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Biomarker assessment of spatial and temporal changes in the composition of flocculent material (floc) in the subtropical wetland of the Florida Coastal Everglades (FCE) from May 2007 to December 2009


At a Glance


Authors: Rudolf Jaffe, Oliva Pisani
Time period: 2007-05-16 to 2009-12-14
Package id: knb-lter-fce.1206.2
Dataset id: ST_OMD_Jaffe_001

How to cite:
Jaffe, R., O. Pisani. 2015. Biomarker assessment of spatial and temporal changes in the composition of flocculent material (floc) in the subtropical wetland of the Florida Coastal Everglades (FCE) from May 2007 to December 2009. Environmental Data Initiative. https://doi.org/10.6073/pasta/e84cc609ffbc63bb45bd484810e6746b. Dataset accessed 2020-10-26.

Geographic Coverage


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Detailed Metadata


  • Dataset Creator(s)
    • Name: Dr. Rudolf Jaffe 
    • Position: Lead Principal Investigator
    • 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

    • Name: Oliva Pisani 
    • Position: Florida International University University Park OE 148
    • Organization: Southeast Environmental Research Center
    • Address: Miami
      Florida, 33199 USA 305-348-3118
    • Phone: 305-348-4096
    • Fax: opisani@fiu.edu
    • Email: Graduate student
    • URL: http://serc.fiu.edu/sercindex/index.htm

  • Dataset Abstract
    Flocculent material (floc) is an important energy source in wetlands. In the Florida Everglades, floc is present in both freshwater marshes and coastal environments and plays a key role in food webs and nutrient cycling. However, not much is known about its environmental dynamics, in particular its biological sources and bio-reactivity. We analysed floc samples collected from different environments in the Florida Everglades and applied biomarkers and pigment chemotaxonomy to identify spatial and seasonal differences in organic matter sources. An attempt was made to link floc composition with algal and plant productivity. Spatial differences were observed between freshwater marsh and estuarine floc. Freshwater floc receives organic matter inputs from local periphyton mats, as indicated by microbial biomarkers and chlorophyll-a estimates. At the estuarine sites, the floc is dominated by mangrove as well as diatom inputs from the marine end-member. The hydroperiod (duration and depth of inundation) at the freshwater sites influences floc organic matter preservation, where the floc at the short-hydroperiod site is more oxidised likely due to periodic dry-down conditions. Seasonal differences in floc composition were not consistent and the few that were observed are likely linked to the primary productivity of the dominant biomass (periphyton in the freshwater marshes and mangroves in the estuarine zone). Molecular evidence for hydrological transport of floc material from the freshwater marshes to the coastal fringe was also observed. With the on-going restoration of the Florida Everglades, it is important to gain a better understanding of the biogeochemical dynamics of floc, including its sources, transformations and reactivity.
  • 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
    Samples were collected in the Taylor Slough and Shark River Slough, within Everglades National Park, South Florida.
    N: 25.550, S: 25.214, E: -80.607, W: -81.078

    Florida Coastal Everglades LTER Study Area: South Florida, Everglades National Park, and Florida Bay
    N: 25.550, S: 25.214, E: -80.607, W: -81.078

    FCE LTER Sites
    SRS2, SRS6, TS/Ph2, and TS/Ph6a.

    All Sites
    Geographic Description
    Bounding Coordinates
    FCE LTER Site SRS2
    N: 25.550, S: 25.550, E: -80.785, W: -80.785
    FCE LTER Site SRS6
    N: 25.365, S: 25.365, E: -81.078, W: -81.078
    FCE LTER Site TS/Ph2
    N: 25.40, S: 25.40, E: -80.61, W: -80.61
    FCE LTER Site TS/Ph6a
    N: 25.21, S: 25.21, E: -80.65, W: -80.65
  • Attributes
    • Data Table:   Biomarker assessment of spatial and temporal changes in the composition of flocculent material (floc) in the subtropical wetland of the Florida Coastal Everglades (FCE)
      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:
      Date
      Attribute Label:
      date
      Attribute Definition:
      Collection date
      Storage Type:
      datetime
      Measurement Scale:
      Missing Value Code:
       

      Attribute Name:
      Depth
      Attribute Label:
      Depth
      Attribute Definition:
      Floc depth
      Storage Type:
      data
      Measurement Scale:
      Units: centimeter
      Precision: 0.1
      Number Type: real
      Missing Value Code:
      -9999.0 (Value will never be recorded )

      Attribute Name:
      Density
      Attribute Label:
      Density
      Attribute Definition:
      Floc density
      Storage Type:
      data
      Measurement Scale:
      Units: gramsPerCubicCentimeter
      Precision: 0.01
      Number Type: real
      Missing Value Code:
      -9999.00 (Value will never be recorded )

      Attribute Name:
      OM
      Attribute Label:
      Organic Matter
      Attribute Definition:
      Percent organic matter obtained by subtracting the ash free dry weight from 100%
      Storage Type:
      data
      Measurement Scale:
      Units: percent
      Precision: 1
      Number Type: real
      Missing Value Code:
      -9999 (Value will never be recorded )

      Attribute Name:
      C/N
      Attribute Label:
      Carbon to nitrogen ratio
      Attribute Definition:
      Carbon to nitrogen ratio
      Storage Type:
      data
      Measurement Scale:
      Units: dimensionless
      Precision: 1
      Number Type: real
      Missing Value Code:
      -9999 (Value will never be recorded )

      Attribute Name:
      ΣChl-a
      Attribute Label:
      Total chlorophyll-a
      Attribute Definition:
      The sum of chlorophyll-a, chlorophyll-a epimer, chlorophyll-a allomer, chlorophyllide-a and pyrochlorophyllide-a.
      Storage Type:
      data
      Measurement Scale:
      Units: milligramsPerGram
      Precision: 0.01
      Number Type: real
      Missing Value Code:
      -9999.00 (Value will never be recorded )

      Attribute Name:
      Σa-derivs
      Attribute Label:
      Total chlorophyll degradation products
      Attribute Definition:
      The sum of pheophytin-a, pyropheophytin-a, pheophorbide-a and pyropheophorbide-a.
      Storage Type:
      data
      Measurement Scale:
      Units: milligramsPerGram
      Precision: 0.01
      Number Type: real
      Missing Value Code:
      -9999.00 (Value will never be recorded )

      Attribute Name:
      Scytonemin
      Attribute Label:
      Scytonemin
      Attribute Definition:
      Scytonemin
      Storage Type:
      data
      Measurement Scale:
      Units: milligramsPerGram
      Precision: 0.01
      Number Type: real
      Missing Value Code:
      -9999.00 (Value will never be recorded )

      Attribute Name:
      Cyano
      Attribute Label:
      Cyanobacteria
      Attribute Definition:
      Cyanobacteria contribution to the floc.
      Storage Type:
      data
      Measurement Scale:
      Units: percent
      Precision: 1
      Number Type: real
      Missing Value Code:
      -9999 (Value will never be recorded )

      Attribute Name:
      Chloro
      Attribute Label:
      Chlorophytes
      Attribute Definition:
      Chlorophyte contribution to the floc.
      Storage Type:
      data
      Measurement Scale:
      Units: percent
      Precision: 1
      Number Type: real
      Missing Value Code:
      -9999 (Value will never be recorded )

      Attribute Name:
      Diatoms
      Attribute Label:
      Diatoms
      Attribute Definition:
      Diatom contribution to the floc.
      Storage Type:
      data
      Measurement Scale:
      Units: percent
      Precision: 1
      Number Type: real
      Missing Value Code:
      -9999 (Value will never be recorded )

      Attribute Name:
      Crypto
      Attribute Label:
      Cryptophytes
      Attribute Definition:
      Cryptophyte contribution to the floc.
      Storage Type:
      data
      Measurement Scale:
      Units: percent
      Precision: 1
      Number Type: real
      Missing Value Code:
      -9999 (Value will never be recorded )

      Attribute Name:
      Dinos
      Attribute Label:
      Dinoflagellates
      Attribute Definition:
      Dinoflagellate contribution to the floc.
      Storage Type:
      data
      Measurement Scale:
      Units: percent
      Precision: 1
      Number Type: real
      Missing Value Code:
      -9999 (Value will never be recorded )

      Attribute Name:
      C29/C17
      Attribute Label:
      C29 and C17 n-alkanes
      Attribute Definition:
      Ratio of the C29 and C17 n-alkanes.
      Storage Type:
      data
      Measurement Scale:
      Units: dimensionless
      Precision: 1
      Number Type: real
      Missing Value Code:
      -9999 (Value will never be recorded )

      Attribute Name:
      Paq
      Attribute Label:
      Aquatic vegetation proxy
      Attribute Definition:
      Proxy for aquatic vegetation inpputs to the floc.
      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:
      C28 n-alkene
      Attribute Label:
      C28 n-alkene
      Attribute Definition:
      C28 n-alkene
      Storage Type:
      data
      Measurement Scale:
      Units: milligramsPerGram
      Precision: 0.01
      Number Type: real
      Missing Value Code:
      -9999.00 (Value will never be recorded )

      Attribute Name:
      C20 HBI
      Attribute Label:
      C20 Highly Branched Isoprenoid
      Attribute Definition:
      C20 Highly Branched Isoprenoid
      Storage Type:
      data
      Measurement Scale:
      Units: milligramsPerGram
      Precision: 0.01
      Number Type: real
      Missing Value Code:
      -9999.00 (Value will never be recorded )


  • Methods
    Sampling Description
    Floc samples are collected quarterly from four LTER sites, stored on ice and transported to the lab. Samples are then frozen, freeze-dried and stored in a freezer until prepared for the pigment and biomarker analyses.

    Method Step

    Description
    Quarterly floc samples were collected in 1-L Teflon jars and stored on ice for transport to the laboratory where they were frozen and freeze-dried. Floc depth and bulk density were measured during each sampling event. A floc subsample was used to obtain the ash free dry weight, the percent organic matter content and the carbon to nitrogen ratio. Pigment chemotaxonomy was performed using reverse-phase high performance liquid chromatography. The floc samples were extracted using 3mL of a solvent mixture of methanol/acetone/dimethylformamide/water (30:30:30:10) containing a known amount of internal standard. The pigment extractions were performed by grinding at ice bath temperature in a Teflon/glass homogenizer. The extract was sonicated in an ice bath and allowed to steep for 1 hour. Extracts were recovered by centrifugation and filtered through a 0.45um filter. The pigments in the extract were separated by reverse phase-high performance liquid chromatography and the quantified pigments include chlorophyll-a, scytonemin, zeaxanthin, echinenone, chlorophyll-b, fucoxanthin, peridinin and alloxanthin. Zeaxanthin and echinenone represent the contribution to the floc from cyanobacteria, chlorophyll-b from chlorophytes, fucoxanthin from diatoms, peridinin from dinoflagellates and alloxanthin from cryptophytes. The floc samples were also analyzed for biomarkers using gas chromatography-mass spectrometry. Aliquots of freeze-dried floc were extracted with 350mL of dichloromethane for 24 hours. The extracts were concentrated and separated into neutral and acid fractions by saponification using 25mL of freshly prepared 1N KOH. The neutral fraction was further fractionated using silica-gel adsorption chromatography and the aliphatic and aromatic hydrocarbon fractions were analysed. Because plants contain high amounts of the C29 n-alkane and algae contain high amounts of the C17 n-alkane, the ratio of the C29 and the C17 n-alkanes was calculated to distinguish between these two sources. The aquatic proxy (Paq) was calculated by dividing the sum of the C23 and C25 n-alkanes by the sum of the C23, C25, C29 and C31 n-alkanes. This parameter is used to distinguish organic matter from submerged-floating and emergent-terrestrial macrophytes because submerged-floating plant species have abundant mid-chain alkanes relative to emergent-terrestrial plants. The C28 n-alkene, which is a biomarker for mangrove inputs, was quantified. The C20 highly branched isoprenoid, a biomarker for periphyton, was quantified.

    Citation
    Neto, R R 2006. Organic biogeochemistry of detrital flocculent material (floc) in a subtropical, coastal wetland. Biogeochemistry, 77: 283-304.

    Instrumentation
    Nalgene 1-L Teflon jars Photodiode array detector 3.9x150mm Waters NovaPack 4-micron C18 column Rheodyne 7125 injector Thermo Fisher Scientific Model 4100 quaternary HPLC pump Agilent HP 6890 gas chromatograph Agilent HP 5730 mass selective detector

    Method Step

    Description
    Quarterly floc samples were collected in 1-L Teflon jars and stored on ice for transport to the laboratory where they were frozen and freeze-dried. Floc depth and bulk density were measured during each sampling event. A floc subsample was used to obtain the ash free dry weight, the percent organic matter content and the carbon to nitrogen ratio. Pigment chemotaxonomy was performed using reverse-phase high performance liquid chromatography. The floc samples were extracted using 3mL of a solvent mixture of methanol/acetone/dimethylformamide/water (30:30:30:10) containing a known amount of internal standard. The pigment extractions were performed by grinding at ice bath temperature in a Teflon/glass homogenizer. The extract was sonicated in an ice bath and allowed to steep for 1 hour. Extracts were recovered by centrifugation and filtered through a 0.45um filter. The pigments in the extract were separated by reverse phase-high performance liquid chromatography and the quantified pigments include chlorophyll-a, scytonemin, zeaxanthin, echinenone, chlorophyll-b, fucoxanthin, peridinin and alloxanthin. Zeaxanthin and echinenone represent the contribution to the floc from cyanobacteria, chlorophyll-b from chlorophytes, fucoxanthin from diatoms, peridinin from dinoflagellates and alloxanthin from cryptophytes. The floc samples were also analyzed for biomarkers using gas chromatography-mass spectrometry. Aliquots of freeze-dried floc were extracted with 350mL of dichloromethane for 24 hours. The extracts were concentrated and separated into neutral and acid fractions by saponification using 25mL of freshly prepared 1N KOH. The neutral fraction was further fractionated using silica-gel adsorption chromatography and the aliphatic and aromatic hydrocarbon fractions were analysed. Because plants contain high amounts of the C29 n-alkane and algae contain high amounts of the C17 n-alkane, the ratio of the C29 and the C17 n-alkanes was calculated to distinguish between these two sources. The aquatic proxy (Paq) was calculated by dividing the sum of the C23 and C25 n-alkanes by the sum of the C23, C25, C29 and C31 n-alkanes. This parameter is used to distinguish organic matter from submerged-floating and emergent-terrestrial macrophytes because submerged-floating plant species have abundant mid-chain alkanes relative to emergent-terrestrial plants. The C28 n-alkene, which is a biomarker for mangrove inputs, was quantified. The C20 highly branched isoprenoid, a biomarker for periphyton, was quantified.

    Citation
    Hagerthey, S E 2006. Evaluation of pigment extraction methods and a recommended protocol for periphyton chlorophyll a determination and chemotaxonomic assessment. Journal of Phycology, 42: 1125-1136.

    Instrumentation
    Nalgene 1-L Teflon jars Photodiode array detector 3.9x150mm Waters NovaPack 4-micron C18 column Rheodyne 7125 injector Thermo Fisher Scientific Model 4100 quaternary HPLC pump Agilent HP 6890 gas chromatograph Agilent HP 5730 mass selective detector

    Method Step

    Description
    Quarterly floc samples were collected in 1-L Teflon jars and stored on ice for transport to the laboratory where they were frozen and freeze-dried. Floc depth and bulk density were measured during each sampling event. A floc subsample was used to obtain the ash free dry weight, the percent organic matter content and the carbon to nitrogen ratio. Pigment chemotaxonomy was performed using reverse-phase high performance liquid chromatography. The floc samples were extracted using 3mL of a solvent mixture of methanol/acetone/dimethylformamide/water (30:30:30:10) containing a known amount of internal standard. The pigment extractions were performed by grinding at ice bath temperature in a Teflon/glass homogenizer. The extract was sonicated in an ice bath and allowed to steep for 1 hour. Extracts were recovered by centrifugation and filtered through a 0.45um filter. The pigments in the extract were separated by reverse phase-high performance liquid chromatography and the quantified pigments include chlorophyll-a, scytonemin, zeaxanthin, echinenone, chlorophyll-b, fucoxanthin, peridinin and alloxanthin. Zeaxanthin and echinenone represent the contribution to the floc from cyanobacteria, chlorophyll-b from chlorophytes, fucoxanthin from diatoms, peridinin from dinoflagellates and alloxanthin from cryptophytes. The floc samples were also analyzed for biomarkers using gas chromatography-mass spectrometry. Aliquots of freeze-dried floc were extracted with 350mL of dichloromethane for 24 hours. The extracts were concentrated and separated into neutral and acid fractions by saponification using 25mL of freshly prepared 1N KOH. The neutral fraction was further fractionated using silica-gel adsorption chromatography and the aliphatic and aromatic hydrocarbon fractions were analysed. Because plants contain high amounts of the C29 n-alkane and algae contain high amounts of the C17 n-alkane, the ratio of the C29 and the C17 n-alkanes was calculated to distinguish between these two sources. The aquatic proxy (Paq) was calculated by dividing the sum of the C23 and C25 n-alkanes by the sum of the C23, C25, C29 and C31 n-alkanes. This parameter is used to distinguish organic matter from submerged-floating and emergent-terrestrial macrophytes because submerged-floating plant species have abundant mid-chain alkanes relative to emergent-terrestrial plants. The C28 n-alkene, which is a biomarker for mangrove inputs, was quantified. The C20 highly branched isoprenoid, a biomarker for periphyton, was quantified.

    Citation
    Jaffe, R 2006. Origin and transport of sedimentary organic matter in two subtropical estuaries: a comparative, biomarker-based study. Organic Geochemistry, 32: 507-526.

    Instrumentation
    Nalgene 1-L Teflon jars Photodiode array detector 3.9x150mm Waters NovaPack 4-micron C18 column Rheodyne 7125 injector Thermo Fisher Scientific Model 4100 quaternary HPLC pump Agilent HP 6890 gas chromatograph Agilent HP 5730 mass selective detector

    Quality Control
    For biomarker measurements, blanks are run between samples to check for carry-over and interferences.
  • Distribution and Intellectual Rights
    Online distribution
    http://fcelter.fiu.edu/perl/public_data_download.pl?datasetid=ST_OMD_Jaffe_001.txt
    Data Submission Date:  2005-08-12

    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, Estuarine, Freshwater marsh, Hydroperiod, Mangrove, Periphyton, Pigment, floc, organic matter, Cyanobacteria, Chlorophytes, Diatoms, Cryptophytes, Dinoflagellates, floc density, floc depth
  • 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:  Biomarker assessment of spatial and temporal changes in the composition of flocculent material (floc) in the subtropical wetland of the Florida Coastal Everglades (FCE)

    Entity Name:
    ST_OMD_Jaffe_001
    Entity Description:
    Biomarker assessment of spatial and temporal changes in the composition of flocculent material (floc) in the subtropical wetland of the Florida Coastal Everglades (FCE)
    Object Name:
    ST_OMD_Jaffe_001
    Number of Header Lines:
    1
    Attribute Orientation:
    column
    Field Delimiter:
    ,
    Number of Records:
    44