chlorophyll a

Soil Biotic Effects Experiment

Abstract: 

Increases in soil temperature and moisture may change the bioavailability of essential elements by altering solubility and diffusion rates in soils, or by changing the amounts of organic compounds. Long-term experiments in the Bonney, Hoare and Fryxell basins have been established with 3 treatments: 1) increased moisture, 2) soil warming (ITEX chambers), and 3) soil warming + increased moisture. The identification and abundance of soil biota are reported.

Core Areas: 

Data set ID: 

4004

Additional Project roles: 

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Short name: 

BEE

Methods: 

Three sites were chosen on generally flat areas of moderately patterned soil. Plots were laid out in an identical design at each site - there are 4 treatments replicated 6 times in blocks. Treatments were randomly assigned to the plots within each block. Each plot measures 1m x 1m (with a 0.83m diameter area within used for experimental treatments and analyses) and there is a 1m buffer strip between adjacent plots. Plots are delineated by nails in the soil, each site is marked by PVC stakes approximately 60cm high. ITEX fiberglass chambers are used to impose the temperature treatment (see Marion et al. citation above). Water treatments are applied annually at a rate of 5.6L per plot. When sites were established, 5 cotton strips per plot were inserted vertically in to the soil. These will be sampled in subsequent seasons to measure decomposition.

Soil samples were taken for organism enumeration and moisture content analysis as follows: Sampling bags were prepared with one sterile 'Whirlpak' bag and clean plastic scoop per sample. Samples were taken from within the 10 cm diameter circular area of each plot. The location of the sampling was recorded each year so that areas were not re-sampled. Using the plastic scoop, soil was collected to 10 cm depth. Very large rocks (greater than 20 mm diameter) were excluded from the sample. The soil was shoveled into the 'Whirlpak' bag until three quarters full (about 1.5 kg soil). The soil was mixed well in the bag, then the bag was closed tightly, expelling as much air as possible. The soil samples were stored in a cooler for transportation. On return to the laboratory (within 8 hours of sampling), the soils were stored at 5C until further processing.

In the laboratory, soil samples were handled in a laminar flow hood to prevent contamination. The Whirlpak bags of soil were mixed thoroughly prior to opening. Approximately 200cm3 of soil was placed in a pre-weighed 800mL plastic beaker. Rocks greater than 3-4mm in diameter were removed from the sample. A sub-sample of approximately 50g was removed and placed in a pre-weighed aluminum dish, and weighed on a balance accurate to 0.01g. This sample was dried at 105C for 24 hours. The sample was removed, placed in desiccator to cool down, and re-weighed. These data were used to calculate water content of the soil and to express data as numbers of soil organisms per unit dry weight of soil. The remaining soil in the plastic beaker was weighed. Cold tap water was added up to 650 mL. The soil suspension was stirred carefully (star stir or figure of 8) for 30 seconds, using a spatula. Immediately the liquid was poured into wet screens - a stack of 40 mesh on top of a 400 mesh. The screens were rinsed gently with ice cold tap water (from a wash bottle) through the top of the stack, keeping the screens at an angle as the water filtered through. The water was kept on ice at all times. The top screen was removed, and the lower screen rinsed top down, never directly on top of the soil, but at the top of the screen and from behind. The water was allowed to cascade down and carry the particles into the bottom wedge of the angled screen. The side of the screen was tapped gently to filter all the water through. The suspension was rinsed from the front and the back, keeping the screen at an angle and not allowing the water to overflow the edge of the screen. The soil particles were backwashed into a 50mL plastic centrifuge tube, tipping the screen into the funnel above the tube and rinsing the funnel gently. The suspension was centrifuged for five minutes at 1744 RPM. The liquid was decanted, leaving a few mL on top of the soil particles. The tube was filled with sucrose solution (454g sucrose per liter of tap water, kept refrigerated) up to 45mL. This was stirred gently with a spatula until the pellet was broken up and suspended. The suspension was centrifuged for one minute at 1744 RPM, decanted into a wet 500 mesh screen, rinsed well with ice cold tap water and backwashed into a centrifuge tube. Samples were refrigerated at 5C until counted. Samples were washed in to a counting dish and examined under a microscope at x10 or x20 magnification. Rotifers and tardigrades were identified and counted. Nematodes were identified to species and sex, and counted. Total numbers in each sample were recorded on data sheets. All species of nematode, and all rotifers and tardigrades found in the sample were recorded. Data were entered in to Excel files, printed, and checked for errors.

For measurements of electrical conductivity 100ml of DI water was added to 20g of soil in a clean, DI- rinsed glass beaker (coarse fragments >3-4 mm were removed). The samples were stirred until thoroughly mixed (about 5-10 sec). After sitting to equilibrate for 10 minutes the samples were stirred again and a reading was taken with a Corning 311 conductivity meter. The values reported are temperature corrected using the following equation: (1,411.8/.01M KCl reading) * sample reading. The 0.01M KCl reading is obtained by measuring the conductivity of a 0.01M KCl solution at the beginning of the 10 minute reading. For measurements of pH, 60 ml of DI water was added to 30 g of soil in a clean, DI- rinsed glass beaker (coarse fragments >2 mm were removed). The samples were stirred until thoroughly mixed (about 5-10 sec). After sitting to equilibrate for 2 hours, the samples were stirred again and a reading was taken with an Orion 720A pH meter. Data were entered in to Excel files, printed, and checked for errors.

Extraction of chlorophyll from the soil. All procedures were carried out in the dark or very low irradiance to avoid degradation of the chlorophyll. The soil samples were mixed thoroughly in the vials, and a sample of approximately 5 g was weighed out in to a 50 mL plastic centrifuge tube with a screw-top cap. 10 mL of a 50:50 DMSO/90% acetone solution was added to each sample and they were mixed thoroughly on a bench-top Vortex mixer for about 5 seconds. The vials were placed in a -4C constant temperature room, in the dark, and left for 12-18 hours. Determination of chlorophyll a concentration - This was determined fluorometrically using a Turner model 111 fluorometer. A calibration using a known concentration of chlorophyll was carried out prior to sample analysis. The machine was blanked using a 50:50 DMSO/90% acetone solution.

Each vial was mixed thoroughly, then centrifuged for 5 minutes at about 1800 RPM. A sample of approximately 4mL of the DMSO/acetone solution was taken from the top of the sample with a pipette, being careful not to get any soil particles in the solution. The sample was placed in a cuvette, in to the fluorometer and the fluorescence was recorded. This was done fairly quickly in order to prevent light from breaking down the chlorophyll. This measurement is called Fo, the initial fluorescence. After taking this reading, 0.1 mL of 1N HCl was added directly to the cuvette and the cuvette was gently agitated. After 20 seconds, the fluorescence was re-measured. (During this step, the acid converts the chlorophyll to phaeophytin by releasing a magnesium ion in an acidic environment). This measurement is called Fa, the fluorescence after acidification . The solution was discarded in to a waste container, and the cuvette rinsed 3 times with DMSO/90% acetone solution before proceeding with the next sample. Data were entered in to Excel files, printed, and checked for errors.

Season Notes on Sampling and Maintenance

* Bonney Dec 1999: 

Comments: Soil samples were taken on 9 Dec 1999 from the Lake Bonney Biotic Effect Experiment (BEE) site at the West Lobe of Lake Bonney in Taylor Valley by Dorota Porazinska and Katie Catapano.  The BEE was established on the same day prior to sampling.  Each sample  was collected from the area outside of a warming chamber but still within the borders of the experimental plots. Soil samples were processed on 10 Dec 99 by Katie Catapano, Dorota Porazinska, and Steve Blecker. [Dorota Porazinska 11 Dec 99].  On 9 Nov 2000, Mike Robertson renamed the "data" worksheet to "raw" and enabled protection for the worksheet.  The worksheet was also copied to create a "calc" sheet.  Formulas were copied from an earlier ".worms" worksheet to calculate the number of individuals per kg of soil for each taxon [Mike Robertson 9 Nov 2000].

File log: This file was created on 11 Dec 1999 by Dorota Porazinska. Data were entered  by Dorota Porazinska on 11 Dec 99. [Dorota Porazinska 11 Dec 99]. Data was proofed by Pilar Tillberg and Kerri Minatre on 01 February 00.  The correction was made by Pilar Tillberg on 01 February 00: the number of dead Eudorylaimus juveniles was changed from 2 to 0 for sample 6TW and from 0 to 2 for sample 6W. [Pilar Tillberg 01 Feb 00]

This file was updated and corrected by MLVandegehochte, 9/11/14 (MLHaddix)

*Fryxell Dec 1999 Comments:

Comments: Soil samples were taken on 4 Dec 1999 from the Lake Fryxell Biotic Effect Experiment (BEE) site at the south side of Lake Fryxell in Taylor Valley (by F6 hut) by Dorota Porazinska, Katie Catapano, Ross Virginia, and John Barrett. The BEE was established on the same day prior sampling.  Each sample was collected from the area outside of a warming chamber but still within the borders of experimental plots. Soil samples were processed on 5 Dec 99 by Katie Catapano, Dorota Porazinska, and John Barrett. [Dorota Porazinska 11 Dec 99].  On 9 Nov 2000, Mike Robertson renamed the "data" worksheet to "raw" and copied this sheet to make a "calc" sheet with all calculations completed [Mike Robertson 9 Nov 2000].

File log: This file was created on 11 Dec 1999 by Dorota Porazinska. Data entered and checked by Dorota Porazinska on 11 Dec 99. [Dorota Porazinska 11 Dec 99].  The data were proofed by Pilar Tillberg and Kerri Minatre on 02 February 2000.  The corrections were made by Pilar Tillberg on 14 February 2000: The number of live female Scottnema for sample 3T was changed from 42 to 142; the number of rotifers for sample 2TW was changed from 0 to 5. [Pilar Tillberg 14 Feb 00]

This file was updated and corrected by MLVandegehochte, 9/11/14 (MLHaddix)

*Hoare Dec 1999 Comments:

Comments: Soil samples were taken on 7 Dec 1999 from the Lake Hoare Biotic Effect Experiment (BEE) site at the south side of Lake Hoare in Taylor Valley by Dorota Porazinska and Katie Catapano.  The BEE was established on the same day prior to sampling.  Each sample was collected from the area outside of a warming chamber but still within the borders of the experimental plots. Soil samples were processed on 8 Dec 99 by Katie Catapano, Dorota Porazinska, and Steve Blecker. [Dorota Porazinska 11 Dec 99]. Sample 5T contained viable egg, and sample 6W a gravid female  (viable egg inside her body).  On 9  Nov 2000, Mike Robertson renamed the "data" worksheet to "raw" and copied this sheet to create a "calc" worksheet with all formulas copied over from an earlier file [Mike Robertson 9 Nov 00].

Nematodes were converted to # per kg in the calc sheet, using the equation provided by Emma Broos: 1000*(# in extr/ (fresh soil in extr - (fresh soil in extr * (moist % / 100)))), and soil moistures were added for this calculation from: LHBEE.soil.Dec99.calc sheet. [Holley Zadeh 6 May 2004]

File log: This file was created on 11 Dec 1999 by Dorota Porazinska. Data were entered  by Dorota Porazinska on 11 Dec 99. [Dorota Porazinska 11 Dec 99]. Data was proofed by Pilar Tillberg and Kerri Minatre on 02 February 2000.  No changes were necessary. [Pilar Tillberg 14 Feb 00]

This file was updated and corrected by MLVandegehochte, 4/02/13 (MLHaddix)

Soil Moisture calculated as the (g of water/ g dry soil) *100 by M L Haddix 8/30/13

*Bonney Dec 2001 Comments:

Comments: Soil samples were taken on 20 Dec 2001 from the Lake Bonney Biotic Effects Experiment (BEE) site at the south side of the west lobe of Lake Bonney by Dorota Porazinska, Nicole DeCrappeo, and Steve Blecker.  Sampling for each plot was done as follows: chla samples were taken from the soil surface (top 2 cm) around the cotton strip using a spoon; one cotton strip was then gently pulled, shaken to remove any loose soil, and wrapped in Al foil (strips were taken from the point farthest from the lake--however, in chamber plots the strips were difficult to find due to sediment accumulation, so the first strip seen was removed).  A soil sample was then taken using a scoop and Whirlpak bag from the place where the cotton strip was removed.  5T chamber shifted north, so that 2 cotton strips were not inside the chamber.  6C had only one cotton strip in the plot, the other 5 blew away.  Soil surface was not marked on the cotton strips in the field but estimated in the lab during processing.  Plots were maintained on the same day right after sampling (water added to appropriate treatments, chambers repositioned, and bungees tightened where necessary).  Samples were placed in a cooler in the field, brought back to Crary and immediately placed in a 4C refrigerator until processing.  Soil samples were processed on 21 Dec 01 by Dorota Porazinska, Nicole DeCrappeo, and Steve Blecker.  Samples were counted on 26 Dec 01 by Dorota Porazinska [Steve Blecker 2 Jan 02].

File log: This file was created on 2 Jan 2002 by Steve Blecker. [Steve Blecker 2 Jan 02].  Data were entered by Nicole DeCrappeo on 6 Jan 2002. [Nicole DeCrappeo 6 Jan 02].  Data were proofed by N. DeCrappeo and Jeb Barrett on 12 Jan 2002 [Jeb Barrett 12 Jan 02].

Nematodes were converted to # per kg in the calc sheet, using the equation provided by Emma Broos: 1000*(# in extr/ (fresh soil in extr - (fresh soil in extr * (moist % / 100)))), and soil moistures were added for this calculation from: LBBEE.soil.Dec01.raw  [Holley Zadeh 20 May 2004]

This file was updated and corrected by MLVandegehochte, 4/02/13 (MLHaddix)

*Fryxell Dec 2001 Comments:

Comments: Soil samples were taken on 18 Dec 2001 from the Lake Fryxell Biotic Effects Experiment (BEE) site at the south side of Lake Fryxell in Taylor Valley (by F6 hut) by Dorota Porazinska, Nicole DeCrappeo, and Steve Blecker.  Sampling for each plot was done as follows: chla samples were taken from the soil surface (top 2 cm) around the cotton strip using a spoon; one cotton strip was then gently pulled, shaken to remove any loose soil, and wrapped in Al foil (LOCATION?).  A soil sample was then taken using a scoop and Whirlpak bag from the place where the cotton strip was removed.  Soil surface was not marked on the cotton strips in the field but estimated in the lab during processing.  Plots were maintained on the same day right after sampling (water added to appropriate treatments, chambers repositioned, and bungees tightened where necessary).  Samples were placed in a cooler in the field, brought back to Crary and immediately placed in a 4C refrigerator until processing. Soil samples were processed on 19 Dec 01 by Dorota Porazinska, Nicole DeCrappeo, and Steve Blecker.  Samples were counted between 21-22 Dec 01 by DP. [Steve Blecker 2 Jan 02]. 

File log: This file was created on 2 Jan 2002 by Steve Blecker.  Data were entered by Nicole DeCrappeo on 6 Jan 02. [Nicole DeCrappeo 6 Jan 02].  These data were proofed by Nicole DeCrappeo and Jeb Barrett on 12 Jan 2002. [Jeb Barrett 12 Jan 02].

Nematodes were converted to # per kg in the calc sheet, using the equation provided by Emma Broos: 1000*(# in extr/ (fresh soil in extr - (fresh soil in extr * (moist % / 100)))), and soil moistures were added for this calculation from F6BEE.soil.Dec01.raw [Holley Zadeh 24 May 2004]

This file was updated and corrected by MLVandegehochte, 4/02/13 (MLHaddix)

Soil Moisture calculated as the (g of water/ g dry soil) *100 by M L Haddix 8/30/13

*Hoare Dec 2001 Comments:

Comments: Soil samples were taken on 23 Dec 2001 from the Lake Hoare Biotic Effects Experiment (BEE) site on the south side of Lake Hoare by Dorota Porazinska, Nicole DeCrappeo and Steve Blecker.  Sampling for each plot was done as follows: chla samples were taken from the soil surface (top 2 cm) around the cotton strip using a spoon; one cotton strip (farthest strip from the lake) was then gently pulled, shaken to remove any loose soil, and wrapped in Al foil.  A soil sample was then taken using a scoop and Whirlpak bag from the place where the cotton strip was removed.  Soil surface was not marked on the cotton strips in the field but estimated in the lab during processing.  Plots were maintained on the same day right after sampling (water added to appropriate treatments, chambers repositioned, and bungees tightened where necessary).  Samples were placed in a cooler in the field, brought back to Crary and immediately placed in a 4C refrigerator until processing.  New chambers were put on the plots 28 Dec 01 and were replaced with the old ones by Jeb Barrett and Andy Parsons on 6 Jan 02.  The new chambers seemed to be of a different composite material (flimsier), harnesses did not seem secure enough, so the old chambers will be left on all the BEE plots.  Soil samples were processed on 26 Dec 01 by Dorota Porazinska, Nicole DeCrappeo, and Steve Blecker.  Samples were counted on 30 Dec 01 by Nicole DeCrappeo [Steve Blecker 2 Jan 02]. 

File log: This file was created on 2 Jan 2002 by Steve Blecker.  Data were entered  by Nicole DeCrappeo on 10 Jan 02. [Nicole DeCrappeo 10 Jan 02].  Data proofed by Nicole DeCrappeo and Steve Blecker on  14 Jan 02. [Steve Blecker 14 Jan 02].

Nematodes were converted to # per kg in the calc sheet, using the equation provided by Emma Broos: 1000*(# in extr/ (fresh soil in extr - (fresh soil in extr * (moist % / 100)))), and soil moistures were added for this calculation from: LHBEE.soil.Dec01.raw  [Holley Zadeh 20 May 2004]

This file was updated and corrected by MLVandegehochte, 4/02/13 (MLHaddix)

*Bonney Jan 2003 Comments: 

File log: This file was created on 8 Jan 2003 by Steve Blecker. Samples were counted by Diana Wall 7 Jan 03 and 8 Jan 03. Soils Data entered and checked by Steve Blecker 8 Jan 03 [Steve Blecker 8 Jan 03].  Worm Data was entered by Jen L Mercer 8 Jan 03 [Jen L Mercer 8 Jan 03].

Comments: Soil samples were taken on 20 Dec 2001 from the Lake Bonney Biotic Effects Experiment (BEE) site at the south side of the west lobe of Lake Bonney by Jen Mercer and Steve Blecker.  Sampling for each plot was done as follows: chla samples were taken from the soil surface (top 2 cm) around the cotton strip using a spoon; one cotton strip was then gently pulled, shaken to remove any loose soil, and wrapped in Al foil (strips were taken from the point farthest from the lake--however, in chamber plots the strips were difficult to find due to sediment accumulation, so the first strip seen was removed).  A soil sample was then taken using a scoop and Whirlpak bag from the place where the cotton strip was removed.  5T chamber shifted north, so that 2 cotton strips were not inside the chamber.  6C had only one cotton strip in the plot, the other 5 blew away.  Soil surface was not marked on the cotton strips in the field but estimated in the lab during processing.  Plots were maintained on the same day right after sampling (water added to appropriate treatments, chambers repositioned, and bungees tightened where necessary).  Samples were placed in a cooler in the field, brought back to Crary and immediately placed in a 4C refrigerator until processing.  Soil samples were processed on 7 Jan 03 by Diana Wall, Andy Parsons and Steve Blecker. NOTE: Due to the vague nomenclature in the "blue methods book", the samples were extracted using a sugar solution prepared by adding 454 lb. of sugar to 1 L of water (specific gravity 1.135 g/cc) instead bringing 454 g of sugar to 1L of volume (1.171 g/cc and 1.33M), the latter being the correct formulation as per Freckman and Virginia (1993).  [Steve Blecker 8 Jan 03].

A ca 100g subsample was extracted using the standard sugar centrufigation method.

This file was updated and corrected by MLVandegehochte, 4/02/13 (MLHaddix)

Soil Moisture calculated as the (g of water/ g dry soil) *100 by M L Haddix 8/30/13

*Fryxell Jan 2003 Comments: 

File log: This file was created on 10 Jan 2003 by Steve Blecker. Soil weight for nematode extraction was entered by SwB 10 Jan 03. [10 Jan 03 Steve Blecker]. Worm data was entered on the raw sheet by Andy Parsons on 15 Jan 03 [Andy Parsons 15 Jan 03]. Data were worked up by Jeb Barrett on Jan 21, 2003. Checked all raw data (Emma Broos and Steve Blecker)

Comments: Samples were taken on 9 January 2003 by Diana Wall, Byron Adams, Andy Parsons and Jeb Barrett from the F6 BEE plots.  Standard soil sampling for Antarctic samples was employed,  with the following details added for clarification. The strip closest to 9 o'clock was sampled, with 12 o'clock being in a northerly direction. Chla samples were taken first, then the cotton strip was removed as gently as possible, any clumps of soil gently removed and then wrapped in Al-foil, then about 1/2 a large whirl pak worth of soil was excavated with a plastic scoop to 10cm, either in the spot the cotton strip was removed, or closer to the 9 o'clock location. Some of the strips in Blocks 1 and 2 were frozen in to the ground and the soil around them had to be excavated prior to removal. 2 strips were torn during removal but both pieces were retrieved. Several of the strips in the +T treatments were buried by new sediment accumulation, this had to be carefully brushed aside to find the strips. Steve says this best: "Locating cotton strips in the chambered plots was difficult at best.  The eolian sediment was scraped away as gently as possible in an effort to locate all the strips (necessary to determine which strip to sample), but orignal surface soil and coarse fragments were disturbed in the process. Recommend that the location of the strips me marked with a flag or nail that sticks above accumulating sediments so the plots do not have to be disturbed so heavily.  Note: the eolian sediment was not sampled."

Samples were placed in backpacks and flown back to the Crary Lab where they were stored at +4C until analysis.

A ca 100g subsample was extracted using the standard sugar centrufigation method. Samples were extracted on 10 January 2003. Samples were counted by Diana Wall on 10 Jan 03 and 11 Jan 03.  [Andy Parsons 15 Jan 03].

There was an 'other' column on the data sheet with 1 for 1T. (Emma Broos 19 Feb 03)

This file was updated and corrected by MLVandegehochte, 4/02/13 (MLHaddix)

Soil Moisture calculated as the (g of water/ g dry soil) *100 by M L Haddix 8/30/13

*Hoare Jan 2003 Comments:

File log: This file was created on 19 Jan 2003 by Steve Blecker.  No data was entered at this time, as there was really no data to enter, plus Sister Ray was playing on iTunes and I couldn't concentrate anyway.  [Steve Blecker 19 Jan 03]. Data entered by Jeb Barrett on Jan. 21, 2003. Soil weight checked [Emma Broos 19Feb03].

Comments:

This file was updated and corrected by MLVandegehochte, 4/02/13 (MLHaddix)

Soil Moisture calculated as the (g of water/ g dry soil) *100 by M L Haddix 8/30/13

*Bonney Jan 2005 Comments:

File log:  Soil data was entered, and log was created, on 21 January 2005 by Holley Zadeh. Data was verified by Holley Zadeh and Vicki on 24 Jan 05.

Comments: These data are for soils collected by Diana Wall and Holley Zadeh. Emma Broos kept track of soil sample kits and sampling locations, cotton strip foil, and made notes in the field book. Byron Adams poured water on treatments, as well as maintained the HOBO. Johnny "The Mule" Chaston replaced soil warming chambers, hauled soils back to the coolers at the helo pad, and generally hoofed things back and forth. Claire Ojima and Emma Broos collected bundt pan samples while Johnny Chaston and Holley Zadeh collected OTC sediments. Holley Zadeh took over for Emma Broos on the bundt pans at #5, and by #7 Hiolley Zadeh and Claire Ojima saw that the soil was wet, and by #8 they saw that Wormherder Creek was full-on flowing.

BEE plot samples were collected at ~1:00, with the lake as 12:00. Exceptions are 6C and 6T, which were both sampled at 2:00, and 6W, which was sampled at 12:00. All but one cotton strip was collected: 1TW was not found.

NOTE: chambers that were used to replace the old beaten ones on all BEE plots are 2" taller than the ones that were removed.

Specimens were extracted on 21 Jan 2005 as follows:

*Holley Zadeh and Claire Ojima under the laminar flow weighing out ext'n soil and pH/EC soil

*Diana "fast-track" Wall sieved soil at the sink

*Byron "poor shot of the day" Adams spun samples at the centrifuge while making only approximately 4 of 50 attempted shots to the burnables can

*Johnny Chaston and Emma Broos counted samples at the scope

All specimens were preserved by EB on 23 Jan 2005 [HZ 23 Jan 2005]

The Microbial Biomass samples were extracted in 50 mls of K2SO4. [RMS 22 Jan 05]

#s/kg were calculated by Holley Zadeh on 11 May 2005 [11 May 05].

Related Files: LBBEE_soil.xls; DNAExtr.xls

This file was updated and corrected by MLVandegehochte, 4/02/13 (MLHaddix)

*Fryxell Dec 2004 Comments:

File log: Data was entered and the log was created on 29 Dec 04 by Holley Zadeh. John Chaston and Ralph the computer voice verified data on 5 Jan 05. Log was checked by all members of the Wall team shortly after it was created.

Comments: Soil samples were collected on a mild day, from the BEE expt at F6, on 27 Dec 2004 by Holley Zadeh, with bagging/labling/keeping-track-of-the-plots assistance from John Chaston. Claire Ojima and Emma Broos removed cotton strips. Holley Zadeh and Emma Broos treated W and TW plots with water. Soil samples were taken from the top left corner (not all the way to the corner) of the plots as you look at them facing North and Lake Fryxell. In the case of a temperature chamber, samples were pulled from within the chamber. Several cotton strips were unrecoverable at this site, due to a large amount of sediment (~10cm deep, but some had more than others). Plots with unrecoverable strips are as follows:

1T

2TW

3TW

4T

5TW

1TW

6T

Big storm came in and we got outta there just in time!

*Sample 4C had a tear in the bag from the field. The sample, in it's original bag, was placed in a clean ziplock bag once we got back to the lab, and the original bag was taped over the hole. When it was double bagged, the ziplock was removed and the taped bag with the hole was placed directly into the second bag.

NOTE: chambers used to replace old ones on all BEE plots are 2" taller than the ones that were removed.

Samples were extracted on 28 Dec 04 as follows:

*Holley Zadeh weighed and recorded soils

*Emma Broos seived each sample

*Claire Ojima worked the centrifuge, added sugar solution, and acted as a runner in her downtime

*John Chaston was at the microscope and doing PCR work

Emma Broos and John Chaston counted these samples on 28 & 29 Dec 04.

 F6 BEE 3C was re-run on 7 Jan 05, in the same way as listed above. Specimens were not counted, however, because we only wanted a Scottnema sample out of it for DNA work.

Nematodes were converted to # per kg in the calc sheet, using the equation: 1000*(# in extr/ (fresh soil in extr - (fresh soil in extr * (moist % / 100)))), and soil moistures were added for this calculation from F6BEE_soil.xls [Holley Zadeh 8 Jan 05].

All specimens were preserved on 4 Jan 2005 by Emma Broos and Holley Zadeh. [Holle Zadeh 23 Jan 05]

Error found in row 27 of calc sheet. Should read 100.65, not 10.65. Corrected by Breana Simmons. E-mail sent to B424 and B423 [Breana Simmons 13 July 06].

Soil Moisture calculated as the (g of water/ g dry soil) *100 by M L Haddix 2/23/14

Numbers per kg dry soil calculated by M L Haddix using formula 1000*(#individuals/(extraction mass*(mass of dry soil/mass of soil used for moisture calc))) 2/23/14

Related Files: F6_BEE_cottonstrips.xls, F6_BEE_soil.xls, see this file for additional comments; also see DNAExtr0405.xls for DNA notes

This file was updated and corrected by MLVandegehochte, 4/02/13 (MLHaddix)

*Hoare Dec 2004 Comments:

File log: Data was entered by Holley Zadeh on 28 Dec 2004, and verified by Holley Zadeh and Victoria on 29 Dec 04. Log was created by Holley Zadeh on 27 Dec 04 and checked by the rest of the team members shortly after.

Comments: Soil was sampled from the BEE plots on the South side of Lake Hoare by John Chaston and Claire Ojima on 23 Dec 04, and decomp strips were gently removed with a metal spatula by Emma Broos, while Holley Zadeh assisted by checking plot numbers and labels and wrapping cotton strips in foil (after gently removing any soil clumped on to the strip); and 'W' plots were treated with water by Emma Broos and Holley Zadeh. Samples were flown back to the Crary lab the same day and incubated in the 4 degree until time for extraction.

NOTE: chambers used to replace old ones on all BEE plots are 2" taller than the ones that were removed.

Samples were extracted on 26 Dec 04 as follows:

*Holley Zadeh weighed and recorded soils

*Emma Broos sieved each sample

*Claire Ojima worked the centrifuge, added sugar solution, and acted as a runner in her downtime

*John Chaston was at the microscope and doing PCR work

Emma Broos and John Chaston counted these samples on 26 & 27 Dec 04.

Sample LHBEE 1TW contained 6 dead juvenile worms with  unique morphological characteristics. This soil was extracted two more times to try to find the same worm, but it was not found again with either extraction, so the worm was not positively ID'd [Holley Zadeh 5 Jan 05].

Comments from JC regarding sample LHBEE 5TW: accurate account, but I erased the numbers on the counter before recording them. They were counted two days later, so maybe some remained in the tube; I thought it was more like 3,0,5,1,3,2, for Scottnema numbers

Samples were preserved on 4 Jan 05 by Emma Broos and John Chaston. Sample LH_BEE 2T was dropped on the bench and only partial sample remains. Was preserved anyway, and this sample was not re-run [Holley Zadeh 5 Jan 05].

Nematodes were converted to # per kg in the calc sheet, using the equation: 1000*(# in extr/ (fresh soil in extr - (fresh soil in extr * (moist % / 100)))), and soil moistures were added for this calculation from LHBEE_soil.xls

This file was updated and corrected by MLVandegehochte, 4/02/13 (MLHaddix)

Soil Moisture calculated as the (g of water/ g dry soil) *100 by M L Haddix 8/30/13

Related Files: LHBEEsoil.Dec04.xls, LHBEE_strips.xls, DNAExtr0405.xls

*Bonney Jan 2007 Comments:

File log: File log was created on 24 Jan 07 by Ed Ayres.

Comments: Soil, chlorophyll a and cotton strip (where posible) samples were collected by Ed Ayres and Dorota Proazinska on 15 Jan 07.  Samples were collected at 2:30 direction at each experimental plot.  Water treatments were applied immediately after sampling to the W and TW plots.

Fauna were extracted by sugar floatation.  Raw data were converted by Ed Ayres using (# individuals/(fresh soil wy extracted/((soil moisture/100)+1)))*1000.

Data extracted 15 Jan 2007

Data preserved 20 Jan 2007

Samples counted by Ed Ayres, Dorota Proazinska and Breana Simmons

Data entered by Breana Simmons on 16 Jan 2007

Data proofed 30 Jan 2007

This file was updated and corrected by MLVandegehochte, 4/02/13 (MLHaddix)

Soil Moisture calculated as the (g of water/ g dry soil) *100 by M L Haddix 8/30/13

Related files: LBBEE_soil.xls, BEE_COC.xls

*Fryxell Jan 2007 Comments:

This log was created by Dorota Porazinska on Jan 10  2007.

All soil samples for nematodes and chloropyll A were collected by Ed Ayres and Dorota Porazinska on 10 Jan 07. Samples were collected at 2:30 direction at each experimental plot. CA single cotton strip was removed only from plots without ITEX chambers (W, C), leaving one more cotton strip in place. Plot4C contained only one strip and so no more cottons strips were left for future sampling. Plots with chambers accumulated so much soil sediment that cotton strips were not visible and thus not accessible.  Immediately after soil samples and coton strips were collected, 5.6 L of water was apllied to apropriate exeprimental treatments (W, TW). Regular maintenance was carried out.

Fauna were extracted by sugar floatation.  Raw data were converted by Ed using (# individuals/(fresh soil wy extracted/((soil moisture/100)+1)))*1000

Data Extracted 11 Jan 2007

Data preserved 14 Jan 2007

Counted by Dorota Porazinska and Ed Ayres

Data entered by Breama Simmons on 22 Jan 2007

Data Proofedb by Ed Ayres

This file was updated and corrected by MLVandegehochte, 4/02/13 (MLHaddix)

Related files: F6BEE_soil.xls, BEE_COC.xls

*Hoare Jan 2007 Comments:

File log: File log was created on 24 Jan 07 by Ed Ayres.

Comments: Soil, chlorophyll a and cotton strip (where posible) samples were collected by Ed Ayres and Dorota Proazinska on 13 Jan 07.  Plots were sampled at the '2:30' position if 12 o'clock is towards the lake.  Water addition treatments were applied to the W and TW plots immediately after sampling.

Fauna were extracted by sugar floatation.  Raw data was converted by Ed Ayres using (# individuals/(fresh soil wt extracted/((soil moisture/100)+1)))*1000

Data extracted  13 Jan 2007

Data preserved 20 Jan 2007

Samples counted by Dorota Proazinska and Ed Ayres

Data entered by Breana Simmons on 16 Jan 2007

Date proofed on 30 Jan 2007

Related files: LHBEE_soil.xls, BEE_COC.xls

This file was updated and corrected by MLVandegehochte, 4/02/13 (MLHaddix)

Soil Moisture calculated as the (g of water/ g dry soil) *100 by M L Haddix 8/30/13

*Bonney Jan 2010 Comments:

LOG: This file created on 1/18/10 by Zachary Sylvain.

Data entered by Zachary Sylvain.

Data checked by Zachary Sylvain.

Calculations by Zachary Sylvain using the formula: (# individuals / dry soil) * 1000

Sampled by Bishwo Adhikara and Diana Wall - no treatments applied afterward because stoich plots were treated.

PLots dry on surface and moist underneath. Tons of sediment in cones.

Cotton Strips: 4C, 2C, 1C, 1W, 3W, 3C, 4W, 6W

Chambers replaced on 1/20/10 by Diana Wall, Uffe Nielsen and Byron Adams. Seam placed East, perpendicular to lake.

This file was updated and corrected by MLVandegehochte, 4/02/13 (MLHaddix)

*Fryxell Jan 2010 Comments:

LOG: This file created on 1/11/10 by Zach Sylvain.

Data entered by Zach Sylvain.

Data checked by Zach Sylvain.

Calculations by Zach Sylvain using the formula: (# individuals / dry soil) * 1000

Sampled at 6 O'Clock by Byron Adams and Diana Wall.

Samples handled by BIshwo Adhikari and Zach SYlvain

Cotton strips present: 1W, 2C, 1C, 4W, 3W, 6TW, 5TW, 5W, 6W

Salinity patches: 3TW 10 to 3 o'clock, 3T at 6 o'clock, 5TW along inside of cone

T-bar hole at 4 o'clock 1W

Sampled at 5 o'clock due to rock 2C

Chambers replaced 1/20/10. Seam facing toward Kukri hills opposite lake. Chambers replaced by Uffe Nielsen, Byron Adams and Diana Wall.

1 chamber badly scratched in transit - placed on 6T

This file was updated and corrected by MLVandegehochte, 4/02/13 (MLHaddix)

Soil Moisture calculated as the (g of water/ g dry soil) *100 by M L Haddix 8/30/13

*Hoare Jan 2003 Comments:

LOG: This file created on 1/18/10 by Zachary Sylvain.

Data entered by Zachary Sylvain.

Data checked by Zachary Sylvain.

Calculations by Zachary Sylvain using the formula: (# individuals / dry soil) * 1000

Sampled at 6 o'clock, upslope

Cotton Strips: 2W, 1C, 2C, 1T, 3W, 3T, 4C, 5W

Sampled by Bishwo Adhikara, Diana Wall, and Zachary Sylvain. Treated by Zachary Sylvain and Bishwo Adhikara with Diana Wall indicating proper plots.

Chambers replaced 1/20/10 and metal collars replaced. Chambers faced S (upslope) toward Kukri Hills. Chambers replaced by Zachary Sylvain and Bishwo Adhikara.

This file was updated and corrected by MLVandegehochte, 4/02/13 (MLHaddix)

Soil Moisture calculated as the (g of water/ g dry soil) *100 by M L Haddix 8/30/13

*Bonney Dec 2011 Comments:

LOG: This file created on 1-4-12 by Zachary Sylvain.

Data entered by Jeremy Whiting.

Data checked by Jeremy Whiting.

Calculations by Zachary Sylvain using the formula: (# individuals / dry soil) * 1000

Notes: Sampled at 3 o'clock oriented facing the plots according to the diagram (looking toward Taylor Glacier)

Cotton strips present at 1C, 1W, 2C, 2W, 3C, 3W, 4C, 4W, 5W and 6W

4C sampled at about 2 o'clock, slightly toward center

5C sampled at about 12 o'clock

This file was updated and corrected by MLVandegehochte, 4/02/13 (MLHaddix)

Soil Moisture calculated as the (g of water/ g dry soil) *100 by M L Haddix 8/30/13

*Fryxell Dec 2011 Comments:

LOG: This file created on 1-4-12 by Zachary Sylvain.

Data entered by Jeremy Whiting.

Data checked by Jeremy Whiting.

Calculations by Zachary Sylvain using the formula: (# individuals / dry soil) * 1000

Notes: Sampled plots at 4 o'clock facing south toward Kukri Hills

Chamber seams all facing south toward Kukri Hills

Cotton strips present at 1W, 2C, 3W, 3C, 4W, 5W, 6W and 6C

Jeremy Whiting had to chisel soil at 1W as it was frozen up to 2cm below the surface

Snowpack in 6W, but not over sampling area at 4 o'clock

This file was updated and corrected by MLVandegehochte, 4/02/13 (MLHaddix)

Soil Moisture calculated as the (g of water/ g dry soil) *100 by M L Haddix 8/30/13

*Hoare Dec 2011 Comments:

LOG: This file created on 1-4-12 by Zachary Sylvain.

Data entered by Jeremy Whiting.

Data checked by Jeremy Whiting.

Calculations by Zachary Sylvain using the formula: (# individuals / dry soil) * 1000

Notes: Sampled at 3 o'clock oriented facing south

Cotton strips present at 1C, 1W, 2C, 2W, 3C, 4C, 5C and 5W

2T cotton strip accidentally removed from under sediment. Strip was bagged and brought back to lab.

This file was updated and corrected by MLVandegehochte, 4/02/13 (MLHaddix)

Metadata Updates New metadata updates on Aug 2013, Inigo San Gil, included all these seasonal notes, all participants (Field Crew, Lab, etc) and better description for units and variable used. Moved to the Drupal Ecological Information Management System on 2014.

Data sources: 

SOILS_BEE

Maintenance: 

This file contains archived data pulled from Nemadisk and the field season directories by Jeb Barrett. 
       
The data page contains the raw data for nematode abundance in # of animals per kg oven dry weight equivalent.
 
May, 2006 - Chris Gardner created this metadata and accompanying Oracle data table from metadata info and an Excel spreadsheet from Jeb Barret. A "COMMENTS" data column was added to indicate where data is missing
   
This file was created on 2 Jan 2002 by Steve Blecker. [SwB 2 Jan 02].  Data were entered by Nicole DeCrappeo on 6 Jan 2002. [ND 6 Jan 02].  Data were proofed by N. DeCrappeo and Jeb Barrett on 12 Jan 2002 [JB 12 Jan 02].
 
Nematodes were converted to # per kg in the calc sheet, using the equation provided by Emma Broos: 1000*(# in extr/ (fresh soil in extr - (fresh soil in extr * (moist % / 100)))), and soil moistures were added for this calculation from: LBBEE.soil.Dec01.raw  [HZ 20 May 2004]
 
This file was updated and corrected by MLVandegehochte, 4/02/13 (MLHaddix)
 
File was abbreviated for website only counts in #/kg dry soil was left along with log, 7/19/13 MLHaddix
 
Data revised and updated in the database in Aug 2013, Inigo San Gil
 
See more history and changes in the methods section.
      

Additional information: 

 Since the attribute table for this dataset is very large, the user must construct the actual column name.  The FIRST letter represents the species, and the following letters represent the life stage/sex/sum type.  The nematode species codes are:
      
      S: Scottnema lindsayae 
      E: Eudorylaimus spp. 
      P: Plectus spp.  
      
For example, in the attribute table,  "(code)ML" has the description "The total number of living male (species) adult nematodes extracted from the soil sample in number of organisms per kg soil oven dry weight equivalent. In this case, a column name called "SML" would be  "The total number of living male Scottnema lindsayae adult nematodes..."
   
TREATMENT Codes
 
In the attribute table, the treatment is the manipulation for a give plot from where the soil was collected. The treatments are:
      (C) control plots (no manipulations), 
      (T) enhanced soil temperature using ITEX conical open-top chambers made of solar fiberglass,
      (W) Nanopure water added to field capacity to 10 cm depth (5.6 L/plot) once per season,
      (TW) temperature enhancement and water addition
 
Preserved Samples
Preserved samples are stored in the NREL Preserved Nematode Collection in room 226, College of Natural Resources, Colorado State University. Original data are stored in Room A208, Natural and Environmental Sciences Building, Colorado State University.
 
     

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