http://lod.bco-dmo.org/id/dataset/732864
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2018-04-04
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
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
2018-04-05
publication
2018-04-05
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2020-02-11
publication
https://doi.org/10.1575/1912/bco-dmo.732864.1
Mya Breitbart
University of South Florida
principalInvestigator
Kristen Nicolle Buck
University of South Florida
principalInvestigator
Chelsea Bonnain
University of South Florida
principalInvestigator
Salvatore Caprara
University of South Florida
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Breitbart, M., Buck, K., Bonnain, C., Caprara, S. (2018) 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. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2018-04-05 [if applicable, indicate subset used]. doi:10.1575/1912/bco-dmo.732864.1 [access date]
Dataset Description: <p>This data was collected as part of a method development study investigating the precipitation and wall loss of labeled ⁵⁷Fe when added to M9 Minimal Media, which is used to grow the model bacterial species <em>Escherichia coli.</em> 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 ⁵⁷Fe and either 0.2 μm or 0.02 μm filtered for comparison of the dissolved and soluble fractions. The ⁵⁷Fe content was monitored over four time points for one week in a shaking incubator, under the same conditions used to culture <em>E. coli</em> for labeling experiments.</p> Methods and Sampling: <p>Refer to Supplemental File, "57Fe Wall Loss Experiment diagram" for the steps indicated in <strong>bold</strong>.</p>
<p>All materials were soaked overnight with heating in 1.5% Citrad Citric Acid liquid cleaner in deionized water, rinsed in RO water, and soaked in 10% HCl in Milli-Q ultrapure water for one week (due to time constraints), then rinsed with MilliQ ultrapure water, let dry in an AirClean 400 work station overnight, and double-bagged in polyethylene bags (Mellett et al., 2017). M9 Minimal Media for bacterial cultures was made using Milli-Q ultrapure water, containing final concentrations of 33.7 mM Na₂HPO₄·2H₂O, 22 mM KH₂PO₄, 8.56 mM NaCl, 18.7 mM NH₄Cl, 0.1 M magnesium chloride, 0.1 M calcium chloride, 2 mg/ml Thiamine HCl in 70% EtOH, and 20% Glucose (Kutter &amp; Sulakvelidze, 2004). Half of the media was chelexed using Chelex-100 resin (Pai et al., 1988) that was not acid-cleaned (<strong>C</strong>), and half remained un-chelexed (<strong>B</strong>). Half of each treatment was spiked with 10 µM labeled ⁵⁷FeSO₄(<strong>2</strong>) while half remained un-spiked (<strong>1</strong>). A volume of 25 ml was then filtered through either a 0.2 µm Sterivex PVDF syringe filter for the dissolved fraction (<strong>D</strong>), or a 0.02 µm Whatman Anatop syringe filter for the soluble fraction (<strong>S</strong>) (Gledhill &amp; Buck, 2012). Samples were directly filtered into trace metal clean polycarbonate Erlenmeyer flasks, placed in a clean bag with a small opening to vent, and left shaking at 37 °C for one week. Samples of each treatment were taken initially, then after the 1st, 3rd, and 7th days (t= 00, 01, 03, 07). The samples were diluted, acidified, and analyzed using an ELEMENT XR High Resolution Inductively Coupled Plasma Mass Spectrometer (HR-ICP-MS). The limit of detection (LOD) for ⁵⁶Fe and ⁵⁷Fe were 0.3 nM and 0.012 nM, respectively (Shrivastava &amp; Gupta, 2011).</p>
<p><strong>Problem Report:</strong><br />
The original measurements of the M9 minimal media ⁵⁶Fe contamination was high, so in an attempt to lower background contamination the media was chelexed. However, the Chelex-100 resin was not rinsed with acid, so was less active for removal of metals. This resulted in higher than expected background concentrations of metals.</p>
<p>Three samples were contaminated with bacterial growth (as indicated by visual turbidity and confirmed using SYBR nucleic acid stain and epifluorescence microscopy) over the course of the week. On t=3, sample B2 was contaminated. By t=7, sample B1D and B1S were contaminated.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1722761 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1722761
completed
Mya Breitbart
University of South Florida
(727) 553-3520
USF College of Marine Sciences 140 7th Avenue South
St Petersburg
FL
33701
USA
mya@marine.usf.edu
pointOfContact
Kristen Nicolle Buck
University of South Florida
541-737-7401
2651 SW Orchard Avenue CEOAS
Corvallis
OR
97331
USA
kristen.buck@oregonstate.edu
pointOfContact
Chelsea Bonnain
University of South Florida
727-553-1538
140 7th Avenue South KRC 2109
St. Petersburg
FL
33701
USA
pointOfContact
Salvatore Caprara
University of South Florida
capraras@oregonstate.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
DATE
SAMPLE_ID
DESCRIPTION
CHELEX
Fe57_SPIKE
FILTER_SIZE
DAY
Fe56
Fe57
Fe57_to_Fe56
NOTES
ELEMENT XR High Resolution Inductively Coupled Plasma Mass Spectrometer
theme
None, User defined
date
sample identification
treatment
filter_size
days
Iron
comments
featureType
BCO-DMO Standard Parameters
Inductively Coupled Plasma Mass Spectrometer
instrument
BCO-DMO Standard Instruments
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
EAGER: Iron-Virus Interactions in the Ocean
https://osprey.bco-dmo.org/project/713367
EAGER: Iron-Virus Interactions in the Ocean
<p>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.</p>
<p>Building 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.</p>
Fe-Virus
largerWorkCitation
project
eng; USA
biota
oceans
2017-11-13
2017-11-13
0
BCO-DMO catalogue of parameters from 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
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/732879.rdf
Name: DATE
Units: unitless
Description: <p>Date (UTC) when media was filtered and experiment initiated (t=0), in format YYYYMMDD</p>
http://lod.bco-dmo.org/id/dataset-parameter/732880.rdf
Name: SAMPLE_ID
Units: unitless
Description: <p>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)</p>
http://lod.bco-dmo.org/id/dataset-parameter/732881.rdf
Name: DESCRIPTION
Units: unitless
Description: <p>Description of treatment type</p>
http://lod.bco-dmo.org/id/dataset-parameter/732882.rdf
Name: CHELEX
Units: unitless
Description: <p>Solution was treated with Chelex-100 resin (Yes) or not (No), units in Yes/No</p>
http://lod.bco-dmo.org/id/dataset-parameter/732883.rdf
Name: Fe57_SPIKE
Units: micromolar (uM)
Description: <p>57FeSO4 spike concentration as added to the media</p>
http://lod.bco-dmo.org/id/dataset-parameter/732884.rdf
Name: FILTER_SIZE
Units: micrometers (um)
Description: <p>Pore size used to filter media, using 0.2 um Sterivex PVDF syringe filter or 0.02 um Anatop syringe filter</p>
http://lod.bco-dmo.org/id/dataset-parameter/732885.rdf
Name: DAY
Units: days
Description: <p>Time when treatment was sampled, t=n, units in days</p>
http://lod.bco-dmo.org/id/dataset-parameter/732886.rdf
Name: Fe56
Units: nanomolar (nM)
Description: <p>Concentration of 56Fe as determined by HR-ICP-MS</p>
http://lod.bco-dmo.org/id/dataset-parameter/732887.rdf
Name: Fe57
Units: nanomolar (nM)
Description: <p>Concentration of 57Fe as determined by HR-ICP-MS</p>
http://lod.bco-dmo.org/id/dataset-parameter/732888.rdf
Name: Fe57_to_Fe56
Units: unitless (percentage)
Description: <p>Ratio of 57Fe concentration to 56Fe concentration as measured by the HR-ICP-MS, multiplied by 100 (in percentage)</p>
http://lod.bco-dmo.org/id/dataset-parameter/732889.rdf
Name: NOTES
Units: unitless
Description: <p>Some samples contaminated by bacterial growth were designated as such</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
4889
https://darchive.mblwhoilibrary.org/bitstream/1912/25362/1/dataset-732864_57fe-wall-loss-experiment__v1.tsv
download
https://doi.org/10.1575/1912/bco-dmo.732864.1
download
onLine
dataset
<p>Refer to Supplemental File, "57Fe Wall Loss Experiment diagram" for the steps indicated in <strong>bold</strong>.</p>
<p>All materials were soaked overnight with heating in 1.5% Citrad Citric Acid liquid cleaner in deionized water, rinsed in RO water, and soaked in 10% HCl in Milli-Q ultrapure water for one week (due to time constraints), then rinsed with MilliQ ultrapure water, let dry in an AirClean 400 work station overnight, and double-bagged in polyethylene bags (Mellett et al., 2017). M9 Minimal Media for bacterial cultures was made using Milli-Q ultrapure water, containing final concentrations of 33.7 mM Na₂HPO₄·2H₂O, 22 mM KH₂PO₄, 8.56 mM NaCl, 18.7 mM NH₄Cl, 0.1 M magnesium chloride, 0.1 M calcium chloride, 2 mg/ml Thiamine HCl in 70% EtOH, and 20% Glucose (Kutter &amp; Sulakvelidze, 2004). Half of the media was chelexed using Chelex-100 resin (Pai et al., 1988) that was not acid-cleaned (<strong>C</strong>), and half remained un-chelexed (<strong>B</strong>). Half of each treatment was spiked with 10 µM labeled ⁵⁷FeSO₄(<strong>2</strong>) while half remained un-spiked (<strong>1</strong>). A volume of 25 ml was then filtered through either a 0.2 µm Sterivex PVDF syringe filter for the dissolved fraction (<strong>D</strong>), or a 0.02 µm Whatman Anatop syringe filter for the soluble fraction (<strong>S</strong>) (Gledhill &amp; Buck, 2012). Samples were directly filtered into trace metal clean polycarbonate Erlenmeyer flasks, placed in a clean bag with a small opening to vent, and left shaking at 37 °C for one week. Samples of each treatment were taken initially, then after the 1st, 3rd, and 7th days (t= 00, 01, 03, 07). The samples were diluted, acidified, and analyzed using an ELEMENT XR High Resolution Inductively Coupled Plasma Mass Spectrometer (HR-ICP-MS). The limit of detection (LOD) for ⁵⁶Fe and ⁵⁷Fe were 0.3 nM and 0.012 nM, respectively (Shrivastava &amp; Gupta, 2011).</p>
<p><strong>Problem Report:</strong><br />
The original measurements of the M9 minimal media ⁵⁶Fe contamination was high, so in an attempt to lower background contamination the media was chelexed. However, the Chelex-100 resin was not rinsed with acid, so was less active for removal of metals. This resulted in higher than expected background concentrations of metals.</p>
<p>Three samples were contaminated with bacterial growth (as indicated by visual turbidity and confirmed using SYBR nucleic acid stain and epifluorescence microscopy) over the course of the week. On t=3, sample B2 was contaminated. By t=7, sample B1D and B1S were contaminated.</p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Processing:</strong><br />
- modified parameter names to conform with BCO-DMO naming conventions&nbsp;(replaced spaces with underscores, removed puncutation, placed letters before numbers);<br />
- formatted year to yyyymmdd;<br />
- replaced blanks with "nd";<br />
- replaced mu symbol with u in DESCRIPTION column.</p>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
ELEMENT XR High Resolution Inductively Coupled Plasma Mass Spectrometer
ELEMENT XR High Resolution Inductively Coupled Plasma Mass Spectrometer
PI Supplied Instrument Name: ELEMENT XR High Resolution Inductively Coupled Plasma Mass Spectrometer PI Supplied Instrument Description:ELEMENT XR High Resolution Inductively Coupled Plasma Mass Spectrometer (HR-ICP-MS) Instrument Name: Inductively Coupled Plasma Mass Spectrometer Instrument Short Name:ICP Mass Spec Instrument Description: 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. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB15/