http://lod.bco-dmo.org/id/dataset/734790
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
2018-05-01
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Vascular plant and microbial biomarkers of dissolved organic matter from San Francisco Bay transects
2019-01-31
publication
2019-01-31
revision
BCO-DMO Linked Data URI
2019-01-31
creation
http://lod.bco-dmo.org/id/dataset/734790
Peter Hernes
University of California-Davis
principalInvestigator
Karl Kaiser
Texas A&M 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: Hernes, P., Kaiser, K. (2019) Vascular plant and microbial biomarkers of dissolved organic matter from San Francisco Bay transects. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 2) Version Date 2019-01-31 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/734790 [access date]
Vascular plant and microbial biomarkers of dissolved organic matter from San Francisco Bay transects Dataset Description: <p>Vascular plant and microbial biomarkers of dissolved organic matter from San Francisco Bay transects. San Francisco Bay transects were collected in December 2014 (Dec-14), June 2015 (Jun-15), and May 2016 (May-16).</p> Methods and Sampling: <p>Samples were collect on the USGS R/V Mary Landsteiner&nbsp;and pumped directly from the surface (1 m deep) with a pump and clean tycoon tubing connected to an inline 0.2 um Whatman Polycap filter.</p>
<p>All filters were pumped and field filtered through 0.7 um Whatman glass fiber filters (GF/F, precombusted at 550 degrees C) using a peristaltic pump after purging the line.</p>
<p>Samples for DOC concentration were acidified to pH 2 and stored in a refrigerator (4 degrees C) until analysis by high-temperature combustion on a Shimadzu TOC-L CPH within two weeks following collection. DOC was calculated as the mean of between three and five injections using a six-point standard curve using established protocols (Mann et al., 2012) and the coefficient of variance was always &lt;2%.</p>
<p>Samples for CDOM absorbance were analyzed in a 1 cm cuvette on a Horiba Aqualog-UV-800-C. Absorbance spectra were measured from 230-800 nm, and corrected for a small offset either due to long-term baseline drift or derived from glass fiber particles during filtration (Blough et al., 1993), by subtracting the mean absorbance measured between 750-800 nm. Two spectral slopes were calculated at 275-295 nm and 350-400 nm (S275-295 and S350-400, respectively), and the spectral slope ratio (SR) was then calculated by dividing the former by the latter (Helms et al., 2008). The CDOM absorption ratio at 250 nm to 365 nm was calculated (a250:a365) and specific ultraviolet absorbance (SUVA254) was calculated by dividing the decadic absorption coefficient at 254 nm by DOC concentration (Weishaar et al., 2003; Fellman et al., 2009).</p>
<p>Fluorescence properties of FDOM were determined using a Horiba Aqualog-UV-800-C. The excitation emission matrices (EEMs) were generated in a 1 cm cuvette at varying integration times (1-10 seconds) to maximize the signal-to-noise ratio based on absorbance values. The EEMs were obtained at excitation (ex) 250-600 nm and at emission (em) 250-600 nm with 5 nm and 2 nm intervals respectively, and the EEMs were corrected for lamp intensity (Cory et al., 2010), inner filter effects (Kothawala et al., 2013), and normalized to Raman units (R.U.) (Stedmon et al., 2003). All corrections were performed using the FDOMcorr toolbox version 1.6 (Murphy, 2011). EEMs were analyzed with parallel factor analysis (PARAFAC) using the procedure described in Murphy et al. (2013). Furthermore, the fluorescence index (FI) (Cory et al., 2010), humification index (HIX) (Ohno, 2002; Zsolnay et al., 1999), and autotrophic productivity index (BIX) (Huguet et al., 2009) were calculated. FI was calculated from the emission wavelengths at 470 nm and 520 nm, obtained at excitation 370 nm (Cory and McKnight, 2005). HIX was calculated using the area under the emission sepctra 435-480 nm divided by the peak area 300-345 + 435-480 nm, at excitation 254 nm (Ohno, 2002). BIX was calculated from the emission intensity of 380 nm and 430 nm, obtained at excitation 310 nm (Wang et al., 2014).</p>
<p>Samples for FT-ICR MS analysis were solid-phase extracted using the procedure described in Dittmar et al., 2008. Filtered samples were acidified to pH 2 before solid phase extraction on 500 mg Agilent Bond Elut PPL cartridges. Each 1 L sample was extracted by eluting 2 mL of of methanol and then diluted to a DOC target concentration of 50 ug C mL-1. Extracted samples were stored at -20 degrees C prior to analysis on a 21 T (Bruker Daltonics, Billerica, MA, USA) FT-ICR MS located at the National High Magnetic Field Laboratory (NHMFL) (Tallahassee, Florida). Direct infusion electrospray ionization (ESI) generates negative ions at a flow rate of 700 nL min-1, and 100 time domain acquisitions were coadded for each mass spectrum.</p>
<p>Molecular formulas were assigned to signals &gt;6RMS baseline noise with EnviroOrg ©,TM software (Koch et al., 2007; Stubbins et al., 2010). Elemental combinations of C1–45H1–92N0–4O1–25S0–2 with a mass accuracy of ≤300 ppb were considered for assignment. Classification of formulas were based on their elemental ratios (Corilo, 2015). The modified aromaticity index (Almod) of each formula was calculated and Almod values of 0.5-0.67 and ≥0.67 were classified as aromatic and condensed aromatic structures (Koch and Dittmar, 2006; Koch and Dittmar, 2016). Other compound classes were unsaturated low oxygen=Almod&lt;0.5, H/C&lt;1.5, O/C&lt;0.5; unsaturated high oxygen=Almod&lt;0.5, H/ C&lt;1.5, O/C&gt;0.5; aliphatics=H/C 1.5-2.0, O/C&lt;0.9, N=0; peptide-like=H/C 1.5-2.0, O/C&lt;0.9, N&gt;0, and sugar-like= O/C&gt;0.9. Sugar-like compounds provide a very minor contribution to %RA (mean = 0.05, ± 0.06 %RA) and so were combined with peptide-like compounds throughout. Although FT-ICR MS allows for the precise assignment of molecular formulas to signals that may represent multiple isomers, they describe the underlying molecular compounds comprising DOM, thus the term compound may be used when describing the signals detected by FT-ICR MS.</p>
<p>Lignin derived phenols were isolated from the dried solid phase extracts followed by cupric oxide oxidation and liquid-liquid extraction modified from Spencer et al., (2010). Briefly, PPL extracts were redissolved in O2 free 2 M NaOH in a 6 mL Teflon vial (Savillex Corp) containing 500 mg CuO, and amended with 100 mg ferrous ammonium sulfate and 50 mg glucose and reacted in a 155 degree C oven for 3 hours. Following oxidation, the samples were centrifuged and supernatants were decanted into 40 mL vials. Oxidation products were acidified to pH 1 with H3PO4 and t-cinnamic acid was added as an internal standard. Liquid-liquid extractions of the oxidation products were undertaken by addition of 4 mL ethyl acetate, vortexing, and centrifugation prior to removal of the ethyl acetate. Extracts were pipetted through drying columns containing sodium sulfate into a 4 mL vial. Samples were dried under ultra-high purity argon between each extraction for a total of three extractions, following the last extraction the sodium sulfate was rinsed with 1 mL of ethyl acetate into the extract vial. Dried ethyl acetate extracts were dissolved in pyridine and derivatized with N/O bis-trimethylsilyltrifluoromethylacetamide (BSTFA) at 60 degrees C for ten minutes. Lignin phenol monomers were measured as trimethylsilane derivatives using an Agilent 6890N GC/5975 MS and were quantified as the relative response factors of each compound compared to the response of t- cinnamic acid and a five-point calibration curve bracketing the concentration range. Eight lignin phenols from three phenol groups were quantified; vanillyl (vanillin, acetovanillone, vanillic acid), syringyl (syringaldehyde, acetosyringone, syringic acid), and coumaryl (coumaric acid, ferulic acid).</p>
<p>Seven neutral sugars (fucose, rhamnose, arabinose, galactose, glucose, mannose, xylose) were analyzed according to Skoog and Benner (1997) with modifications. Briefly, samples were hydrolyzed in 1.2 mol L−1 sulfuric acid and neutralized with a self-absorbed ion retardation resin (Kaiser and Benner, 2000). After desalting with a mixture of cation and anion exchange resins, neutral sugars were isocratically separated with 25 mM NaOH on a PA 1 column in a Dionex 500 system with a pulsed amperiometric detector (PAD).</p>
<p>The following amino acids were analyzed using the method of Kaiser and Benner, 2005: histidine, serine, arginine, glycine, aspartic acid, glutamic acid, threonine, alanine, lysine, tyrosine, methionine, valine, norvaline, isoleucine, leucine, phenylalanine.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1464396 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1464396
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1335622 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1335622
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1333633 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1333633
completed
Peter Hernes
University of California-Davis
530-754-4327
Dept. of Land, Air and Water Resources
Davis
CA
95616
USA
pjhernes@ucdavis.edu
pointOfContact
Karl Kaiser
Texas A&M University
409-740-4879
1001 Texas Clipper Rd Dept. of Marine Sciences, Texas A&M University, Galveston Campus
Galveston
TX
77554
USA
kaiserk@tamug.edu
pointOfContact
asNeeded
Dataset Version: 2
Unknown
Date
Salinity
Lat
Long
Temp
pH
DO
Turbidity
TSS
DOC_uM
DOC_mgL
FI
HIX
HIX_Norm
BIX
abs_250
abs_254
abs_350
abs_365
abs_412
abs_440
abs_ratio_250_365
SUVA254
S275_295
S350_400
Sr
C1
C2
C3
C4
C5
C6
C7
C8
C9
C10
Ctotal
Num_formula
Aliphatic_HighOC
Aliphatic_LowOC
Condensed_aromatics
Highly_Unsaturated_and_Phenolic_HighOC
Highly_Unsaturated_and_Phenolic_LowOC
Peptide_like
Polyphenolic_HighOC
Polyphenolic_LowOC
conc_Sum8
conc_Sum6
Cnorm_Sum8
Cnorm_Sum6
S_to_V
C_to_V
Ad_to_Al_v
Ad_to_Al_s
THAA
Asp
Glu
Ser
His
Thr
Gly
Arg
Ala
Tyr
Val
Ile
Phe
Leu
Lys
THNS
Fuc
Rha
Ara
Gal
Glc
Man
Xyl
Horiba Aqualog-UV-800-C
FT-ICR MS
Agilent 6890N GC/5975 MS
Dionex 500 system
Agilent 6890N GC/5975 MS
Shimadzu TOC-L CPH
theme
None, User defined
date
salinity
latitude
longitude
water temperature at measurement depth
pH
dissolved Oxygen
turbidity
No BCO-DMO term
dissolved organic Carbon
absorption coefficient
amino acid concentration
featureType
BCO-DMO Standard Parameters
Fluorometer
Fourier Transform Ion Cyclotron Resonance Mass Spectrometer
Gas Chromatograph
Ion Chromatograph
Mass Spectrometer
Shimadzu TOC-L Analyzer
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: Calibration and application of vascular plant and aqueous microbial biomarkers to examine transformations of dissolved organic matter
https://osprey.bco-dmo.org/project/732791
Collaborative Research: Calibration and application of vascular plant and aqueous microbial biomarkers to examine transformations of dissolved organic matter
<p><em>NSF abstract:</em><br />
Organic matter (OM) fluxes between and within terrestrial and oceanic reservoirs play an important role in the global carbon cycle. A clearer understanding of OM dynamics is critical for understanding fundamental processes and effects on greenhouse gases and climate. At present, researchers have an abundance of analytical methods and tools for investigating dissolved organic matter (DOM) cycling, but the field struggles to move past a qualitative understanding of sources, processing, and fates toward a quantitative understanding. Researchers from University of California-Davis, Woods Hole Oceanographic Institute, and Texas A&M University will develop biomarker tools to advance quantitative understanding of DOM cycling in riverine and estuarine environments in California, specifically targeting vascular plant and microbial markers. Results from this study will allow for future biomarker studies to quantitatively address DOM source and processing in aquatic environments and improve the limited understanding of the fate of terrestrial DOM in the ocean.</p>
<p>Broader Impacts: This study will provide interdisciplinary scientific training and development for undergraduate and graduate students, including individuals from underrepresented groups. Results from the study will be disseminated to the public, California stakeholders, and college students to educate them about the carbon cycle.</p>
DOM biomarkers
largerWorkCitation
project
eng; USA
oceans
-122.508
-121.265
37.679
38.478
2014-12-01
2016-05-31
San Francisco Bay Delta
0
BCO-DMO catalogue of parameters from Vascular plant and microbial biomarkers of dissolved organic matter from San Francisco Bay transects
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/734805.rdf
Name: Date
Units: unitless
Description: <p>Date of sample collection. Format: month-year. (e.g. Dec-14 = December 2014, Jun-15 = June 2015, May-16 = May 2016)</p>
http://lod.bco-dmo.org/id/dataset-parameter/734806.rdf
Name: Salinity
Units: PSU
Description: <p>Salinity</p>
http://lod.bco-dmo.org/id/dataset-parameter/734807.rdf
Name: Lat
Units: decimal degrees
Description: <p>Latitude of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/734808.rdf
Name: Long
Units: decimal degrees
Description: <p>Longitude of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/734809.rdf
Name: Temp
Units: degrees Celsius
Description: <p>Temperature</p>
http://lod.bco-dmo.org/id/dataset-parameter/734810.rdf
Name: pH
Units: unitless
Description: <p>pH</p>
http://lod.bco-dmo.org/id/dataset-parameter/734811.rdf
Name: DO
Units: milligrams per liter (mg/L)
Description: <p>Dissolved oxygen</p>
http://lod.bco-dmo.org/id/dataset-parameter/734812.rdf
Name: Turbidity
Units: FNU
Description: <p>Turbidity</p>
http://lod.bco-dmo.org/id/dataset-parameter/734813.rdf
Name: TSS
Units: milligrams per liter (mg/L)
Description: <p>Total suspended solids</p>
http://lod.bco-dmo.org/id/dataset-parameter/734814.rdf
Name: DOC_uM
Units: micromolar (uM)
Description: <p>Dissolved organic carbon in uM</p>
http://lod.bco-dmo.org/id/dataset-parameter/734815.rdf
Name: DOC_mgL
Units: milligrams per liter (mg/L)
Description: <p>Dissolved organic carbon in mg/L</p>
http://lod.bco-dmo.org/id/dataset-parameter/734816.rdf
Name: FI
Units: unitless
Description: <p>Fluorescence Index (DOM composition metric)</p>
http://lod.bco-dmo.org/id/dataset-parameter/734817.rdf
Name: HIX
Units: unitless
Description: <p>Humification Index (DOM composition metric)</p>
http://lod.bco-dmo.org/id/dataset-parameter/734818.rdf
Name: HIX_Norm
Units: unitless
Description: <p>Humification Index Norm (DOM composition metric)</p>
http://lod.bco-dmo.org/id/dataset-parameter/734819.rdf
Name: BIX
Units: unitless
Description: <p>Autotrophic productivity index (DOM composition metric)</p>
http://lod.bco-dmo.org/id/dataset-parameter/734820.rdf
Name: abs_250
Units: reciprocal meters (m-1)
Description: <p>CDOM absorbance at 250 nm</p>
http://lod.bco-dmo.org/id/dataset-parameter/734821.rdf
Name: abs_254
Units: m-1
Description: <p>CDOM absorbance at 254 nm</p>
http://lod.bco-dmo.org/id/dataset-parameter/734822.rdf
Name: abs_350
Units: m-1
Description: <p>CDOM absorbance at 350 nm</p>
http://lod.bco-dmo.org/id/dataset-parameter/734823.rdf
Name: abs_365
Units: m-1
Description: <p>CDOM absorbance at 365 nm</p>
http://lod.bco-dmo.org/id/dataset-parameter/734824.rdf
Name: abs_412
Units: m-1
Description: <p>CDOM absorbance at 412 nm</p>
http://lod.bco-dmo.org/id/dataset-parameter/734825.rdf
Name: abs_440
Units: m-1
Description: <p>CDOM absorbance at 440 nm</p>
http://lod.bco-dmo.org/id/dataset-parameter/734826.rdf
Name: abs_ratio_250_365
Units: unitless
Description: <p>Absorbance ratio; absorbance at 250/365</p>
http://lod.bco-dmo.org/id/dataset-parameter/734827.rdf
Name: SUVA254
Units: L mgC-1 m-1
Description: <p>Specific UV absorbance at 254 nm</p>
http://lod.bco-dmo.org/id/dataset-parameter/734828.rdf
Name: S275_295
Units: unitless
Description: <p>Spectral slope range 275-295</p>
http://lod.bco-dmo.org/id/dataset-parameter/734829.rdf
Name: S350_400
Units: unitless
Description: <p>Spectral slope range 350-400</p>
http://lod.bco-dmo.org/id/dataset-parameter/734830.rdf
Name: Sr
Units: unitless
Description: <p>Spectral slope ratio (275-295/350-400)</p>
http://lod.bco-dmo.org/id/dataset-parameter/734831.rdf
Name: C1
Units: Raman units
Description: <p>Fluorescence intensity of component 1</p>
http://lod.bco-dmo.org/id/dataset-parameter/734832.rdf
Name: C2
Units: Raman units
Description: <p>Fluorescence intensity of component 2</p>
http://lod.bco-dmo.org/id/dataset-parameter/734833.rdf
Name: C3
Units: Raman units
Description: <p>Fluorescence intensity of component 3</p>
http://lod.bco-dmo.org/id/dataset-parameter/734834.rdf
Name: C4
Units: Raman units
Description: <p>Fluorescence intensity of component 4</p>
http://lod.bco-dmo.org/id/dataset-parameter/734835.rdf
Name: C5
Units: Raman units
Description: <p>Fluorescence intensity of component 5</p>
http://lod.bco-dmo.org/id/dataset-parameter/734836.rdf
Name: C6
Units: Raman units
Description: <p>Fluorescence intensity of component 6</p>
http://lod.bco-dmo.org/id/dataset-parameter/734837.rdf
Name: C7
Units: Raman units
Description: <p>Fluorescence intensity of component 7</p>
http://lod.bco-dmo.org/id/dataset-parameter/734838.rdf
Name: C8
Units: Raman units
Description: <p>Fluorescence intensity of component 8</p>
http://lod.bco-dmo.org/id/dataset-parameter/734839.rdf
Name: C9
Units: Raman units
Description: <p>Fluorescence intensity of component 9</p>
http://lod.bco-dmo.org/id/dataset-parameter/734840.rdf
Name: C10
Units: Raman units
Description: <p>Fluorescence intensity of component 10</p>
http://lod.bco-dmo.org/id/dataset-parameter/734841.rdf
Name: Ctotal
Units: Raman units
Description: <p>Fluorescence intensity total</p>
http://lod.bco-dmo.org/id/dataset-parameter/734842.rdf
Name: Num_formula
Units: unitless
Description: <p>FT-ICR MS: Number of formula assigned</p>
http://lod.bco-dmo.org/id/dataset-parameter/734843.rdf
Name: Aliphatic_HighOC
Units: % relative abundance
Description: <p>Aliphatic High OC (FT-ICR MS compound class)</p>
http://lod.bco-dmo.org/id/dataset-parameter/734844.rdf
Name: Aliphatic_LowOC
Units: % relative abundance
Description: <p>Aliphatic Low OC (FT-ICR MS compound class)</p>
http://lod.bco-dmo.org/id/dataset-parameter/734845.rdf
Name: Condensed_aromatics
Units: % relative abundance
Description: <p>Condensed Aromatics (FT-ICR MS compound class)</p>
http://lod.bco-dmo.org/id/dataset-parameter/734846.rdf
Name: Highly_Unsaturated_and_Phenolic_HighOC
Units: % relative abundance
Description: <p>Highly unsaturated and phenolic high OC (FT-ICR MS compound class)</p>
http://lod.bco-dmo.org/id/dataset-parameter/734847.rdf
Name: Highly_Unsaturated_and_Phenolic_LowOC
Units: % relative abundance
Description: <p>Highly unsaturated and phenolic low OC (FT-ICR MS compound class)</p>
http://lod.bco-dmo.org/id/dataset-parameter/734848.rdf
Name: Peptide_like
Units: % relative abundance
Description: <p>Peptide-like (FT-ICR MS compound class)</p>
http://lod.bco-dmo.org/id/dataset-parameter/734849.rdf
Name: Polyphenolic_HighOC
Units: % relative abundance
Description: <p>Polyphenolic high OC (FT-ICR MS compound class)</p>
http://lod.bco-dmo.org/id/dataset-parameter/734850.rdf
Name: Polyphenolic_LowOC
Units: % relative abundance
Description: <p>Polyphenolic low OC (FT-ICR MS compound class)</p>
http://lod.bco-dmo.org/id/dataset-parameter/734851.rdf
Name: conc_Sum8
Units: micrograms per liter (ug/L)
Description: <p>Lignin Phenols Concentration Sum of 8</p>
http://lod.bco-dmo.org/id/dataset-parameter/734852.rdf
Name: conc_Sum6
Units: micrograms per liter (ug/L)
Description: <p>Lignin Phenols Concentration Sum of 6</p>
http://lod.bco-dmo.org/id/dataset-parameter/734853.rdf
Name: Cnorm_Sum8
Units: mg/100 mg OC
Description: <p>Lignin Phenols C-normalized Sum of 8</p>
http://lod.bco-dmo.org/id/dataset-parameter/734854.rdf
Name: Cnorm_Sum6
Units: mg/100 mg OC
Description: <p>Lignin Phenols C-normalized Sum of 6</p>
http://lod.bco-dmo.org/id/dataset-parameter/734855.rdf
Name: S_to_V
Units: unitless
Description: <p>S:V (syringyl to vanillyl ratio)</p>
http://lod.bco-dmo.org/id/dataset-parameter/734856.rdf
Name: C_to_V
Units: unitless
Description: <p>C:V (cinnamyl to vanillyl ratio)</p>
http://lod.bco-dmo.org/id/dataset-parameter/734857.rdf
Name: Ad_to_Al_v
Units: unitless
Description: <p>(Ad:Al)v (Vanillic acid to aledhyde ratio)</p>
http://lod.bco-dmo.org/id/dataset-parameter/734858.rdf
Name: Ad_to_Al_s
Units: unitless
Description: <p>(Ad:Al)s (Syringic acid to aledhyde ratio)</p>
http://lod.bco-dmo.org/id/dataset-parameter/754574.rdf
Name: THAA
Units: micromoles per liter (umol/L)
Description: <p>Total hydrolyzable amino acids</p>
http://lod.bco-dmo.org/id/dataset-parameter/754575.rdf
Name: Asp
Units: mol%
Description: <p>Aspartic acid</p>
http://lod.bco-dmo.org/id/dataset-parameter/754576.rdf
Name: Glu
Units: mol%
Description: <p>Glutamic acid</p>
http://lod.bco-dmo.org/id/dataset-parameter/754577.rdf
Name: Ser
Units: mol%
Description: <p>Serine</p>
http://lod.bco-dmo.org/id/dataset-parameter/754578.rdf
Name: His
Units: mol%
Description: <p>Histidine</p>
http://lod.bco-dmo.org/id/dataset-parameter/754579.rdf
Name: Thr
Units: mol%
Description: <p>Threonine</p>
http://lod.bco-dmo.org/id/dataset-parameter/754580.rdf
Name: Gly
Units: mol%
Description: <p>Glycine</p>
http://lod.bco-dmo.org/id/dataset-parameter/754581.rdf
Name: Arg
Units: mol%
Description: <p>Arginine</p>
http://lod.bco-dmo.org/id/dataset-parameter/754582.rdf
Name: Ala
Units: mol%
Description: <p>Alanine</p>
http://lod.bco-dmo.org/id/dataset-parameter/754583.rdf
Name: Tyr
Units: mol%
Description: <p>Tyrosine</p>
http://lod.bco-dmo.org/id/dataset-parameter/754584.rdf
Name: Val
Units: mol%
Description: <p>Valine</p>
http://lod.bco-dmo.org/id/dataset-parameter/754585.rdf
Name: Ile
Units: mol%
Description: <p>Isoleucine</p>
http://lod.bco-dmo.org/id/dataset-parameter/754586.rdf
Name: Phe
Units: mol%
Description: <p>Phenylalanine</p>
http://lod.bco-dmo.org/id/dataset-parameter/754587.rdf
Name: Leu
Units: mol%
Description: <p>Leucine</p>
http://lod.bco-dmo.org/id/dataset-parameter/754588.rdf
Name: Lys
Units: mol%
Description: <p>Lysine</p>
http://lod.bco-dmo.org/id/dataset-parameter/754589.rdf
Name: THNS
Units: micromoles per liter (umol/L)
Description: <p>Total hydrolyzable neutral sugars</p>
http://lod.bco-dmo.org/id/dataset-parameter/754590.rdf
Name: Fuc
Units: mol%
Description: <p>Fucose</p>
http://lod.bco-dmo.org/id/dataset-parameter/754591.rdf
Name: Rha
Units: mol%
Description: <p>Rhamnose</p>
http://lod.bco-dmo.org/id/dataset-parameter/754592.rdf
Name: Ara
Units: mol%
Description: <p>Arabinose</p>
http://lod.bco-dmo.org/id/dataset-parameter/754593.rdf
Name: Gal
Units: mol%
Description: <p>Galactose</p>
http://lod.bco-dmo.org/id/dataset-parameter/754594.rdf
Name: Glc
Units: mol%
Description: <p>Glucose</p>
http://lod.bco-dmo.org/id/dataset-parameter/754595.rdf
Name: Man
Units: mol%
Description: <p>Mannose</p>
http://lod.bco-dmo.org/id/dataset-parameter/754596.rdf
Name: Xyl
Units: mol%
Description: <p>Xylose</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
15179
https://datadocs.bco-dmo.org/file/KAAGNLGC9nExq8/SFB_Transects.csv
SFB_Transects.csv
Primary data file for dataset ID 734790
download
https://osprey.bco-dmo.org/dataset/734790/data/download
download
onLine
dataset
<p>Samples were collect on the USGS R/V Mary Landsteiner&nbsp;and pumped directly from the surface (1 m deep) with a pump and clean tycoon tubing connected to an inline 0.2 um Whatman Polycap filter.</p>
<p>All filters were pumped and field filtered through 0.7 um Whatman glass fiber filters (GF/F, precombusted at 550 degrees C) using a peristaltic pump after purging the line.</p>
<p>Samples for DOC concentration were acidified to pH 2 and stored in a refrigerator (4 degrees C) until analysis by high-temperature combustion on a Shimadzu TOC-L CPH within two weeks following collection. DOC was calculated as the mean of between three and five injections using a six-point standard curve using established protocols (Mann et al., 2012) and the coefficient of variance was always &lt;2%.</p>
<p>Samples for CDOM absorbance were analyzed in a 1 cm cuvette on a Horiba Aqualog-UV-800-C. Absorbance spectra were measured from 230-800 nm, and corrected for a small offset either due to long-term baseline drift or derived from glass fiber particles during filtration (Blough et al., 1993), by subtracting the mean absorbance measured between 750-800 nm. Two spectral slopes were calculated at 275-295 nm and 350-400 nm (S275-295 and S350-400, respectively), and the spectral slope ratio (SR) was then calculated by dividing the former by the latter (Helms et al., 2008). The CDOM absorption ratio at 250 nm to 365 nm was calculated (a250:a365) and specific ultraviolet absorbance (SUVA254) was calculated by dividing the decadic absorption coefficient at 254 nm by DOC concentration (Weishaar et al., 2003; Fellman et al., 2009).</p>
<p>Fluorescence properties of FDOM were determined using a Horiba Aqualog-UV-800-C. The excitation emission matrices (EEMs) were generated in a 1 cm cuvette at varying integration times (1-10 seconds) to maximize the signal-to-noise ratio based on absorbance values. The EEMs were obtained at excitation (ex) 250-600 nm and at emission (em) 250-600 nm with 5 nm and 2 nm intervals respectively, and the EEMs were corrected for lamp intensity (Cory et al., 2010), inner filter effects (Kothawala et al., 2013), and normalized to Raman units (R.U.) (Stedmon et al., 2003). All corrections were performed using the FDOMcorr toolbox version 1.6 (Murphy, 2011). EEMs were analyzed with parallel factor analysis (PARAFAC) using the procedure described in Murphy et al. (2013). Furthermore, the fluorescence index (FI) (Cory et al., 2010), humification index (HIX) (Ohno, 2002; Zsolnay et al., 1999), and autotrophic productivity index (BIX) (Huguet et al., 2009) were calculated. FI was calculated from the emission wavelengths at 470 nm and 520 nm, obtained at excitation 370 nm (Cory and McKnight, 2005). HIX was calculated using the area under the emission sepctra 435-480 nm divided by the peak area 300-345 + 435-480 nm, at excitation 254 nm (Ohno, 2002). BIX was calculated from the emission intensity of 380 nm and 430 nm, obtained at excitation 310 nm (Wang et al., 2014).</p>
<p>Samples for FT-ICR MS analysis were solid-phase extracted using the procedure described in Dittmar et al., 2008. Filtered samples were acidified to pH 2 before solid phase extraction on 500 mg Agilent Bond Elut PPL cartridges. Each 1 L sample was extracted by eluting 2 mL of of methanol and then diluted to a DOC target concentration of 50 ug C mL-1. Extracted samples were stored at -20 degrees C prior to analysis on a 21 T (Bruker Daltonics, Billerica, MA, USA) FT-ICR MS located at the National High Magnetic Field Laboratory (NHMFL) (Tallahassee, Florida). Direct infusion electrospray ionization (ESI) generates negative ions at a flow rate of 700 nL min-1, and 100 time domain acquisitions were coadded for each mass spectrum.</p>
<p>Molecular formulas were assigned to signals &gt;6RMS baseline noise with EnviroOrg ©,TM software (Koch et al., 2007; Stubbins et al., 2010). Elemental combinations of C1–45H1–92N0–4O1–25S0–2 with a mass accuracy of ≤300 ppb were considered for assignment. Classification of formulas were based on their elemental ratios (Corilo, 2015). The modified aromaticity index (Almod) of each formula was calculated and Almod values of 0.5-0.67 and ≥0.67 were classified as aromatic and condensed aromatic structures (Koch and Dittmar, 2006; Koch and Dittmar, 2016). Other compound classes were unsaturated low oxygen=Almod&lt;0.5, H/C&lt;1.5, O/C&lt;0.5; unsaturated high oxygen=Almod&lt;0.5, H/ C&lt;1.5, O/C&gt;0.5; aliphatics=H/C 1.5-2.0, O/C&lt;0.9, N=0; peptide-like=H/C 1.5-2.0, O/C&lt;0.9, N&gt;0, and sugar-like= O/C&gt;0.9. Sugar-like compounds provide a very minor contribution to %RA (mean = 0.05, ± 0.06 %RA) and so were combined with peptide-like compounds throughout. Although FT-ICR MS allows for the precise assignment of molecular formulas to signals that may represent multiple isomers, they describe the underlying molecular compounds comprising DOM, thus the term compound may be used when describing the signals detected by FT-ICR MS.</p>
<p>Lignin derived phenols were isolated from the dried solid phase extracts followed by cupric oxide oxidation and liquid-liquid extraction modified from Spencer et al., (2010). Briefly, PPL extracts were redissolved in O2 free 2 M NaOH in a 6 mL Teflon vial (Savillex Corp) containing 500 mg CuO, and amended with 100 mg ferrous ammonium sulfate and 50 mg glucose and reacted in a 155 degree C oven for 3 hours. Following oxidation, the samples were centrifuged and supernatants were decanted into 40 mL vials. Oxidation products were acidified to pH 1 with H3PO4 and t-cinnamic acid was added as an internal standard. Liquid-liquid extractions of the oxidation products were undertaken by addition of 4 mL ethyl acetate, vortexing, and centrifugation prior to removal of the ethyl acetate. Extracts were pipetted through drying columns containing sodium sulfate into a 4 mL vial. Samples were dried under ultra-high purity argon between each extraction for a total of three extractions, following the last extraction the sodium sulfate was rinsed with 1 mL of ethyl acetate into the extract vial. Dried ethyl acetate extracts were dissolved in pyridine and derivatized with N/O bis-trimethylsilyltrifluoromethylacetamide (BSTFA) at 60 degrees C for ten minutes. Lignin phenol monomers were measured as trimethylsilane derivatives using an Agilent 6890N GC/5975 MS and were quantified as the relative response factors of each compound compared to the response of t- cinnamic acid and a five-point calibration curve bracketing the concentration range. Eight lignin phenols from three phenol groups were quantified; vanillyl (vanillin, acetovanillone, vanillic acid), syringyl (syringaldehyde, acetosyringone, syringic acid), and coumaryl (coumaric acid, ferulic acid).</p>
<p>Seven neutral sugars (fucose, rhamnose, arabinose, galactose, glucose, mannose, xylose) were analyzed according to Skoog and Benner (1997) with modifications. Briefly, samples were hydrolyzed in 1.2 mol L−1 sulfuric acid and neutralized with a self-absorbed ion retardation resin (Kaiser and Benner, 2000). After desalting with a mixture of cation and anion exchange resins, neutral sugars were isocratically separated with 25 mM NaOH on a PA 1 column in a Dionex 500 system with a pulsed amperiometric detector (PAD).</p>
<p>The following amino acids were analyzed using the method of Kaiser and Benner, 2005: histidine, serine, arginine, glycine, aspartic acid, glutamic acid, threonine, alanine, lysine, tyrosine, methionine, valine, norvaline, isoleucine, leucine, phenylalanine.</p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Processing:</strong><br />
- modified parameter names to conform with BCO-DMO naming conventions&nbsp;(removed units,&nbsp;replaced spaces with underscores);<br />
- replaced "NaN" with "nd" (no data);<br />
- 31-Jan-2019: updated dataset to version submitted on 20-Dec-2018.</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
Horiba Aqualog-UV-800-C
Horiba Aqualog-UV-800-C
PI Supplied Instrument Name: Horiba Aqualog-UV-800-C PI Supplied Instrument Description:Samples for CDOM absorbance were analyzed in a 1 cm cuvette on a Horiba Aqualog-UV-800-C (benchtop fluorometer). Fluorescence properties of FDOM were also determined using a Horiba Aqualog-UV-800-C. Instrument Name: Fluorometer Instrument Short Name:Fluorometer Instrument Description: A fluorometer or fluorimeter is a device used to measure parameters of fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light. The instrument is designed to measure the amount of stimulated electromagnetic radiation produced by pulses of electromagnetic radiation emitted into a water sample or in situ. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/113/
FT-ICR MS
FT-ICR MS
PI Supplied Instrument Name: FT-ICR MS PI Supplied Instrument Description:Samples were analyzed on a 21 T (Bruker Daltonics, Billerica, MA, USA) FT-ICR MS located at the National High Magnetic Field Laboratory (NHMFL) (Tallahassee, Florida). Instrument Name: Fourier Transform Ion Cyclotron Resonance Mass Spectrometer Instrument Short Name:FTICR MS Instrument Description: In Fourier Transform Ion Cyclotron Resonance Mass Spectrometry, the mass-to-charge ratio (m/z) of an ion is experimentally determined by measuring the frequency at which the ion processes in a magnetic field. These frequencies, which are typically in the 100 KHz to MHz regime, can be measured with modern electronics making it possible to determine the mass of an ion to within +/- 0.000005 amu or 5 ppm.
Agilent 6890N GC/5975 MS
Agilent 6890N GC/5975 MS
PI Supplied Instrument Name: Agilent 6890N GC/5975 MS PI Supplied Instrument Description:Lignin phenol monomers were measured as trimethylsilane derivatives using an Agilent 6890N GC/5975 MS. Instrument Name: Gas Chromatograph Instrument Short Name:Gas Chromatograph Instrument Description: Instrument separating gases, volatile substances, or substances dissolved in a volatile solvent by transporting an inert gas through a column packed with a sorbent to a detector for assay. (from SeaDataNet, BODC) Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB02/
Dionex 500 system
Dionex 500 system
PI Supplied Instrument Name: Dionex 500 system PI Supplied Instrument Description:Neutral sugars were isocratically separated in a Dionex 500 system with a pulsed amperiometric detector (PAD). Instrument Name: Ion Chromatograph Instrument Short Name:Ion Chromatograph Instrument Description: Ion chromatography is a form of liquid chromatography that measures concentrations of ionic species by separating them based on their interaction with a resin. Ionic species separate differently depending on species type and size. Ion chromatographs are able to measure concentrations of major anions, such as fluoride, chloride, nitrate, nitrite, and sulfate, as well as major cations such as lithium, sodium, ammonium, potassium, calcium, and magnesium in the parts-per-billion (ppb) range. (from http://serc.carleton.edu/microbelife/research_methods/biogeochemical/ic.html)
Agilent 6890N GC/5975 MS
Agilent 6890N GC/5975 MS
PI Supplied Instrument Name: Agilent 6890N GC/5975 MS PI Supplied Instrument Description:Lignin phenol monomers were measured as trimethylsilane derivatives using an Agilent 6890N GC/5975 MS. 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/
Shimadzu TOC-L CPH
Shimadzu TOC-L CPH
PI Supplied Instrument Name: Shimadzu TOC-L CPH PI Supplied Instrument Description:DOC concentration was determined on a Shimadzu TOC-L CPH. Instrument Name: Shimadzu TOC-L Analyzer Instrument Short Name:Shimadzu TOC-L Instrument Description: A Shimadzu TOC-L Analyzer measures DOC by high temperature combustion method.
Developed by Shimadzu, the 680 degree C combustion catalytic oxidation method is now used worldwide. One of its most important features is the capacity to efficiently oxidize hard-to-decompose organic compounds, including insoluble and macromolecular organic compounds. The 680 degree C combustion catalytic oxidation method has been adopted for the TOC-L series.
http://www.shimadzu.com/an/toc/lab/toc-l2.html Community Standard Description: http://onto.nerc.ac.uk/CAST/124.html