Arctic LTER Database

Conditions of Use

The re-use of scientific data has the potential to greatly increase communication, collaboration and synthesis within and among disciplines, and thus is fostered, supported and encouraged. Permission to use this dataset is granted to the Data User free of charge subject to the following terms:

1) Acceptable use. Use of the dataset will be restricted to academic, research, educational, government, recreational, or other not-for-profit professional purposes. The Data User is permitted to produce and distribute derived works from this dataset provided that they are released under the same license terms as those accompanying this Data Set. Any other uses for the Data Set or its derived products will require explicit permission from the dataset owner.
2 ) Redistribution. The data are provided for use by the Data User. The metadata and this license must accompany all copies made and be available to all users of this Data Set. The Data User will not redistribute the original Data Set beyond this collaboration sphere.
3 ) Citation. It is considered a matter of professional ethics to acknowledge the work of other scientists. Thus, the Data User will properly cite the Data Set in any publications or in the metadata of any derived data products that were produced using the Data Set. Citation should take the following general form: Creator, Year of Data Publication, Title of Dataset, Publisher, Dataset identifier. For example:

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 

4 ) Acknowledgement. The Data User should acknowledge any institutional support or specific funding awards referenced in the metadata accompanying this dataset in any publications where the Data Set contributed significantly to its content. Acknowledgements should identify the supporting party, the party that received the support, and any identifying information such as grant numbers. For example:

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.

5 ) Notification. The Data User will notify the Data Set Contact when any derivative work or publication based on or derived from the Data Set is distributed. The Data User will provide the data contact with two reprints of any publications resulting from use of the Data Set and will provide copies, or on-line access to, any derived digital products. Notification will include an explanation of how the Data Set was used to produce the derived work.
6 ) Collaboration. The Data Set has been released in the spirit of open scientific collaboration. Data Users are thus strongly encouraged to consider consultation, collaboration and/or co-authorship with the Data Set Creator.

By accepting this Data Set, the Data User agrees to abide by the terms of this agreement. The Data Owner shall have the right to terminate this agreement immediately by written notice upon the Data User's breach of, or non-compliance with, any of its terms. The Data User may be held responsible for any misuse that is caused or encouraged by the Data User's failure to abide by the terms of this agreement.

Disclaimer

While substantial efforts are made to ensure the accuracy of data and documentation contained in this Data Set, complete accuracy of data and metadata cannot be guaranteed. All data and metadata are made available "as is". The Data User holds all parties involved in the production or distribution of the Data Set harmless for damages resulting from its use or interpretation.

Dataset URLs:METADATA: HTML, Rich Text, XML(EML compliant)
DATA: Comma Delimited, Excel file with Metadata and data
Dataset ID:2012_GS_ITEX_PF_ShootHarvestData.05
Dataset Title:Harvest data including the shoot leaf area index, position in the canopy, and shoot and plant tissue area, count and mass for each shoot harvested at three levels in the canopy from 19 1m x 1m plots dominated by S. pulchra and B. nana shrubs near LTER Shrub plots at Toolik Field Station, AK the summer of 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:shoot photosynthesis; shrub canopy; point frame; A/Ci curve; light response curve; A/Ci Curve; leaf mass per area (LMA); leaf area index (LAI); ImageJ; opaque conifer chamber; Li-Cor 6400
Abstract:Leaf and plant tissue area and mass from shoots harvested from 19 1m x 1m point frame plots near Toolik Field Station, AK during the summer of 2012. Six shoots were harvested from each plot, two from each canopy layer: upper, middle, and low. Each shoot came from a different plant, and the species selected was based on the species dominant in that canopy layer. The leaf area and mass were used to correct A/Ci and light response curves taken on each shoot [data published separately]. At the time of collection, the location relative to the point frame, height, and leaf area index (LAI) of each shoot was measured; those data are included here.
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.10142&urlTail=terrest/tracegas/data/2012_GS_ITEX_PF_ShootHarvestData.csv
Data File Name 2012_GS_ITEX_PF_ShootHarvestData
Beginning Date 6/23/2012
End Date 8/7/2012
Number of Data Records 116
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 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: Metadata updated to newer form (with sites sheet). CH April 2013.
Version 4: Corrected eml excel file name wrong extension. JimL 16May13
Version 5: Change excel extension from xlsm to xlsx Jim L
 
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:HARVEST METHOD:
The methods for setting up each point frame plot are described below in the section 'POINT FRAME PIN-DROP METHODS'. The methods here describe how each shoot was harvested from the plots which were used for the point frame method.

Six shoots were harvested from each of 19 1m x 1m point frame plots which were dominated either by Salix pulchra or Betula nana tall, shrub species. The "shoots" described here are branch clippings between eight to ten inches long. Whenever possible they were selected for appearing relatively healthy, intact leaves, and each shoot was taken from a different plant. As these shoots were used for shoot-level and leaf-level measurements, shoots with bi-furcated stems -- or two stems from the same branch/height were cut -- one for leaf-level and the second for shoot-level analyses.

Before being cut, we measured the distance from the point frame to the highest tip on the shoot as well as the distance from the point frame to the shoot five inches from the tip. This way, we could approximate the angle of the shoot relative to the ground. Using the same criteria as for the pin-drop measurements, we measured the distance from the top of the shoot to the soil. In addition, the row number and pin-hole number nearest to the shoot's location with respect to the point frame was also recorded .

We then measured the leaf area index (LAI) of the shoot by holding an LAI-2000 (Li-Cor Inc., Lincoln, Nebraska, USA) in the exact location where the shoot had been and taking the average of three readings (one above, three below). For these measurements we used the one-quarter cut out and took care to always hold the instrument level and with the technician's body casting a uniform shadow over the instrument's eye, with the technician standing between the instrument and the sun. On occasion when it was raining during the shoot harvest, the area near where the shoot had been was marked with flagging tape, and the the LAI measurement was taken at a later date, using the height from frame/distance from ground meausrements as well as the row number and pin hole measurements as a guide.

Once cut, the shoot was placed immediately into water and transported to the lab. Once in the lab, the end of each shoot was clipped under water to ensure that there were no air bubbles in the stem that would inhibit the flow of water. Shoots were then allowed to sit at ambient room conditions (~20-25 degrees Celsius) until the the photosynthetic rates could be measured.

AREA CALCULATIONS:
Area calculations were made using the open source software Image J, available at http://rsbweb.nih.gov/ij/download.html. The procedures for each kind of area calculation are outlined here:

SHOOT SILHOUETTE AREA: Digital image capture of intact stem and leaves
1. Arrange the shoot on a white background (e.g. blank paper or foam board) as it sat in the LiCor conifer chamber. Add a note of sample number and date.
2. Place a ruler that you can later use as a reference. Ensure ruler/stem do not overlap.
3. Use a tripod to hold the camera in a steady position and as close as possible to the stem, keep this distance constant throughout the samples if possible to avoid the need to re-calibrate Image J.
4. Take a digital image of the shoot in very bright light conditions, using diffuser or reflector panels as needed to minimize shadows. [Shadows can be mistakenly analyzed in the software as plant tissue if not careful.]
5. Download the images in the computer, save them as TIFF files.
 
SHOOT TISSUE AREA: Image capture of shoot tissues (leaf, petiole, stipule, organ, green/brown stem) using a scanner
 1. Pluck the sample with forceps, arrange leaves, petioles, stipules, green and brown stems and inflorescences separately, grouped by type onto the white background of a plastic board. Place a ruler that you can later use as a reference. Add a note of sample number and date.
2. Press flat with the clear plastic cover. Ensure ruler/plant parts are not overlapping.
3. Place plastic side down on scanner (ensure no parts have overlapped when inverting plastic board).
4. Scan the images to the computer, save them as TIFF files.
 
BOTH SILHOUETTE AND TISSUE AREA ANALYSES:
In the Image J software program:  
1. Open leaf image via Select File ? Open? your file name
2. Convert scanned colour image of leaf to greyscale:
3. Image?Type?8 bit
4. Set measurement scale: Draw a line over a 50 mm section of the ruler then Analyze ?Set Scale
 5. In Set Scale window enter 50 into the 'Known Distance' box and change the 'Unit of Measurement' box to mm , check 'Global' (the Global option will apply the same scale to all the images you open after this, if you took the photos from different heights you might need to repeat this procedure every time)
6. Draw a new line and confirm that the measurement scale is correct.
7. Threshold the leaf image: Image? adjust? threshold
8. Play with sliders to include all of leaf in red and click ‘Apply’
 9. Calculate area of entire silhouette area and area of each tissue type:
Enclose the region of the shoot or tissues that you wish to calculate the area for with the rectangular selection tool, then Analyze ? Analyze Particles
 10. Select the options of display masks and display results.
Area of measured pixels is displayed. Check that only your leaf is included in the outline (not the ruler or extraneous tissue types).
The data of the leaf area is displayed on a new window ‘summary’, this data can be copied into Excel or the data can be saved directly as an Excel file. Keep summary window open between picture analyses to maintain a record of measured areas.
 11. Save new black and white image as well as its original colour photo with an appropriate file name.

DRYING AND WEIGHING:
Once digital images of each shoot and tissue had been made, each plant tissue was separated, counted, and placed in a labeled coin envelope. These samples were then dried for a minimum of three days at 60 degrees Celsius prior to being weighed on a four-point balance with glass enclosure.

Plant tissues were weighed in aggregate, thus the average mass included in these data are the total tissue mass divided by the count of that tissue (e.g. number of leaves, petioles, etc). In the same manner, plant tissure area was calculated in aggregate, thus the average area per leaf/petiole/stipule is based on the total area of that tissue divided by the count of that tissue.

At the start of this project, we did not take care to distinguish leaves, petioles, or stipules. While not thought to make a significant difference in the area or mass calculations for most samples, we did not want to include the petioles in the CHN analyses. Thus, for those samples that had removeable petioles (all B. nana, most S. pulchra, but no Vaccinium spp. or L. palustre samples), the petioles were clipped after drying and the leaves re-weighed. In some cases the mass of the leaves with petioles removed was greater than the original mass; in these cases, the original mass was preserved. [The original mass of all samples weighed is listed in the ORIGINAL LEAF MASS W/ PETIOLE data-column.]

NOTE: The area used for correcting the LiCor A/Ci and light curve data included leaves, petioles, and stipules.

CHN ANALYSIS:
Grinding: All leaf samples were dried in an oven at 60°C before grinding. Samples were small enough to grind the entire sample without subsampling. Leaves were ground using the Retsch MM 200 for 3 minutes or until a talcum powder consistency was achieved.

Weighing: After grinding, samples were stored in glass scintillation vials and dried again at 60°C for at least 36 hours. Once samples were removed, vials were tightly re-capped. When not in use, vials were stored in dessicators. 3.5-4.5 mg of each sample was weighed into a 10x12 mm tin capsule. A standard calibration curve was created using increasing amounts of aspartic acid (from about 0.2 mg to 5.0 mg). A chemical standard, acetanilide, and an organic sample, apple leaf, were run after the standard curve. Every ten samples, an aspartic acid check standard and a duplicate of an already-packed sample were run.

CN analysis: CN analysis was run between 10/4/2012 and 11/15/2012 by Rachel Rubin using the ThermoScientific 2000 at the Ecosystems Center, MBL, Woods Hole, MA. Duplicate sample values were averaged (mass, %N and %C) before inclusion into final results. The CHN data is available in the file "2012_GS_ITEX_PF_CHN_Data"


POINT FRAME PIN-DROP METHODS:
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.

Data Table

Variable Name Variable Description Data Type Units DateTime Format Code Information Missing Value Code
YEAR year of measurement datetime   YYYY    
DATE date of measurement 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        
TREATMENT control or fertilized annually (with N and P) text        
PLOT SIZE 1m x 1m point frame size text        
DOMINANT VEGETATION Dominant canopy vegetation text        
SPP Shoot species sampled text        
SHOOT ID Identification for each shoot sampled (NOT unique); consists of canopy position (up/mid/low), species abbreviation, and a number text        
CANOPY POSN Relative position of shoot in the canopy text        
ROW# Row number on the point frame where pin-drop measurement were taken number number     #N/A=Missing or Not Measured
PIN HOLE# Pin hole where pin-drop measurements were taken number number     #N/A=Missing or Not Measured
DIST TO TOP OF SHOOT Distance (cm) from the point frame to the highest tip of the shoot number centimeter     #N/A=Missing or Not Measured
DIST TO BOTTOM OF SHOOT Distance (cm) from the point frame to the place point 5 inches from the tip number centimeter     #N/A=Missing or Not Measured
DIST TO GROUND Distance (cm) of the highest tip of shoot to the soil number centimeter     #N/A=Missing or Not Measured
LAI (LAI-2000) Leaf area index measured at shoot location (meter squared leaf per meter square ground) number meterSquaredPerMeterSquared     #N/A=Missing or Not Measured
TOT SILHOUETTE AREA Area of whole shoot as viewed with shoot intact (square cm shoot) number centimeterSquared     #N/A=Missing or Not Measured
SUM(GREEN LEAF, PETIOLE, STIPULE) AREA Area of the shoot leaves, petioles, and stipules used to correct A/Ci and light curve data (square cm leaf+petiole+stipule) number centimeterSquared     #N/A=Missing or Not Measured
GREEN LEAF AREA Area of green leaves on shoot (square cm leaves) number centimeterSquared     #N/A=Missing or Not Measured
PETIOLE AREA Area of green petioles on shoot (square cm petiole) number centimeterSquared     #N/A=Missing or Not Measured
STIPULE AREA Area of green stipules on shoot (square cm stipule) number centimeterSquared     #N/A=Missing or Not Measured
OTHER GREEN ORGAN Area of green organs on shoot (square cm organ) number centimeterSquared     #N/A=Missing or Not Measured
BROWN STEM AREA Area of brown stem on shoot (square cm brown stemP number centimeterSquared     #N/A=Missing or Not Measured
GREEN STEM AREA Area of green stem on shoot (square cm green stem) number centimeterSquared     #N/A=Missing or Not Measured
TOTAL GREEN AREA Sum of green tissue area (leaf, petiole, stipule , organ, stem) on shoot number centimeterSquared     #N/A=Missing or Not Measured
TOTAL SHOOT AREA (LEAVES, STEM, ORGAN) Sum of the area of all tissues (green and brown) on shoot (square cm shoot) number centimeterSquared     #N/A=Missing or Not Measured
LEAF COUNT Number of leaves on shoot number number     #N/A=Missing or Not Measured
PETIOLE COUNT Number of petioles on shoot number number     #N/A=Missing or Not Measured
STIPULE COUNT Number of stipules on shoot number number     #N/A=Missing or Not Measured
GREEN ORGAN COUNT Number of organs on shoot number number     #N/A=Missing or Not Measured
TOT LEAF DRY MASS Dry mass of all leaves (g leaf) number gram     #N/A=Missing or Not Measured
TOT DRY PETIOLE MASS Dry mass of all petioles (g petiole) number gram     #N/A=Missing or Not Measured
TOT DRY STIPULE MASS Dry mass of all stipules (g stipule) number gram     #N/A=Missing or Not Measured
AVG MASS PER LEAF Mass of leaves divided by leaf count (g per leaf) number gramPerNumber     #N/A=Missing or Not Measured
AVG MASS PER PETIOLE Mass of petioles divided by petiole count (g per petiole) number gramPerNumber     #N/A=Missing or Not Measured
AVG MASS PER STIPULE Mass of stipules divided by stipule count (g per stipule) number gramPerNumber     #N/A=Missing or Not Measured
AVG MASS PER ORGAN Mass of organs divided by organ count (g per organ) number gramPerNumber     #N/A=Missing or Not Measured
BROWN STEM DRY MASS Dry mass of brown stem (g brown stem) number gram     #N/A=Missing or Not Measured
GREEN STEM DRY MASS Dry mass of green stem (g green stem) number gram     #N/A=Missing or Not Measured
TOT SHOOT DRY MASS Dry mass of total shoot (g shoot) number gram     #N/A=Missing or Not Measured
AVG AREA PER LEAF Total leaf area divided by leaf count (square meter per leaf) number meterSquaredPerNumber     #N/A=Missing or Not Measured
LMA Leaf mass per unit area (g leaf per square cm leaf) number gramPerMeterSquared     #N/A=Missing or Not Measured
ORIGINAL LEAF MASS W/ PETIOLE Dry mass of leaves with petioles prior to being separated and re-weighed (uncorrected g leaf) number gram     #N/A=Missing or Not Measured
COMMENTS Notes on data quality and measurements text