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Microbial Sampling from Shark River Slough and Taylor Slough, Everglades National Park, South Florida, USA (FCE LTER), January 2001 - ongoing


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Authors: Henry Briceno
Time period: 2001-01-01 to 2022-12-21
Package id: knb-lter-fce.1056.12
Dataset id: LT_ND_Dailey_001

How to cite:
Briceno, H.. 2023. Microbial Sampling from Shark River Slough and Taylor Slough, Everglades National Park, South Florida, USA (FCE LTER), January 2001 - ongoing. Environmental Data Initiative. https://doi.org/10.6073/pasta/3f0e0898e39240fdd350179bef704745. Dataset accessed 2024-11-21.

Geographic Coverage


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Detailed Metadata


  • Dataset Creator(s)
    • Name: Dr. Henry Briceno 
    • Position: Collaborator
    • Organization: Southeast Environmental Research Center (SERC)
    • Address: 11200 SW 8th Street
      Florida International University
      University Park
      OE 148
      Miami, FL 33199 USA
    • Phone: 305-348-1269
    • Fax: 305-348-4096
    • Email: bricenoh@fiu.edu
    • URL: http://sercweb.fiu.edu/

  • Dataset Abstract
    We collected monthly observations of water microbial characteristics from each of the FCE LTER sites beginning in February 2001. Bacteria counts using DAPI epifluorescence, heterotrophic bacteria production with tritiated Thymidine uptake, and algal energetics and chl a using the PAM fluorometer were determined from each of the water samples. Bacteria counts in Shark River Slough in the freshwater end of the transect revealed highest bacteria numbers upon marsh rewetting after the dry down. The highest overall count of bacteria was found at the most freshwater point adjacent to the perimeter of the water conservation area but only in March of 2001. Peak numbers of bacteria in the saline end of Shark River transect occurred in December and July. There is some evidence that these higher bacteria numbers in the SR transect are associated with higher salinities. Highest bacteria counts along the Taylor slough transect were observed at the mouth of the Taylor River with peak counts in the wet season in October. Bacteria densities also increased from the eastern to western end of the transect in Florida Bay. Heterotrophic bacterial production did not relate closely bacteria numbers and exhibited highest numbers in the dry season. There was no discernible relationship between salinity and bacteria production as seen in bacteria numbers. Monthly observations using PAM fluorometry revealed that brown algae was the greatest contribution to the algal chal a pool and this relationship was consistent across all FCE LTER sites. Converse to the pattern of bacteria abundance along the Shark River transect, there was evidence that algal biomass decreases from freshwater to estuary. In the Shark River, algal energetics increased from marsh to estuary as well as in the panhandle region of the Taylor River transect. From these observations we conclude the behavior of the microbial loop and interactions generated between functional guilds is highly variable along individual transects and between the Shark River and Taylor River transect. Wet dry season dynamics partially explain temporal variability in microbial dynamics along the individual transects yet responses were unique for each section of the transect as freshwater versus estuarine versus Bay. Relationships between salinity and microbial parameters in this case, were not easily discerned but were more consistent within the two river transects than between river transects. As of 2020-06-05, PAM is no longer considered accurate and pigment data are no longer reported.
  • Geographic Coverage
    Study Extent Description
    The Study Extent of this dataset includes the FCE Shark River Slough and Taylor Slough 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: 25.550, S: 25.550, E: -80.785, W: -80.785

    SRS3
    N: 25.468, S: 25.468, E: -80.853, W: -80.853

    SRS4
    N: 25.410, S: 25.410, E: -80.964, W: -80.964

    SRS5
    N: 25.377, S: 25.377, E: -81.032, W: -81.032

    SRS6
    N: 25.365, S: 25.365, E: -81.078, W: -81.078

    TS/Ph1b
    N: 25.439, S: 25.439, E: -80.590, W: -80.590

    TS/Ph2
    N: 25.404, S: 25.404, E: -80.607, W: -80.607

    TS/Ph3
    N: 25.252, S: 25.252, E: -80.663, W: -80.663

    TS/Ph4
    N: 25.315, S: 25.315, E: -80.522, W: -80.522

    TS/Ph5
    N: 25.295, S: 25.295, E: -80.520, W: -80.520

    TS/Ph6a
    N: 25.214, S: 25.214, E: -80.649, W: -80.649

    TS/Ph7a
    N: 25.191, S: 25.191, E: -80.639, W: -80.639

    TS/Ph8
    N: 25.233, S: 25.233, E: -80.525, W: -80.525

    TS/Ph9
    N: 25.177, S: 25.177, E: -80.490, W: -80.490

    TS/Ph10
    N: 25.025, S: 25.025, E: -80.681, W: -80.681

    TS/Ph11
    N: 24.913, S: 24.913, E: -80.938, W: -80.938

    SRS1b
    N: 25.758, S: 25.758, E: -80.726, W: -80.726

    SRS1c
    N: 25.755, S: 25.755, E: -80.574, W: -80.574

    SRS1d
    N: 25.746, S: 25.746, E: -80.654, W: -80.654

    TS/Ph1a
    N: 25.424, S: 25.424, E: -80.590, W: -80.590

    FCE LTER Sites
    SRS1a,SRS1b, SRS1c, SRS1d, SRS2, SRS3, SRS4, SRS5, SRS6, TS/Ph1b,TS/Ph1a,TS/Ph2,TS/Ph3, TS/Ph4, TS/Ph5, TS/Ph6a, TS/Ph7a, TS/Ph8, TS/Ph9, TS/Ph10, TS/Ph11

  • Attributes
    • Data Table:   Microbial Sampling from Shark River Slough and Taylor Slough, Everglades National Park, South Florida
      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:
      SURV
      Attribute Label:
      ID Number
      Attribute Definition:
      Survey ID Number
      Storage Type:
      ordinal
      Measurement Scale:
      Survey ID Number
      Missing Value Code:
       

      Attribute Name:
      Date
      Attribute Label:
      date
      Attribute Definition:
      Sample Collection Date
      Storage Type:
      datetime
      Measurement Scale:
      Missing Value Code:
      -9999 (Value will never be recorded )

      Attribute Name:
      BacteriaProductionHourlyRate
      Attribute Label:
      rate
      Attribute Definition:
      Bacteria Hourly Production
      Storage Type:
      data
      Measurement Scale:
      Units: microgramsPerLiterPerHour
      Precision: 0.0001
      Number Type: real
      Missing Value Code:
      -9999.0000 (Value will never be recorded )

      Attribute Name:
      BacteriaProductionDailyRate
      Attribute Label:
      rate
      Attribute Definition:
      Bacteria Daily Production
      Storage Type:
      data
      Measurement Scale:
      Units: microgramsPerLiterPerDay
      Precision: 0.0001
      Number Type: real
      Missing Value Code:
      -9999.0000 (Value will never be recorded )

      Attribute Name:
      BacteriaAbundance
      Attribute Label:
      abundance
      Attribute Definition:
      Bacteria Abundance
      Storage Type:
      data
      Measurement Scale:
      Units: numberPerMilliliter
      Precision: 1
      Number Type: real
      Missing Value Code:
      -9999 (Value will never be recorded )

      Attribute Name:
      Chl_a_Blue
      Attribute Label:
      PAM fluorometry
      Attribute Definition:
      Chl a Blue
      Storage Type:
      data
      Measurement Scale:
      Units: microgramsPerLiter
      Precision: 0.01
      Number Type: real
      Missing Value Code:
      -9999.00 (Value will never be recorded )

      Attribute Name:
      Chl_a_Green
      Attribute Label:
      PAM fluorometry
      Attribute Definition:
      Chl a Green
      Storage Type:
      data
      Measurement Scale:
      Units: microgramsPerLiter
      Precision: 0.01
      Number Type: real
      Missing Value Code:
      -9999.00 (Value will never be recorded )

      Attribute Name:
      Chl_a_Brown
      Attribute Label:
      PAM fluorometry
      Attribute Definition:
      Chl a Brown
      Storage Type:
      data
      Measurement Scale:
      Units: microgramsPerLiter
      Precision: 0.01
      Number Type: real
      Missing Value Code:
      -9999.00 (Value will never be recorded )

      Attribute Name:
      Sum_Chl_a_PAM
      Attribute Label:
      PAM fluorometry
      Attribute Definition:
      Sum Chl a PAM
      Storage Type:
      data
      Measurement Scale:
      Units: microgramsPerLiter
      Precision: 0.01
      Number Type: real
      Missing Value Code:
      -9999.00 (Value will never be recorded )

      Attribute Name:
      QuantumYield_SUM
      Attribute Label:
      PAM fluorometry
      Attribute Definition:
      Quantum Yield SUM
      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:
      Ch1Alpha
      Attribute Label:
      PAM fluorometry
      Attribute Definition:
      Channel 1 Alpha
      Storage Type:
      data
      Measurement Scale:
      Units: dimensionless
      Precision: 0.001
      Number Type: real
      Missing Value Code:
      -9999.000 (Value will never be recorded )

      Attribute Name:
      Ch2Alpha
      Attribute Label:
      PAM fluorometry
      Attribute Definition:
      Channel 2 Alpha
      Storage Type:
      data
      Measurement Scale:
      Units: dimensionless
      Precision: 0.001
      Number Type: real
      Missing Value Code:
      -9999.000 (Value will never be recorded )

      Attribute Name:
      Ch3Alpha
      Attribute Label:
      PAM fluorometry
      Attribute Definition:
      Channel 3 Alpha
      Storage Type:
      data
      Measurement Scale:
      Units: dimensionless
      Precision: 0.001
      Number Type: real
      Missing Value Code:
      -9999.000 (Value will never be recorded )

      Attribute Name:
      Ch4Alpha
      Attribute Label:
      PAM fluorometry
      Attribute Definition:
      Channel 4 Alpha
      Storage Type:
      data
      Measurement Scale:
      Units: dimensionless
      Precision: 0.001
      Number Type: real
      Missing Value Code:
      -9999.000 (Value will never be recorded )

      Attribute Name:
      Ch1_ETRmax
      Attribute Label:
      PAM fluorometry
      Attribute Definition:
      Channel 1 Electron Transport Rate Max
      Storage Type:
      data
      Measurement Scale:
      Units: dimensionless
      Precision: 0.1
      Number Type: real
      Missing Value Code:
      -9999.0 (Value will never be recorded )

      Attribute Name:
      Ch2_ETRmax
      Attribute Label:
      PAM fluorometry
      Attribute Definition:
      Channel 2 Electron Transport Rate Max
      Storage Type:
      data
      Measurement Scale:
      Units: dimensionless
      Precision: 0.1
      Number Type: real
      Missing Value Code:
      -9999.0 (Value will never be recorded )

      Attribute Name:
      Ch3_ETRmax
      Attribute Label:
      PAM fluorometry
      Attribute Definition:
      Channel 3 Electron Transport Rate Max
      Storage Type:
      data
      Measurement Scale:
      Units: dimensionless
      Precision: 0.1
      Number Type: real
      Missing Value Code:
      -9999.0 (Value will never be recorded )

      Attribute Name:
      Ch4_ETRmax
      Attribute Label:
      PAM fluorometry
      Attribute Definition:
      Channel 4 Electron Transport Rate Max
      Storage Type:
      data
      Measurement Scale:
      Units: dimensionless
      Precision: 0.1
      Number Type: real
      Missing Value Code:
      -9999.0 (Value will never be recorded )

      Attribute Name:
      Ch1_Ik
      Attribute Label:
      PAM fluorometry
      Attribute Definition:
      Channel 1 Initial Slope Irradiance
      Storage Type:
      data
      Measurement Scale:
      Units: dimensionless
      Precision: 0.1
      Number Type: real
      Missing Value Code:
      -9999.0 (Value will never be recorded )

      Attribute Name:
      Ch2_Ik
      Attribute Label:
      PAM fluorometry
      Attribute Definition:
      Channel 2 Initial Slope Irradiance
      Storage Type:
      data
      Measurement Scale:
      Units: dimensionless
      Precision: 0.1
      Number Type: real
      Missing Value Code:
      -9999.0 (Value will never be recorded )

      Attribute Name:
      Ch3_Ik
      Attribute Label:
      PAM fluorometry
      Attribute Definition:
      Channel 3 Initial Slope Irradiance
      Storage Type:
      data
      Measurement Scale:
      Units: dimensionless
      Precision: 0.1
      Number Type: real
      Missing Value Code:
      -9999.0 (Value will never be recorded )

      Attribute Name:
      Ch4_Ik
      Attribute Label:
      PAM fluorometry
      Attribute Definition:
      Channel 4 Initial Slope Irradiance
      Storage Type:
      data
      Measurement Scale:
      Units: dimensionless
      Precision: 0.1
      Number Type: real
      Missing Value Code:
      -9999.0 (Value will never be recorded )

      Attribute Name:
      AlphaBlue
      Attribute Label:
      PAM fluorometry
      Attribute Definition:
      Algal Energetics Light Curve Slope Cyanobacteria
      Storage Type:
      data
      Measurement Scale:
      Units: dimensionless
      Precision: 0.001
      Number Type: real
      Missing Value Code:
      -9999.000 (Value will never be recorded )

      Attribute Name:
      AlphaGreen
      Attribute Label:
      PAM fluorometry
      Attribute Definition:
      Algal Energetics Light Curve Slope Brown
      Storage Type:
      data
      Measurement Scale:
      Units: dimensionless
      Precision: 0.001
      Number Type: real
      Missing Value Code:
      -9999.000 (Value will never be recorded )

      Attribute Name:
      AlphaBrown
      Attribute Label:
      PAM fluorometry
      Attribute Definition:
      Algal Energetics Light Curve Slope Green
      Storage Type:
      data
      Measurement Scale:
      Units: dimensionless
      Precision: 0.001
      Number Type: real
      Missing Value Code:
      -9999.000 (Value will never be recorded )

      Attribute Name:
      ETRmax_Blue
      Attribute Label:
      PAM fluorometry
      Attribute Definition:
      Electron Transport Rate Maximum Cyanobacteria
      Storage Type:
      data
      Measurement Scale:
      Units: dimensionless
      Precision: 0.1
      Number Type: real
      Missing Value Code:
      -9999.0 (Value will never be recorded )

      Attribute Name:
      ETRmax_Green
      Attribute Label:
      PAM fluorometry
      Attribute Definition:
      Electron Transport Rate Maximum Green
      Storage Type:
      data
      Measurement Scale:
      Units: dimensionless
      Precision: 0.1
      Number Type: real
      Missing Value Code:
      -9999.0 (Value will never be recorded )

      Attribute Name:
      ETRmax_Brown
      Attribute Label:
      PAM fluorometry
      Attribute Definition:
      Electron Transport Rate Maximum Brown
      Storage Type:
      data
      Measurement Scale:
      Units: dimensionless
      Precision: 0.1
      Number Type: real
      Missing Value Code:
      -9999.0 (Value will never be recorded )

      Attribute Name:
      Ik_Blue
      Attribute Label:
      PAM fluorometry
      Attribute Definition:
      Initial Slope Irradiance Maximum Cyanobacteria
      Storage Type:
      data
      Measurement Scale:
      Units: dimensionless
      Precision: 0.1
      Number Type: real
      Missing Value Code:
      -9999.0 (Value will never be recorded )

      Attribute Name:
      Ik_Green
      Attribute Label:
      PAM fluorometry
      Attribute Definition:
      Initial Slope Irradiance Maximum Brown
      Storage Type:
      data
      Measurement Scale:
      Units: dimensionless
      Precision: 0.1
      Number Type: real
      Missing Value Code:
      -9999.0 (Value will never be recorded )

      Attribute Name:
      Ik_Brown
      Attribute Label:
      PAM fluorometry
      Attribute Definition:
      Initial Slope Irradiance Maximum Green
      Storage Type:
      data
      Measurement Scale:
      Units: dimensionless
      Precision: 0.1
      Number Type: real
      Missing Value Code:
      -9999.0 (Value will never be recorded )


  • Methods
    Sampling Description
    Sterile, brown 1 L bottles rinsed 3 times with sample water collected 10 cm below the water surface.

    Method Step

    Description
    Microbial Analyses, Water samples were collected, processed, and analyzed to determine bacterial abundance, algal energetics and chl a by phytoplankton guild, enzyme activity, and heterotrophic bacterial production. Samples for microbial analyses were collected in washed, acid-rinsed, ADDIH2O rinsed, then sample rinsed brown, 250 ml, Nalgene bottles. Depth of sampling was 10 cm below the water surface. A sample for PAM analysis was set aside for a 10 hr dark acclimation period. Bacterial abundance was determined through epifluorenscence microscopy using DAPI DNA stain after preservation with 2 percent bacterial free phosphate buffered formalin and dark storage. Slides were made within 14 days of collection and counted immediately after they were prepared. Algal dynamics were determined through PAM (pulse-amplitude modulation) fluorescence within 24 hours of collection. (NOTE (2/22/2021): PhytoPAM measurements were not calibrated, per Henry Briceno). Algal energetics samples were analyzed using PAM fluormetry for chl a content and productivity irradiance curves. Heterotrophic bacterial production was determined using tritiated thymidine uptake within 24 hours of collection. We incubated each of the duplicate samplings per site with 3 replicates and one blank of 10 ml for each sample. The blank was killed with BFF to a final concentration of 4 percent. Stock tritiated thymidine was made with 2.58 mCi radioisotope with 30 ml of filter sterilized (0.2 um) water from Shark River. Each replicate and blank received 0.86 uCi ml-1 and was incubated at 22 degrees C for one hour. We also determined the specific activity for each incubation. We stopped the incubation period with TCA to final concentration of 5 percent then put the samples on ice for 15 to 45 minutes before filtering the sample onto nitrocellulose filters. A series of 3 rinses with 5 percent TCA and 80 percent ETOH of 1 ml each and filters were placed in scintillation vials. We added liquid scintillation cocktail and counted the samples after 24 hours with a Beckman liquid scintillation counter (Model 3801).

    Citation
    Bell, Russel T 1993. Estimating Production of Heterotrophic Bacterioplankton via Incorporation of Tritiated Thymidine. p. 495-503 in Kemp, Paul F , Barry F Sherr, Evelyn B Sherr, Jonathan J Cole. , (eds). In Handbook of Methods in Aquatic Microbial Ecology. Lewis Publishers, Boca Raton, Florida ,

    Instrumentation
    Zeiss microscope autoclave laboratory balance PAM desktop model fluorometer Gilford V Spectrofluorometer Beckman liquid scintillation counter (Model 3801) Hydrolab Probe Meter 4A Mini Sonde datasonde and YSI.

    Method Step

    Description


    Citation
    Lebaron, P , P Catala, N Parthuisot. 1998. Effectiveness of SYTOX green stain for bacterial viability assessment. Applied and Environmental Microbiology, 64: 2697-2700.


    Quality Control
    SERC QAQC for nutrient data, blank controls and isotope blanks for tritiated thymidine uptake incubations per sample, negative controls for bacteria counts using DAPI epifluorescence techniques, PAM chl a versus acetone extraction chl a calibration, BOD incubations for algal prodcution versus PAM energetics parameters. Each datum was checked individually with raw chart data or computer files generated during analysis. Data entries and calculations were verified independently by three investigators.
  • Distribution and Intellectual Rights
    Online distribution
    https://pasta.lternet.edu/package/data/eml/knb-lter-fce/1056/12/e0069c0220b968565fa5f1a83cf51df0
    Data Submission Date:  2023-08-25

    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
    nutrients, estuaries, primary production, FCE, Florida Coastal Everglades LTER, ecological research, long-term monitoring, microbial dynamics, Shark River Slough, Everglades National Park, bacteria abundance, heterotrophic bacteria production, algal abundance, algal energetics, PAM, bacteria production rates, Taylor Slough, bacteria, productivity, transects, water, freshwater, river
  • Dataset Contact
    • Name: Henry Briceno 
    • Position: Collaborator
    • Organization: Southeast Environmental Research Center (SERC)
    • Address: 11200 SW 8th Street
      Florida International University
      University Park
      OE 148
      Miami, FL 33199 USA
    • Phone: 305-348-1269
    • Fax: 305-348-4096
    • Email: bricenoh@fiu.edu
    • URL: http://sercweb.fiu.edu/

    • 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: http://fcelter.fiu.edu

  • Data Table and Format
    Data Table:  Microbial Sampling from Shark River Slough and Taylor Slough, Everglades National Park, South Florida

    Entity Name:
    LT_ND_Dailey_001.csv
    Entity Description:
    Microbial Sampling from Shark River Slough and Taylor Slough, Everglades National Park, South Florida
    Object Name:
    LT_ND_Dailey_001.csv
    Number of Header Lines:
    1
    Attribute Orientation:
    column
    Field Delimiter:
    ,
    Number of Records:
    4253