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Examination of protein-like fluorophores in chromophoric dissolved organic matter (CDOM) in a wetland and coastal environment for the wet and dry seasons of the years 2002 and 2003 (FCE)


At a Glance


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Authors: Rudolf Jaffe
Time period: 2002-03-01 to 2003-10-01
Package id: knb-lter-fce.1100.3
Dataset id: ST_ND_Jaffe_006

How to cite:
Jaffe, R.. 2024. Examination of protein-like fluorophores in chromophoric dissolved organic matter (CDOM) in a wetland and coastal environment for the wet and dry seasons of the years 2002 and 2003 (FCE). Environmental Data Initiative. https://doi.org/10.6073/pasta/e043bac2f37ee341e9524d880a25c28b. Dataset accessed 2024-04-27.

Geographic Coverage


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Detailed Metadata


  • Dataset Abstract
    Water samples are collected at the end of the dry and the wet season from all LTER sites and stored on ice until return to the lab. They are pre-filtered through pre-combusted GF/F filters and ultrafiltered and concentrated with a Pellicon 2 Mini tangential flow ultrafiltration system.Concentrated samples were then analyzed using fluorescence and SEC-HPLC. This CDOM optical study revealed the presence of two classes of compounds associated with the protein-like peak (peak T; excitation/emission (Ex/Em) maxima at around 280 nm/325 nm), which have very different chemical structures and ecological roles. In addition to proteins, we propose phenolic compounds as possible origins of peak T in coastal and wetland environments. In this study, natural water samples were obtained from subtropical rivers and estuarine environments within the Florida Coastal Everglades (FCE) ecosystem. The samples were ultra-filtered and excitation-emission fluorescence matrices (EEMs) were obtained. The EEMs showed the presence of four peaks with Ex/Em maxima at around 280 nm/325 nm (T), less than 260 nm/460 nm (A), 300 nm/412nm (M), and 350 nm/470 nm (C). To better understand the nature of peak T, the components originating this peak were separated using size exclusion chromatography (SEC) and detected by fluorescence emission at Ex/Em = 280 nm/325 nm. The elution curves revealed the presence of two elution peaks at a molecular weight of greater than 50K (void volume; T1) and around 7.6K (T2). This result suggested the need of cautious interpretation in the use of peak T as a proxy for the detection of proteinaceous materials in wetland and estuarine environments, since significant amounts of potentially interfering phenolic compounds are leached from senescent biomass in wetland and coastal ecosystems. As such EEM spectra of gallic acid an important component of hydrolysable tannins, and condensed tannins extracted from red mangroves (Rhizophora mangle) showed the presence of a peak maxima at a similar position to peak T (260/346 and 275/313 nm, respectively), suggesting these phenolic compounds can be possible sources of peak T.
  • Geographic Coverage
    Study Extent Description
    The Study Extent of this dataset includes the FCE Shark River Slough, Taylor Slough, and Florida Bay research sites within Everglades National Park, South Florida

    Bounding Coordinates
    SRS1a
    N: 25.761, S: 25.761, E: -80.727, W: -80.727

    SRS2
    N: 25.54972811, S: 25.54972811, E: -80.78520692, W: -80.78520692

    SRS3
    N: 25.46820617, S: 25.46820617, E: -80.85327617, W: -80.85327617

    SRS4
    N: 25.40976421, S: 25.40976421, E: -80.96431016, W: -80.96431016

    SRS5
    N: 25.37702258, S: 25.37702258, E: -81.03234716, W: -81.03234716

    SRS6
    N: 25.36462994, S: 25.36462994, E: -81.07794623, W: -81.07794623

    TS/Ph1a
    N: 25.42388762, S: 25.42388762, E: -80.59029790000001, W: -80.59029790000001

    TS/Ph2
    N: 25.40357188, S: 25.40357188, E: -80.60690341, W: -80.60690341

    TS/Ph3
    N: 25.25240534, S: 25.25240534, E: -80.66271768, W: -80.66271768

    TS/Ph6a
    N: 25.21418102, S: 25.21418102, E: -80.6490792, W: -80.6490792

    TS/Ph7a
    N: 25.19080491, S: 25.19080491, E: -80.63910514, W: -80.63910514

    TS/Ph8
    N: 25.23269749, S: 25.23269749, E: -80.52455665, W: -80.52455665

    TS/Ph9
    N: 25.17692874, S: 25.17692874, E: -80.48978207, W: -80.48978207

    TS/Ph10
    N: 25.02476744, S: 25.02476744, E: -80.68097374, W: -80.68097374

    TS/Ph11
    N: 24.91293492, S: 24.91293492, E: -80.93798347, W: -80.93798347

    TS/Ph4
    N: 25.32, S: 25.32, E: -80.52, W: -80.52

    TS/Ph5
    N: 25.3, S: 25.3, E: -80.52, W: -80.52

    C-111
    N: 25.32, S: 25.32, E: -80.52, W: -80.52

    FCE LTER Sites
    SRS1a, SRS2, SRS3, SRS4, SRS5, SRS6, TS/Ph1a, TS/Ph2, TS/Ph3, TS/Ph4, TS/Ph5, TS/Ph6a, TS/Ph7a, TS/Ph8, TS/Ph9, TS/Ph10, TS/Ph11, and C-111.

  • Attributes
    • Data Table:   Examination of protein-like fluorophores in chromophoric dissolved organic matter (CDOM) in a wetland and coastal environment
      Attribute Name:
      SITENAME
      Attribute Label:
      sitename
      Attribute Definition:
      Name of LTER site
      Storage Type:
      text
      Measurement Scale:
      text
      Missing Value Code:
       

      Attribute Name:
      Sampling Season
      Attribute Label:
      sampling season
      Attribute Definition:
      Collection season
      Storage Type:
      text
      Measurement Scale:
      text
      Missing Value Code:
       

      Attribute Name:
      N/C
      Attribute Label:
      Nitrogen to carbon ratio
      Attribute Definition:
      Nitrogen to carbon ratio
      Storage Type:
      data
      Measurement Scale:
      Units: percent
      Precision: 0.001
      Number Type: real
      Missing Value Code:
      -9999.000 (Value will never be recorded)

      Attribute Name:
      T
      Attribute Label:
      Tryptophan
      Attribute Definition:
      Emission intensity of tryptophan peak
      Storage Type:
      data
      Measurement Scale:
      Units: QSUPerMilligramPerLiter
      Precision: 0.01
      Number Type: real
      Missing Value Code:
      -9999.00 (Value will never be recorded)

      Attribute Name:
      A1
      Attribute Label:
      Fixed humic substance peak
      Attribute Definition:
      Excitation wavelength = 260nm and emission wavelength = 460 nm
      Storage Type:
      data
      Measurement Scale:
      Units: QSUPerMilligramPerLiter
      Precision: 0.01
      Number Type: real
      Missing Value Code:
      -9999.00 (Value will never be recorded)

      Attribute Name:
      A2
      Attribute Label:
      UV humic peak
      Attribute Definition:
      Excitation wavelength = 260 nm, emission maximum
      Storage Type:
      data
      Measurement Scale:
      Units: QSUPerMilligramPerLiter
      Precision: 0.01
      Number Type: real
      Missing Value Code:
      -9999.00 (Value will never be recorded)

      Attribute Name:
      C
      Attribute Label:
      Visible humic peak
      Attribute Definition:
      Excitation wavelength = 350 nm, emission wavelength = 470 nm.
      Storage Type:
      data
      Measurement Scale:
      Units: QSUPerMilligramPerLiter
      Precision: 0.01
      Number Type: real
      Missing Value Code:
      -9999.00 (Value will never be recorded)

      Attribute Name:
      %T1
      Attribute Label:
      Protein derived T1
      Attribute Definition:
      Protein derived T1
      Storage Type:
      data
      Measurement Scale:
      Units: QSUPerMilligramPerLiter
      Precision: 0.01
      Number Type: real
      Missing Value Code:
      -9999.00 (Value will never be recorded)

      Attribute Name:
      SEC_%T1
      Attribute Label:
      SEC_%T1
      Attribute Definition:
      Percentage of protein-like material (high molecular weight fraction) determined by size exclusion chromatography. Detector excitation wavelength = 280 nm, emission wavelength = 325 nm.
      Storage Type:
      data
      Measurement Scale:
      Units: percent
      Precision: 1
      Number Type: real
      Missing Value Code:
      -9999 (Value will never be recorded)

      Attribute Name:
      Max_WL
      Attribute Label:
      Maximum Wavelength
      Attribute Definition:
      Emission wavelength that gives maximum emission intensity at a fixed excitation of 313 nm
      Storage Type:
      data
      Measurement Scale:
      Units: nanometer
      Precision: 1
      Number Type: real
      Missing Value Code:
      -9999 (Value will never be recorded)

      Attribute Name:
      Max_I
      Attribute Label:
      Maximum Intensity
      Attribute Definition:
      Emission intensity of maximum emission wavelength at a fixed excitation of 313 nm.
      Storage Type:
      data
      Measurement Scale:
      Units: QSUPerMilligramPerLiter
      Precision: 0.1
      Number Type: real
      Missing Value Code:
      -9999.0 (Value will never be recorded)

      Attribute Name:
      FI
      Attribute Label:
      Fluorescence Index
      Attribute Definition:
      Ratio of emission intensities at 450 and 500 nm at a fixed excitation wavelength of 370 nm.
      Storage Type:
      data
      Measurement Scale:
      Units: dimensionless
      Precision: 0.01
      Number Type: real
      Missing Value Code:
      -9999.00 (Value will never be recorded)

      Attribute Name:
      %285
      Attribute Label:
      %285
      Attribute Definition:
      Obtained from synchronous fluorescence spectrum at a constant offset of 30 nm (excitation wavelengths = 285, 350, 385, 460 nm). Percentage of the first peak intensity (285 nm).
      Storage Type:
      data
      Measurement Scale:
      Units: percent
      Precision: 1
      Number Type: real
      Missing Value Code:
      -9999 (Value will never be recorded)

      Attribute Name:
      Peak_1
      Attribute Label:
      Peak_1
      Attribute Definition:
      Fluorescence intensity at an excitation of 285 nm in synchronous scan.
      Storage Type:
      data
      Measurement Scale:
      Units: QSUPerMilligramPerLiter
      Precision: 0.1
      Number Type: real
      Missing Value Code:
      -9999.0 (Value will never be recorded)

      Attribute Name:
      A_254
      Attribute Label:
      Absorbance at 254 nm
      Attribute Definition:
      UV absorbance at 254 nm.
      Storage Type:
      data
      Measurement Scale:
      Units: dimensionless
      Precision: 0.001
      Number Type: real
      Missing Value Code:
      -9999.000 (Value will never be recorded)


  • Methods
    Sampling Description
    Water samples were collected at the end of the dry and the wet season from all LTER sites, stored on ice and filtered through combusted GF/F glass fiber filters upon arrival to the lab.

    Method Step

    Description
    Natural water samples (16 to 50 L) were collected in Nalgene low density polyethylene carboys at the end of the dry (Mar-Apr) and the wet (Sep-Oct) season of 2002 and 2003 from all LTER sites. They were stored on ice and filtered through pre-combusted GF/F glass fiber filters upon arrival to the lab. The filtrate was processed through a tangential flow ultrafiltration system (TFF) equipped with 0.2um nominal molecular weight cutoff regenerated cellulose membranes, followed by a concentration with 1kDalton molecular weight cutoff membrane while samples were kept in iced water. Following the concentration procedure, the samples were diafiltered three times with 1-L of Milli-Q Water to eliminate salts. The concentrated UDOM samples were then freeze-dried and stored at room temperature in a dessicator. Before fluorescence or SEC-HPLC analysis, samples were re-hydrated with 0.05M Tris(hydroxymethl)aminomethane (THAM) (adjusted to pH at 7.0 with phosphoric acid) to a concentration of 20 mgCL-1 for Florida Bay samples (TS/Ph 9,10,and 11) and 5 mgCL-1 for all other samples.A series of emission fluorescence spectra of the samples were obtained at a ratio mode (emission signal-to-excitation lamp output) from lamda +10nm to lamda + 250nm at 1nm intervals, where lamda is the excitation wavelength. The excitation wavelength was scanned from 260 to 455 nm every 5 nm in a 1 cm quartz fluorescence cell at room temperature (20 degrees C). Fluorescence values were corrected for internal absorbance quenching following the procedures outlined in McKnight et al (2001). The Fluorescence spectra were also corrected for the internal instrument configuration using excitation and emission correction factors for the range of observations supplied by the manufacturer (e.g. Coble 1996; Kowalczuk et al. 2003). Fluorescence was reported as quinine sulfate units according to Maie et al. (2005). MilliQ-water was measured as the blank and subtracted from the sample spectra. UV-visible absorption spectra were measured with a UV-Vis scanning spectrophotometer using a 1 cm quartz cell. The molecular weight distribution of the UDOM was determined by size exclusion chromatography (SEC) (Maie et al. 2004; Scully et al. 2004). Analytical conditions were as follows: column, YMC-Pack Diol-120G (pore size 12 nm, I.D. 8.0mm x length 500mm), eluent, 0.05 M THAM (adjusted to pH at 7.0 with phosphoric acid); flow rate, 0.7 ml min-1; detection, fluorescence emission at 325 nm with an excitation at 280nm; injection volume, 200ul; temperature 22 degrees C. The void volume (VO; 13.8 min.) and void volume plus inner volume (VO+VI; 32.3 min.) were determined using Blue Dextran 2000 and tryptophan, respectively. The column was calibrated with several different dextran standards of know molecular weight. Total organic C and N content was measured on a Carlo Erba NA 1500 Nitrogen/Carbon Analyzer. Prior to analysis trace amounts of carbonate were removed by exposing the powered UDOM in a silver capsule to hydrochloric acid vapor for 4 hours (Hedges and Stern 1984). The samples were then dried under vacuum to eliminate any residual hydrochloric acid and sealed for later analysis.

    References:

    Coble, Paula G 1996. Characterization of marine and terrestrial DOM in seawater using excitation-emission matrix spectroscopy. Marine Chemistry, 51: 325-346.

    Hedges, J I 1984. Carbon and nitrogen determinations of carbonate-containing solids. Limnology and Oceanography, 29: 657-663.

    Kowalczuk, P 2003. Characterization of CDOM in an organic-rich river and surrounding coastal ocean in the South Atlantic Bight. Aquatic Science, 65: 384-401.

    Maie, Nagamitsu 2004. Chemical characteristics and potential source of fulvic acids leached from the plow layer of paddy soil.. Geoderma, 120: 309-323.

    Maie, Nagamitsu 2005. Chemical characteristics of dissolved organic matter (DOM) in an extremely oligotrophic subtropical wetland.. Limnology and Oceanography, 50: 23-25.

    McKnight, D M 2001. Spectrofluorometric characterization of dissolved organic matter for the identification of percursor organic material and aromaticity.. Limnology and Oceanography, 46: 38-48.

    Scully, N M 2004. Early diagenesis of plant derived dissolved organic matter along a wetland, mangrove, estuary ecotone.. Limnology and Oceanography, 49: 1667-1678.

    Instrumentation
    Whatman GF/F glass fiber filters, Nalgene polyethylene carboys, Pellicon 2 Mini Flow Ultrafiltration System, Jobin Yvon Horiba Fluoromax 3, Shimadzu 2101PC Spectrophotometer, Carlo Erba NA 1500 Nitrogen/Carbon Analyzer (Carlo Erba Milan Italy).

    Quality Control
    Fluorescence measurements are corrected for internal absorbance quenching (McKnight et al., 2001). Fluorescence spectra are corrected for internal instrument configuration using excitation and emission correction factors (Coble, 1996 and Kowalczuk et al., 2003). SEC-HPLC results were corrected by calibrating the column with several different dextran standards of known molecular weight.
  • Distribution and Intellectual Rights
    Online distribution
    https://pasta.lternet.edu/package/data/eml/knb-lter-fce/1100/3/08834b918d10a5a8a1d34cfd31a3aa0e
    Data Submission Date:  2005-09-08

    Intellectual Rights
    This information is released under the Creative Commons license - Attribution - CC BY (https://creativecommons.org/licenses/by/4.0/). The consumer of these data ("Data User" herein) is required to cite it appropriately in any publication that results from its use. The Data User should realize that these data may be actively used by others for ongoing research and that coordination may be necessary to prevent duplicate publication. The Data User is urged to contact the authors of these data if any questions about methodology or results occur. Where appropriate, the Data User is encouraged to consider collaboration or co-authorship with the authors. The Data User should realize that misinterpretation of data may occur if used out of context of the original study. While substantial efforts are made to ensure the accuracy of data and associated documentation, complete accuracy of data sets cannot be guaranteed. All data are made available "as is." The Data User should be aware, however, that data are updated periodically and it is the responsibility of the Data User to check for new versions of the data. The data authors and the repository where these data were obtained shall not be liable for damages resulting from any use or misinterpretation of the data. Thank you.

  • Keywords
    organic matter, FCE, Florida Coastal Everglades LTER, ecological research, long-term monitoring, Everglades National Park, emissions, Shark River Slough, fluorescence, water, organisms, seasonality, wetlands, nitrogen, UDOM Fluorescence, Optical measurements, Fluorescence spectroscopy, SEC-HPLC, phenolic compounds, Taylor Slough
  • Dataset Contact
    • Name: Rudolf Jaffe 
    • Position: Project Collaborator
    • Organization: Florida Coastal Everglades LTER Program
    • Address: Florida International University
      University Park
      OE 148
      Miami, Florida 33199 USA
    • Phone: 305-348-2456
    • Fax: 305-348-4096
    • Email: jaffer@fiu.edu
    • URL: http://serc.fiu.edu/sercindex/index.htm

    • Position: Information Manager
    • Organization: Florida Coastal Everglades LTER
    • Address: Florida International University
      11200 SW 8th Street, OE 148
      Miami, FL 33199 USA
    • Email: fcelter@fiu.edu
    • URL: https://fcelter.fiu.edu

  • Data Table and Format
    Data Table:  Examination of protein-like fluorophores in chromophoric dissolved organic matter (CDOM) in a wetland and coastal environment

    Entity Name:
    ST_ND_Jaffe_006
    Entity Description:
    Examination of protein-like fluorophores in chromophoric dissolved organic matter (CDOM) in a wetland and coastal environment
    Object Name:
    ST_ND_Jaffe_006.csv
    Number of Header Lines:
    1
    Attribute Orientation:
    column
    Field Delimiter:
    ,
    Number of Records:
    72