I. Data Set Descriptors A. Title: Lishen Mao. 2023. Pulse amplitude modulated (PAM) 5-minute chlorophyll fluorescence (ChlF) with accompanying environmental variables from the GCE-LTER Keenan Field site on Sapelo Island, GA in July 2020. Georgia Coastal Ecosystems LTER Data Catalog (data set MSH-GCET-2302; /data/MSH-GCET-2302) B. Accession Number: MSH-GCET-2302 C. Description 1. Originator(s): Name: Lishen Mao Address: Department of Geography Georgraphy-Geology Building, Room 313 Athens, Georgia 30602 Country: USA Email: lmao@uga.edu 2. Abstract: Pulse amplitude modulated (PAM) chlorophyll fluorescence (ChlF) from July 11, 2020 to July 27, 2020 collected over a Spartina alterniflora marsh located on the western side of Sapelo Island bounded by the Duplin River. PAM ChlF were processed in WinControl-3.25. Additional biophysical variables included are photosynthetically active radiation (PAR) from onsite quantum sensors (Licor-192), and tide height from an onsite pressure transducer (Hobo U20). 3. Study Type: Graduate Thesis Study 4. Study Themes: Marsh Ecology 5. LTER Core Areas: Primary Production 6. Georeferences: none 7. Submission Date: Feb 09, 2023 D. Keywords: chlorophyll, Duplin River, fluorescence, GCE, Georgia, Georgia Coastal Ecosystems, LTER, photosynthesis, Plant Monitoring, Primary Production, Pulse amplitude modulated (PAM) fluorometry, salt marshes, Sapelo Island, Spartina alterniflora, USA II. Research Origin Descriptors A. Overall Project Description 1. Project Title: Georgia Coastal Ecosystems LTER - IV 2. Principal Investigators: Name: Merryl Alber Address: Dept. of Marine Sciences University of Georgia Athens, Georgia 30602-3636 Country: USA Email: malber@uga.edu 3. Funding Period: Feb 01, 2019 to Jan 31, 2025 4. Objectives: The GCE-LTER project has four goals. 1) Track environmental and human drivers that can cause perturbations in our focal ecosystems. This will be accomplished this through continuing long-term measurements of climate, water chemistry, oceanic exchange, and human activities on the landscape. 2) Describe temporal and spatial variability in physical, chemical, geological and biological characteristics of the study system (coastal wetland complexes) and how they respond to external drivers. This will be accomplished through field monitoring in combination with remote sensing and modeling. 3) Characterize the ecological responses of intertidal marshes to disturbance. This will be accomplished by ongoing monitoring and experimental work to evaluate system responses to major perturbations in three key marsh habitats (changes in inundation and predator exclusion in Spartina-dominated salt marshes; increases in salinity in fresh marshes; changes in runoff in high marshes), by implementing standardized experimental disturbances along salinity and elevation gradients, and by tracking responses to natural disturbances. 4) Evaluate ecosystem properties at the landscape level (habitat distribution, net and gross primary production, C budgets) and assess the cumulative effects of disturbance on these properties. The project will also develop relationships between drivers and response variables, which can be used to predict the effects of future changes. This will be accomplished through a combination of data synthesis, remote sensing and modeling. 5. Abstract: The Georgia Coastal Ecosystems (GCE) Long Term Ecological Research (LTER) program, based at the University of Georgia Marine Institute on Sapelo Island, Georgia, was established in 2000 to study long-term change in coastal ecosystems. Estuaries (places where salt water from the ocean mixes with fresh water from the land) and their adjacent marshes provide food and refuge for fish, shellfish and birds; protect the shoreline from storms; help to keep the water clean; and store carbon. The GCE LTER researchers study marshes and estuaries to understand how these ecosystems function, to track how they change over time, and to predict how they might be affected by future changes in climate and human activities. They accomplish this by tracking the major factors that can cause long-term change in coastal areas (e.g. sea level, rainfall, upstream development), and measuring the effects of these factors on the study site. They also conduct focused studies to assess how key marsh habitats will respond to major changes expected in the future, including large-scale experiments to evaluate the effects of a) increases in the salinity of the water that floods freshwater marshes (mimicking drought and/or sea level rise), b) changes in water runoff from land into the upland marsh border (mimicking drought or upland development), and c) exclusion of larger organisms in the salt marsh (mimicking long-term declines in predators). During this award they will initiate additional studies to systematically evaluate how coastal wetlands respond to disturbances. Disturbances, or disruptions in the environment, are particularly important to understand in the context of long-term background changes such as increasing sea level, and GCE researchers are working to assess the cumulative effects of multiple disturbances on the landscape. The GCE education and outreach program works to share an understanding of coastal ecosystems with teachers and students, coastal managers, citizen scientist and the general public. 6. Funding Source: NSF OCE 1832178 B. Sub-project Description 1. Site Description a. Geographic Location: GCE_Flux -- GCE Flux Tower Marsh, Sapelo Island, Georgia Kenan_Field_KF -- Kenan_Field_KF Coordinates: GCE_Flux -- NW: 081 17 19.06 W, 31 27 23.72 N NE: 081 16 21.23 W, 31 27 23.72 N SE: 081 16 21.23 W, 31 26 12.12 N SW: 081 17 19.06 W, 31 26 12.12 N Kenan_Field_KF -- 81 16 42.0 W, 31 27 06.0 N b. Physiographic Region: GCE_Flux -- Lower coastal plain Kenan_Field_KF -- unspecified c. Landform Components: GCE_Flux -- Intertidal salt marsh bordering maritime forest Kenan_Field_KF -- unspecified d. Hydrographic Characteristics: GCE_Flux -- Site is along the Duplin River, and bounded by Barn Creek on the south and east, and is subject to 2-3m semi-diurnal tides Kenan_Field_KF -- unspecified e. Topographic Attributes: GCE_Flux -- Flat, with elevations ranging from 0-3m above mean low tide Kenan_Field_KF -- unspecified f. Geology, Lithology and Soils: GCE_Flux -- unspecified Kenan_Field_KF -- unspecified g. Vegetation Communities: GCE_Flux -- Dominated by Spartina alterniflora Kenan_Field_KF -- unspecified h. History of Land Use and Disturbance: none recorded i. Climate: Climate summary for Sapelo Island, Georgia, based on NWS data from 1980-2010: Daily-aggregated Values: Mean (sample standard deviation) mean air temperature: 20.09°C (7.28°C) minimum air temperature: 15.02°C (7.96°C) maximum air temperature: 24.82°C (6.98°C) total precipitation: 3.26mm (10.3mm) Yearly-aggregated Daily Values: Mean (sample standard deviation) total precipitation (1980-2010): 1124mm (266mm) 2. Experimental or Sampling Design a. Design Characteristics: We deployed separate Pulse Amplitude Modulation (PAM) fluorometry PAM fluorometers, at the Keenan Field marsh site on the west side of Sapelo Island (Latitude 31.444°, Longitude -81.283°). S. alterniflora in this area varies in height along an elevation gradient, with tall-form plants (> 100 cm) along the low elevation creekbank, medium (50 to 100 cm), and short-forms (< 50 cm) in intermediate and high marshes, respectively. b. Permanent Plots: Keenan Field marsh site on the west side of Sapelo Island (Latitude 31.444°, Longitude -81.283°). 9713 data points were acquired from July 11, 2020 to July 27, 2020 at 5 min interval. c. Data Collection Duration and Frequency: We collected leaf-level Chlorophyll fluorescence (ChlF) and incident Photosynthetic Photon Flux Density (PPFD) at the top and bottom of canopy (It is referred as TOC and BOC in the datasheet respectively) where the sensors were attached to two to three pairs of green and healthy leaves, TOC and BOC was at approximately 105 cm and 35 cm from the soil surface. We also record water table measurements that is taken by a separate HOBO U20 Water Level Data Logger ~4.8 m east of the ChlF measuring system. Beginning of Observations: Jul 11, 2020 End of Observations: Jul 27, 2020 3. Research Methods a. Field and Laboratory Methods: PSII Operating Efficiency (fPSII) calculations -- These are completely new analysis which was done to address questions related to the differences in the photosynthesis rates between air-exposed and submerged parts of the canopy. fPSII is the operating efficiency of the Photosystem-II (PSII) within the plant leaves (where photosynthesis occur). fPSII is the fluorescence parameter that indicates the efficiency at which light absorbed by PSII that is used for photosynthesis. fPSII is calculated as: fPSII = (Fm' - F') / Fm' Where, Fm' is the fluorescence maximum in the light-adapted state, and F' is the fluorescence yield at which the absorbed radiant energy is emitted from the S. alterniflora leaf in actinic light conditions. The position of the top sensor was determined by the marsh plant height (average canopy height was 110 ± 2.3 cm during sampling). The bottom sensor position was determined by the height of the leaves lowest on the plant stem. See the attached picture taken in the field. It shows how the TOC and BOC sensors were deployed. b. Protocols: none c. Instrumentation: HOBO U20 Water Level Data Logger (Onset Computer Corporation, Bourne, MA) LI-192 quantum sensors (LI-COR Biosciences, Lincoln, NE) d. Taxonomy and Systematics: not applicable e. Speclies List: f. Permit History: not applicable 4. Project Personnel a. Personnel: 1: Lishen Mao 2: Deepak Mishra 3: Peter Hawman 4: Caroline Narron 5: Jessica L. O'Connell 6: David L. Cotten b. Affiliations: 1: University of Georgia, Athens, Georgia 2: University of Georgia, Athens, Georgia 3: University of Georgia, Athens, Georgia 4: University of Georgia, Athens, Georgia 5: University of Texas at Austin, Port Aransas, Texas 6: Oak Ridge National Laboratory III. Data Set Status and Accessibility A. Status 1. Latest Update: 16-Feb-2023 2. Latest Archive Date: 16-Feb-2023 3. Latest Metadata Update: 16-Feb-2023 4. Data Verification Status: Reviewed by GCE IM B. Accessibility 1. Storage Location and Medium: Stored at GCE-LTER Data Management Office Dept. of Marine Sciences Univ. of Georgia Athens, GA 30602-3636 USA on media: electronic data download (WWW) or compact disk 2. Contact Person: Name: Adam Sapp Address: Department of Marine Sciences University of Georgia Athens, Georgia 30602 Country: USA Email: asapp@uga.edu 3. Copyright Restrictions: not copyrighted 4. Restrictions: This information is licensed under a Creative Commons Attribution 4.0 International License (see: https://creativecommons.org/licenses/by/4.0/). The consumer of these data ("Data User" herein) has an ethical obligation 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. a. Release Date: Affiliates: Feb 09, 2023, Public: Feb 09, 2023 b. Citation: Data provided by the Georgia Coastal Ecosystems Long Term Ecological Research Project, supported by funds from NSF OCE 1832178 (data set MSH-GCET-2302) c. Disclaimer: The user assumes all responsibility for errors in judgement based on interpretation of data and analyses presented in this data set. 5. Costs: free electronic data download via WWW, distribution on CD may be subject to nominal processing and handling fee IV. Data Structural Descriptors A. Data Set File 1. File Name: MSH-GCET-2302_1_0.CSV 2. Size: 4897 records 3. File Format: ASCII text (comma-separated value format) 3a. Delimiters: single comma 4. Header Information: 5 lines of ASCII text 5. Alphanumeric Attributes: 6. Quality Control Flag Codes: Q = questionable value, I = invalid value, E = estimated value 7. Authentication Procedures: 8. Calculations: 9. Processing History: Software version: GCE Data Toolbox Version 3.9.9b (06-Mar-2019) Data structure version: GCE Data Structure 1.1 (29-Mar-2001) Original data file processed: MSH-GCET-2302.txt (4897 records) Data processing history: 16-Feb-2023: new GCE Data Structure 1.1 created ('newstruct') 16-Feb-2023: 4897 rows imported from ASCII data file 'MSH-GCET-2302.txt' ('imp_ascii') 16-Feb-2023: 13 metadata fields in file header parsed ('parse_header') 16-Feb-2023: data structure validated ('gce_valid') 16-Feb-2023: automatically assigned study date metadata descriptors based on the range of date values in date/time columns (add_studydates) 16-Feb-2023: updated 1 metadata fields in the Dataset section(s) ('addmeta') 16-Feb-2023: imported Dataset, Project, Site, Study, Status, Supplement metadata descriptors from the GCE Metabase ('imp_gcemetadata') 16-Feb-2023: updated 57 metadata fields in the Dataset, Project, Site, Status, Study, Supplement section(s) ('addmeta') 16-Feb-2023: updated 1 metadata fields in the Dataset section(s) ('addmeta') 16-Feb-2023: imported Dataset, Project, Site, Study, Status, Supplement metadata descriptors from the GCE Metabase ('imp_gcemetadata') 16-Feb-2023: updated 57 metadata fields in the Dataset, Project, Site, Status, Study, Supplement section(s) ('addmeta') 16-Feb-2023: updated 1 metadata fields in the Dataset section(s) ('addmeta') 16-Feb-2023: imported Dataset, Project, Site, Study, Status, Supplement metadata descriptors from the GCE Metabase ('imp_gcemetadata') 16-Feb-2023: updated 57 metadata fields in the Dataset, Project, Site, Status, Study, Supplement section(s) ('addmeta') 16-Feb-2023: updated 1 metadata fields in the Dataset section(s) ('addmeta') 16-Feb-2023: imported Dataset, Project, Site, Study, Status, Supplement metadata descriptors from the GCE Metabase ('imp_gcemetadata') 16-Feb-2023: updated 57 metadata fields in the Dataset, Project, Site, Status, Study, Supplement section(s) ('addmeta') 16-Feb-2023: manually edited data set metadata ('ui_editmetadata') 16-Feb-2023: updated 6 metadata fields in the Data section(s) ('addmeta') 16-Feb-2023: updated 15 metadata fields in the Status, Data sections to reflect attribute metadata ('updatecols') 16-Feb-2023: parsed and formatted metadata ('listmeta') B. Variable Information 1. Variable Name: column 1. Date column 2. Time column 3. TOC_PAR column 4. BOC_PAR column 5. TOC_F column 6. TOC_Fm column 7. TOC_PSII column 8. BOC_F column 9. BOC_Fm column 10. BOC_PSII column 11. Tide_Level 2. Variable Definition: column 1. Calendar date of observation column 2. Calendar time of observation column 3. Photosynthetically active radiation measured at the top of the canopy column 4. Photosynthetically active radiation measured at the bottom of the canopy column 5. ChlF measured from leaves at the top of the canopy column 6. Maximum ChlF measured from leaves at the top of the canopy column 7. PSII operating efficiency for leaves at top the canopy column 8. ChlF measured from leaves at the bottom of the canopy column 9. Maximum ChlF measured from leaves at the bottom of the canopy column 10. PSII operating efficiency for leaves at the bottom of the canopy column 11. Tide level above the soil surface 3. Units of Measurement: column 1. YYYY-MM-DD column 2. hh:mm:ss column 3. umol/m2/s column 4. umol/m2/s column 5. none column 6. none column 7. none column 8. none column 9. none column 10. none column 11. meters 4. Data Type a. Storage Type: column 1. string column 2. string column 3. floating-point column 4. floating-point column 5. floating-point column 6. floating-point column 7. floating-point column 8. floating-point column 9. floating-point column 10. floating-point column 11. floating-point b. Variable Codes: c. Numeric Range: column 1. (none) column 2. (none) column 3. 0 to 1868.8625 column 4. 0 to 2210.3547 column 5. 133 to 522 column 6. 381 to 973 column 7. 0.203 to 0.766 column 8. 8 to 493 column 9. 14 to 717 column 10. 0.061 to 0.815 column 11. -0.063 to 0.723 d. Missing Value Code: 5. Data Format a. Column Type: column 1. text column 2. text column 3. numerical column 4. numerical column 5. numerical column 6. numerical column 7. numerical column 8. numerical column 9. numerical column 10. numerical column 11. numerical b. Number of Columns: 11 c. Decimal Places: column 1. 0 column 2. 0 column 3. 4 column 4. 4 column 5. 0 column 6. 0 column 7. 3 column 8. 0 column 9. 0 column 10. 3 column 11. 3 6. Logical Variable Type: column 1. datetime (none) column 2. datetime (none) column 3. data (continuous) column 4. data (continuous) column 5. data (continuous) column 6. data (continuous) column 7. data (continuous) column 8. data (continuous) column 9. data (continuous) column 10. data (continuous) column 11. data (continuous) 7. Flagging Criteria: column 1. none column 2. none column 3. none column 4. none column 5. none column 6. none column 7. none column 8. none column 9. none column 10. none column 11. none C. Data Anomalies: V. Supplemental Descriptors A. Data Acquisition 1. Data Forms: 2. Form Location: 3. Data Entry Validation: B. Quality Assurance/Quality Control Procedures: C. Supplemental Materials: D. Computer Programs: E. Archival Practices: F. Publications: not specified G. History of Data Set Usage 1. Data Request History: not specified 2. Data Set Update History: none 3. Review History: none 4. Questions and Comments from Users: none