http://lod.bco-dmo.org/id/dataset/861133
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
2021-09-21
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Siderophore concentrations found in supernatants of Azotobacter vinelandii str. OP, Azotobacter chroococcum str. B3, and Azotobacter chroococcum str. NCIMB 8003 from laboratory experiments in 2015
2021-10-05
publication
2021-10-05
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2021-10-05
publication
https://doi.org/10.26008/1912/bco-dmo.861133.1
Dr Francois Morel
Princeton University
principalInvestigator
Oliver Baars
Princeton University
principalInvestigator
Xinning Zhang
Princeton University
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: Morel, F. (2021) Siderophore concentrations found in supernatants of Azotobacter vinelandii str. OP, Azotobacter chroococcum str. B3, and Azotobacter chroococcum str. NCIMB 8003 from laboratory experiments in 2015. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 2) Version Date 2021-10-05 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.861133.2 [access date]
Methods and Sampling: <p><strong>Sampling and analytical procedures:</strong></p>
<p>Wild type Azotobacter chroococcum strain B3 (ATCC strain 7486) and strain NCIMB 8003 (ATCC strain 4412) were grown aerobically in a modified Burk’s medium under diazotrophic conditions by shaking at room temperature as previously described.14,48 For HR-LC-MS analysis of siderophores, the availability of Fe was limited by addition of 100 M EDTA to 0.1 M FeCl3 for AC-B3, whereas a concentration of 5 M FeCl3 was added to achieve sufficient growth with AC-8003. To study the effect of Fe sources, Fe was added as (1) 100 M EDTA and 0.1 M FeCl3; (2) 100 M EDTA and 5 M FeCl3; and (3) precipitated amorphous Fe oxides. Bacterial growth was monitored at an optical density (OD) of 620 nm (OD620nm).</p>
<p>To follow concentrations of siderophores in AC-B3, 1 mL sample aliquots were taken at different times throughout the growth, filtered through 0.2 m syringe filters, acidified (0.1% acetic acid and 0.1% formic acid) and analyzed by direct injection on a single quadrupole LC-MS system (Agilent 6120). The analysis&nbsp;of all siderophores, except for crochelin A, was performed with a C18 column (Agilent Eclipse Plus C18 3.5 m, 4.6mm x 100 mm) and a gradient of solution A (water + 0.1% FA + 0.1% acetic acid) and B (acetonitrile + 0.1% FA + 0.1% acetic acid; gradient from 0–100% A over 30 min; flow rate of 0.8 mL/min). To achieve sufficient retention on the same C18 column, the analysis of crochelin A required the use of the ion-pairing reagent heptafluorobutyric acid (HFBA) added to solutions A (water + 0.05% HFBA) and B (acetonitrile + 0.05% HFBA) with a gradient from 0–100% A over 30 min; flow rate of 0.8 mL/min. The column outflow was diverted to waste for the first 5.25 min ensuring that the sample was completely desalted before introduction into the mass spectrometer. Siderophores were quantified by single ion monitoring (SIM) using a list of target m/z values of the identified siderophores. For quantification, LC-MS peak areas were determined and converted to concentrations by calibration with standards of vibrioferrin A,16 amphibactins ACA, S, and crochelin A. For catechol siderophores and azotobactins, LC-MS and UV-vis peak areas were determined using MassHunter software (Agilent). Relative peak areas were converted to concentrations by calibration with isolated standards of vibrioferrin, 2,3-dihydroxybenzoic acid (DHBA), azotochelin,&nbsp;protochelin, and azotobactin d. Seven technical replicates of a spent medium siderophore mix ‘‘standard’’ showed relative standard deviations of &lt;10% when present at concentrations above 0.5 M. The detection limit of vibrioferrin A, amphibactins, and crochelin A in the supernatant sample was in the range of 0.02 to 0.10 M.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1657639 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1657639
completed
Dr Francois Morel
Princeton University
609-258-2416
Department of Geosciences Guyot Hall, Washington Rd.
Princeton
NJ
08544
USA
morel@princeton.edu
pointOfContact
Oliver Baars
Princeton University
609-356-8195
obaars@ncsu.edu
pointOfContact
Xinning Zhang
Princeton University
xinningz@princeton.edu
pointOfContact
asNeeded
Dataset Version: 2
Unknown
Time_days
Organism
Condition
vibrioferrin
amphibactins
crochelin_A
catechol_siderophores
azotobactins
OD620
FigRef
Agilent 6120 LC-MS (Agilent, Santa Clara, CA, USA)
theme
None, User defined
time_elapsed
sample description
treatment
abundance
optical_density
reference_paper
featureType
BCO-DMO Standard Parameters
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.
Iron uptake by marine bacteria: regulation and function of weak and strong siderophores
https://osprey.bco-dmo.org/project/856898
Iron uptake by marine bacteria: regulation and function of weak and strong siderophores
<p>NSF abstract:<br />
Organic molecules that bind and transport iron are called siderophores. Because iron is an essential trace element for biological systems and exists at very, very low concentrations in the open ocean, siderophores perform a critical role in capturing iron for cellular function. It is known that marine bacteria can produce two different types of siderophores that either tightly bind iron or only weakly do so, with different ecological consequences. This researcher will leverage an exceptional career on metal-organism interactions to examine the unsolved question of exactly what environmental and biochemical conditions (for example the availability of iron) control bacterial production of various siderophores. Results will generate significant new understanding of a critical chemical oceanographic process, and cap this researcher's groundbreaking discoveries that have built to this project. Funding for this research will also support the advancement of women in science by both providing the highest quality training of a female scientist and providing the opportunity for her to host an oceanography booth at the Princeton Plasma Physics Lab's "Young Women in Science" conference.</p>
<p>This study will use Vibrio harveyi as a model organism to investigate a variety of questions surrounding the marine bacterial production of weak and strong siderophores. To start, the investigation will look into how siderophore production is controlled by varying iron availability and quorum sensing (i.e. a coordinated response correlated to population density and/or certain signaling molecules). This also includes in-depth investigation of the impact of life phase and biochemical changes with growth as they relate to coordinated use of weak and strong siderophores. Using established protocols for genetic manipulation of V. harveyi, the researcher plans to discover how varying combinations of weak and strong siderophores maximize the uptake of iron. The broader biogeochemical implications of this study to the field of chemical oceanography, with regard to the microbial use of, and cellular responses to, many essential micronutrients in the ocean would be to significantly influence understanding of elemental distributions beyond the specific study of iron and siderophore cycling in the ocean.</p>
Bacteria Iron Siderophores
largerWorkCitation
project
eng; USA
oceans
2015-01-01
2015-01-01
laboratory
0
BCO-DMO catalogue of parameters from Siderophore concentrations found in supernatants of Azotobacter vinelandii str. OP, Azotobacter chroococcum str. B3, and Azotobacter chroococcum str. NCIMB 8003 from laboratory experiments in 2015
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/862305.rdf
Name: Time_days
Units: days
Description: <p>Sampling time from start of incubation (decimal days).</p>
http://lod.bco-dmo.org/id/dataset-parameter/862306.rdf
Name: Organism
Units: unitless
Description: <p>Species and strain of Azotobacter bacterium used in the culture (e.g. Achroococcum_8003).</p>
http://lod.bco-dmo.org/id/dataset-parameter/862307.rdf
Name: Condition
Units: unitless
Description: <p>Growth conditions were one of the following three: precipitated amorphous Fe oxides / 100 mM EDTA and 5 mM FeCl3 / 100 mM EDTA and 0.1 mM FeCl3</p>
http://lod.bco-dmo.org/id/dataset-parameter/862308.rdf
Name: vibrioferrin
Units: micromoles per liter (umol/L, uM)
Description: <p>Concentration of the siderophore vibrioferrin.</p>
http://lod.bco-dmo.org/id/dataset-parameter/862309.rdf
Name: amphibactins
Units: micromoles per liter (umol/L, uM)
Description: <p>Summed concentration of a suite of amphibactin siderophores.</p>
http://lod.bco-dmo.org/id/dataset-parameter/862310.rdf
Name: crochelin_A
Units: micromoles per liter (umol/L, uM)
Description: <p>Concentration of the siderophore crochelin A.</p>
http://lod.bco-dmo.org/id/dataset-parameter/862311.rdf
Name: catechol_siderophores
Units: micromoles per liter (umol/L, uM)
Description: <p>Summed concentration of the siderphores protochelin, azotochelin, aminochelin, and 2,3-dihydroxybenzoic acid.</p>
http://lod.bco-dmo.org/id/dataset-parameter/862312.rdf
Name: azotobactins
Units: micromoles per liter (umol/L, uM)
Description: <p>Summed concentration of various azotobactin type siderophores described in Baars, Oliver, et al. (2006).</p>
http://lod.bco-dmo.org/id/dataset-parameter/862313.rdf
Name: OD620
Units: unitless
Description: <p>Optical density of the culture measured at 620 nm</p>
http://lod.bco-dmo.org/id/dataset-parameter/862314.rdf
Name: FigRef
Units: unitless
Description: <p>Citation and figure where data are published (see Related Publications for full citation)</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
6894
https://darchive.mblwhoilibrary.org/bitstream/1912/27611/1/dataset-861133_azotobactersiderophoreconcentrations__v2.tsv
download
6894
https://darchive.mblwhoilibrary.org/bitstream/1912/27603/1/dataset-861133_azotobactersiderophoreconcentrations__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.861133.1
download
onLine
dataset
<p><strong>Sampling and analytical procedures:</strong></p>
<p>Wild type Azotobacter chroococcum strain B3 (ATCC strain 7486) and strain NCIMB 8003 (ATCC strain 4412) were grown aerobically in a modified Burk’s medium under diazotrophic conditions by shaking at room temperature as previously described.14,48 For HR-LC-MS analysis of siderophores, the availability of Fe was limited by addition of 100 M EDTA to 0.1 M FeCl3 for AC-B3, whereas a concentration of 5 M FeCl3 was added to achieve sufficient growth with AC-8003. To study the effect of Fe sources, Fe was added as (1) 100 M EDTA and 0.1 M FeCl3; (2) 100 M EDTA and 5 M FeCl3; and (3) precipitated amorphous Fe oxides. Bacterial growth was monitored at an optical density (OD) of 620 nm (OD620nm).</p>
<p>To follow concentrations of siderophores in AC-B3, 1 mL sample aliquots were taken at different times throughout the growth, filtered through 0.2 m syringe filters, acidified (0.1% acetic acid and 0.1% formic acid) and analyzed by direct injection on a single quadrupole LC-MS system (Agilent 6120). The analysis&nbsp;of all siderophores, except for crochelin A, was performed with a C18 column (Agilent Eclipse Plus C18 3.5 m, 4.6mm x 100 mm) and a gradient of solution A (water + 0.1% FA + 0.1% acetic acid) and B (acetonitrile + 0.1% FA + 0.1% acetic acid; gradient from 0–100% A over 30 min; flow rate of 0.8 mL/min). To achieve sufficient retention on the same C18 column, the analysis of crochelin A required the use of the ion-pairing reagent heptafluorobutyric acid (HFBA) added to solutions A (water + 0.05% HFBA) and B (acetonitrile + 0.05% HFBA) with a gradient from 0–100% A over 30 min; flow rate of 0.8 mL/min. The column outflow was diverted to waste for the first 5.25 min ensuring that the sample was completely desalted before introduction into the mass spectrometer. Siderophores were quantified by single ion monitoring (SIM) using a list of target m/z values of the identified siderophores. For quantification, LC-MS peak areas were determined and converted to concentrations by calibration with standards of vibrioferrin A,16 amphibactins ACA, S, and crochelin A. For catechol siderophores and azotobactins, LC-MS and UV-vis peak areas were determined using MassHunter software (Agilent). Relative peak areas were converted to concentrations by calibration with isolated standards of vibrioferrin, 2,3-dihydroxybenzoic acid (DHBA), azotochelin,&nbsp;protochelin, and azotobactin d. Seven technical replicates of a spent medium siderophore mix ‘‘standard’’ showed relative standard deviations of &lt;10% when present at concentrations above 0.5 M. The detection limit of vibrioferrin A, amphibactins, and crochelin A in the supernatant sample was in the range of 0.02 to 0.10 M.</p>
Specified by the Principal Investigator(s)
<p>Peaks were identified by a combination of their characteristic masses, retention times, and their UV-vis absorbance using MassHunter (Agilent).<br />
<br />
BCO-DMO Data Manager Processing Notes (v1):<br />
* Imported data table from file "Azotobacter_SiderophoreConcentrations.csv" into the BCO-DMO data system.<br />
* Renamed columns to meet BCO-DMO naming conventions: https://www.bco-dmo.org/page/bco-dmo-data-processing-conventions<br />
<br />
BCO-DMO Data Manager Processing Notes (v2):<br />
* Reference in abstract corrected from 2016 to 2019.<br />
* Data column FigReg from&nbsp;"Azotobacter_SiderophoreConcentrations.csv" to&nbsp; replace "ZhangBaars_Metallomics_2018_Fig6" with&nbsp;"ZhangBaars_Metallomics_2019_Fig6"</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
Agilent 6120 LC-MS (Agilent, Santa Clara, CA, USA)
Agilent 6120 LC-MS (Agilent, Santa Clara, CA, USA)
PI Supplied Instrument Name: Agilent 6120 LC-MS (Agilent, Santa Clara, CA, USA) Instrument Name: Mass Spectrometer Instrument Short Name:Mass Spec Instrument Description: General term for instruments used to measure the mass-to-charge ratio of ions; generally used to find the composition of a sample by generating a mass spectrum representing the masses of sample components. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB16/