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 

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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 via LTER Data Poral
Dataset ID:2012_GS_ITEX_SunScan_LAI.05
Dataset Title:Leaf Area Index data taken with the Delta-T SunScan wand every 15 cm of 1m x 1m chamber flux and point frame plots as well as sites where dataloggers monitored PAR above, within and below S. pulchra and B. nana canopies during the growing season at the Toolik Field Station in AK, 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
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
Zip Code:02543
Country:United States
Investigator 3: 
First Name:Mathew
Last Name:Williams
Organization:University of Edinburgh
Address line 2:School of Geosciences
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
Zip Code:02543
Country:United States
Associate Investigators:
Keywords:photosynthesis, shrub canopy, chamber flux measurement, point frame, dataloggers, leaf area index
Abstract:Leaf area index (LAI) measurements were taken with the Delta-T SunScan wand every 15 cm from the ground to above the canopy under both direct and diffuse light. conditions The data includes all outputs from the SunScan wand: time of measurement, transmitted light, spread of PAR sensors, beam fraction, and zenith angle. These measurements were taken for 1m x 1m chamber flux and point frame plots sampled in tall Salix pulchra and Betula nana shrub canopies as well as sites monitored remotely by PAR sensors situated above, within, and below tall shrub canopies at the Toolik Field Station in the summer of 2012.
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
Online URL:
Data File URL
Data File Name 2012_GS_ITEX_SunScan_LAI
Beginning Date 6/23/2012
End Date 8/13/2012
Number of Data Records 1126
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
Maintenance Description This was a seasonal 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: Metadata updated to newer form (with sites sheet). CH April 2013.
Version 4 corrected eml exel file name JimL 16May13
Version 5: Corrected Distrubution URL. It had xlsfiles in the path. Jim L 19Jun14
RESEARCH LOCATION:                  
Location Name LTER Shrub Block 1 LTER Shrub Block 2 Toolik Field Station Lab 2 Toolik Field Station Gate 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. Lab2; used briefly as a location for the beam fraction sensor (BF3) to autolog. This site is located on the shore of Toolik Lake behind the Lab 2 building. It was chosen for convenient access, though ultimately was changed because of the prevalence of nearby structures. Toolik Gate; this was the preferred logging location for the beam fraction sensor (BF3). This site was located just up the road from the entrance to the field station. It was chosen for the complete absence of nearby structures and the ease of access. 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 68.6271861111111 68.6272416666666 In Decimal Degrees In Decimal Degrees In Decimal Degrees In Decimal Degrees  
Longitude -149.568666666666 -149.588083333333 -149.598469444444 -149.585425 In Decimal Degrees In Decimal Degrees In Decimal Degrees In Decimal Degrees  
Elevation 747 m 730 m 720 m 743 m In Meters In Meters In Meters In Meters  
Link to Google Map View on Google Map View on Google Map View on Google Map View on Google Map          
Organisms studied Betula nana; Salix pulchra; Salix glauca
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).

Measurements of the canopies monitored by the datalogger sensors were taken in the same way as those for the chamber flux and point frame canopies with the following exceptions:
* The measurements were taken near the end of the growing season when leaves were already beginning to senesce.
* Although the SunScan wand was traditionally used in conjunction with a Beam Fraction sensor (BF3), this sensor was malfunctioning when the datalogger sites were sampled , and thus it was not used. Instead of the BF3 sensor, wand measurements above the canopy were made immediately prior to each data measurement to record the ambiant total irradiance levels. [This same practice was followed for all sites sampled while the BF3 sensor was not functioning.]
* The weather conditions during the datalogger site measurements were almost uniform cloud cover; thus nearly all of the measurements were taken under "diffuse" light conditions (diffuse light fraction greater than 0.7). The measurements taken with "direct" light conditions were taken on partly cloudy days.
* Five replicates (rather than three) were taken at each height within the canopy. Locations were chosen to be those immediately surrounding the datalogger sensors.

In addition to the LAI values, the Delta-T SunScan instrument gives an output of other variables including: transmitted light, spread among sensors, beam fraction, and zenith angle. These values are further described here:

Transmitted Light: the fraction of incident light that passes through a given canopy. It can refer to Direct, Diffuse, or Total incident light.

Spread: the standard deviation of the 64-PAR sensors on the SunScan wand.

Beam Fraction: the fraction of the Total incident PAR in the Direct beam.

Zenith Angle: the angle between the centre of the sun and the point directly overhead.
Zenith angles are calculated from latitude, longitude, and local time using standard astronomical equations as given in Practical Astronomy. The location used to determine the local zenith angle was: 68 37' 39" N, Longitude 149 35' 51" W.

*"ELADP is a way of characterizing the horizontal or vertical tendency of leaves in a canopy." p 37 of SS1 User Manual v2.0 (SunScan Canopy Analysis System, type SS1. Delta-T Devices Ltd. May 19, 2008)


In order to monitor canopy conditions of the shrub species of interest--Betula nana and Salix pulchra--two CR1000 dataloggers (Campbell Scientific, 815 W. 1800, North Logan, UT, USA) were installed at the sites used for the ITEX shrub canopy studies at Toolik Field Station in Alaska the summer of 2012. The sites (see "Group" category) are labeled as "Upland" and "Outlet"--descriptions of the sample site in relation to Toolik Lake. The Upland site is colocated with Block 1 of the LTER shrub vegetation plots; the Outlet site is colocated with Block 2. The dataloggers were adjacent to, rather than within, LTER plots.

Both the Upland and Outlet datalogger had the following sensors which logged every five minutes:
(5) Photosynthetically active radiation (PAR) sensors: LI-190SB Quantum Sensor (Li-Cor Biosciences, 4647 Superior St, Lincoln, NE, USA)
* Sensors were placed as follows: (1) Above all vegetation at a height of 2.2 meters

(1) Mid-way within the B. nana canopies (approximately 40 cm above the soil)

(1) Mid-way within the S. pulchra canopies (approximately 40 cm above the soil)

(1) Below the B. nana canopies (approximately 10 cm above the soil)

(1) Below the S. pulchra canopies (approximately 10 cm above the soil)

(3) Relative humidity (RH) and temperature sensors: HMP50/HMP60 Probe (Campbell Scientific, North Logan, UT, USA)
* Sensors each had either a 6- or 10-plate radiation shield (Campbell Scientific model 41303-5A or 41003-5)
* Sensors were placed as follows: (1) Above all vegetation at a height of 2 meters

(1) Below the B. nana canopies (approximately 10 cm above the soil)

(1) Below the S. pulchra canopies (approximately 10 cm above the soil)

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.

We preferentially selected tall shrub canopies dominated either by Betula nana or Salix pulchra, that is canopies that were greater than 75 cm height. Care was taken to select fairly uniform canopies, that is avoiding the edge of a shrub stand or areas where the canopy had a large gaps, suggesting the area may have been disturbed.

We used point frames constructed from a 1.1 m x 1.1 m aluminum square with holes in each corner to accomodate steel rod posts used as the legs of the point frame. In this way, the frame could rest upon the four leg posts that had been hammered into the ground and remain adjustable in each corner. The frame had a level on each side, and great care was taken to ensure that the frame was (a) unable to be pushed deeper into the ground and, (b) level on all four sides prior to taking measurements. These factors were important to the measurement to have accurate data regarding the distance from the frame and the overall height of each point sampled in the canopy.

The aluminum frame had numbered, regularly spaced holes on two opposite sides in order to accomodate a metal bar that could be placed across the frame and locked into place. [These holes on the frame are the row numbers.] The bar that was placed across the frame similarly had numbered, evenly spaced holes in order to accomodate a pin--a long (100-200cm) metal rod with a diameter of ~3.175 mm. [The holes on this bar are the pin hole numbers.] Measurements were only ever taken from odd row numbers, and alternated even/odd pin hole numbers with each row; in this way, for every plot 25 evenly spaced locations were sampled covering an area of one square meter.

The length of the pin was marked every half-centimeter so that the distance could be read easily. Measurements were made by lowering the pin through a pin hole and, once encountering a leaf or stem, recording the following: row#, pin hole#, hit#, and the species hit. If the object hit was not a leaf, the plant tissue was noted; the diameter of each stem hit was estimated in millimeters, and the length of every graminoid blade hit was recorded from the point at which it was hit to the tip. As the primary species of interest for this project were for a select number of species (B. nana, S. pulchra, S. glauca, S. reticulata, V. uliginosum, V. vitis, L. palustre), species that were not the target of interest were classified as functional groups--e.g. graminoid spp., forb, moss.

The last pin-hit recorded for each pin hole was always at the "soil" which was considered to be the transition between the green and brown plant material, often in a mossy layer.

These data can be used in conjunction with the other data collected from these same plots--leaf area index, light and A-Ci response curves of shoots taken at different segments of the canopy.

Data Table

Variable Name Variable Description Data Type Units DateTime Format Code Information Missing Value Code
YEAR year of measurement datetime   YYYY    
DATE Date measurement was made datetime   DD-MMM-YY    
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      
MEASUREMENT TYPE Distinguishes chamber flux (CH) and point frame (PF) measurements text        
PLOT SIZE 1m x 1m chamber or point frame size text        
DOM VEG Dominant canopy vegetation text        
TIME 24-hour time measurement was taken datetime   HH:MM:SS    
TRANSMITTED light fraction that passes through the canopy (umol PAR transimitted per umol PAR above canopy) number micromolePerMole     #N/A=Missing or Not Measured
SPREAD Standard deviation of the 64-PAR sensors (umol PAR per meter square ground per second) number micromolePerMeterSquaredPerSecond     #N/A=Missing or Not Measured
INCIDENT Incident radiation measured on BF3 sensor (umol PAR per meter squared per second) number micromolePerMeterSquaredPerSecond     #N/A=Missing or Not Measured
BEAM FRACTION Fraction of light that is a direct beam (umol direct PAR per umol total PAR) number micromolePerMole     #N/A=Missing or Not Measured
ZENITH ANGLE angle of the sun above the horizon - estimated based on latitude and time of day number degree     #N/A=Missing or Not Measured
LAI leaf area index measured with SunScan wand (square meter leaf per square meter ground) number meterSquaredPerMeterSquared     #N/A=Missing or Not Measured
HEIGHT FROM GROUND height in centimeters of the SunScan wand from ground in cm text centimeter     #N/A=Missing or Not Measured
LIGHT CONDITION Description of the light condition during measurement text        
ROW / NOTES Row number indicating repetition number (1-3) or comments about the measurement text