BCO-DMO ERDDAP
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Row Type Variable Name Attribute Name Data Type Value
attribute NC_GLOBAL access_formats String .htmlTable,.csv,.json,.mat,.nc,.tsv
attribute NC_GLOBAL acquisition_description String Refer to Supplemental File, \\\"57Fe Wall Loss Experiment diagram\\\" for the\nsteps indicated in bold.\n \nAll materials were soaked overnight with heating in 1.5% Citrad Citric Acid\nliquid cleaner in deionized water, rinsed in RO water, and soaked in 10% HCl\nin Milli-Q ultrapure water for one week (due to time constraints), then rinsed\nwith MilliQ ultrapure water, let dry in an AirClean 400 work station\novernight, and double-bagged in polyethylene bags (Mellett et al., 2017). M9\nMinimal Media for bacterial cultures was made using Milli-Q ultrapure water,\ncontaining final concentrations of 33.7 mM Na\\u2082HPO\\u2084\\u00b72H\\u2082O,\n22 mM KH\\u2082PO\\u2084, 8.56 mM NaCl, 18.7 mM NH\\u2084Cl, 0.1 M magnesium\nchloride, 0.1 M calcium chloride, 2 mg/ml Thiamine HCl in 70% EtOH, and 20%\nGlucose (Kutter & Sulakvelidze, 2004). Half of the media was chelexed using\nChelex-100 resin (Pai et al., 1988) that was not acid-cleaned (C), and half\nremained un-chelexed (B). Half of each treatment was spiked with 10 \\u00b5M\nlabeled \\u2075\\u2077FeSO\\u2084(2) while half remained un-spiked (1). A volume\nof 25 ml was then filtered through either a 0.2 \\u00b5m Sterivex PVDF syringe\nfilter for the dissolved fraction (D), or a 0.02 \\u00b5m Whatman Anatop\nsyringe filter for the soluble fraction (S) (Gledhill & Buck, 2012). Samples\nwere directly filtered into trace metal clean polycarbonate Erlenmeyer flasks,\nplaced in a clean bag with a small opening to vent, and left shaking at 37\n\\u00b0C for one week. Samples of each treatment were taken initially, then\nafter the 1st, 3rd, and 7th days (t= 00, 01, 03, 07). The samples were\ndiluted, acidified, and analyzed using an ELEMENT XR High Resolution\nInductively Coupled Plasma Mass Spectrometer (HR-ICP-MS). The limit of\ndetection (LOD) for \\u2075\\u2076Fe and \\u2075\\u2077Fe were 0.3 nM and 0.012\nnM, respectively (Shrivastava & Gupta, 2011).\n \nProblem Report:  \n \\u200bThe original measurements of the M9 minimal media \\u2075\\u2076Fe\ncontamination was high, so in an attempt to lower background contamination the\nmedia was chelexed. However, the Chelex-100 resin was not rinsed with acid, so\nwas less active for removal of metals. This resulted in higher than expected\nbackground concentrations of metals.\n \nThree samples were contaminated with bacterial growth (as indicated by visual\nturbidity and confirmed using SYBR nucleic acid stain and epifluorescence\nmicroscopy) over the course of the week. On t=3, sample B2 was contaminated.\nBy t=7, sample B1D and B1S were contaminated.
attribute NC_GLOBAL awards_0_award_nid String 713366
attribute NC_GLOBAL awards_0_award_number String OCE-1722761
attribute NC_GLOBAL awards_0_data_url String http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1722761 (external link)
attribute NC_GLOBAL awards_0_funder_name String NSF Division of Ocean Sciences
attribute NC_GLOBAL awards_0_funding_acronym String NSF OCE
attribute NC_GLOBAL awards_0_funding_source_nid String 355
attribute NC_GLOBAL awards_0_program_manager String Michael E. Sieracki
attribute NC_GLOBAL awards_0_program_manager_nid String 50446
attribute NC_GLOBAL cdm_data_type String Other
attribute NC_GLOBAL comment String 57Fe Wall Loss Experiment \n  PIs: Kristen Buck & Mya Breitbart (USF) \n  Co-PIs: Salvatore Caprara & Chelsea Bonnain (USF) \n  Verion: 04 April 2018
attribute NC_GLOBAL Conventions String COARDS, CF-1.6, ACDD-1.3
attribute NC_GLOBAL creator_email String info at bco-dmo.org
attribute NC_GLOBAL creator_name String BCO-DMO
attribute NC_GLOBAL creator_type String institution
attribute NC_GLOBAL creator_url String https://www.bco-dmo.org/ (external link)
attribute NC_GLOBAL data_source String extract_data_as_tsv version 2.3  19 Dec 2019
attribute NC_GLOBAL date_created String 2018-04-04T17:40:41Z
attribute NC_GLOBAL date_modified String 2020-02-11T18:33:18Z
attribute NC_GLOBAL defaultDataQuery String &time<now
attribute NC_GLOBAL doi String 10.1575/1912/bco-dmo.732864.1
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/732864 (external link)
attribute NC_GLOBAL institution String BCO-DMO
attribute NC_GLOBAL instruments_0_acronym String ICP Mass Spec
attribute NC_GLOBAL instruments_0_dataset_instrument_description String ELEMENT XR High Resolution Inductively Coupled Plasma Mass Spectrometer (HR-ICP-MS)
attribute NC_GLOBAL instruments_0_dataset_instrument_nid String 732867
attribute NC_GLOBAL instruments_0_description String An ICP Mass Spec is an instrument that passes nebulized samples into an inductively-coupled gas plasma (8-10000 K) where they are atomized and ionized. Ions of specific mass-to-charge ratios are quantified in a quadrupole mass spectrometer.
attribute NC_GLOBAL instruments_0_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L05/current/LAB15/ (external link)
attribute NC_GLOBAL instruments_0_instrument_name String Inductively Coupled Plasma Mass Spectrometer
attribute NC_GLOBAL instruments_0_instrument_nid String 530
attribute NC_GLOBAL instruments_0_supplied_name String ELEMENT XR High Resolution Inductively Coupled Plasma Mass Spectrometer
attribute NC_GLOBAL keywords String bco, bco-dmo, biological, chelex, chemical, data, dataset, date, day, description, dmo, erddap, fe56, fe57, Fe57_SPIKE, Fe57_to_Fe56, filter, FILTER_SIZE, management, notes, oceanography, office, preliminary, sample, SAMPLE_ID, size, spike
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/732864/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/732864 (external link)
attribute NC_GLOBAL param_mapping String {'732864': {}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/732864/parameters (external link)
attribute NC_GLOBAL people_0_affiliation String University of South Florida
attribute NC_GLOBAL people_0_affiliation_acronym String USF
attribute NC_GLOBAL people_0_person_name String Mya Breitbart
attribute NC_GLOBAL people_0_person_nid String 51740
attribute NC_GLOBAL people_0_role String Principal Investigator
attribute NC_GLOBAL people_0_role_type String originator
attribute NC_GLOBAL people_1_affiliation String University of South Florida
attribute NC_GLOBAL people_1_affiliation_acronym String USF
attribute NC_GLOBAL people_1_person_name String Kristen N. Buck
attribute NC_GLOBAL people_1_person_nid String 51624
attribute NC_GLOBAL people_1_role String Principal Investigator
attribute NC_GLOBAL people_1_role_type String originator
attribute NC_GLOBAL people_2_affiliation String University of South Florida
attribute NC_GLOBAL people_2_affiliation_acronym String USF
attribute NC_GLOBAL people_2_person_name String Chelsea Bonnain
attribute NC_GLOBAL people_2_person_nid String 732872
attribute NC_GLOBAL people_2_role String Co-Principal Investigator
attribute NC_GLOBAL people_2_role_type String originator
attribute NC_GLOBAL people_3_affiliation String University of South Florida
attribute NC_GLOBAL people_3_affiliation_acronym String USF
attribute NC_GLOBAL people_3_person_name String Salvatore Caprara
attribute NC_GLOBAL people_3_person_nid String 732874
attribute NC_GLOBAL people_3_role String Co-Principal Investigator
attribute NC_GLOBAL people_3_role_type String originator
attribute NC_GLOBAL people_4_affiliation String Woods Hole Oceanographic Institution
attribute NC_GLOBAL people_4_affiliation_acronym String WHOI BCO-DMO
attribute NC_GLOBAL people_4_person_name String Shannon Rauch
attribute NC_GLOBAL people_4_person_nid String 51498
attribute NC_GLOBAL people_4_role String BCO-DMO Data Manager
attribute NC_GLOBAL people_4_role_type String related
attribute NC_GLOBAL project String Fe-Virus
attribute NC_GLOBAL projects_0_acronym String Fe-Virus
attribute NC_GLOBAL projects_0_description String Iron is an essential micronutrient for phytoplankton that is required for photosynthesis and respiration. Insufficient iron has been shown to limit phytoplankton growth in large regions of the surface ocean, and correspondingly, iron cycling is directly linked to carbon cycling in much of the marine environment. Nearly all iron in seawater (>99%) exists as complexes with organic molecules called ligands, which govern the concentration of iron dissolved in the water and the bioavailability of that iron to phytoplankton. However, despite the importance of iron-binding organic ligands, their sources and identities are largely unknown. Viruses, the majority of which are phages (viruses that infect bacteria), are extremely abundant in seawater and are in the same size fraction as dissolved iron. Recent evidence that non-marine phages contain iron as part of their structures has led to the proposal that marine phages may represent a previously overlooked class of organic iron-binding ligands. This project is determining the contribution of marine phages to dissolved iron pools and culture phage-host systems in the laboratory to determine if phages utilize bacterial iron-uptake receptors for infection in the manner of a Trojan horse. As the first study to examine the biogeochemical impact of trace elements contained within the structure of highly abundant marine phage particles, successful completion of the proposed research will be transformative for biological and chemical oceanography and have far-reaching implications for other fields, including human health where iron availability plays an important role in microbial pathogenesis. This project contributes to the multidisciplinary training of a graduate student and postdoctoral researcher. Research results will be disseminated through scientific publications and presentations, and the public will be educated about linkages between viruses and ocean chemistry via a hands-on exhibit for the annual St. Petersburg Science Festival.\nBuilding upon evidence from non-marine model systems demonstrating the presence of iron ions in phage tail proteins and phage utilization of cell surface receptors for siderophore-bound iron, this project combines field and laboratory-based experiments to test the following three hypotheses regarding iron-virus interactions in the oceans: (1) Iron incorporated into phage tails originates from bacterial cell reserves, reducing the amount of iron available for remineralization upon lysis; (2) Phages constitute important iron-binding ligands in the oceans, accounting for a substantial portion of organically complexed colloidal dissolved iron; (3) Marine phages compete with siderophore-bound iron for uptake receptors on the bacterial cell surface and use iron in their tails as a Trojan horse for infection. Initial calculations predict that phages could account for up to 70% of the colloidal fraction of organically complexed dissolved iron in the surface ocean; therefore, this project is critical for advancing knowledge of trace-metal cycling as well as phage-host interactions. Additionally, if a portion of the cellular iron thought to be released from bacterial cells for remineralization following lysis is already incorporated into phage tails, then these findings will have significant implications for oceanic biogeochemical models. Through a combination of laboratory-based culture experiments and field sample measurements, this project could reveal the identity of a ubiquitous component of colloidal organic iron-binding ligands, modify the estimates of iron concentrations and species released through viral lysis, and potentially identify a novel receptor type for marine phage that may compete with the acquisition of siderophore-bound iron by host bacteria.
attribute NC_GLOBAL projects_0_end_date String 2019-01
attribute NC_GLOBAL projects_0_name String EAGER: Iron-Virus Interactions in the Ocean
attribute NC_GLOBAL projects_0_project_nid String 713367
attribute NC_GLOBAL projects_0_start_date String 2017-02
attribute NC_GLOBAL publisher_name String Biological and Chemical Oceanographic Data Management Office (BCO-DMO)
attribute NC_GLOBAL publisher_type String institution
attribute NC_GLOBAL sourceUrl String (local files)
attribute NC_GLOBAL standard_name_vocabulary String CF Standard Name Table v55
attribute NC_GLOBAL subsetVariables String DATE
attribute NC_GLOBAL summary String This data was collected as part of a method development study investigating the precipitation and wall loss of labeled \\u2075\\u2077Fe when added to M9 Minimal Media, which is used to grow the model bacterial species Escherichia coli. The bulk media was prepared with the same components and a portion was treated with Chelex-100 to remove metals, while the other portion remained un-chelexed. Half of each treatment was spiked with labeled \\u2075\\u2077Fe and either 0.2 \\u03bcm or 0.02 \\u03bcm filtered for comparison of the dissolved and soluble fractions. The \\u2075\\u2077Fe content was monitored over four time points for one week in a shaking incubator, under the same conditions used to culture E. coli for labeling experiments.
attribute NC_GLOBAL title String [57Fe Wall Loss Experiment] - 57Fe Wall Loss Experiment data collected as part of a method development study investigating the precipitation and wall loss of labeled 57Fe when added to M9 Minimal Media (EAGER: Iron-Virus Interactions in the Ocean)
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.3
variable DATE int
attribute DATE _FillValue int 2147483647
attribute DATE actual_range int 20171113, 20171113
attribute DATE bcodmo_name String date
attribute DATE description String Date (UTC) when media was filtered and experiment initiated (t=0), in format YYYYMMDD
attribute DATE long_name String DATE
attribute DATE nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/ADATAA01/ (external link)
attribute DATE units String unitless
variable SAMPLE_ID String
attribute SAMPLE_ID bcodmo_name String sample
attribute SAMPLE_ID description String Sample identifier designated B for un-chelexed, or C for chelexed; 1 for un-spiked with 57FeSO4, 2 for spiked with 10 uM 57FeSO4; D for dissolved (0.2 um filtered) or S for soluble (0.02 um filtered)
attribute SAMPLE_ID long_name String SAMPLE ID
attribute SAMPLE_ID nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/ACYC/ (external link)
attribute SAMPLE_ID units String unitless
variable DESCRIPTION String
attribute DESCRIPTION bcodmo_name String treatment
attribute DESCRIPTION description String Description of treatment type
attribute DESCRIPTION long_name String DESCRIPTION
attribute DESCRIPTION units String unitless
variable CHELEX String
attribute CHELEX bcodmo_name String treatment
attribute CHELEX description String Solution was treated with Chelex-100 resin (Yes) or not (No), units in Yes/No
attribute CHELEX long_name String CHELEX
attribute CHELEX units String unitless
variable Fe57_SPIKE byte
attribute Fe57_SPIKE _FillValue byte 127
attribute Fe57_SPIKE actual_range byte 0, 10
attribute Fe57_SPIKE bcodmo_name String treatment
attribute Fe57_SPIKE description String 57FeSO4 spike concentration as added to the media
attribute Fe57_SPIKE long_name String Fe57 SPIKE
attribute Fe57_SPIKE units String micromolar (uM)
variable FILTER_SIZE String
attribute FILTER_SIZE bcodmo_name String filter_size
attribute FILTER_SIZE description String Pore size used to filter media, using 0.2 um Sterivex PVDF syringe filter or 0.02 um Anatop syringe filter
attribute FILTER_SIZE long_name String FILTER SIZE
attribute FILTER_SIZE units String micrometers (um)
variable DAY byte
attribute DAY _FillValue byte 127
attribute DAY actual_range byte 0, 7
attribute DAY bcodmo_name String days
attribute DAY description String Time when treatment was sampled, t=n, units in days
attribute DAY long_name String DAY
attribute DAY units String days
variable Fe56 float
attribute Fe56 _FillValue float NaN
attribute Fe56 actual_range float 10.73, 738.92
attribute Fe56 bcodmo_name String Fe
attribute Fe56 description String Concentration of 56Fe as determined by HR-ICP-MS
attribute Fe56 long_name String Fe56
attribute Fe56 units String nanomolar (nM)
variable Fe57 float
attribute Fe57 _FillValue float NaN
attribute Fe57 actual_range float 2.13, 10857.82
attribute Fe57 bcodmo_name String Fe
attribute Fe57 description String Concentration of 57Fe as determined by HR-ICP-MS
attribute Fe57 long_name String Fe57
attribute Fe57 units String nanomolar (nM)
variable Fe57_to_Fe56 float
attribute Fe57_to_Fe56 _FillValue float NaN
attribute Fe57_to_Fe56 actual_range float 2.27, 2459.01
attribute Fe57_to_Fe56 bcodmo_name String Fe
attribute Fe57_to_Fe56 description String Ratio of 57Fe concentration to 56Fe concentration as measured by the HR-ICP-MS, multiplied by 100 (in percentage)
attribute Fe57_to_Fe56 long_name String Fe57 To Fe56
attribute Fe57_to_Fe56 units String unitless (percentage)
variable NOTES String
attribute NOTES bcodmo_name String comment
attribute NOTES description String Some samples contaminated by bacterial growth were designated as such
attribute NOTES long_name String NOTES
attribute NOTES units String unitless

 
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