Dataset title: Monthly fluorescence parallel factor analysis (PARAFAC) components for Shark River Slough, Taylor Slough, and Florida Bay, Everglades National Park (FCE LTER), Florida, USA, April 2011 - ongoing Dataset ID: doi:10.6073/pasta/78b3ae1e8c115eb5a9ef6024eb35bdb9 Dataset Creator Name: Dr. John Kominoski Organization: Florida Coastal Everglades LTER Address: Florida International University 11200 SW 8th Street, OE 148 Miami, FL 33199 United States Phone: 305-348-7117 Email: jkominos@fiu.edu Name: Dr. Matthew Smith Organization: U.S. Army Corps of Engineers Email: Matthew.A.Smith2@usace.army.mil Metadata Provider Organization: Florida Coastal Everglades LTER Address: Florida International University 11200 SW 8th Street, OE 148 Miami, FL 33199 USA Phone: 305-348-6054 Email: fcelter@fiu.edu URL: https://fcelter.fiu.edu Dataset Abstract Dissolved organic matter plays an important role in biogeochemical processes in aquatic environments such as elemental cycling, microbial loop energetics, and the transport of materials across landscapes. Since most of N (> 90%) and P (around 90%) is in the organic form in the oligotrophic subtropical Florida Coastal Everglades (FCE), study of the source and dynamics of dissolved organic matter (DOM) in the ecosystem is crucial for the better understanding of the biogeochemical cycling of nutrients. FCE are composed of estuaries with distinct regions with different biogeochemical processes. Freshwater marsh primarily receives terrestrial input and local autochthonous vegetation production. Mangrove ecotone, nevertheless, is affected by the tidal contributions from Florida Bay and local mangrove production. Florida Bay (FB) is a wedge-shaped shallow oligotrophic estuary which lays south of the Everglades, the bottom of which is covered with a dense biomass of seagrass. The sources of both freshwater and nutrients in FCE are difficult to quantify, owing to the non-point source nature of runoff from the Everglades and the dendritic cross channels in the mangroves. Furthermore, the combination of multiple DOM sources (freshwater marsh vegetation, mangroves, phytoplankton, seagrass, etc.), and the potential seasonal variability of their relative contribution, along with the history of (photo)chemical and microbial diagenetic processing, and complex advective circulation, makes the study of DOM dynamics in FCE particularly difficult using standard schemes of estuarine ecology. Quantitative information of DOM is very useful to investigate the biogeochemical cycling of DOM to a certain degree, however, qualitative information is necessary to better understand the source and dynamics of DOM. Since fluorescence spectroscopic techniques are very sensitive, quick and simple, they have been applied to investigate the fate of DOM in estuaries. Here, we have quantified a series of six distinct signatures of DOM composition using parallel factor analysis (PARAFAC). These components comprise the majority of DOM source and composition across the Florida Coastal Everglades ecosystem. Data collection for this project began in April 2011 and is ongoing. Monthly fluorescence monitoring data in this data package supersede those in package knb-lter-fce.1234 (https://portal.edirepository.org/nis/mapbrowse?scope=knb-lter-fce&identifier=1234). Additional monthly monitoring fluorescence data (covering 2004-2014) from FCE are available in package knb-lter-fce.1174 (https://portal.edirepository.org/nis/mapbrowse?scope=knb-lter-fce&identifier=1174) but are not interoperable with fluorescence data provided in this package. Geographic Coverage Bounding Coordinates Geographic description: SRS1d West bounding coordinate: -80.654 East bounding coordinate: -80.654 North bounding coordinate: 25.7463 South bounding coordinate: 25.7463 Geographic description: SRS2 West bounding coordinate: -80.78520692 East bounding coordinate: -80.78520692 North bounding coordinate: 25.54972811 South bounding coordinate: 25.54972811 Geographic description: SRS3 West bounding coordinate: -80.85327617 East bounding coordinate: -80.85327617 North bounding coordinate: 25.46820617 South bounding coordinate: 25.46820617 Geographic description: SRS4 West bounding coordinate: -80.96431016 East bounding coordinate: -80.96431016 North bounding coordinate: 25.40976421 South bounding coordinate: 25.40976421 Geographic description: SRS5 West bounding coordinate: -81.03234716 East bounding coordinate: -81.03234716 North bounding coordinate: 25.37702258 South bounding coordinate: 25.37702258 Geographic description: SRS6 West bounding coordinate: -81.07794623 East bounding coordinate: -81.07794623 North bounding coordinate: 25.36462994 South bounding coordinate: 25.36462994 Geographic description: TS/Ph1 West bounding coordinate: -80.59029790000001 East bounding coordinate: -80.59029790000001 North bounding coordinate: 25.42388762 South bounding coordinate: 25.42388762 Geographic description: TS/Ph2 West bounding coordinate: -80.60690341 East bounding coordinate: -80.60690341 North bounding coordinate: 25.40357188 South bounding coordinate: 25.40357188 Geographic description: TS/Ph3 West bounding coordinate: -80.66271768 East bounding coordinate: -80.66271768 North bounding coordinate: 25.25240534 South bounding coordinate: 25.25240534 Geographic description: TS/Ph6a West bounding coordinate: -80.6490792 East bounding coordinate: -80.6490792 North bounding coordinate: 25.21418102 South bounding coordinate: 25.21418102 Geographic description: TS/Ph7a West bounding coordinate: -80.63910514 East bounding coordinate: -80.63910514 North bounding coordinate: 25.19080491 South bounding coordinate: 25.19080491 Geographic description: TS/Ph9 West bounding coordinate: -80.48978207 East bounding coordinate: -80.48978207 North bounding coordinate: 25.17692874 South bounding coordinate: 25.17692874 Geographic description: TS/Ph10 West bounding coordinate: -80.68097374 East bounding coordinate: -80.68097374 North bounding coordinate: 25.02476744 South bounding coordinate: 25.02476744 Geographic description: TS/Ph11 West bounding coordinate: -80.93798347 East bounding coordinate: -80.93798347 North bounding coordinate: 24.91293492 South bounding coordinate: 24.91293492 Temporal Coverage Start Date: 2011 End Date: 2022 Data Table Entity Name: FCE1256_Smith_Fluorescence_Dataset Entity Description: Monthly fluorescence parallel factor analysis (PARAFAC) components for Shark River Slough, Taylor Slough, and Florida Bay, Everglades National Park (FCE LTER), Florida, USA Object Name: FCE1256_Smith_Fluorescence_Dataset.csv Data Format Number of Header Lines: 1 Attribute Orientation: column Field Delimiter: , Number of Records: Attributes Attribute Name: Sample Attribute Label: Sample Attribute Definition: Sample ID Storage Type: string Measurement Scale: text Missing Value Code: Attribute Name: Latitude Attribute Label: Latitude Attribute Definition: Latitude Storage Type: float Measurement Scale: Units: degree Number Type: real Missing Value Code: -9999 (No data available) Attribute Name: Longitude Attribute Label: Longitude Attribute Definition: Longitude Storage Type: float Measurement Scale: Units: degree Number Type: real Missing Value Code: -9999 (No data available) Attribute Name: Transect Attribute Label: Transect Attribute Definition: Transect Number Storage Type: string Measurement Scale: SRS= Shark River Slough TS= Taylor Slough Missing Value Code: Attribute Name: TransectCategory Attribute Label: TransectCategory Attribute Definition: Transect distance from ocean: marsh (3), mangrove (2), marine (1) Storage Type: string Measurement Scale: 1= Transect category (Marine) - distance from ocean 2= Transect category (Mangrove) - distance from ocean 3= Transect category (Marsh) - distance from ocean Missing Value Code: Attribute Name: Ecotype Attribute Label: Ecotype Attribute Definition: Ecotype Storage Type: string Measurement Scale: Mangrove= Mangrove Ecotype Marine= Marine Ecotype Marsh= Marsh Ecotype Missing Value Code: Attribute Name: Site Attribute Label: Site Attribute Definition: Site Number Storage Type: float Measurement Scale: Units: dimensionless Number Type: real Missing Value Code: NA (No data available) Attribute Name: Month Attribute Label: Month Attribute Definition: Month of Collection Storage Type: float Measurement Scale: Units: dimensionless Number Type: real Missing Value Code: -9999 (No data available) Attribute Name: Year Attribute Label: Year Attribute Definition: Year of Collection Storage Type: dateTime Measurement Scale: Missing Value Code: -9999 (No data available) Attribute Name: FMax_C1 Attribute Label: FMax_C1 Attribute Definition: Fluorescence maximum Storage Type: float Measurement Scale: Units: dimensionless Number Type: real Missing Value Code: -9999 (No data available) Attribute Name: FMax_C2 Attribute Label: FMax_C2 Attribute Definition: Fluorescence maximum Storage Type: float Measurement Scale: Units: dimensionless Number Type: real Missing Value Code: -9999 (No data available) Attribute Name: FMax_C3 Attribute Label: FMax_C3 Attribute Definition: Fluorescence maximum Storage Type: float Measurement Scale: Units: dimensionless Number Type: real Missing Value Code: -9999 (No data available) Attribute Name: FMax_C4 Attribute Label: FMax_C4 Attribute Definition: Fluorescence maximum Storage Type: float Measurement Scale: Units: dimensionless Number Type: real Missing Value Code: -9999 (No data available) Attribute Name: FMax_C5 Attribute Label: FMax_C5 Attribute Definition: Fluorescence maximum Storage Type: float Measurement Scale: Units: dimensionless Number Type: real Missing Value Code: -9999 (No data available) Attribute Name: FMax_C6 Attribute Label: FMax_C6 Attribute Definition: Fluorescence maximum Storage Type: float Measurement Scale: Units: dimensionless Number Type: real Missing Value Code: -9999 (No data available) Attribute Name: Percent_C1 Attribute Label: Percent_C1 Attribute Definition: Percent (%) of DOM sample contributed by Component 1 Storage Type: float Measurement Scale: Units: percent Number Type: real Missing Value Code: -9999 (No data available) Attribute Name: Percent_C2 Attribute Label: Percent_C2 Attribute Definition: Percent (%) of DOM sample contributed by Component 2 Storage Type: float Measurement Scale: Units: percent Number Type: real Missing Value Code: -9999 (No data available) Attribute Name: Percent_C3 Attribute Label: Percent_C3 Attribute Definition: Percent (%) of DOM sample contributed by Component 3 Storage Type: float Measurement Scale: Units: percent Number Type: real Missing Value Code: -9999 (No data available) Attribute Name: Percent_C4 Attribute Label: Percent_C4 Attribute Definition: Percent (%) of DOM sample contributed by Component 4 Storage Type: float Measurement Scale: Units: percent Number Type: real Missing Value Code: -9999 (No data available) Attribute Name: Percent_C5 Attribute Label: Percent_C5 Attribute Definition: Percent (%) of DOM sample contributed by Component 5 Storage Type: float Measurement Scale: Units: percent Number Type: real Missing Value Code: -9999 (No data available) Attribute Name: Percent_C6 Attribute Label: Percent_C6 Attribute Definition: Percent (%) of DOM sample contributed by Component 6 Storage Type: float Measurement Scale: Units: percent Number Type: real Missing Value Code: -9999 (No data available) Attribute Name: dilution_factor Attribute Label: dilution_factor Attribute Definition: Amount of dilution (using MilliQ water) of original sample Storage Type: float Measurement Scale: Units: dimensionless Number Type: real Missing Value Code: -9999 (No data available) Attribute Name: FI_FI370 Attribute Label: FI_FI370 Attribute Definition: Fluorescence Index at excitation 370 nm (unitless) Storage Type: float Measurement Scale: Units: dimensionless Number Type: real Missing Value Code: -9999 (No data available) Attribute Name: BIX_FI310 Attribute Label: BIX_FI310 Attribute Definition: Biological Index at excitation 310 nm (unitless) Storage Type: float Measurement Scale: Units: dimensionless Number Type: real Missing Value Code: -9999 (No data available) Attribute Name: HIX_FI254 Attribute Label: HIX_FI254 Attribute Definition: Humification Index at excitation 254 nm (unitless) Storage Type: float Measurement Scale: Units: dimensionless Number Type: real Missing Value Code: -9999 (No data available) Attribute Name: Abs254 Attribute Label: Abs254 Attribute Definition: Absorbance at 254 nm at 1 cm path length (unitless) Storage Type: float Measurement Scale: Units: dimensionless Number Type: real Missing Value Code: -9999 (No data available) Attribute Name: DOC_umol_L Attribute Label: DOC_umol_L Attribute Definition: Dissolved organic carbon concentration Storage Type: float Measurement Scale: Units: micromolePerLiter Number Type: real Missing Value Code: -9999 (No data available) Attribute Name: DOC_mg_L Attribute Label: DOC_mg_L Attribute Definition: Dissolved organic carbon concentration Storage Type: float Measurement Scale: Units: milligramPerLiter Number Type: real Missing Value Code: -9999 (No data available) Attribute Name: SUVA254 Attribute Label: SUVA254 Attribute Definition: Specific UV Absorbance at 254 nm with 1 cm path length (unitless) Storage Type: float Measurement Scale: Units: dimensionless Number Type: real Missing Value Code: -9999 (No data available) Attribute Name: slp274_295 Attribute Label: slp274_295 Attribute Definition: Slope of excitation from 274 to 295 nm (unitless) Storage Type: float Measurement Scale: Units: dimensionless Number Type: real Missing Value Code: -9999 (No data available) Attribute Name: slp350_400 Attribute Label: slp350_400 Attribute Definition: Slope of excitation from 350 to 400 nm (unitless) Storage Type: float Measurement Scale: Units: dimensionless Number Type: real Missing Value Code: -9999 (No data available) Attribute Name: SR Attribute Label: SR Attribute Definition: Slope ratio (division of slope of 275 to 295 nm by slope of 350 to 400 nm), unitless Storage Type: float Measurement Scale: Units: dimensionless Number Type: real Missing Value Code: -9999 (No data available) Attribute Name: ES_E3 Attribute Label: ES_E3 Attribute Definition: Ratio of the absorbance from 250 to 365 nm (unitless) Storage Type: float Measurement Scale: Units: dimensionless Number Type: real Missing Value Code: -9999 (No data available) Methods Method Step Description Sampling Description Water samples are collected monthly (ongoing since April 2011) from a total of 14 sampling stations located in the coastal estuaries of the southern tip of the Florida Peninsula, USA. These stations were established for an on-going water quality monitoring program (http://www.serc.fiu.edu/wqmnetwork). Sampling stations can be largely grouped into 3 distinct districts based on the geomorphological features, that is, Florida Bay (FB, 3 sampling stations), Shark River Slough (SRS, 6 sampling stations), and Taylor Slough (TSPH, 8 sampling stations). Surface water samples were taken from the these stations. The samples were collected using pre-washed, brown Nalgen polyethylene bottles (Nalge Nunc International). Salinity of the water samples was measured in the field using an Orion salinity meter. The samples were stored on ice and returned to the laboratory within 8 h for analysis. Subsamples for spectroscopic analysis were filtered through precombusted Whatman GF/F glass fiber filters once received in the laboratory and analyzed immediately. Instrumentation Whatman 0.7um glass fiber filters, Shimadzu TOC-5000A Analyzer, Jobin Yvon Horiba (France) Aqualog-2 fluorometer, Varian CARY 50 Bio UV visible spectrophotometer Method Step Description Laboratory Analysis Description Total organic carbon (TOC) concentrations were analyzed by a high-temperature combustion method with a Shimadzu TOC-5000A TOC analyzer. In advance the analysis, samples were acidified with 3M HCl, and purged with N2 gas to remove inorganic C. Ancillary physical and chemical parameters were measured using standard methods as part of on-going estuarine water quality monitoring program http://www.serc.fiu.edu/wqmnetwork. Detailed methods will be found elsewhere. For escitation-emission matrix (EEM) measurements, fluorescences spectra were measured with a Jobin-Yvon-Horiba (France) Aqualog-2 fluorometer equipped with a 150-W continuous output xenon arc lamp under condition of 5.7-nm excitation and 2-nm emission slit widths and a 0.25 second response time. Forty-four emission scans were acquired at excitation wavelengths (lamda ex) between 240 and 455 nm at 5 nm intervals. Them emission wavelengths were scanned from lamda ex + 10 nm to lamda ex + 250 nm at 2 nm intervals (Coble et al., 1993 and Coble, 1996). All fluorescence spectra were acquired in ratio mode, whereby the sample (emission signal, S) and reference (excitation lamp output, R) signals were collected and the ratio (S/R) was calculated. The ratio mode eliminates the influence of possible fluctuation and wavelength dependency of excitation lamp output. Several post-acquisition steps were involved in the correction of the fluorescence spectra. First, an inner filter corrections was applied to the fluorescence data according to McKnight et al. (2001). After inner filter corrections the sample EEM underwent spectral subtraction of the Milli-Q water to remove most of the effects due to Raman scattering. Instrument bias related to wavelength dependent efficiencies of the specific instrument's optical components (gratings, mirrors, etc.) were then corrected by applying multiplication factors, supplied by the manufacturer, for both excitation and emission wavelengths for the range of observations. Finally, the fluorescence intensity values were converted to quinine sulfate unit (QSU;1QSU=1 ngL-1 of quinine sulfate monohydroxide) to facilitate inter-laboratory comparisons (Coble et al., 1993). From the 370 nm scan a fluorescence index (FI) was calculated (McKnight et al., 2001). The humification index (HIX) was quantified as the area under the emission curve between 435-480 nm divided by the area under the emission curve between 300-345 nm, for excitation at 254 nm (Zsolnay et al. 1999). The biological index (BIX), an indicator of the relative contribution of new autochthonous production to the DOM pool, was calculated as the emission at 380 nm divided by the emission at 430 nm, for excitation at 310 nm (Huguet et al. 2009). The slope ratio (SR), a measure of the average molecular weight, was calculated as the best-fir slope of the natural-log of abosorbance from 275 to 295 nm divided by the best-fit slope of the natural-log of absorbance from 350 to 400 nm (Helms et al. 2008). Milli-Q water was used as a reference for all fluorescence analysis. UV-visible measurements of the water samples were carried out with 1cm quartz UV-visible cells at room temperature (20 degrees C), using a Varian CARY 50 Bio UV-visible spectrophotometer. Milli-Q water was used as the reference. Quality Control: Fluorescence measurements are corrected for internal absorbance quenching. Fluorescence spectra are corrected for internal instrument configuration using excitation and emission correction factors. For DOC, Humic carbon and carbohydrate data, we create calibration curves with standards and then graph the data. References: Coble, P. G. (1996). Characterization of marine and terrestrial DOM in seawater using excitation-emission matrix spectroscopy. Marine chemistry, 51(4), 325-346. Coble, P. G., Schultz, C. A., & Mopper, K. (1993). Fluorescence contouring analysis of DOC intercalibration experiment samples: a comparison of techniques. Marine chemistry, 41(1-3), 173-178. Helms, J. R., Stubbins, A., Ritchie, J. D., Minor, E. C., Kieber, D. J., & Mopper, K. (2008). Absorption spectral slopes and slope ratios as indicators of molecular weight, source, and photobleaching of chromophoric dissolved organic matter. Limnology and oceanography, 53(3), 955-969. Huguet, A., Vacher, L., Relexans, S., Saubusse, S., Froidefond, J. M., & Parlanti, E. (2009). Properties of fluorescent dissolved organic matter in the Gironde Estuary. Organic Geochemistry, 40(6), 706-719. References: Coble, P. G. (1996). Characterization of marine and terrestrial DOM in seawater using excitation-emission matrix spectroscopy. Marine chemistry, 51(4), 325-346. Coble, P. G., Schultz, C. A., & Mopper, K. (1993). Fluorescence contouring analysis of DOC intercalibration experiment samples: a comparison of techniques. Marine chemistry, 41(1-3), 173-178. Helms, J. R., Stubbins, A., Ritchie, J. D., Minor, E. C., Kieber, D. J., & Mopper, K. (2008). Absorption spectral slopes and slope ratios as indicators of molecular weight, source, and photobleaching of chromophoric dissolved organic matter. Limnology and oceanography, 53(3), 955-969. Huguet, A., Vacher, L., Relexans, S., Saubusse, S., Froidefond, J. M., & Parlanti, E. (2009). Properties of fluorescent dissolved organic matter in the Gironde Estuary. Organic Geochemistry, 40(6), 706-719. Method Step Description PARAFAC Analysis Description Processing of absorbance and fluorescence data and parallel-factor analysis (PARAFAC) modeling were carried out using the DrEEM 3.0 toolbox in MATLAB R2022a (Murphy et al., 2013). First, we normalized EEMs by total sample fluorescence, and then we fit a PARAFAC model to n = 842 EEMs as described by Stedmon and Bro (2008). We validated the model using split-half validation, random initialization tests, and visual examination of the residuals. References: Murphy, K. R., Stedmon, C. A., Graeber, D., & Bro, R. (2013). Fluorescence spectroscopy and multi-way techniques. PARAFAC. Analytical methods, 5(23), 6557-6566. Stedmon, C. A., & Bro, R. (2008). Characterizing dissolved organic matter fluorescence with parallel factor analysis: a tutorial. Limnology and Oceanography: Methods, 6(11), 572-579. Method Step Description This method step describes provenance-based metadata as specified in the LTER EML Best Practices. Distribution Online distribution: https://pasta.lternet.edu/package/data/eml/knb-lter-fce/1256/4/071b3224c71575a8256112277e8ea27c 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. Dataset Keywords FCE LTER Florida Coastal Everglades LTER Dissolved Organic Matter PARAFAC Dissolved Organic Carbon ecosystem Fluorescence Index Humification Index Biological Index Specific UV Absorbance LTER biogeochemistry disturbance organic matter disturbance organic matter Maintenance 1256.4: Removed sample duplicate, removed 37 samples that were not part of the DOM fluorescence monthly sampling campaign and were no longer included in the updated PARAFAC model, added 66 samples, updated data based on a new model run, updated metadata to include QUDT unit annotations. Dataset Contact 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 Name: Dr. Matthew Smith Organization: U.S. Army Corps of Engineers Email: Matthew.A.Smith2@usace.army.mil