http://lod.bco-dmo.org/id/dataset/861154
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)
Amphi-enterobactins and related siderophore concentrations found in Vibrio harveyi supernatants and pellets from laboratory experiments in 2017
2021-10-01
publication
2021-10-01
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2021-10-05
publication
https://doi.org/10.26008/1912/bco-dmo.861154.1
Dr Francois Morel
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) Amphi-enterobactins and related siderophore concentrations found in Vibrio harveyi supernatants and pellets from laboratory experiments in 2017. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2021-10-01 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.861154.1 [access date]
Methods and Sampling: <p><strong>Sampling and analytical procedures:</strong></p>
<p>V. harveyi cells were cultured at 30C with shaking at 200 RPM. Growth experiments were conducted using a fully chemically defined artificial seawater medium consisting of basic salts (3x10-1 M NaCl, 1.05x10-2 M CaCl2Ÿ2H2O, 5x10-2 M MgSO4Ÿ7H2O, 4.85x10-4 M H3BO3) as well as 1x10-4 M K2HPO4, 6.51x10-2 M glycerol, 2.65 x10-8 M riboflavin, 2.96 x 10-6 M thiamine and Aquil trace metals without added Fe. Aquil trace metals contain 100 M EDTA, background Fe concentrations were determined by inductively coupled plasma MS (ICP-MS) to be ~100 nM. Nitrogen was added as MEM essential and non-essential amino acids (Sigma M5550, 92 mL L-1 ; Sigma M7145, 46 mL L-1 ). All cells were pre-cultured for ~24 hours in low Fe medium before the start of experiments to exhaust background trace metal supplies.</p>
<p>For quantification of siderophores ~50 mL of V. harveyi culture was centrifuged at 16,000 xg for 6 minutes. Supernatant samples were decanted, filtered (0.2 m) and acidified with 0.1% formic acid. Samples were then extracted using Oasis HLB (Waters) columns with the following conditions: 20 mL methanol, 20 mL MilliQ H2O, 50 mL sample, 20 mL 0.03% trifluoroacetic acid, 10 mL 0.03% formic acid and final elution with 30 mL of 40% methanol. Cell pellets were extracted overnight (~18 hours) with 5 mL of 80% methanol with 0.1% formic acid. Four mL of the resulting supernatant was diluted to 20% methanol with acidic (0.1% formic acid) MilliQ and extracted using an HLB column: 20 mL methanol, 20 mL MilliQ, 16 mL sample, 20 mL MilliQ and elution with 30 mL of 100% methanol. Samples were dried under vacuum (SpeedVac, ThermoFisher) and resuspended in either 1 mL MilliQ (supernatants) or 1 mL of 80% methanol (pellets). &nbsp;Extracted samples were acidified (0.1% acetic acid and 0.1% formic acid) and analyzed using electrospray-ionization LC-MS (Agilent 6120, Agilent, Santa Clara, CA, USA), with a UV-vis diode array detector and a C18 column (Agilent 4 Eclipse Plus C18, 3.5 m, 4.6 mm x 100 mm). Injected samples (100 L) were separated using a gradient of solutions A and B (A: water, 1% formic acid, 1% acetic acid, 1% acetonitrile; solution B: acetonitrile, 1% formic acid, 1% acetic acid, 2% water; gradient 0-100% B) over 30 min, with a flow rate of 0.8 mL min-1 . Full-scan mass spectra were collected in both positive- and negative-ion (m/z=140-1400).<br />
<br />
Location: Laboratory experiments conducted at Princeton University.</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
asNeeded
Dataset Version: 1
Unknown
Time
Strain
Siderophore
Conc
STDEVSiderophore
OD500
STDEVOD
FigRef
Agilent 6120 LC-MS (Agilent, Santa Clara, CA, USA)
theme
None, User defined
time_elapsed
sample description
abundance
standard deviation
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
2017-01-01
2017-01-01
laboratory
0
BCO-DMO catalogue of parameters from Amphi-enterobactins and related siderophore concentrations found in Vibrio harveyi supernatants and pellets from laboratory experiments in 2017
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/862315.rdf
Name: Time
Units: hours
Description: <p>Sampling time from start of incubation (decimal hours).</p>
http://lod.bco-dmo.org/id/dataset-parameter/862316.rdf
Name: Strain
Units: unitless
Description: <p>Vibrio harveyi strain used. BB120 is the wild type strain (BAA-1116), JAF548 has a mutation that prevents it from responding to quorum sensing molecules (see Lilley and Bassler, 2000)</p>
http://lod.bco-dmo.org/id/dataset-parameter/862317.rdf
Name: Siderophore
Units: unitless
Description: <p>Specific siderophore being quantified. Amph-Ent refers to m/z 965</p>
http://lod.bco-dmo.org/id/dataset-parameter/862318.rdf
Name: Conc
Units: micromoles per liter (umol/L, uM)
Description: <p>Siderophore concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/862319.rdf
Name: STDEVSiderophore
Units: micromoles per liter (umol/L, uM)
Description: <p>Standard deviation of biological duplicates for Siderophore concentration ("Conc" column).</p>
http://lod.bco-dmo.org/id/dataset-parameter/862320.rdf
Name: OD500
Units: unitless
Description: <p>Optical density of the culture measured at 500 nm</p>
http://lod.bco-dmo.org/id/dataset-parameter/862321.rdf
Name: STDEVOD
Units: unitless
Description: <p>Standard deviation of biological duplicates for optical density ("OD500" column).</p>
http://lod.bco-dmo.org/id/dataset-parameter/862322.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
1968
https://darchive.mblwhoilibrary.org/bitstream/1912/27602/1/dataset-861154_vharveyisiderophoreconcentrations__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.861154.1
download
onLine
dataset
<p><strong>Sampling and analytical procedures:</strong></p>
<p>V. harveyi cells were cultured at 30C with shaking at 200 RPM. Growth experiments were conducted using a fully chemically defined artificial seawater medium consisting of basic salts (3x10-1 M NaCl, 1.05x10-2 M CaCl2Ÿ2H2O, 5x10-2 M MgSO4Ÿ7H2O, 4.85x10-4 M H3BO3) as well as 1x10-4 M K2HPO4, 6.51x10-2 M glycerol, 2.65 x10-8 M riboflavin, 2.96 x 10-6 M thiamine and Aquil trace metals without added Fe. Aquil trace metals contain 100 M EDTA, background Fe concentrations were determined by inductively coupled plasma MS (ICP-MS) to be ~100 nM. Nitrogen was added as MEM essential and non-essential amino acids (Sigma M5550, 92 mL L-1 ; Sigma M7145, 46 mL L-1 ). All cells were pre-cultured for ~24 hours in low Fe medium before the start of experiments to exhaust background trace metal supplies.</p>
<p>For quantification of siderophores ~50 mL of V. harveyi culture was centrifuged at 16,000 xg for 6 minutes. Supernatant samples were decanted, filtered (0.2 m) and acidified with 0.1% formic acid. Samples were then extracted using Oasis HLB (Waters) columns with the following conditions: 20 mL methanol, 20 mL MilliQ H2O, 50 mL sample, 20 mL 0.03% trifluoroacetic acid, 10 mL 0.03% formic acid and final elution with 30 mL of 40% methanol. Cell pellets were extracted overnight (~18 hours) with 5 mL of 80% methanol with 0.1% formic acid. Four mL of the resulting supernatant was diluted to 20% methanol with acidic (0.1% formic acid) MilliQ and extracted using an HLB column: 20 mL methanol, 20 mL MilliQ, 16 mL sample, 20 mL MilliQ and elution with 30 mL of 100% methanol. Samples were dried under vacuum (SpeedVac, ThermoFisher) and resuspended in either 1 mL MilliQ (supernatants) or 1 mL of 80% methanol (pellets). &nbsp;Extracted samples were acidified (0.1% acetic acid and 0.1% formic acid) and analyzed using electrospray-ionization LC-MS (Agilent 6120, Agilent, Santa Clara, CA, USA), with a UV-vis diode array detector and a C18 column (Agilent 4 Eclipse Plus C18, 3.5 m, 4.6 mm x 100 mm). Injected samples (100 L) were separated using a gradient of solutions A and B (A: water, 1% formic acid, 1% acetic acid, 1% acetonitrile; solution B: acetonitrile, 1% formic acid, 1% acetic acid, 2% water; gradient 0-100% B) over 30 min, with a flow rate of 0.8 mL min-1 . Full-scan mass spectra were collected in both positive- and negative-ion (m/z=140-1400).<br />
<br />
Location: Laboratory experiments conducted at Princeton University.</p>
Specified by the Principal Investigator(s)
<p>Peaks related to amphi-enterobactins were identified by a combination of their characteristic masses and their absorbance at 310 nm using MassHunter (Agilent).<br />
<br />
BCO-DMO Data Manager Processing Notes:<br />
* Imported data table from file "Vharveyi-SiderophoreConcentrations.csv" into the BCO-DMO data system.<br />
* Renamed columns to meet BCO-DMO naming conventions:&nbsp;https://www.bco-dmo.org/page/bco-dmo-data-processing-conventions</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/