Dataset title: 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 Dataset ID: ST_OMD_Jaffe_001 Research type: Short-Term Dataset Creator 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 Metadata Provider Organization: Florida Coastal Everglades LTER Program Address: Florida International University University Park OE 148 Miami, FL 33199 USA Phone: 305-348-6054 Email: fcelter@fiu.edu URL: http://fcelter.fiu.edu 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 Geographic description: Samples were collected in the Taylor Slough and Shark River Slough, within Everglades National Park, South Florida. West bounding coordinate: -81.078 East bounding coordinate: -80.607 North bounding coordinate: 25.550 South bounding coordinate: 25.214 Geographic description: Florida Coastal Everglades LTER Study Area: South Florida, Everglades National Park, and Florida Bay West bounding coordinate: -81.078 East bounding coordinate: -80.607 North bounding coordinate: 25.550 South bounding coordinate: 25.214 FCE LTER Sites: SRS2, SRS6, TS/Ph2, and TS/Ph6a. All Sites Geographic Description:FCE LTER Site SRS2 Longitude:-80.785 Latitude:25.550 Geographic Description:FCE LTER Site SRS6 Longitude:-81.078 Latitude:25.365 Geographic Description:FCE LTER Site TS/Ph2 Longitude:-80.61 Latitude:25.40 Geographic Description:FCE LTER Site TS/Ph6a Longitude:-80.65 Latitude:25.21 Temporal Coverage Start Date: 2007-05-16 End Date: 2009-12-14 Data Table 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 Data Format Number of Header Lines: 1 Attribute Orientation: column Field Delimiter: , Number of Records: Attributes 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 Online distribution: http://fcelter.fiu.edu/perl/public_data_download.pl?datasetid=ST_OMD_Jaffe_001.txt 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. Dataset 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 Data Submission Date: 2005-08-12 Maintenance This is a short-term organic matter dynamic dataset. 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 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 Dataset Submission Date 2005-08-12