectrometer is an optical instrument used to measure properties of light over a specific portion of the electromagnetic spectrum.";
    String instruments_1_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L22/current/TOOL0460/";
    String instruments_1_instrument_name "Spectrometer";
    String instruments_1_instrument_nid "667";
    String instruments_1_supplied_name "UV-Visible spectrometer, BioTek Instruments Inc Model EPOCH";
    String instruments_2_dataset_instrument_description "Beckman Coulter Allegra X-12 centrifuge";
    String instruments_2_dataset_instrument_nid "764491";
    String instruments_2_description "A machine with a rapidly rotating container that applies centrifugal force to its contents, typically to separate fluids of different densities (e.g., cream from milk) or liquids from solids.";
    String instruments_2_instrument_name "Centrifuge";
    String instruments_2_instrument_nid "629890";
    String instruments_2_supplied_name "Beckman Coulter Allegra X-12 centrifuge";
    String instruments_3_dataset_instrument_description "Canberra ultrahigh purity germanium well gamma detector Model GCW3024";
    String instruments_3_dataset_instrument_nid "764492";
    String instruments_3_description "Instruments measuring the relative levels of electromagnetic radiation of different wavelengths in the gamma-ray waveband.";
    String instruments_3_instrument_name "Gamma Ray Spectrometer";
    String instruments_3_instrument_nid "670659";
    String instruments_3_supplied_name "Canberra ultrahigh purity germanium well gamma detector Model GCW3024";
    String keywords "act, bco, bco-dmo, biological, biopolymer, Biopolymer_fraction, cell, Cell_type, chemical, data, dataset, dmo, erddap, fe59, Fe59_act_pcnt, fraction, management, oceanography, office, pcnt, pcnt_URA_TCHO, preliminary, protein, Protein_C_TCHO_C, pu238, Pu238_act_pcnt, tcho, type, ura";
    String license "https://www.bco-dmo.org/dataset/764480/license";
    String metadata_source "https://www.bco-dmo.org/api/dataset/764480";
    String param_mapping "{'764480': {}}";
    String parameter_source "https://www.bco-dmo.org/mapserver/dataset/764480/parameters";
    String people_0_affiliation "Texas A&M, Galveston";
    String people_0_affiliation_acronym "TAMUG";
    String people_0_person_name "Peter Santschi";
    String people_0_person_nid "735998";
    String people_0_role "Principal Investigator";
    String people_0_role_type "originator";
    String people_1_affiliation "Texas A&M, Galveston";
    String people_1_affiliation_acronym "TAMUG";
    String people_1_person_name "Antonietta Quigg";
    String people_1_person_nid "736000";
    String people_1_role "Co-Principal Investigator";
    String people_1_role_type "originator";
    String people_2_affiliation "Texas A&M, Galveston";
    String people_2_affiliation_acronym "TAMUG";
    String people_2_person_name "Kathleen Schwehr";
    String people_2_person_nid "736002";
    String people_2_role "Co-Principal Investigator";
    String people_2_role_type "originator";
    String people_3_affiliation "Texas A&M, Galveston";
    String people_3_affiliation_acronym "TAMUG";
    String people_3_person_name "Chen Xu";
    String people_3_person_nid "736004";
    String people_3_role "Co-Principal Investigator";
    String people_3_role_type "originator";
    String people_4_affiliation "Woods Hole Oceanographic Institution";
    String people_4_affiliation_acronym "WHOI BCO-DMO";
    String people_4_person_name "Mathew Biddle";
    String people_4_person_nid "708682";
    String people_4_role "BCO-DMO Data Manager";
    String people_4_role_type "related";
    String project "Biopolymers for radionuclides";
    String projects_0_acronym "Biopolymers for radionuclides";
    String projects_0_description 
"NSF Award Abstract:
Particle-associated natural radioisotopes are transported to the ocean floor mostly via silica and carbonate ballasted particles, allowing their use as tracers for particle transport. Th(IV), Pa (IV,V), Po(IV), Pb(II) and Be(II) radionuclides are important proxies in oceanographic investigations, used for tracing particle and colloid cycling, estimating export fluxes of particulate organic carbon, tracing air-sea exchange, paleoproductivity, and/or ocean circulation in paleoceanographic studies. Even though tracer approaches are considered routine, there are cases where data interpretation or validity has become controversial, largely due to uncertainties about inorganic proxies and organic carrier molecules. Recent studies showed that cleaned diatom frustules and pure silica particles, sorb natural radionuclides to a much lower extent (by 1-2 orders of magnitude) than whole diatom cells (with or without shells). Phytoplankton that build siliceous or calcareous shells, such as the diatoms and coccolithophores, are assembled via bio-mineralization processes using biopolymers as nanoscale templates. These templates could serve as possible carriers for radionuclides and stable metals.
In this project, a research team at the Texas A & M University at Galveston hypothesize that radionuclide sorption is controlled by selective biopolymers that are associated with biogenic opal (diatoms), CaCO3 (coccolithophores) and the attached exopolymeric substances (EPS), rather than to pure mineral phase. To pursue this idea, the major objectives of their research will include separation, identification and molecular-level characterization of the individual biopolymers (e.g., polysaccharides, uronic acids, proteins, hydroquinones, hydroxamate siderophores, etc.) that are responsible for binding different radionuclides (Th, Pa, Pb, Po and Be) attached to cells or in the matrix of biogenic opal or CaCO3 as well as attached EPS mixture, in laboratory grown diatom and coccolithophore cultures. Laboratory-scale radiolabeling experiments will be conducted, and different separation techniques and characterization techniques will be applied.
Intellectual Merit : It is expected that this study will help elucidate the molecular basis of the templated growth of diatoms and coccoliths, EPS and their role in scavenging natural radionuclides in the ocean, and help resolve debates on the oceanographic tracer applications of different natural radioisotopes (230,234Th, 231Pa, 210Po, 210Pb and 7,10Be). The proposed interdisciplinary research project will require instrumental approaches for molecular-level characterization of these radionuclides associated carrier molecules.
Broader Impacts: The results of this study will be relevant for understanding biologically mediated ocean scavenging of radionuclides by diatoms and coccoliths which is important for carbon cycling in the ocean, and will contribute to improved interpretation of data obtained by field studies especially through the GEOTRACES program. This new program will enhance training programs at TAMUG for postdocs, graduate and undergraduate students. Lastly, results will be integrated in college courses and out-reach activities at Texas A&M University, including NSF-REU, Sea Camp, Elder Hostel and exhibits at the local science fair and interaction with its after-school program engaging Grade 9-12 students from groups traditionally underrepresented.";
    String projects_0_end_date "2018-02";
    String projects_0_name "Biopolymers as carrier phases for selected natural radionuclides (of Th, Pa, Pb, Po, Be) in diatoms and coccolithophores";
    String projects_0_project_nid "735996";
    String projects_0_start_date "2014-03";
    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 "Iron (Fe), a micronutrient for algal growth, and plutonium (Pu), an anthropogenic radionuclide, share some common features. This includes similar oceanic distributions when different input modes are taken into account, as well as their chemical behavior, such as a high affinity to natural organic matter (NOM). The NOM produced by various phytoplankton communities can potentially influence Fe cycling in the ocean, and likely also influence the transport behavior of Pu. We conducted laboratory incubation experiments using the coccolithophore Emiliania huxleyi and the diatom Skeletonema costatum, in the presence of 59Fe and 238Pu as radiotracers, in order to differentiate Fe and Pu uptake by extracellular exopolymeric substances (EPS) and intracellular biopolymers. The Fe and Pu distributions in select organic compound classes including proteins, total carbohydrates (TCHO) and uronic acids (URA) produced by these two types of phytoplankton were compared. Our results indicated that most of the Fe and Pu (>95%) were found concurrently concentrated in E. huxleyi-derived non-attached EPS, while much less (<2%) was present in the intracellular fraction of E. huxleyi. By contrast, in the diatom S. costatum, both Fe and Pu distribution was EPS > intracellular biopolymers > outer cell covering (i.e., frustule). In fact, over 50% of Fe was concentrated in S. costatum-derived attached EPS and intracellular biopolymers. The diatom derived Fe-EPS complexes were more hydrophobic, with stronger tendency to aggregate in seawater. Fe binding to biopolymers in both E. huxleyi and S. costatum cultures was related to URA concentrations, but the overall distribution of URA between these two phytoplankton species was different. Our findings suggest that the presence of URA in S. costatum cellular surface (i.e., attached EPS) and its intracellular fraction could be an indicator for the Fe transport from the surrounding seawater to the diatom cells. However, for the coccolithophore E. huxleyi, Fe appeared not to be efficiently taken up during its growth. Instead, the more hydrophilic non-attached EPS (i.e., low protein/TCHO ratio) produced by E. huxleyi could have stabilized Fe in the colloidal form as Fe-EPS complexes. Similar partitioning behavior of Fe and Pu suggests that Pu isotopes can potentially serve as a tracer for the Fe biogeochemistry in the ocean.";
    String title "Partitioning of iron and plutonium in exopolymeric substances and intracellular biopolymers: a comparison study between the coccolithophore Emiliania huxleyi and the diatom Skeletonema costatum";
    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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