Plum Island Ecosystems LTER Database

Acceptance and utilization of LTER data requires that:

(1) The Principal Investigator be sent a notice stating reasons for acquiring any data and a description of the publication intentions.
(2) The Principal Investigator of the data set be sent a copy of the report or manuscript prior to submission and be adequately cited in any resultant publications.
(3) A copy of any resultant publications should be sent to:

Principal Investigator
Ecosystems Center
Marine Biological Laboratory
7 MBL St.
Woods Hole, MA 02543

Dataset URLs:METADATA: HTML, Rich Text, XML(EML compliant)
DATA: Comma Delimited, Excel file with Metadata and data
Dataset ID:MAR-NE-EddyFlux-2013.01
Dataset Title:Eddy flux measurements during 2013 from high marsh (Spartina patens/short Spartina alterniflora) off Nelson Island Creek, Rowley, Massachusetts
Investigator 1: 
First Name:Anne
Last Name:Giblin
Address line 1:Ecosystems Center
Address line 2:MBL
Address line 3:7 MBL St
City:Woods Hole
State:MA
Zip Code:02543
Country:USA
Investigator 2: 
First Name:Inke
Last Name:Forbrich
Address line 1:Ecosystems Center
Address line 2:MBL
Address line 3:7 MBL St
City:Woods Hole
State:MA
Zip Code:02543
Country:USA
Associate Investigators:
Keywords:PIE LTER, Plum Island Ecosystems, Massachusetts, primary production, organic matter, carbon flux, high marsh, net ecosystem exchange
Abstract:We deployed an eddy covariance system to measure ecosystem-atmosphere exchange of CO2 above a high marsh system (Spartina patens, short Spartina alterniflora) located on the Parker River Wildlife Refuge in marshes of Plum Island Sound, Rowley MA. This data represents the growing season CO2 exchange (May-October) in 2013.
Contact: Plum Island Ecosystems LTER Information Manager
The Ecosystems Center
Marine Biological Lab
7 MBL St
Woods Hole, MA 02543
Phone (508) 289 7485
Email: pie_im@mbl.edu
Online URL: http://pie-lter.ecosystems.mbl.edu
DATA FILE INFORMATION:
Data File URL http://ecosystems.mbl.edu/PIE/data/MAR/data/MAR-NE-EddyFlux-2013.csv
Data File Name MAR-NE-EddyFlux-2013
Beginning Date 1/1/2013
End Date 12/31/2013
Number of Data Records 17520
Other Files to Reference
Availability Status Type 1
Quality Control Information
Maintenance Description Data collection and processing complete
Log of Changes: Version 01: January 21, 2016, data and metadata created to comply with importation to Drupal and LTER PASTA. Used MarcrosExportEML_HTML (working)pie_excel2007_Jan2015.xlsm 1/15/15 4:26 PM for QA/QC to EML 2.1.0
 
RESEARCH LOCATION: MON-RO-NE-MAR-PRNWR Eddy Station Site 2
Geographic Description PIE Eddy Flux station in high marsh (S. patens, short S. alterniflora) off Nelson Island Creek, Parker River National Wildlife Refuge, Rowley, MA  
Location Bounding Box    
West Bounding Coordinate    
East Bounding Coordinate    
North Bounding Coordinate    
South Bounding Coordinate    
OR if single point location    
Latitude 42.73938889  
Longitude -70.828  
Elevation ca. 1.4 meters (NAVD88)  
     
     
 
TAXONOMIC COVERAGE:
Taxonomic Protocols
Organisms studied Spartina patens; Spartina alterniflora
 
Methods:We deployed one eddy covariance system to measure NEE of the dominant high marsh at PIE. The location of the tower is ca. 2km away from the parking lot at Stackyard Road within the Nelson Creek catchment. Deployment of the system is seasonal from mid-April to mid-November. The site was equipped with a Campbell Scientific® Closed Path System (CPEC200). Micrometeorological instrumentation was mounted on a tower at a height of 4.16m above the marsh surface at low tide. 10Hz rawdata were stored on a 2 Gb PCMCIA card and downloaded every two to three weeks. Power for the datalogger and instrumentation was located ca.8 m to the northeast of the tower and consisted of four south-facing solar panels and four 6 V 225 amp-hour batteries.
Environmental data were recorded as 10min averages. Air temperature and relative humidity were monitored at the same height as the anemometer (Campbell Scientific HC2S3 enclosed in a naturally aspirated radiation shield). A four-component net radiometer (Hukseflux NR01) was mounted 1.5 m aboveground of the high marsh. At the same height, two sensors (LI190SB, Licor) monitored incoming and reflected photosynthetically active radiation (PAR). In addition, a pressure transducer (Campbell Scientific CS456) recorded water table height at the high marsh. Soil temperature at a depth of 2cm, 6cm, 10cm, 20cm and 40cm was measured with (TCAV-L; Campbell Scientific; Logan, Utah, USA), and soil heat flux at a depth of 8 cm was measured with two soil heat flux plates (HFP01-SC; Campbell Scientific; Logan, Utah, USA). This data was recorded on a separate CR3000 datalogger.

Turbulent fluxes of momentum, sensible heat, latent heat and CO2 were determined by the eddy covariance technique (Baldocchi et al. 1988). Half hourly CO2 and H2O fluxes were calculated as the covariance between the turbulent departures from the mean of the 10 Hz vertical wind speed measured with a 3D sonic anemometer (CSAT3; Campbell Scientific; Logan, Utah, USA) and the CO2 and H2O dry mixing ratio measured with the closed path analyzer. Fluxes were processed using EdiRe software (Robert Clement, University of Edinburgh) and reported using the meteorological sign convention where negative NEE indicates carbon uptake and positive NEE indicates carbon loss from the ecosystem. Two coordinate rotations were performed on the wind components, and the time lag between wind and CO2 mixing ratio measurements was determined and removed for each averaging interval of 30min. For every 30 min period, a factor for the correction of the frequency attenuation of the flux was calculated according to Moore [1986] and applied to the flux. Fluxes were calculated using the Edire software (version 1.5.0.32, R. Clement, University of Edinburgh, UK). Afterward, fluxes were filtered for system malfunctioning and calibration periods, integral turbulence characteristics, stationarity, and wind direction [Foken etal., 2012]. We also excluded measurements when less than 75% of the flux was generated within the study area. Thresholds in friction velocity (u*) for nighttime fluxes were determined according to Papale et al. [2006] and was set to 0.14m/s..

To continuously monitor aboveground biomass, we calculated a broadband normalized difference vegetation index (NDVI) based on the approach of Wilson and Meyers [2007]. Incoming (i) and reflected (r) Solar (S) and photosynthetically active radiation (PAR) measurements were converted into red and near-infrared reflectance. Solar zenith effects were removed by using data exclusively around solar noon (10 A.M.–2 P.M. EST). In our system, spring tides occurred around noon, so
that simultaneous radiation measurements recorded the effect of tidal inundation at that time. A decrease in NDVI would reflect that during inundation the amount of biomass that was air exposed was smaller than under nonflooded conditions. We included this effect in our NEE model by creating two continuous time series of NDVI to simulate flooded and nonflooded conditions: NDVIall which included spring tide effects, and a reference time series, NDVIref, which represented nonflooded conditions.

NEE is gap-filled with a modified PLIRTLE model (NEE=GPP+Reco), using NDVI_all, air temperature and PAR as input. GPP_all and Reco_all are estimated using the two sub-models of the PLIRTLE model. GPP_ref and Reco_ref are modelled with NDVI_ref as input variable and thus represent the fluxes occurring if no tidal inundation had occurred.

References:
Baldocchi et al. [1988]: Measuring Biosphere-Atmosphere Exchanges of Biologically Related Gases with Micrometeorological Methods. Ecology, Vol. 69, No. 5, pp. 1331-1340.
Moore [1986]: Frequency response correction s for eddy correlation systems. Boundary Layer Meteorology, Vol. 37, pp. 17-35.
Foken et al. [2012]: Corrections and Data Quality Control. In: Aubinet, Vesala, Papale (editors): Eddy covariance - a practical guide to measurement and data analysis.
Papale et al. [2006]: Towards a standardized processing of Net Ecosystem Exchange measured with eddy covariance technique: algorithms and uncertainty estimation . Biogeosciences, Vol. 3, pp. 571-583.

Data Table

Variable Name Variable Description Units Measurement Scale Code Information Number Type DateTime Format Missing Value Code Missing Value Code Explanation
Date Date of measurements   datetime     DD-MON-YYYY    
Time Timestamp of measurements (center of 30min averaging period)   datetime     hh:mm    
zcorr measurement height of micromet instrumentation above surface meter ratio   real   NaN NaN = not available
PA atmospheric pressure kilopascal ratio   real   NaN NaN = not available
RH relative humidity percent ratio   real   NaN NaN = not available
Temp air temperature celsius ratio   real   NaN NaN = not available
PAR photosynthetic active radiation micromolePerMeterSquaredPerSecond ratio   real   NaN NaN = not available
WT water table height relative to high marsh surface meter ratio   real   NaN NaN = not available
NDVI_all Normalized difference vegetation index (NDVI) including response to inundation number ratio   real   NaN NaN = not available
NDVI_ref Normalized difference vegetation index (NDVI) excluding response to inundation number ratio   real   NaN NaN = not available
vpd vapor pressure deficit hectoPascal ratio   real   NaN NaN = not available
WD wind direction degree ratio   real   NaN NaN = not available
u wind speed meterPerSecond ratio   real   NaN NaN = not available
umax max wind speed in averaging period meterPerSecond ratio   real   NaN NaN = not available
v_sigma standard deviation in v component (after coordinate rotation) meterPerSecond ratio   real   NaN NaN = not available
u_sigma standard deviation in u component (after coordinate rotation) meterPerSecond ratio   real   NaN NaN = not available
w_sigma standard deviation in w component (after coordinate rotation) meterPerSecond ratio   real   NaN NaN = not available
ustar friction velocity meterPerSecond ratio   real   NaN NaN = not available
ZL stability parameter z/L number ratio   real   NaN NaN = not available
meanCO2 mean CO2 dry mixing ratio (micromole CO2 per mole of dry air) micromolePerMole ratio   real   NaN NaN = not available
meanTs mean sonic temperature celsius ratio   real   NaN NaN = not available
ITC test result integral turbulence characteristics (after Foken and Wichura 1996) percent ratio   real   NaN NaN = not available
CO2_stat steady state test result for CO2 percent ratio   real   NaN NaN = not available
flag_csat flag for anemometer (ideal conditions=0) number ratio   real   NaN NaN = not available
flag_irga flag for infrared gas analyzer (ideal conditions=0) number ratio   real   NaN NaN = not available
flag_mode flag for system mode (measurement mode=1) number ratio   real   NaN NaN = not available
fp_620m percent of flux originating within 620m from tower (threshold 75% used) calculated with analytical footprint model after Kormann and Meixner (2001) percent ratio   real   NaN NaN = not available
NEE_qc quality controlled CO2 flux micromolePerMeterSquaredPerSecond ratio   real   NaN NaN = not available
storage Storage CO2 flux micromolePerMeterSquaredPerSecond ratio   real   NaN NaN = not available
NEE_f gap-filled CO2 flux micromolePerMeterSquaredPerSecond ratio   real   NaN NaN = not available
GPP_all modelled gross primary production (as CO2) including response to inundation micromolePerMeterSquaredPerSecond ratio   real   NaN NaN = not available
Reco_all modelled ecosystem respiration (as CO2) including response to inundation micromolePerMeterSquaredPerSecond ratio   real   NaN NaN = not available
GPP_ref modelled gross primary production (as CO2) assuming no response to inundation micromolePerMeterSquaredPerSecond ratio   real   NaN NaN = not available
Reco_ref modelled ecosystem respiration (as CO2) assuming no response to inundation micromolePerMeterSquaredPerSecond ratio   real   NaN NaN = not available