Summary of soil temperature, moisture, and thaw depth for 14 chamber flux measurements sampled near LTER shrub sites at Toolik Field Station, Alaska, summer 2012.


Soil temperature at 5cm and 10cm depth [°C], volumetric water content (VWC) [%] and depth of thaw [cm] for 14 shrub canopy flux plots measured in vicinity of the Toolik Field Station, AK in 2012.

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Published on EDI/LTER Data Portal


Shaver, G. 2013. Summary of soil temperature, moisture, and thaw depth for 14 chamber flux measurements sampled near LTER shrub sites at Toolik Field Station, Alaska, summer 2012. Environmental Data Initiative.



Additional People: 

Data Manager
Field Crew
Associated Researcher
Associated Researcher

Date Range: 

Saturday, June 23, 2012 to Tuesday, August 7, 2012

Publication Date: 



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.

After taking the volume measurements of the chamber base, we characterized the soil conditions within the chamber by measuring the soil temperature, soil moisture, and thaw depth at six different locations central to the 1m x 1m chamber flux plot.

The soil temperature was measured at 5cm and 10cm below the soil surface at using traceable soil temperature probes (Fischer Scientific). Temperatures were recorded once the thermometer reading was stable for at least 30 seconds. On occasions when flux measurements spanned multiple days, soil temperature measurements were taken on each day, though measurements were made on the perimeter of the flux chamber base so to minimize the disturbance to the soil and vegetation until all flux measurements were complete.

Volumetric water content (VWC) was measured to estimate percent soil moisture using a Hydrosense Water Content Sensor (TDR probe) with 12cm tines (Campbell Scientific). The tines were inserted into the soil at a 45-degree angle for instantaneous readings. If the soil was too rocky to penetrate to the desired depth for any measurement this is indicated in the notes column. The VWC values were corrected for arctic tundra soils using a calculation developed by J. Powers in 2003 [see below]. Both original and corrected values are listed in the data sheet.

Thaw depth measurements were made using a 110 cm thaw depth probe marked every 0.5 cm. The probe was inserted into the ground as far as possible, and the depth from the tip of the probe to the soil's surface, considered to be the depth where no green moss or vegetation was visible.

The TDR probe is calibrated at manufacture for use in agricultural soils; for tundra soils meter readings are corrected using the equation:

actual VWC (%) = 0.5952(meter reading) + 7.684
R2 = 0.8649

(J Powers 2003)

Version Changes: 

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.
Version 2: Missing values changed to #N/A. CH 28Jan2013
Version 3: Updated metadata to new 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
Version 5: Corrected Distrubution URL. It had xlsfiles in the path. Jim L 19Jun14
Version 6: Changed Distrubution URL since the LTER network DAS system is being discontinued. JimL 9Apr2015

Sites sampled.

Full Metadata and data files (either comma delimited (csv) or Excel) - Environmental Data Initiative repository.

Use of the data requires acceptance of the data use policy --> Arctic LTER Data Use Policy