1b:I[42426,["/_next/static/immutable/chunks/1xctgzqre-wsy.js","/_next/static/immutable/chunks/06_-wz6pdtp2b.js","/_next/static/immutable/chunks/30e52g49hg40p.js","/_next/static/immutable/chunks/02yq6tul2z-oh.js","/_next/static/immutable/chunks/10bx_ec2vj7n_.js","/_next/static/immutable/chunks/33bfn03fo8xnt.js","/_next/static/immutable/chunks/0tfjf78scu61b.js","/_next/static/immutable/chunks/31xnvej4n1bi9.js"],"default"] 1c:T9cb,

Sampling and analytical procedures:

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.

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). 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).

Location: Laboratory experiments conducted at Princeton University.

1d:T90d,NSF abstract: 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. 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.6:["$","$L1b",null,{"dataset":{"_id":"861154","description":"","problem":"","acquisition":"$1c","processing":"

Peaks related to amphi-enterobactins were identified by a combination of their characteristic masses and their absorbance at 310 nm using MassHunter (Agilent).

BCO-DMO Data Manager Processing Notes:
\n* Imported data table from file \"Vharveyi-SiderophoreConcentrations.csv\" into the BCO-DMO data system.
\n* Renamed columns to meet BCO-DMO naming conventions: https://www.bco-dmo.org/page/bco-dmo-data-processing-conventions

\n","bcodmoProcessing":"","title":"Amphi-enterobactins and related siderophore concentrations found in Vibrio harveyi supernatants and pellets from laboratory experiments in 2017","nickname":"Vharveyi_SiderophoreConcentrations","dataUrl":"","currentState":"Final no updates expected","currentStateId":"7","validated":true,"restricted":false,"version":"1","version_date":"2021-10-01T04:00:00.000Z","abstract":"Amphi-enterobactins and related siderophore concentrations found in Vibrio harveyi supernatants and pellets from laboratory experiments in 2017. These data were published in McRose et al. (2018, Fig. 4).","citation":"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]","citationParts":{"identifier":"doi:10.26008/1912/bco-dmo.861154.1","versionDate":"2021-10-01","versionId":"1","year":"2021","title":"Amphi-enterobactins and related siderophore concentrations found in Vibrio harveyi supernatants and pellets from laboratory experiments in 2017","authors":"Morel, F.","publisher":"Biological and Chemical Oceanography Data Management Office (BCO-DMO)."},"doi":"10.26008/1912/bco-dmo.861154.1","release_date":null,"field_dataset_location":"","temporal_extent":{"start":"2017-01-01T05:00:00.000Z","end":"2017-01-01T05:00:00.000Z"},"temporal":{"resolution":"time:unitYear","type":"time:Instant","start":{"value":"","label":""},"end":{"value":"","label":""}},"spatial_extent":{"shape":"","center":{"latitude":0,"longitude":0},"wkt":"","north":0,"east":0,"south":0,"west":0},"dataset_type":["experimental"],"keywords":["oceans"],"data_files":[{"id":"903492","title":"vharveyi_conc.csv","url":"https://datadocs.bco-dmo.org/dataset/861154/file/ZZZgxXgfD1XPz5/vharveyi_conc.csv","showTableUrl":"https://www.bco-dmo.org/dataset/861154/data/view/903492","description":"Primary data file for dataset ID 861154","filename":"vharveyi_conc.csv","bytesize":1968,"checksum":{"value":"9e5255118a70dd884e1093eedfc6c8dd","Algorithm":{"_id":"190","name":"MD5"}},"mimetype":"text/csv","fileType":{"_id":"192","name":"Comma Separated Values (.csv)"},"isErddap":"","date":"","isPublicDuringEmbargo":false,"primaryDataFile":true,"showTable":true,"restricted":false}],"supplemental_files":[],"roles":[{"role":{"_id":"138","name":"Principal Investigator"},"performedBy":{"_id":"564738","name":"Dr Francois Morel"},"performedAtOrganization":{"_id":"61","name":"Princeton University"}},{"role":{"_id":"128","name":"Student"},"performedBy":{"_id":"861204","name":"Darcy McRose"},"performedAtOrganization":{"_id":"61","name":"Princeton University"}},{"role":{"_id":"133","name":"Contact"},"performedBy":{"_id":"861204","name":"Darcy McRose"},"performedAtOrganization":{"_id":"61","name":"Princeton University"}},{"role":{"_id":"145","name":"BCO-DMO Data Manager"},"performedBy":{"_id":"643627","name":"Amber D. York"},"performedAtOrganization":{"_id":"191","name":"Woods Hole Oceanographic Institution"}}],"deployments":[],"funding":[{"_id":"856897","name":"OCE-1657639","fundingSource":{"_id":"355","name":"NSF Division of Ocean Sciences"},"url":"https://www.nsf.gov/awardsearch/show-award?AWD_ID=1657639"}],"instruments":[{"_id":"861160","name":"Agilent 6120 LC-MS (Agilent, Santa Clara, CA, USA)","description":"","type_id":"685","type_name":"Mass Spectrometer","type_desc":"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.","type_acronym":"Mass Spec"}],"parameters":[{"_id":"862315","name":"Time","format":"","frictionlessType":"string","description":"

Sampling time from start of incubation (decimal hours).

","units":{"_id":"","name":"hours"},"type":{"_id":"1838","name":"time_elapsed","description":"

Elapsed time. Units can be seconds, minutes, etc.

"}},{"_id":"862316","name":"Strain","format":"","frictionlessType":"string","description":"

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)

","units":{"_id":"","name":"unitless"},"type":{"_id":"1741","name":"sample_descrip","description":"

text description or other traits of the sample collected

"}},{"_id":"862317","name":"Siderophore","format":"","frictionlessType":"string","description":"

Specific siderophore being quantified. Amph-Ent refers to m/z 965

","units":{"_id":"","name":"unitless"},"type":{"_id":"1741","name":"sample_descrip","description":"

text description or other traits of the sample collected

"}},{"_id":"862318","name":"Conc","format":"","frictionlessType":"number","description":"

Siderophore concentration

","units":{"_id":"","name":"micromoles per liter (umol/L, uM)"},"type":{"_id":"735","name":"abundance","description":"

Amount (number, mass, diversity/species variation) of the specific taxa/group counted per unit area or volume

"}},{"_id":"862319","name":"STDEVSiderophore","format":"","frictionlessType":"number","description":"

Standard deviation of biological duplicates for Siderophore concentration ("Conc" column).

","units":{"_id":"","name":"micromoles per liter (umol/L, uM)"},"type":{"_id":"1974","name":"standard deviation","description":"

Generic standard deviation value, taking on the units of the parameter that it is tied to.

"}},{"_id":"862320","name":"OD500","format":"","frictionlessType":"number","description":"

Optical density of the culture measured at 500 nm

","units":{"_id":"","name":"unitless"},"type":{"_id":"514906","name":"optical_density","description":"

Measurement of the degree to which light at specific wavelengths pass through a medium. The more dense the medium, the less light passes through. Optical density is usually measured with a spectrophotometer set at a specific wavelength for a specific medium or solution. Optical density can be used to measure the concentration of bacteria or phytoplankton.

"}},{"_id":"862321","name":"STDEVOD","format":"","frictionlessType":"number","description":"

Standard deviation of biological duplicates for optical density ("OD500" column).

","units":{"_id":"","name":"unitless"},"type":{"_id":"1974","name":"standard deviation","description":"

Generic standard deviation value, taking on the units of the parameter that it is tied to.

"}},{"_id":"862322","name":"FigRef","format":"","frictionlessType":"string","description":"

Citation and figure where data are published (see Related Publications for full citation)

","units":{"_id":"","name":"unitless"},"type":{"_id":"476271","name":"reference_paper","description":"

A list of papers referred to as a data column, or a publication referenced in a dataset or study.

"}}],"related_publications":[{"id":"861162","citation":"Lilley, B. N., & Bassler, B. L. (2000). Regulation of quorum sensing in Vibrio harveyi by LuxO and Sigma-54. Molecular Microbiology, 36(4), 940–954. doi:10.1046/j.1365-2958.2000.01913.x\r\n","relation_type":["Methods"],"relation_desc":""},{"id":"861161","citation":"McRose, D. L., Baars, O., Seyedsayamdost, M. R., & Morel, F. M. M. (2018). Quorum sensing and iron regulate a two-for-one siderophore gene cluster inVibrio harveyi. Proceedings of the National Academy of Sciences, 115(29), 7581–7586. doi:10.1073/pnas.1805791115\r\n","relation_type":["Results"],"relation_desc":""},{"id":"861164","citation":"Naka, H., Reitz, Z. L., Jelowicki, A. L., Butler, A., & Haygood, M. G. (2018). Amphi-enterobactin commonly produced among Vibrio campbellii and Vibrio harveyi strains can be taken up by a novel outer membrane protein FapA that also can transport canonical Fe(III)-enterobactin. JBIC Journal of Biological Inorganic Chemistry, 23(7), 1009–1022. doi:10.1007/s00775-018-1601-5\r\n","relation_type":["Methods"],"relation_desc":""},{"id":"861163","citation":"Zane, H. K., Naka, H., Rosconi, F., Sandy, M., Haygood, M. G., & Butler, A. (2014). Biosynthesis of Amphi-enterobactin Siderophores by Vibrio harveyi BAA-1116: Identification of a Bifunctional Nonribosomal Peptide Synthetase Condensation Domain. Journal of the American Chemical Society, 136(15), 5615–5618. doi:10.1021/ja5019942\r\n","relation_type":["Methods"],"relation_desc":""}],"related_datasets":[{"_id":"861194","name":"Vharveyi_Spectra","url":"","relation_type":"IsReferencedBy","type_desc":"

A dataset that was used as a source of information.

\n","relation_desc":"High-resolution mass spectra for amphi-enterobactin from this same experiment.","citation":"Morel, F. (2021) High resolution mass spectra for amphi-enterobactin related siderophores from Vibrio harveyi from laboratory experiments in 2017. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2021-09-21 doi:10.26008/1912/bco-dmo.861194.1"}],"services":[{"grouping":"","items":[{"name":"View Data","description":"An in-browser view of the primary tabular data file","url":"https://www.bco-dmo.org/dataset/861154/data/view","contentType":"text/html","actionType":"view"}]},{"grouping":"Metadata","items":[{"name":"HTML","description":"A simple HTML page of the dataset metadata","url":"https://www.bco-dmo.org/dataset/861154/description","contentType":"text/html","actionType":"view"},{"name":"PDF","description":"A PDF of the HTML dataset metadata","url":"https://www.bco-dmo.org/dataset/861154/Dataset_description.pdf","contentType":"application/pdf","actionType":"download"},{"name":"ISO 19115-2 (NOAA Profile)","description":"","url":"https://www.bco-dmo.org/dataset/861154/iso","contentType":"application/xml","actionType":"download"}]}],"programs":[],"projects":[{"_id":"856898","name":"Iron uptake by marine bacteria: regulation and function of weak and strong siderophores","acronym":"Bacteria Iron Siderophores","description":"$1d"}],"archives":[{"id_value":"10.26008/1912/bco-dmo.861154.1","url":"https://doi.org/10.26008/1912/bco-dmo.861154.1","date_assigned":"2021-10-05","version_date":"2021-10-01","archiver":"Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)","archiver_id":"272"}],"license":{"name":"Creative Commons Attribution 4.0","id":"CC-BY-4.0","uri":"https://creativecommons.org/licenses/by/4.0/","spdxUri":"https://spdx.org/licenses/CC-BY-4.0"},"metrics":{"views":{"count":91},"downloads":{"count":293}}},"fileId":"903492"}]