water content

Soil Elevational Transect Experiment

Abstract: 

Investigation of the effect of elevation and topography on soil biota and soil properties was part of the McMurdo Dry Valleys Long Term Ecological Research (LTER) project. The number of soil organisms (nematodes, rotifers and tardigrades), divided by species, sex and maturity was monitored at 3 elevations, initially in Taylor Valley (1993) then Garwood and Miers Valleys (2012) in order to accomplish this.

Core Areas: 

Data set ID: 

4003

Additional Project roles: 

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Short name: 

Elev_tran

Methods: 

In 1993, three sites were chosen on generally flat benches of the glaciated slope near South Side Lake Hoare in Taylor Valley: A at 83 m above sea level, B at 121 m above sea level, and C at 188 m above sea level. In 2012 two further Valleys were added to this experiment: Garwood and Miers. As with Taylor Valley, three sites were chosen in each on generally flat benches of the glaciated slope: Garwood A at 369 m above sea level, B at 377 m above sea level, and C at 392 m above sea level. Miers A at 179 m above sea level, B at 220 m above sea level, and C at 290 m above sea level.

A 20X 20 m grid was placed at each elevation, and soil samples were taken at the four corners of the grid, at the middle point of each side, and at the center of the square. A smaller 2 X 2 m grid was placed at the northwest corner of the larger grid, and samples were collected with the same scheme, though no second samples were taken from the overlapping corner.

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 into a counting dish and examined under a microscope at x 10 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 pH, an aqueous soil solution was made. DI-H2O was added to soil in a 1:2 soil:water ratio 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 h (all years up to 2002-03) or 10 min (all years 2004-05 and later), the samples were stirred again and a reading was taken with a pH meter. For measurements of electrical conductivity, DI-H2O was added to soil in a 1:5 soil:water ratio. The samples were stirred until thoroughly mixed (about 5-10 sec). After sitting to equilibrate for 2 h (all years up to 2002-03) or 10 min (all years 2004-05 and later), the samples were stirred again and a reading was taken with a conductivity meter. For 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/90percent 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 -4°C constant temperature room, in the dark, and left for 12-18 hours. Determination of chlorophyll a concentration 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/90percent acetone solution. 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, into 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/90percent acetone solution before proceeding with the next sample. For mineral N content, a 20 g subsample was extracted in 50 ml 2M KCl for 1 h and filtered through Whatman #42 filter paper. Extracts were frozen prior to analysis for NH4-N and NO2+NO3-N on a Lachat Quikchem. For total C and N, a subsample of soil was hand-ground using a sapphire mortar and pestle, from which a subsample was run on a Carlo Erba NA 1500 N Elemental Analyzer (Carlo Erba Instruments, Milan, Italy). For organic C, 1 mg of ground soil was acidified with 1 ml 6 N HCl and dried at 95°C for 48 h. A subsample was run on a Carlo Erba, and the value was corrected for the change in weight associated with acidification. Microbial C and N were measured using the chloroform fumigation extraction technique with a 1:2.5 ratio of soil and 0.5 M K2SO4. Approximately 20 g of soil from each sample was extracted in 50 ml of 0.5 M K2SO4. Extracts were shaken at 240 rpm for 45 minutes, then centrifuged at 15000 rpm for 15 min, and the supernatant brought to pH~2 with 0.5 ml 6N HCl. A duplicate 20-g subsample was placed in a vacuum desiccator and fumigated with ethanol-free chloroform for 120 h. After fumigation, soils were extracted as described above. All extracts were frozen prior to analysis on a Shimadzu TOC analyzer for DOC and DIN.

Season Notes

2002-2003

File log:

This file was created on 15 Jan 2003 by Steve Blecker. Extraction weight entered at this time [Steve Blecker 15 Jan 03].  Nema data entered on 21 Jan 03 by Steve Blecker [Steve Blecker 21 Jan 03]. Calculation done by Jeb Barrett 22 Jan 03. Raw data checked and corrected [Emma Broos 4 March 03].

Numbers per kg dry soil changed by M L Haddix using formula 1000*(#individuals/(extraction mass*(mass of dry soil/mass of soil used for moisture calc))) 7/22/13

Soil Moisture calculated as the (g of water/ g dry soil) *100 by M L Haddix 9/06/13

File was abbreviated for website only counts in #/kg dry soil was left along with log, 7/22/13 MLHaddix 2004-2005

File log:  Soil data was entered, and log was created, on 14 Jan 2005 by Holley Zadeh. Data verified by Holley Zadeh on 23 Jan 05.

Comments:

These data are for soils collected by Diana Wall, John Chaston, and Holley Zadeh. Emma Broos and Claire Ojima kept track of sample locations, logged them in their field books, and made sure sample bags were correct. See map of sampling locations in drawing box below.

To note: A1 was not mixed in the field, and we forgot to mix it before sampling. Also, C3 was counted, but after counting was dropped, so we do not have a sample to preserve.

Samples were extracted at the Crary lab on 12 Jan 2005 as follows:

*Holley Zadeh weighed soil under the laminar flow hood and recorded weights

*Diana Wall sieved soil at the sink

*Byron Adams spun samples in the centrifuge

*John Chaston and Emma Broos counted specimens at the microscope. They were counted on the 13th and 14th of January 2005.

Numbers per kg dry soil changed by M L Haddix using formula 1000*(#individuals/(extraction mass*(mass of dry soil/mass of soil used for moisture calc))) 7/22/13

Soil Moisture calculated as the (g of water/ g dry soil) *100 by M L Haddix 9/06/13

Related Files: ET_worms.xls; DNAExtr0405.xls

File was abbreviated for website only counts in #/kg dry soil was left along with log, 7/22/13 MLHaddix 2006-2007

Comments: Soil samples for faunal extraction and chlorophyll a were collected by Ed Ayres, Breana Simmons, Dorota Porazinska on 18 Jan 2007.  Local scale sampling of spatial variation was conducted at the '6' location of each ET plot.  Soil samples were collected ~10 cm from the nail at 1 o'clock (if 12 o'clock is upslope).  Take extra nails for small scale sampling next time (at least 9). Soil was extracted on 20 Jan 2007. Nematodes preserved 23 Jan 2007.  Worms counted by Dorota Porazinska Data entered on 22 Jan 2007 by Ed Ayres.  Data was proofed by Dorota Porazinska.

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

Numbers per kg dry soil changed by M L Haddix using formula 1000*(#individuals/(extraction mass*(mass of dry soil/mass of soil used for moisture calc))) 7/03/13

Soil Moisture calculated as the (g of water/ g dry soil) *100 by M L Haddix 9/06/13

Related Files: ET_labels.doc, ET_soils.xls, ET_COC.xls

2008-2009

LOG: This file created on 12/29/08 by Karen "rainbow Sprinkles" Seaver.

COMMENTS:

Samples were collected from the LTER core study, the Elevational Transect by Breana Simmons, Karen Seaver? and ??.

Note: A sulfur smell was noted at the C elevation?

Nematodes were extracted by     on

Data entered by Karen Seaver and Uffe Nielsen on 12/28/08 

Data checked by Karen Seaver and her electronic boyfriend Alex on 12/29/08.

RELATED FILES:

Bre - microbial biomass if we get it, ?

ET_LABEL.XLS

ET_SOILS.xls

LTM_ET_COC.xls

Dryvalleydisturbance_08_09.xls (In Reports Folder)  GPS coordinates

Numbers per kg dry soil changed by M L Haddix using formula 1000*(#individuals/(extraction mass*(mass of dry soil/mass of soil used for moisture calc))) 7/11/13

Soil Moisture calculated as the (g of water/ g dry soil) *100 by M L Haddix 9/06/13

File was abbreviated for website only counts in #/kg dry soil was left along with log, 5/01/14 MLHaddix Inigo San Gil revised data, updated database records and metadata

2011-2012

Garwood

LOG: This file created on 1/13/12 by Zachary Sylvain.

Data entered by Zachary Sylvain.

Data checked by Zachary Sylvain.

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

Numbers per kg dry soil adjusted by Martijn L Vandegehuchte using formula 1000*(#individuals/(extraction mass*(mass of dry soil/mass of soil used for moisture calc)))

Soil Moisture calculated as the (g of water/ g dry soil) *100 by M L Haddix 11/26/13

ET

LOG: This file created on 1/13/12 by Zachary Sylvain.

Data entered by Jeremy Whiting.

Data checked by Jeremy Whiting.

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

The majority of the worms were counted on Jan 6. Some worms were counted on the 5th and 7th as well.

Numbers per kg dry soil adjusted by Martijn L Vandegehuchte using formula 1000*(#individuals/(extraction mass*(mass of dry soil/mass of soil used for moisture calc)))

Soil Moisture calculated as the (g of water/ g dry soil) *100 by M L Haddix 9/06/13

Miers

LOG: This file created on 1/11/12 by Zachary Sylvain.

Data entered by Jeremy Whiting.

Data checked by Jeremy Whiting.

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

C Transect

     Polygon C3: 26m x 16m

     Spike: S78.08898, E163.77657

     Polygon C2: 14.5m x 12.3m

     Spike: S78.08907, E163.77563

     Polygon C1: 15.5m x 15.5m

     Spike: S78.08899, E163.77509

B Transect

     Polygon B1 Spike: S78.09200, E163.77771

     Polygon B2 Spike: S78.09188, E163.77815

     Polygon B3 Spike: S78.09203, E163.77843

A Transect

     Polygon A1: 12.6m x 14.2m

     Spike: S78.09403, E163.78671

     Polygon A2: 12.7m x 12m

     Spike: S78.09420, E163.78677

     Polygon A3: 9.7m x 9.3m

     Spike: S78.09421, E163.78763

MC3 sampled in a line downslope toward stream

MC2 sampled down toward lake

MC2 sampled upslope

MB1 sampled toward northern edge of lake

MB2 sampled downslope toward MB3

MB3 sampled toward northern edge of lake

MA1 sampled downslope

MA2 sampled downslope

MA3 sampled upslope

Numbers per kg dry soil adjusted by Martijn Vandegehuchte using formula 1000*(#individuals/(extraction mass*(mass of dry soil/mass of soil used for moisture calc)))

Soil Moisture calculated as the (g of water/ g dry soil) *100 by M L Haddix 11/26/13

2012-2013

ET

LOG: This file created on 20 January 2013 by Ashley Shaw.

Data entered by Ashley Shaw.

Data checked by Sabrina Saurey.

Calculations by Martijn Vandegehuchte using the formula:

1000*(#individuals/(extraction mass*(mass of dry soil/mass of soil used for moisture calc)))

Soil Moisture calculated as the (g of water/ g dry soil) *100 by M L Haddix 9/06/13

Garwood

LOG: This file created on Jan 18 by Sabrina Saurey.

Data entered by Sabrina Saurey.

Data checked by Ashley Shaw.

Calculations by Martijn Vandegehuchte using the formula:

1000*(#individuals/(extraction mass*(mass of dry soil/mass of soil used for moisture calc)))

Soil Moisture calculated as the (g of water/ g dry soil) *100 by M L Haddix 11/13/13

Miers

LOG: This file created on Jan 19 by Sabrina Saurey.

Data entered by Sabrina Saurey.

Data checked by Ashley Shaw on 20 January 2013

Calculations by Martijn Vandegehuchte using the formula:

1000*(#individuals/(extraction mass*(mass of dry soil/mass of soil used for moisture calc)))

Soil Moisture calculated as the (g of water/ g dry soil) *100 by M L Haddix 11/13/13

Data sources: 

SOILS_ELEVATION_TRN

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. 

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 nermatode  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..."
      In the data,
 
      ND = no data; sample not taken
      BD = below detection limit
      
     

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