http://lod.bco-dmo.org/id/dataset/861145
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 Rhodopseudomonas palustris str. CGA009 grown under different aerobic and anaerobic conditions from laboratory experiments in 2016
2021-09-21
publication
2021-09-21
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2021-10-05
publication
https://doi.org/10.26008/1912/bco-dmo.861145.1
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., Baars, O., Zhang, X. (2021) Siderophore concentrations found in supernatants of Rhodopseudomonas palustris str. CGA009 grown under different aerobic and anaerobic conditions from laboratory experiments in 2016. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2021-09-21 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.861145.1 [access date]
Methods and Sampling: <p>&nbsp;</p>
<p><strong>Sampling and analytical procedures:</strong></p>
<p>R. palustris strain CGA009 was grown in batch culture at room temperature in the presence or absence of added iron and molybdate under (i) aerobic chemoheterotrophic growth supplemented with 2 mM ammonium, (ii) photoheterotrophic nitrogen-fixing growth under anaerobic conditions and (iii) photoheterotrophic nitrogen-fixing under anaerobic conditions with added NaS and cysteine as reductants. Aerobic cultures (30 ml) in Nunc flasks (75 cm2) were shaken at 45 rpm. Before the start of the incubations, bacteria were adjusted for &gt;12 generations (&gt; 2 transfers into fresh media) to the growth conditions. Photoheterotrophic anaerobic cultures (10 ml) were grown with a constant light source in Baltch-type glass tubes (25 ml volume) with a nitrogen headspace, sealed with a butyl rubber stopper. For all anaerobic incubations, bacteria were grown for &gt;30 generations (5 transfers into fresh media) in media supplemented with Fe but without Mo. This was necessary to dilute Mo originally present in the medium to levels low enough for a clear measurable Mo growth limitation. All incubations were performed in duplicate. Bacterial growth was monitored spectrophotometrically as optical density at 660 nm. To confirm the absence of oxygen in rhodopetrobactin producing cultures, samples were taken occasionally in a glovebox (COY&nbsp;Vinyl) for measurement of dissolved oxygen with an oxygen probe (Hach HQ40d) and redox potential with an ORP probe (Hana HI-98120) or the redox indicator resazurine. Dissolved oxygen concentrations were always below the detection limit of the oxygen sensor (&lt; 0.02 mg/l). Redox potential measurements with the ORP probe in anaerobic treatments were &lt;90 mV and &lt;150 mV vs. NHE in media without and with added reductants. Reductant additions to anaerobic media clarified the redox indicator resazurine indicating a redox potential &lt;110 mV and had a noticeable H2S smell.</p>
<p>Bacterial incubation samples (1 ml) were collected throughout growth, filtered through 0.2 m syringe filters (Millipore MILLEX GP 0.22 m) and the supernatants were stored at 2208C until analysis. Quantification of rhodopetrobactins was performed on a single quadrupole LC-MS system (Agilent 6120), equipped with a diode array detector. Prior to analysis, the samples were acidified with 0.1% acetic acid and 0.1% formic acid. Samples (100 L) were injected onto a C18 column (Agilent Eclipse Plus C18,&nbsp;3.5 m, 4.6x100 mm) equipped with a matching guard column. The separation proceeded with A and B solutions (solution A: water,&nbsp;0.1% formic acid, 0.1% acetic acid; solution B: acetonitrile, 0.1% formic acid, 0.1% acetic acid) over 30 min, at a flow rate of 0.8 ml/min.&nbsp;Using a 6-port valve, the column outflow was diverted to waste for the first 5.25 min ensuring that the sample was desalted before introduction into the mass spectrometer. For quantification, UV/Vis traces were extracted at 294 nm, and peak areas corresponding to the elution of rhodopetrobactin A and B were determined using MassHunter software (Agilent). Concentrations were determined with standard solutions of 3,4-dihydroxybenzoic acid and isolated rhodopetrobactins. The detection limit for rhodopetrobactins was approximately 0.1 M.</p>
<p>Iron concentrations in the supernatants were measured by inductively coupled plasma-mass spectrometry (Thermo iCAP-Q in KED mode) after acidification (10% HNO3) and dilution (1:5). The detection limit for iron (<sup>56</sup>Fe) was approximately 0.065 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: 1
Unknown
Time_days
Condition
rhodopetrobactin_A
rhodopetrobactin_B
OD660
dissolvedFe
FigRef
Agilent 6120 LC-MS (Agilent, Santa Clara, CA, USA)
theme
None, User defined
time_elapsed
treatment
abundance
optical_density
Iron
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
2016-01-01
2016-01-01
laboratory
0
BCO-DMO catalogue of parameters from Siderophore concentrations found in supernatants of Rhodopseudomonas palustris str. CGA009 grown under different aerobic and anaerobic conditions from laboratory experiments in 2016
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/862298.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/862299.rdf
Name: Condition
Units: unitless
Description: <p>Growth conditions were one of the following: (a) Aerobic and chemoheterotrophic | (b) Anaerobic photoheterotrophic N2-fixing | (c) Anaerobic photoheterotrophic N2-fixing with a chemically reduced medium using Na2S and cysteine. Each of the above conditions was micronutrient replete (+Fe/+Mo) or limited for either Fe (-Fe/+Mo), Mo (+Fe/-Mo) or both micronutrients (-Fe/-Mo).</p>
http://lod.bco-dmo.org/id/dataset-parameter/862300.rdf
Name: rhodopetrobactin_A
Units: micromoles per liter (umol/L, uM)
Description: <p>Concentration of the siderophore rhodopetrobactin A.</p>
http://lod.bco-dmo.org/id/dataset-parameter/862301.rdf
Name: rhodopetrobactin_B
Units: micromoles per liter (umol/L, uM)
Description: <p>Concentration of the siderophore rhodopetrobactin B.</p>
http://lod.bco-dmo.org/id/dataset-parameter/862302.rdf
Name: OD660
Units: micromoles per liter (umol/L, uM)
Description: <p>Optical density of the culture measured at 660 nm.</p>
http://lod.bco-dmo.org/id/dataset-parameter/862303.rdf
Name: dissolvedFe
Units: micromoles per liter (umol/L, uM)
Description: <p>Concentration dissolved iron</p>
http://lod.bco-dmo.org/id/dataset-parameter/862304.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
3041
https://darchive.mblwhoilibrary.org/bitstream/1912/27604/1/dataset-861145_rpalustrissiderophoreconcentrations__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.861145.1
download
onLine
dataset
<p>&nbsp;</p>
<p><strong>Sampling and analytical procedures:</strong></p>
<p>R. palustris strain CGA009 was grown in batch culture at room temperature in the presence or absence of added iron and molybdate under (i) aerobic chemoheterotrophic growth supplemented with 2 mM ammonium, (ii) photoheterotrophic nitrogen-fixing growth under anaerobic conditions and (iii) photoheterotrophic nitrogen-fixing under anaerobic conditions with added NaS and cysteine as reductants. Aerobic cultures (30 ml) in Nunc flasks (75 cm2) were shaken at 45 rpm. Before the start of the incubations, bacteria were adjusted for &gt;12 generations (&gt; 2 transfers into fresh media) to the growth conditions. Photoheterotrophic anaerobic cultures (10 ml) were grown with a constant light source in Baltch-type glass tubes (25 ml volume) with a nitrogen headspace, sealed with a butyl rubber stopper. For all anaerobic incubations, bacteria were grown for &gt;30 generations (5 transfers into fresh media) in media supplemented with Fe but without Mo. This was necessary to dilute Mo originally present in the medium to levels low enough for a clear measurable Mo growth limitation. All incubations were performed in duplicate. Bacterial growth was monitored spectrophotometrically as optical density at 660 nm. To confirm the absence of oxygen in rhodopetrobactin producing cultures, samples were taken occasionally in a glovebox (COY&nbsp;Vinyl) for measurement of dissolved oxygen with an oxygen probe (Hach HQ40d) and redox potential with an ORP probe (Hana HI-98120) or the redox indicator resazurine. Dissolved oxygen concentrations were always below the detection limit of the oxygen sensor (&lt; 0.02 mg/l). Redox potential measurements with the ORP probe in anaerobic treatments were &lt;90 mV and &lt;150 mV vs. NHE in media without and with added reductants. Reductant additions to anaerobic media clarified the redox indicator resazurine indicating a redox potential &lt;110 mV and had a noticeable H2S smell.</p>
<p>Bacterial incubation samples (1 ml) were collected throughout growth, filtered through 0.2 m syringe filters (Millipore MILLEX GP 0.22 m) and the supernatants were stored at 2208C until analysis. Quantification of rhodopetrobactins was performed on a single quadrupole LC-MS system (Agilent 6120), equipped with a diode array detector. Prior to analysis, the samples were acidified with 0.1% acetic acid and 0.1% formic acid. Samples (100 L) were injected onto a C18 column (Agilent Eclipse Plus C18,&nbsp;3.5 m, 4.6x100 mm) equipped with a matching guard column. The separation proceeded with A and B solutions (solution A: water,&nbsp;0.1% formic acid, 0.1% acetic acid; solution B: acetonitrile, 0.1% formic acid, 0.1% acetic acid) over 30 min, at a flow rate of 0.8 ml/min.&nbsp;Using a 6-port valve, the column outflow was diverted to waste for the first 5.25 min ensuring that the sample was desalted before introduction into the mass spectrometer. For quantification, UV/Vis traces were extracted at 294 nm, and peak areas corresponding to the elution of rhodopetrobactin A and B were determined using MassHunter software (Agilent). Concentrations were determined with standard solutions of 3,4-dihydroxybenzoic acid and isolated rhodopetrobactins. The detection limit for rhodopetrobactins was approximately 0.1 M.</p>
<p>Iron concentrations in the supernatants were measured by inductively coupled plasma-mass spectrometry (Thermo iCAP-Q in KED mode) after acidification (10% HNO3) and dilution (1:5). The detection limit for iron (<sup>56</sup>Fe) was approximately 0.065 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:<br />
* Imported data table from file "Rpalustris_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</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/