http://lod.bco-dmo.org/id/dataset/935786
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
2024-08-19
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
HPLC data from field sampling sites in the Neuse River Estuary, Pamlico Sound, and Onslow Bay in the coastal North Atlantic, offshore from North Carolina, USA, in 2021 and 2022
2024-08-19
publication
2024-08-19
revision
BCO-DMO Linked Data URI
2024-08-19
creation
http://lod.bco-dmo.org/id/dataset/935786
Ryan Paerl
North Carolina State 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: Paerl, R., Curtis, N. (2024) HPLC data from field sampling sites in the Neuse River Estuary, Pamlico Sound, and Onslow Bay in the coastal North Atlantic, offshore from North Carolina, USA, in 2021 and 2022. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-08-19 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/935786 [access date]
Methods and Sampling: <p>Sampling summary: Discrete samples were all obtained from ~0.2m using a diaphragm pump and weighted, marked hose. All containers were kept in dark coolers at ambient temperature during transport to the laboratory.&nbsp; All filtration was done within a few hours of collection and when conditions permitted, on board the research vessel.<br />
<br />
Diagnostic phytoplankton photopigments were identified, separated and quantified by high performance liquid chromatography (HLPC)&nbsp;coupled to an in-line photodiode array spectrophotometer (Jeffrey et al.&nbsp; 1997):&nbsp; Known volumes of water sample (500-1000 milliliters, enough to obtain color on the filter) were vacuum filtered (less than 25 kiloPascals) through 25 or 47 millimeter Whatman glass microfibre filters (GF/F) under reduced light conditions.&nbsp; The filters were blotted dry, folded in half, wrapped in foil and then immediately frozen at -20 degrees Celsius until analysis.&nbsp; The filters were placed in 15 milliliter centrifuge tubes containing 1.5-3.0 milliliters of 100% acetone (HPLC Grade), sonicated for 30-60 seconds using a Fisher Sonic Dismembrator 300 with microtip and extracted at -20 degrees Celsius for 12-24 hours.&nbsp; After extraction the samples were centrifuged at 4500 rpm and the supernatant (i.e.- the combined extracted pigments) collected &amp; filtered into amber glass autosampler vials using Millipex Millipore 0.45 micometer PTFE.&nbsp; Two hundred microliters of extractant from each vial was injected into the HPLC system using a Spectra Physics (now Thermo Separations Products) AS3000 autosampler and SP8800 pump, running a non-linear, 55 minute, 2-solvent gradient adapted from Van Heukelem et.al. 1994.&nbsp; The nonlinear, variable flow, binary gradient consisted of solvent A [80% methanol : 20% ammonium acetate (0.5 M adjusted to pH 7.2)] and B (80% methanol : 20% acetone).&nbsp; The extractant was separated into individual pigments using a series of C18 reverse-phase columns to optimize photopigment separations:&nbsp; The column order was a Rainin Microsorb guard column (0.46 x 1.5 centimeters, 3 micrometer packing) followed by a single monomeric reverse-phase C18 column (Rainin Microsorb-MV, 0.46 x 10 cm, 3 µm packing) followed by two polymeric reverse-phase C18 columns (Vydac 201TP5, 0.46 x 25 cm, 5 µm packing).&nbsp; The columns were kept at a constant 52 degrees Celsius in an Alltech 330 column heater.&nbsp; The separated pigments were then passed through an in line Shimadzu SPD-M10AV photodiode array detector which measured the absorbance of the sample/extractant, scanning the range of 350-800 nanometers every 2 seconds.&nbsp; The data was collected and analyzed using Shimadzu's EZChrom software (Agilent Technologies, Inc&nbsp;<span style="color:rgb(0, 0, 0); font-family:helvetica,arial,sans-serif; font-size:13.68px">(n.d.)</span>).&nbsp; Individual pigments are identified using a combination of peak retention time and absorbance spectrum shape.&nbsp; Retention times and absorbance spectra are identified for each pigment by analyzing known pigments (either as pure standards or pigments or isolated from algal cultures).&nbsp; Pigments are quantified from their peak areas, calculated at 440nm. A calibration curve is generated by injecting various volumes of a mixed standard composed of known quantities of seven pure pigment standards (fucoxanthin, zeaxanthin, bacteriochlorophyll a, canthaxathin, chlorophyll b, chlorophyll a, echinenone and ß-carotene) and calculating the peak areas of those pigments&nbsp; &nbsp;The peak areas are regressed against the known quantities of each pigment to calculate the slope (Response Factor) for that pigment.&nbsp; Response factors for pigments we do not have reference standards for are calculated using the ratio of absorbance coefficients of each pigment to its closest structurally related reference pigment, multiplying the known pigment's response factor by that ratio. Pigments extracted from the samples are then quantified by multiplying the peak areas of a chromatogram at 440nm by the response factors. Pigment values listed as below detection were below the software threshold for peak detection or had spectra below a similarity of 0.9 compared to library spectra. Technician expert judgment&nbsp;was used in difficult cases.<br />
<br />
See the "Related Datasets" section for in-situ hydrography methods and data collected&nbsp;as part of the same study at the same field sampling locations.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2049388 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2049388
onGoing
Ryan Paerl
North Carolina State University
919.515.7276
135 Jordan Hall 2800 Faucette Drive
Raleigh
NC
27695
USA
rpaerl@ncsu.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Station
Trip_Code
Site
Lat
Lon
Date
Chlide_a
Chl_c1c2
Perid
Perid_flag
But_fuco
But_fuco_flag
Fuco
Hex_fuco
Hex_fuco_flag
Neo
Viola
Diadino
Anth
Myxo
Myxo_flag
Allo
Diato
Diato_flag
Monado
Monado_flag
Lut
Zea
Gyro
Gyro_flag
Cantha
Cantha_flag
Chl_b
Chl_a
Echin
Echin_flag
B_car
B_car_flag
TotalChla
Shimadzu UV-160U spectrophotometer
theme
None, User defined
station
deployment number
site
latitude
longitude
date_local
chlorophyllide a
chl_c1_c2
peridinin
flag
19-prime-butanoyloxyfucoxanthin
19-prime-hexanoyloxyfucoxanthin
neoxanthin
violaxanthin
diadinoxanthin
antherax
myxoxanthophyll
alloxanthin
diatoxanthin
monad
lutein
zeaxanthin
Gyroxanthin-Diester
No BCO-DMO term
chlorophyll b
chlorophyll a
carotene-beta
sum of chlorophyll a like compounds
featureType
BCO-DMO Standard Parameters
High-Performance Liquid Chromatograph
Laboratory Autosampler
Spectrophotometer
Turner Designs Trilogy fluorometer
UV Spectrophotometer-Shimadzu
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.
Collaborative Research: Vitamin B1 Limitation and Advantageous Use of B1-related Compounds by Marine Bacterioplankton
https://osprey.bco-dmo.org/project/834222
Collaborative Research: Vitamin B1 Limitation and Advantageous Use of B1-related Compounds by Marine Bacterioplankton
<p><strong>NSF Award Abstract:</strong><br />
Planktonic marine bacteria significantly impact global elemental cycling, productivity, and water quality. Recent evidence shows that abundant and diverse marine bacterioplankton require external vitamin B1 or precursors (B1 herein) to survive, and addition of these nutrients stimulates bacterial production. This suggests that it is favorable for most marine bacteria to rely on supplied B1, making B1 dynamics an environmentally relevant test case to study nutrient exchanges within the planktonic microbiome. Notably though, links between extracellular B1 availability and the composition, function, and fitness of marine bacteria are poorly understood. This project sheds light on 1) which activities and interactions are modulated by B1 availability, and 2) the benefits of exogenous B1 use by ubiquitous marine bacterioplankton. Experiments are being conducted to address uncertainty regarding B1 limitation of natural bacterioplankton, help predict plankton responses to natural or anthropogenic increases in B1 and reveal more on the rules governing nutrient exchange between plankton. Greater knowledge of the advantages of bacterial B1 use will benefit fields beyond oceanography, such as synthetic biology which focuses on streamlined microbial product generation. B1-deficiency in animals is a current concern in marine ecosystems. Greater knowledge of costs and quotas at the microbial level will best position the larger community to ask deficiency questions at other trophic levels. The teaching and training components of this project include support for graduate students and a post-doctoral scholar. The major outreach component is a newly conceived Mobile Aquatic Microbial Laboratory (MAML) that seeks to improve public awareness of aquatic microbes and their ecosystem impact, as well as convey concepts of nutrient limitation and why cells need vitamins. Pre- and post-assessment and social distancing measures are integrated into MAML, as are incentives for participants to share via social media images and contribute to the program.</p>
<p>This project investigates the impact of vitamin B1 and B1 congeners on bacterioplankton in marine ecosystems where vitamins have garnered little recent consideration as influential nutrients. The work is conducted in the Neuse River estuary, the second largest estuary in the lower USA, and in the offshore coastal ocean. Nutrient amendment experiments are being conducted to test whether B1/congeners modulate bacterioplankton growth, composition, and gene transcription (reflecting putative function). Complementary lab-based experiments with wildtype and genetically engineered bacterioplankton are being conducted to test whether use of exogenous B1/congener significantly improves cell fitness and to address why reliance upon exogenous B1/congener is so prevalent among wild bacterioplankton. Additional lab experiments with isolates are being conducted to examine the protein-related cost of B1 <em>de novo</em> biosynthesis versus exogenous B1/congener use as well as cell quotas of B1 and precursors using mass spectrometry techniques. The work reaches beyond recent genome-based extrapolations to address how exogenous B1/congener availability shapes bacterioplankton metabolism, community structure, microbial interactions, and fitness. </p>
VBLAM
largerWorkCitation
project
eng; USA
oceans
-76.6771
-76.2006
34.609368
35.1225
2021-09-27
2022-08-29
Pamlico Albemarle Sound System, NC and Coastal N. Atlantic Ocean.
0
BCO-DMO catalogue of parameters from HPLC data from field sampling sites in the Neuse River Estuary, Pamlico Sound, and Onslow Bay in the coastal North Atlantic, offshore from North Carolina, USA, in 2021 and 2022
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/966799.rdf
Name: Station
Units: unitless
Description: <p>Sampled station</p>
http://lod.bco-dmo.org/id/dataset-parameter/966800.rdf
Name: Trip_Code
Units: unitless
Description: <p>Individual trip code</p>
http://lod.bco-dmo.org/id/dataset-parameter/966801.rdf
Name: Site
Units: unitless
Description: <p>Site name (geolocation)</p>
http://lod.bco-dmo.org/id/dataset-parameter/966802.rdf
Name: Lat
Units: decimal degrees
Description: <p>Site latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/966803.rdf
Name: Lon
Units: decimal degrees
Description: <p>Site longitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/966804.rdf
Name: Date
Units: unitless
Description: <p>Date when the in situ measurements were made. When the collection was split over two days, a single date was used based on the upstream or majority stations. (local time zone EST/EDT)</p>
http://lod.bco-dmo.org/id/dataset-parameter/966805.rdf
Name: Chlide_a
Units: micrograms per liter (ug/L)
Description: <p>Chlorophyllide a concentration by HPLC analysis.</p>
http://lod.bco-dmo.org/id/dataset-parameter/966806.rdf
Name: Chl_c1c2
Units: micrograms per liter (ug/L)
Description: <p>Chlorophyll c1 and c2 concentration by HPLC analysis.</p>
http://lod.bco-dmo.org/id/dataset-parameter/966807.rdf
Name: Perid
Units: micrograms per liter (ug/L)
Description: <p>Peridinin concentration by HPLC analysis.</p>
http://lod.bco-dmo.org/id/dataset-parameter/966808.rdf
Name: Perid_flag
Units: unitless
Description: <p>Perid flag. Indicates if the blank value in the Perid column is due to the following: BDL = "Below the detection limit", NA= "Parameter was not analyzed/measured/recorded"</p>
http://lod.bco-dmo.org/id/dataset-parameter/966809.rdf
Name: But_fuco
Units: micrograms per liter (ug/L)
Description: <p>19'-Butanoyloxyfucoxanthin concentration by HPLC analysis.</p>
http://lod.bco-dmo.org/id/dataset-parameter/966810.rdf
Name: But_fuco_flag
Units: unitless
Description: <p>But_fuco flag. Indicates if the blank value in the But_fuco column is due to the following: BDL = "Below the detection limit", NA= "Parameter was not analyzed/measured/recorded"</p>
http://lod.bco-dmo.org/id/dataset-parameter/966811.rdf
Name: Fuco
Units: micrograms per liter (ug/L)
Description: <p>Peridinin concentration by HPLC analysis.</p>
http://lod.bco-dmo.org/id/dataset-parameter/966812.rdf
Name: Hex_fuco
Units: micrograms per liter (ug/L)
Description: <p>19'-Hexanoyloxyfucoxanthin concentration by HPLC analysis (micrograms per liter).</p>
http://lod.bco-dmo.org/id/dataset-parameter/966813.rdf
Name: Hex_fuco_flag
Units: unitless
Description: <p>Hex_fuco flag. Indicates if the blank value in the Hex_fuco column is due to the following: BDL = "Below the detection limit", NA= "Parameter was not analyzed/measured/recorded"</p>
http://lod.bco-dmo.org/id/dataset-parameter/966814.rdf
Name: Neo
Units: micrograms per liter (ug/L)
Description: <p>9'-cis Neoxanthin concentration by HPLC analysis.</p>
http://lod.bco-dmo.org/id/dataset-parameter/966815.rdf
Name: Viola
Units: micrograms per liter (ug/L)
Description: <p>Violaxanthin concentration by HPLC analysis.</p>
http://lod.bco-dmo.org/id/dataset-parameter/966816.rdf
Name: Diadino
Units: micrograms per liter (ug/L)
Description: <p>Diadinoxanthin concentration by HPLC analysis.</p>
http://lod.bco-dmo.org/id/dataset-parameter/966817.rdf
Name: Anth
Units: micrograms per liter (ug/L)
Description: <p>Antheraxanthin concentration by HPLC analysis.</p>
http://lod.bco-dmo.org/id/dataset-parameter/966818.rdf
Name: Myxo
Units: micrograms per liter (ug/L)
Description: <p>Myxoxanthophyll concentration by HPLC analysis.</p>
http://lod.bco-dmo.org/id/dataset-parameter/966819.rdf
Name: Myxo_flag
Units: unitless
Description: <p>Myxo flag. Indicates if the blank value in the Myxo column is due to the following: BDL = "Below the detection limit", NA= "Parameter was not analyzed/measured/recorded"</p>
http://lod.bco-dmo.org/id/dataset-parameter/966820.rdf
Name: Allo
Units: micrograms per liter (ug/L)
Description: <p>Alloxanthin concentration by HPLC analysis.</p>
http://lod.bco-dmo.org/id/dataset-parameter/966821.rdf
Name: Diato
Units: micrograms per liter (ug/L)
Description: <p>Diatoxanthin concentration by HPLC analysis.</p>
http://lod.bco-dmo.org/id/dataset-parameter/966822.rdf
Name: Diato_flag
Units: unitless
Description: <p>Diato flag. Indicates if the blank value in the Diato column is due to the following: BDL = "Below the detection limit", NA= "Parameter was not analyzed/measured/recorded"</p>
http://lod.bco-dmo.org/id/dataset-parameter/966823.rdf
Name: Monado
Units: micrograms per liter (ug/L)
Description: <p>Monadoxanthin concentration by HPLC analysis.</p>
http://lod.bco-dmo.org/id/dataset-parameter/966824.rdf
Name: Monado_flag
Units: unitless
Description: <p>Monado flag. Indicates if the blank value in the Monado column is due to the following: BDL = "Below the detection limit", NA= "Parameter was not analyzed/measured/recorded"</p>
http://lod.bco-dmo.org/id/dataset-parameter/966825.rdf
Name: Lut
Units: micrograms per liter (ug/L)
Description: <p>Lutein concentration by HPLC analysis.</p>
http://lod.bco-dmo.org/id/dataset-parameter/966826.rdf
Name: Zea
Units: micrograms per liter (ug/L)
Description: <p>Zeaxanthin concentration by HPLC analysis.</p>
http://lod.bco-dmo.org/id/dataset-parameter/966827.rdf
Name: Gyro
Units: micrograms per liter (ug/L)
Description: <p>Gyroxanthin concentration by HPLC analysis.</p>
http://lod.bco-dmo.org/id/dataset-parameter/966828.rdf
Name: Gyro_flag
Units: unitless
Description: <p>Gyro flag. Indicates if the blank value in the Gyro column is due to the following: BDL = "Below the detection limit", NA= "Parameter was not analyzed/measured/recorded"</p>
http://lod.bco-dmo.org/id/dataset-parameter/966829.rdf
Name: Cantha
Units: micrograms per liter (ug/L)
Description: <p>Canthaxanthin concentration by HPLC analysis.</p>
http://lod.bco-dmo.org/id/dataset-parameter/966830.rdf
Name: Cantha_flag
Units: unitless
Description: <p>Cantha flag. Indicates if the blank value in the Cantha column is due to the following: BDL = "Below the detection limit", NA= "Parameter was not analyzed/measured/recorded"</p>
http://lod.bco-dmo.org/id/dataset-parameter/966831.rdf
Name: Chl_b
Units: micrograms per liter (ug/L)
Description: <p>Chlorophyll b concentration by HPLC analysis.</p>
http://lod.bco-dmo.org/id/dataset-parameter/966832.rdf
Name: Chl_a
Units: micrograms per liter (ug/L)
Description: <p>Chlorophyll a concentration by HPLC analysis.</p>
http://lod.bco-dmo.org/id/dataset-parameter/966833.rdf
Name: Echin
Units: micrograms per liter (ug/L)
Description: <p>Echinenone concentration by HPLC analysis.</p>
http://lod.bco-dmo.org/id/dataset-parameter/966834.rdf
Name: Echin_flag
Units: unitless
Description: <p>Echin flag. Indicates if the blank value in the Echin column is due to the following: BDL = "Below the detection limit", NA= "Parameter was not analyzed/measured/recorded"</p>
http://lod.bco-dmo.org/id/dataset-parameter/966835.rdf
Name: B_car
Units: micrograms per liter (ug/L)
Description: <p>B-Carotene (beta-carotene) concentration by HPLC analysis.</p>
http://lod.bco-dmo.org/id/dataset-parameter/966836.rdf
Name: B_car_flag
Units: unitless
Description: <p>B_car flag. Indicates if the blank value in the B_car column is due to the following: BDL = "Below the detection limit", NA= "Parameter was not analyzed/measured/recorded"</p>
http://lod.bco-dmo.org/id/dataset-parameter/966837.rdf
Name: TotalChla
Units: micrograms per liter (ug/L)
Description: <p>Total chlorophyll a concentration derived from the sum of Chlorophytes, Cryptophytes, Cyanobacteria, Diatoms, and Dinoflagellates (all in ug L-1). This concentration should equal total chlorophyll a generated from HPLC analysis.</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
https://osprey.bco-dmo.org/dataset/935786/data/download
download
onLine
dataset
<p>Sampling summary: Discrete samples were all obtained from ~0.2m using a diaphragm pump and weighted, marked hose. All containers were kept in dark coolers at ambient temperature during transport to the laboratory.&nbsp; All filtration was done within a few hours of collection and when conditions permitted, on board the research vessel.<br />
<br />
Diagnostic phytoplankton photopigments were identified, separated and quantified by high performance liquid chromatography (HLPC)&nbsp;coupled to an in-line photodiode array spectrophotometer (Jeffrey et al.&nbsp; 1997):&nbsp; Known volumes of water sample (500-1000 milliliters, enough to obtain color on the filter) were vacuum filtered (less than 25 kiloPascals) through 25 or 47 millimeter Whatman glass microfibre filters (GF/F) under reduced light conditions.&nbsp; The filters were blotted dry, folded in half, wrapped in foil and then immediately frozen at -20 degrees Celsius until analysis.&nbsp; The filters were placed in 15 milliliter centrifuge tubes containing 1.5-3.0 milliliters of 100% acetone (HPLC Grade), sonicated for 30-60 seconds using a Fisher Sonic Dismembrator 300 with microtip and extracted at -20 degrees Celsius for 12-24 hours.&nbsp; After extraction the samples were centrifuged at 4500 rpm and the supernatant (i.e.- the combined extracted pigments) collected &amp; filtered into amber glass autosampler vials using Millipex Millipore 0.45 micometer PTFE.&nbsp; Two hundred microliters of extractant from each vial was injected into the HPLC system using a Spectra Physics (now Thermo Separations Products) AS3000 autosampler and SP8800 pump, running a non-linear, 55 minute, 2-solvent gradient adapted from Van Heukelem et.al. 1994.&nbsp; The nonlinear, variable flow, binary gradient consisted of solvent A [80% methanol : 20% ammonium acetate (0.5 M adjusted to pH 7.2)] and B (80% methanol : 20% acetone).&nbsp; The extractant was separated into individual pigments using a series of C18 reverse-phase columns to optimize photopigment separations:&nbsp; The column order was a Rainin Microsorb guard column (0.46 x 1.5 centimeters, 3 micrometer packing) followed by a single monomeric reverse-phase C18 column (Rainin Microsorb-MV, 0.46 x 10 cm, 3 µm packing) followed by two polymeric reverse-phase C18 columns (Vydac 201TP5, 0.46 x 25 cm, 5 µm packing).&nbsp; The columns were kept at a constant 52 degrees Celsius in an Alltech 330 column heater.&nbsp; The separated pigments were then passed through an in line Shimadzu SPD-M10AV photodiode array detector which measured the absorbance of the sample/extractant, scanning the range of 350-800 nanometers every 2 seconds.&nbsp; The data was collected and analyzed using Shimadzu's EZChrom software (Agilent Technologies, Inc&nbsp;<span style="color:rgb(0, 0, 0); font-family:helvetica,arial,sans-serif; font-size:13.68px">(n.d.)</span>).&nbsp; Individual pigments are identified using a combination of peak retention time and absorbance spectrum shape.&nbsp; Retention times and absorbance spectra are identified for each pigment by analyzing known pigments (either as pure standards or pigments or isolated from algal cultures).&nbsp; Pigments are quantified from their peak areas, calculated at 440nm. A calibration curve is generated by injecting various volumes of a mixed standard composed of known quantities of seven pure pigment standards (fucoxanthin, zeaxanthin, bacteriochlorophyll a, canthaxathin, chlorophyll b, chlorophyll a, echinenone and ß-carotene) and calculating the peak areas of those pigments&nbsp; &nbsp;The peak areas are regressed against the known quantities of each pigment to calculate the slope (Response Factor) for that pigment.&nbsp; Response factors for pigments we do not have reference standards for are calculated using the ratio of absorbance coefficients of each pigment to its closest structurally related reference pigment, multiplying the known pigment's response factor by that ratio. Pigments extracted from the samples are then quantified by multiplying the peak areas of a chromatogram at 440nm by the response factors. Pigment values listed as below detection were below the software threshold for peak detection or had spectra below a similarity of 0.9 compared to library spectra. Technician expert judgment&nbsp;was used in difficult cases.<br />
<br />
See the "Related Datasets" section for in-situ hydrography methods and data collected&nbsp;as part of the same study at the same field sampling locations.</p>
Specified by the Principal Investigator(s)
<p>Formatting and organization of data was completed in Excel (Microsoft).</p>
Specified by the Principal Investigator(s)
BCO-DMO Data Manager Processing Notes:
* Data from source file BLAMM_METADATA_HPLC_7_3_24_RWP.xlsx Sheet "HPLC ugL" were exported from Excel as a csv file. The csv file was imported into the BCO-DMO data system.
* Additional *_flag columns added. For example, Cantha_flag for the Cantha column. _flag columns provide information about what type of missing data each blank value corresponds to or if substituted data was used. Flags (-7777,-9999) within data columns moved to the new _flag columns as (NA or BDL), respectively. See the Parameters section for more details on flag meanings.
** Missing data in the BCO-DMO system displays as a blank (null values) by default and will vary depending upon the file format downloaded (blank in csv files, NaN in .mat matlab files, etc).
* Parameters (column names) renamed to comply with BCO-DMO naming conventions. See https://www.bco-dmo.org/page/bco-dmo-data-processing-conventions
* Site name (geolocation), lat, lon were added to the data table from an additional sheet provided in related dataset excel file (hydrography) BLAMM_METADATA_7_3_24_RWP.xlsx
* Decimals rounded to 5 decimal places.
* DateTime (UTC) column added in ISO 8601 format yyyy-mm-ddTHH:MM:SSZ using local date and time provided (EST/EDT). Date and time format changed to ISO 8601 format.
Specified by BCO-DMO Data Managers
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
PI Supplied Instrument Name: PI Supplied Instrument Description:High performance liquid chromatography (HLPC) coupled to an in-line photodiode array spectrophotometer (Jeffrey et al. 1997).
Study also used a Shimadzu SPD-M10AV photodiode array detector. Instrument Name: High-Performance Liquid Chromatograph Instrument Short Name:HPLC Instrument Description: A High-performance liquid chromatograph (HPLC) is a type of liquid chromatography used to separate compounds that are dissolved in solution. HPLC instruments consist of a reservoir of the mobile phase, a pump, an injector, a separation column, and a detector. Compounds are separated by high pressure pumping of the sample mixture onto a column packed with microspheres coated with the stationary phase. The different components in the mixture pass through the column at different rates due to differences in their partitioning behavior between the mobile liquid phase and the stationary phase. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB11/
PI Supplied Instrument Name: PI Supplied Instrument Description:Spectra Physics (now Thermo Separations Products) AS3000 autosampler and SP8800 pump Instrument Name: Laboratory Autosampler Instrument Short Name: Instrument Description: Laboratory apparatus that automatically introduces one or more samples with a predetermined volume or mass into an analytical instrument.
PI Supplied Instrument Name: PI Supplied Instrument Description:High performance liquid chromatography (HLPC) coupled to an in-line photodiode array spectrophotometer (Jeffrey et al. 1997). Instrument Name: Spectrophotometer Instrument Short Name:Spectrophotometer Instrument Description: An instrument used to measure the relative absorption of electromagnetic radiation of different wavelengths in the near infra-red, visible and ultraviolet wavebands by samples. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB20/
PI Supplied Instrument Name: Instrument Name: Turner Designs Trilogy fluorometer Instrument Short Name:Turner Trilogy Instrument Description: The Trilogy Laboratory Fluorometer is a compact laboratory instrument for making fluorescence, absorbance, and turbidity measurements using the appropriate snap-in application module. Fluorescence modules are available for discrete sample measurements of various fluorescent materials including chlorophyll (in vivo and extracted), rhodamine, fluorescein, cyanobacteria pigments, ammonium, CDOM, optical brighteners, and other fluorescent compounds.
Shimadzu UV-160U spectrophotometer
Shimadzu UV-160U spectrophotometer
PI Supplied Instrument Name: Shimadzu UV-160U spectrophotometer Instrument Name: UV Spectrophotometer-Shimadzu Instrument Short Name:UV Spectrophotometer-Shimadzu Instrument Description: The Shimadzu UV Spectrophotometer is manufactured by Shimadzu Scientific Instruments (ssi.shimadzu.com). Shimadzu manufacturers several models of spectrophotometer; refer to dataset for make/model information. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB20/