Arctic LTER Database

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Shaver, G. 1989. Above ground biomass in acidic tussock tundra experimental site, 1989, Arctic LTER, Toolik, Alaska. Arctic LTER, Marine Biological Lab, Woods Hole, Ma 02543. 1989gsttbm http://ecosystems.mbl.edu/arc/terrest/biomass/index.shtml 

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Data sets were provided by the Arctic LTER. This material is based upon work supported by the National Science Foundation under Grants #DEB-981022, 9211775, 8702328; #OPP-9911278, 9911681, 9732281, 9615411, 9615563, 9615942, 9615949, 9400722, 9415411, 9318529; #BSR 9019055, 8806635, 8507493.

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Dataset URLs:	METADATA: HTML, Rich Text, XML(EML compliant) DATA: Comma Delimited, Excel file with Metadata and data
Dataset ID:	2012_GS_ITEX_LC_ParameterSummary.04
Dataset Title:	Summary of measured and modeled light curve parameters for diffuse, direct, and intermediate light curves for 14 whole-canopy 1mx1m plots sampled near the shrub LTER sites at Toolik Field Station, Alaska, summer 2012.
Investigator 1:
First Name:	Gaius
Last Name:	Shaver
Organization:	Ecosystems Center at the Marine Biological Laboratory
Address line 2:	7 MBL Street
Address line 3:
City:	Woods Hole
State:	MA
Zip Code:	02543
Country:	United States
Investigator 2:
First Name:	Edward
Last Name:	Rastetter
Organization:	Ecosystems Center at the Marine Biological Laboratory
Address line 2:	7 MBL Street
City:	Woods Hole
State:	MA
Zip Code:	02543
Country:	United States
Investigator 3:
First Name:	Mathew
Last Name:	Williams
Organization:	University of Edinburgh
Address line 2:	School of Geosciences
City:	Edinburgh
State:
Zip Code:	EH9 EJU
Country:	United Kingdom
Investigator 4:
First Name:	James
Last Name:	Laundre
Organization:	Ecosystems Center at the Marine Biological Laboratory
Address line 2:	7 MBL Street
Address line 3:
City:	Woods Hole
Zip Code:	02543
Country:	United States
Investigator 5:
First Name:	Laura
Last Name:	van der Pol
Organization:	Ecosystems Center at the Marine Biological Laboratory
Address line 2:	7 MBL Street
City:	Woods Hole
State:	MA
Zip Code:	02543
Country:	United States
Associate Investigators:
Keywords:	photosynthesis; shrub canopy, chamber flux measurement; light curve, direct light, diffuse light fraction
Abstract:	14 1m x 1m shrub plots were sampled the summer of 2012 under direct and diffuse light conditions. Light response curves were measured under each light condition for each plot using a Li-Cor 6400 to measure net ecosystem exchange (NEP); these measurements were modelled using a saturatingMichaelis-Menton formula. The best fit parameters for those models are contained here (Pmax, K, RE, Eo, and light compensation point) for each individual NEP light response curve (direct, diffuse, and intermediate light conditions) measured with corresponding NDVI , LAI, diffuse light fraction, and average temperature. Sorting variables and curve ID numbers for each curve match the corresponding data in the flux data file.
For questions about the Metadata and data contact the Investigators. For information about this web site contact:	Arctic LTER Information Manager The Ecosystems Center Marine Biological Lab 7 MBL St Woods Hole, MA 02543 Phone (508) 289 7496 Email: arc_im@mbl.edu Online URL: http://ecosystems.mbl.edu/ARC/
DATA FILE INFORMATION:
Data File URL	http://metacat.lternet.edu/das/dataAccessServlet?docid=knb-lter-arc.10150&urlTail=terrest/tracegas/data/2012_GS_ITEX_LC_ParameterSummary.csv
Data File Name	2012_GS_ITEX_LC_ParameterSummary
Beginning Date	6/23/2012
End Date	8/7/2012
Number of Data Records	34
Other Files to Reference	2012_GS_ITEX_BF3_DiffuseLightData; 012_GS_ITEX_CH_SoilData; 2012_GS_ITEX_CHFluxData; 2012_GS_ITEX_LC_ParameterSummary; 2012_GS_ITEX_MaxCanopyHeight; 2012_GS_ITEX_PercentCover; 2012_GS_ITEX_CHN_Data; 2012_GS_ITEX_PF_LAISummary; 2012_GS_ITEX_RawPinDrop_Data; 2012_GS_ITEX_ShootACiData; 2012_GS_ITEX_ShootHarvestData; 2012_GS_ITEX_ShrubCanopy_DailyLogger; 2012_GS_ITEX_InstantLogger; 2012_GS_ITEX_SunScan_LAI; 2012_GS_ITEX_SunScan_PAR; 2012_GS_PFandCH_GPS; 2012_GS_ITEX_PF_ShootLightCurve; 2003-2004gsfluxleafN; 2003-2009gscurveparameters; 2003-2009gsflux; 2003-2009gsGPSandveg; 2003-2009gsharvestLAI-N; 2003-2009gsspecieslist; 2004-2009gscoverft; 2004-2009gscoversp;
Availability Status	1
Quality Control Information	For measurements with a linear change in CO2 (r2>0.97), NEP is calculated from the last 45 seconds of the measurement. [The first 12 seconds of data were always discarded as the LiCor 6400 bases its flux calculations on 10sec averages.] When abnormalities in CO2 slope were observed due to leaks, very small changes in CO2, or changes in light levels, certain portions of the measurement were discaded. CO2 slope was always taken from contiguous data points (i.e. points were never removed from the middle of the measurement period)
Maintenance Description	This was a season-long project | though it followed similar methods to ITEX projects performed starting in 2003 that are likely to be replicated in the future for reasearch at the Toolik Field Station, AK.
Log of Changes:	Version 2: Missing values changed to #N/A. CH 28Jan2013
	Version 3: Updated metadata to newer form (with sites sheet) CH April 2013.
	Version 4: Corrected the extension of the eml Excel file - it was saved as .xls instead of .xlsx JimL 17May13

RESEARCH LOCATION:
Location Name	LTER Shrub Block 1	LTER Shrub Block 2	Select Site or enter New One	Select Site or enter New One	Select Site or enter New One	Select Site or enter New One	Select Site or enter New One	Select Site or enter New One
Geographic Description	Upland site; co-located in Block 1 of the Shrub LTER sites; IVO 68° 38'18.8" N | 149° 34' 07.2" W +/- 50m. Except for plots marked "FERT" | plots are outside of the designated LTER treatments | though are exposed to the same environmental conditions. All plots were chosen by the dominant shrub canopy (either Salix pulchraor Betula nana) and preferentially selected to be 90cm+ in height.	Outlet site; co-located in Block 2 of the Shrub LTER sites; IVO 68° 38'008.1" N | 149° 35' 017.1" W +/- 50m. Except for plots marked "FERT" | plots are outside of the designated LTER treatments | though are exposed to the same environmental conditions. All plots were chosen by the dominant shrub canopy (either Salix pulchraor Betula nana) and preferentially selected to be 90cm+ in height.	Enter Description	Enter Description	Enter Description	Enter Description	Enter Description	Enter Description
Location Bounding Box
West Bounding Coordinate
East Bounding Coordinate
North Bounding Coordinate
South Bounding Coordinate
OR if single point location
Latitude	68.6385555555555	68.6355833333333	In Decimal Degrees	In Decimal Degrees	In Decimal Degrees	In Decimal Degrees	In Decimal Degrees	In Decimal Degrees
Longitude	-149.568666666666	-149.588083333333	In Decimal Degrees	In Decimal Degrees	In Decimal Degrees	In Decimal Degrees	In Decimal Degrees	In Decimal Degrees
Elevation	747 m	730 m	In Meters	In Meters	In Meters	In Meters	In Meters	In Meters
Link to Google Map	View on Google Map	View on Google Map

TAXONOMIC COVERAGE:
Organisms studied	Betula nana; Salix pulchra; Salix glauca
Methods:	CHAMBER FLUX MEASUREMENTS CO2 and H2O fluxes were measured using a Licor 6400 photosynthesis system (Li-Cor Inc., Lincoln, Nebraska, USA) connected to a 1m x 1m plexiglass chamber in canopies dominated either by Salix pulchra or Betula nana shrub species. The height of the chamber varied depending on the height of the canopy being measured; chamber bases were constructed of PVC pipe to accomodate canopies with heights up to 125 cm. In addition to the plexiglass chamber, we also constructed a plexiglass "sleeve" that could extend the height of the rigid portion of the chamber by 0.25m. To set up each chamber, a location was chosen where the base would be level enough to ensure a complete seal with the plexiglass chamber and shrub branches could be moved either in or out of the chamber without creating large gaps in the canopy inside the chamber. Branches were included within the chamber if they were rooted within the chamber and excluded otherwise. Once the base was in place, we drove hollow PVC pipe legs into the permafrost and inserted an aluminum frame with foam campermount tape along the top edge for the plexiglass chamber and/or sleeve to rest upon, creating an airtight seal. The aluminum frame had taped to it semi-transparent, plastic skirt which extended to the ground (+30cm). We sealed the skirt to the tundra by weighting the skirt with heavy chains, pushing them firmly into the moss layer where possible and adding additional plastic materials as needed to ensure a good seal. We screwed the LiCor custom chamber head attachment over the holes drilled into the plexiglass chamber, again sealing with a rubber gasket. The air in the chamber was mixed using 4-8 small fans (depending on chamber height) powered by a 12v battery. At each plot we took measurements to create two light curves: one under direct light and one under diffuse light conditions. In order to determine the fraction of diffuse light, we used a DeltaT Beam Fraction Sensor (BF3, Delta-T Devices Ltd, Burwell Cambridge, UK) which quantifies the total irradianc and total diffuse light from which the diffuse light fraction (diffuse light/total light) can be calculated. For each day of flux measurements, the BF3 logged an instantaneous reading every 30-60 seconds set up on a leveled tripod at approximately 2 m above the ground. For the purpose of correlating the diffuse light fraction with each flux measurement, the LiCor 6400 and BF3 sensor were synchronized to read the same time (+/- 1 sec) at the start of each day. Different light levels for both diffuse and direct light curves were achieved by taking measurements under a variety of conditions: ambient light (no manipulation), successive shading levels (covering the chamber with 1-5 fine mesh net cloths), and intercepting direct light with photographic diffuser panels, as well as reflecting light into the chamber to increase the amount of diffuse light with white photographic panels. When the diffuser panels were used, they were carefully positioned to intercept all direct light that would otherwise enter the chamber. Whenwhite reflector panels were used, they were positioned on the side of the chamber opposite the sun and angled towards the chamber so as to increase the amount of diffuse light entering the chamber (these were used in conjuction with the diffuser panels). For these 'artificial' diffuse light measurements, we did not diffuse the BF3 sensor, thus the diffuse fraction calculations during these flux measurements do not represent the light conditions in the chamber. After field tests of using the diffuser and reflector panels, we determined that the panels effectively block all direct light, and thus we assume the diffuse light fraction is greater than 0.7 for these measurements. At each light level a flux measurement lasted 45 - 60 secs in total, with CO2 and H2O concentrations in the chamber recorded by the LiCor 6400 every 2 secs. After each measurement we lifted the chamber until CO2 and H2O concentrations had stabilized at ambient levels. We made an effort to obtain a wide range of flux measurements for light levels between 0-1600, and used whatever chamber light treatments were needed to achieve that based on the ambient light conditions. In addition to light measurements, we made at least three measurements in the dark for each day we took flux measurements. These were achieved by covering the chamber in an opaque tarpaulin cloth. These measurements represent the ecosystem respiration. After each light curve we determined chamber volume by taking depth measurements from the top of the chamber base to the ground. We measured the chamber base depth with 36 measurements made at regular 20cm intervals determined by placing a 1m x1m plastic frame with a 20cm x 20cm string grid on top of the base. The volume determined by these depth measurements (chamber surface area*average depth) was added to the volume of the plexiglass chamber (and sleeve, as needed) . The surface area of the inside of the 1 m x 1 m plexiglass chamber was 0.8836m2. For measurements with a linear change in CO2 (r2>0.97), NEP is calculated from the last 45 seconds of the measurement. [The first 12 seconds of data were always discarded as the LiCor 6400 bases its flux calculations on 10sec averages.] When abnormalities in CO2 slope were observed due to leaks, very small changes in CO2, or changes in light levels, certain portions of the measurement were discaded. CO2 slope was always taken from contiguous data points (i.e. points were never removed from the middle of the measurement period). Often at low light levels near the light compensation point, very small changes in CO2 resulted in measurements within the detection limits of the LiCor 6400, and large segments of the measurement had to be discarded to use a representative, linear segment of the data. All other variablels (H2O flux, pressure, chamber air temperature, CO2 concentration, PAR, PAR range) are calculated over the same time window as NEP. These variables were computed as the average over the course of the measurement. Each flux measurement was placed in one of four categories: direct, diffuse, intermediate, or respiration. These categories are defined as follows: Direct (sunny measurements): diffuse light fraction < 0.40 Diffuse (cloudy or diffused-light): diffuse light fraction > 0.70 Intermediate (partial sun/cloud): 0.40 < diffuse light fraction < 0.70 Respiration (dark): measurements taken in complete darkness; used for all light curve calculations NDVI UNISPEC DATA We measured NDVI on each flux a single channel Unipec spectral analysis system (PP Systems Inc, Amesbury, MA, USA). The unispec spectral analyser measures reflected light intensity in 256 portions of the visible spectrum from ~300nm to ~1100nm. A foreoptic cable transmits light reflected from the target to the instrument, a measurement scan lasts for ~10ms. Nine scans were measured in a regular grid for each of the flux plots. The end of the fibre optic was kept approximately 30cm vertically above the top of the canopy. The NDVI values were calculated using the equation below and then the NDVI values averaged together for each of the nine scans. Each scan was corrected for both incident radiation as well as sensor error. The incident radiation was accounted fo with a "reference scan" taken by holding the foreoptic cable vertically above a white, reference standard under the same light conditions as subsequent measurements. The scans were also corrected for with a "dark scan" taken with the sensor exposed to complete darkness (covering the sensor input with a black cloth) to account for the intrinsic error in the sensor itself. The program Multispec5.1.5.exe was used to compile and integrate the Unispec reflectance spectra from the raw target spectra. CHAMBER LIGHT RESPONSE CURVES The net ecocystem photosynthesis rate (NEP) was estimated by modelling the chamber flux measurements for each plot under direct and diffuse light with a saturating (michaelis-Menton type) function fitted to the measured data. Best-fit parameters are calcuated by minimising the sum of the squared errors between measured and modeled NEP values, using the Excel sover add-in. This model was run separately for each light curve, thus each chamber has a diffuse light curve, a direct light curve, and some have a so-called "intermediate" light curve if there were a substantial number of measurements taken that were under diffuse fraction conditions greater than 0.40 but less than 0.70. The model equation and parameters are described below. LAI SUNSCAN DATA The methods used to collect leaf area index (LAI) estimates at many heights within each canopy were the same used to collect PAR (see "SunScan_PAR_Data"). We measured the LAI using a DeltaT SunScan wand in conjuction with the BF3 sensor (Delta-T Devices Ltd, Burwell Cambridge, UK). The SunScan wand compares indident light readings measured on the BF3 sensor with the 64-PAR readings on the light wand to calculate LAI along the length of the 1m-long wand. LAI was measured by inserting the SunScan wand as near to the ground as possible--typically ~5cm from the ground as the wand rested on top of moss--and then measured vertically every 15 cm with the last measurement being above the canopy. Measurements were taken from the side of the chamber or point frame opposite the sun at three locations under both direct (ambient) and diffuse light conditions . In many cases the replicates at each height were differentiated by row (1-3, or occasionaly 3-8 which correspond to the point frame pins). Typically diffuse light conditions were achieved by shading both the BF3 sensor and the shrub canopy with photographic diffuser panels. On occasion, measurements were taken during cloudy light conditions where the diffuse light fraction was greater than 0.7 and no diffuser panel was needed; on these occasions the direct and diffuse light estimates may have been taken in slightly different locations as they were taken at different times and the precise position of the SunScan wand could not be replicated exactly. The SunScan wand measures PAR along 64 points along a 1-m horizontal profile. When sampling PAR within the shrub canopy, the data are from the raw output from each PAR sensor. When sampling LAI, there is an internal calculation performed though the Delta-T software that compares the reading above the canopy to the reading within the canopy, and takes into account the percent of absorbed PAR (assumed to be 0.85), and the ellipsoidal leaf angle distribution parameter (ELADP*) (assumed to be 1.0). While the LAI data from each height in the chamber flux canopies are available, the data here are only from the lowest, ground-level measurements (~5cm) to represent the canopy LAI. CALCULATIONS: INDIVIDUAL FLUX MEASUREMENTS: Fluxes are calculated from the slope of chamber CO2 (umol mol-1) [or H2O (mmol mol-1)] concentration against time. NEP = rho x vol x dCdry/dt rho = P_av x 1000 SA R T where NEP = net CO2 flux [umol m-2 s-1] rho = air density [mol/m3] P_av = pressure [kPa] R = ideal gas consant 8.314 [J mol K-1] T = temperature [K] = Temp_av [0c] + 273. vol = chamber volume {m3} dCdry/dt = slope of chamber water-dilution-corrected CO2 conc against time [umol mol-1 s-1] SA = chamber surface area [m2] = 0.8836 For net fluxes, a negative flux represents CO2 uptake by vegetation, a positive flux represents CO2 loss from the ecosystem to the atmosphere. RE = NEP during dark measurement GEP = RE - NEP LIGHT RESPONSE CURVE MODEL: Light response curves are modeled as: NEP = Re - Pmax*PAR K + PAR where Re = ecosystem respiration [µmol C m-2 ground s-1] Pmax = light saturated ecosystem photosynthesis [µmol C m-2 ground s-1] K = half saturation constant [µmol PAR m-2 ground s-1] E0 = ecosystem light use efficiency [µmol C µmol-1 PAR] LCP = ecosystem light compensation point [µmol PAR m-2 ground s-1] The initial slope of the light response curve (light use efficiency or E0), the light compensation point (LCP), and the gross primary productivty at a PPFD of 600 µmol m-2 s-1 (or GPP600) are calculated from these parameters as: E0 =Pmax/K LCP = RE*K Pmax-RE GPP600 = Pmax*600 K + 600 The 'Avg time of measurement' was calculated in Excel by converting the time of each flux measurement to a decimal, averaging the decimal-time values in a Pivot table, and then changing the averaged value format back into the HH:MM:SS format contained here. The respiration measurement times were not included in these averages, nor were they included in the average chamber air temperature. NDVI FROM UNISPEC NDVI = (RII-RI) (RI + RII) where RI = average reflectance from 570nm to 680nm RII = average reflectance from 725nm to 1000nm. REFERENCE: ITEX Manual, as updated in 2011

Data Table

Variable Name	Variable Description	Data Type	Units	DateTime Format	Code Information	Missing Value Code
YEAR	year of measurement	datetime		YYYY		#N/A=Missing or Not Measured
DATE	date of measurement	datetime		DD-MMM-YY		#N/A=Missing or Not Measured
SITE	Toolik	text
GROUP	Measurement location in relation to Toolik Lake LTER Shrub plots; In vicinity of Block1 =Upland, IVO Block 2 =Outlet	text
PLOT	Individual plot identifier	text
TREAT	none or fertilised annually (FERT) (with N and P)	text
PLOT SIZE	1m x 1m chamber size	text
PHASE	Measurement series (round of measurements within each year) ; not used in this dataset	number	number			#N/A=Missing or Not Measured
CURVE ID	Light curve identifier	text
AVG TIME OF MEASUREMENT	avg time light curve taken	datetime		HH24:Mi:SS		#N/A=Missing or Not Measured
NDVI	NDVI of flux plot	number	dimensionless			#N/A=Missing or Not Measured
Pmax	light saturated photosynthesis (umol PAR per meter squared ground per second)	number	micromolePerMeterSquaredPerSecond			#N/A=Missing or Not Measured
K	half saturation constant (umol PAR per umol CO2)	number	micromolePerMicromole			#N/A=Missing or Not Measured
AVG Measured Re	measured ecosystem respiration (umol CO2 per meter square ground per second)	number	micromolePerMeterSquaredPerSecond			#N/A=Missing or Not Measured
Eo	ecosystem light use efficiency (umol CO2 per umol PAR)	number	micromolePerMicromole			#N/A=Missing or Not Measured
LCP	ecosystem light compensation point (umol PAR per meter squared ground per second)	number	micromolePerMeterSquaredPerSecond			#N/A=Missing or Not Measured
AVG CH AIRTEMP	average chamber air temp during measurment (deg Celsius)	number	celsius			#N/A=Missing or Not Measured
MAX PAR	maximum ambient PAR at which a flux measurement is taken for that light curve (umol PAR per meter squared per second)	number	micromolePerMeterSquaredPerSecond			#N/A=Missing or Not Measured
GPP600	Gross primary productivity at a PPFD of 600 µmol m-2 s-1 (umol CO2 per meter squared ground per second)	number	micromolePerMeterSquaredPerSecond			#N/A=Missing or Not Measured
AVG BF3 TOT IRRAD	Average total irradiation measured with DeltaT Beam Fraction sensor (umol PAR per meter squared ground per second)	number	micromolePerMeterSquaredPerSecond			#N/A=Missing or Not Measured
AVG BF3 DIFFUSE IRRAD	Average total diffuse light measured with DeltaT Beam Fraction sensor (umol diffuse PAR per meter squared ground per second)	number	micromolePerMeterSquaredPerSecond			#N/A=Missing or Not Measured
AVG DIRECT:DIFFUSE LIGHT FRACTION	Average diffuse light divided by total irradiance (umol diffuse PAR per umol total PAR)	number	micromolePerMicromole			#N/A=Missing or Not Measured
STDEV BF3 TOT IRRAD	Standard deviation of total irradiation measured with DeltaT Beam Fraction sensor (umol PAR per meter squared ground per second)	number	micromolePerMeterSquaredPerSecond			#N/A=Missing or Not Measured
STDEV BF3 DIFFUSE IRRAD	Standard deviation total diffuse light measured with DeltaT Beam Fraction sensor (umol diffuse PAR per meter squared ground per second)	number	micromolePerMeterSquaredPerSecond			#N/A=Missing or Not Measured
STDEV DIRECT:DIFFUSE LIGHT FRACTION	Standard deviation diffuse light divided by total irradiance (umol diffuse PAR per umol total PAR)	number	micromolePerMicromole			#N/A=Missing or Not Measured
DOM VEG	Dominant canopy vegetation	text
DIRECT LAI-5cm	LAI estimate taken under DIRECT light at 5cm from ground (squared meter leaf per square meter ground)	number	meterSquaredPerMeterSquared			#N/A=Missing or Not Measured
DIFFUSE LAI-5cm	LAI estimate taken under DIFFUSE light at 5cm from ground (squared meter leaf per square meter ground)	number	meterSquaredPerMeterSquared			#N/A=Missing or Not Measured
AVG Modeled Re	modelled ecosystem respiration (umol CO2 per square meter ground per second)	number	micromolePerMeterSquaredPerSecond			#N/A=Missing or Not Measured
COMMENTS	Comments on NDVI/Unispec measurements	text
	Please contact arc_im@mbl.edu with questions, comments, or for technical assistance regarding this web site.