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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


Authors: Rudolf Jaffe
Time period: 2002-03-01 to 2003-10-01
Package id: knb-lter-fce.1100.2
Dataset id: ST_ND_Jaffe_006

How to cite:
Jaffe, R.. 2006. 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/6d2e26bc8c8cd2322981d22a095ab968. Dataset accessed 2020-10-26.

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
    Samples were collected in the Taylor Slough and Shark River Slough, within Everglades National Park, South Florida.
    N: 25.761, S: 24.913, E: -80.490, W: -81.078

    Florida Coastal Everglades LTER Study Area: South Florida, Everglades National Park, and Florida Bay
    N: 25.761, S: 24.913, E: -80.490, W: -81.078

    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.

    All Sites
    Geographic Description
    Bounding Coordinates
    FCE LTER Site SRS1a
    N: 25.761, S: 25.761, E: -80.727, W: -80.727
    FCE LTER Site SRS2
    N: 25.550, S: 25.550, E: -80.785, W: -80.785
    FCE LTER Site SRS3
    N: 25.468, S: 25.468, E: -80.853, W: -80.853
    FCE LTER Site SRS4
    N: 25.410, S: 25.410, E: -80.964, W: -80.964
    FCE LTER Site SRS5
    N: 25.377, S: 25.377, E: -81.032, W: -81.032
    FCE LTER Site SRS6
    N: 25.365, S: 25.365, E: -81.078, W: -81.078
    FCE LTER Site TS/Ph1a
    N: 25.42, S: 25.42, E: -80.59, W: -80.59
    FCE LTER Site TS/Ph2
    N: 25.40, S: 25.40, E: -80.61, W: -80.61
    FCE LTER Site TS/Ph3
    N: 25.25, S: 25.25, E: -80.66, W: -80.66
    FCE LTER Site TS/Ph4
    N: 25.32, S: 25.32, E: -80.52, W: -80.52
    FCE LTER Site TS/Ph5
    N: 25.30, S: 25.30, E: -80.52, W: -80.52
    FCE LTER Site TS/Ph6
    N: 25.21, S: 25.21, E: -80.65, W: -80.65
    FCE LTER Site TS/Ph7
    N: 25.19, S: 25.19, E: -80.64, W: -80.64
    FCE LTER Site TS/Ph8
    N: 25.23, S: 25.23, E: -80.53, W: -80.53
    FCE LTER Site TS/Ph9
    N: 25.18, S: 25.18, E: -80.49, W: -80.49
    FCE LTER Site TS/Ph10
    N: 25.02, S: 25.02, E: -80.68, W: -80.68
    FCE LTER Site TS/Ph11
    N: 24.91, S: 24.91, E: -80.94, W: -80.94
    C-111
    N: 25.32, S: 25.32, E: -80.52, W: -80.52
  • 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:
      Name of LTER site
      Missing Value Code:
       

      Attribute Name:
      Sampling Season
      Attribute Label:
      sampling season
      Attribute Definition:
      Collection season
      Storage Type:
      text
      Measurement Scale:
      Collection season
      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.

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

    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).

    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.

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

    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).

    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.

    Citation
    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.

    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).

    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.

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

    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).

    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.

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

    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).

    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.

    Citation
    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.

    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).

    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.

    Citation
    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
    http://fcelter.fiu.edu/perl/public_data_download.pl?datasetid=ST_ND_Jaffe_006.txt
    Data Submission Date:  2005-09-08

    Intellectual Rights
    These data are classified as 'Type II' whereby original FCE LTER experimental data collected by individual FCE researchers to be released to restricted audiences according to terms specified by the owners of the data. Type II data are considered to be exceptional and should be rare in occurrence. The justification for exceptions must be well documented and approved by the lead PI and Site Data Manager. Some examples of Type II data restrictions may include: locations of rare or endangered species, data that are covered under prior licensing or copyright (e.g., SPOT satellite data), or covered by the Human Subjects Act, Student Dissertation data and those data related to the FCE LTER Program but not funded by the National Science Foundation (NSF) under LTER grants #DEB-9910514, and # DBI-0620409. Researchers that make use of Type II Data may be subject to additional restrictions to protect any applicable commercial or confidentiality interests. All publications based on this dataset must cite the data Contributor, the Florida Coastal Everglades Long-Term Ecological Research (LTER) Program and that this material is based upon work supported by the National Science Foundation through the Florida Coastal Everglades Long-Term Ecological Research program under Cooperative Agreements #DEB-1237517, #DBI-0620409, and #DEB-9910514. Additionally, two copies of the manuscript must be submitted to the Florida Coastal Everglades LTER Program Office, LTER Program Manager, Florida International University, Southeast Environmental Research Center, OE 148, University Park, Miami, Florida 33199. For a complete description of the FCE LTER Data Access Policy and Data User Agreement, please go to FCE Data Management Policy at http://fcelter.fiu.edu/data/DataMgmt.pdf and LTER Network Data Access Policy at http://fcelter.fiu.edu/data/core/data_user_agreement/distribution_policy.html.

  • Keywords
    FCE, Florida Coastal Everglades LTER, ecological research, long-term monitoring, Everglades National Park, emissions, Shark River Slough, fluorescence, water, organisms, seasonality, organic matter, wetlands, nitrogen, UDOM Fluorescence, Optical measurements, Fluorescence spectroscopy, SEC-HPLC, phenolic compounds, Taylor Slough
  • Dataset Contact
    • Position: Information Manager
    • Organization: LTER Network Office
    • Address: UNM Biology Department, MSC03-2020
      1 University of New Mexico
      Albuquerque, NM 87131-0001 USA
    • Phone: 505 277-2535
    • Fax: 505 277-2541
    • Email: tech-support@lternet.edu
    • URL: http://www.lternet.edu

    • 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 Program
    • Address: Florida International University
      University Park
      OE 148
      Miami, FL 33199 USA
    • Phone: 305-348-6054
    • Fax: 305-348-4096
    • Email: fcelter@fiu.edu
    • URL: http://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
    Number of Header Lines:
    1
    Attribute Orientation:
    column
    Field Delimiter:
    ,
    Number of Records:
    72