Name: soil lysimeter excavation for coupled hydrological, geochemical, and microbiological investigations
Uploaded: 2016-09-11T15:00:00
Description: Watch this Scientific Journal Video about Soil Lysimeter Excavation for Coupled Hydrological, Geochemical, and Microbiological Investigations at JoVE.com

We thank Ty P.A. Ferr&#233;, Till Volkman, Edwin Donker, Mauricio Vera for helping us during the excavation, and Triffon J. Tatarin, Manpreet Sahnan and Edward Hunt for their help in sample analysis. This work was carried out at Biosphere 2, University of Arizona and funded by National Science Foundation grant EAR_1344552 and Honors Research Program of Biosphere 2.

1. Devise a Sampling Matrix to Ensure Systematic and Comprehensive Sampling of Lysimeter
<ol>
	<li>Divide lysimeter into voxels of fixed length, width, and depth.
	<ol>
		<li>Use a Euclidean space coordinate system and divide the total distance along each direction (X, Y and Z) into an adequate number of equally spaced intervals. Consider discarding the soil near the walls of the lysimeter to avoid boundary effects. 
		NOTE: A buffer of 5 cm along the four walls is adopted in this experiment to avoid boundary effe...

<ol>
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P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Landscape+evolution+(A+Review).">Landscape evolution (A Review).</a> Proc. Natl. Acad. Sci. U. S. A. 79, 4477-4486 (1982).</li><li>Temme, A., Montgomery, D. R., Bierman, P. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Predicting+the+effect+of+changing+climate+on+landscapes+with+computer+based+landscape+evolution+models.">Predicting the effect of changing climate on landscapes with computer based landscape evolution models.</a> Key Concepts in Geomorphology. , (2013).</li><li>Troch, P. 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M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Contributions+of+atmospheric+CO+and+hydrogen+uptake+to+microbial+dynamics+on+recent+Hawaiian+volcanic+deposits.">Contributions of atmospheric CO and hydrogen uptake to microbial dynamics on recent Hawaiian volcanic deposits.</a> Appl. Environ. Microbiol. 69 (7), 4067-4075 (2003).</li><li>Meyer, W. S., Barrs, H. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Roots+in+irrigated+clay+soils:+Measurement+techniques+and+responses+to+rootzone+conditions.">Roots in irrigated clay soils: Measurement techniques and responses to rootzone conditions.</a> Irrig. Sci. 12 (3), 125-134 (1991).</li><li>Graham, C. B., Woods, R. A., McDonnell, J. 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Landscape evolution is the cumulative effect of hydrological, geochemical, and biological processes12. These processes control flow and transport of water and elements, and biogeochemical reactions in evolving landscapes. However, capturing the interactions simultaneously requires precisely coordinated experimental design and sampling. Additionally, studying incipient landscape evolution is difficult in natural systems, with limited capabilities to identify &#34;time zero&#34; conditions. Literature reports on...

Soil and landscape dynamics are shaped by the complex interaction of physical, chemical, and biological processes1. Water flow, geochemical weathering, and biological activity shape the overall development of the landscape into a stable ecosystem2,3. While surface changes are the most conspicuous features of landscape4, understanding cumulative effects of hydrological, geochemical, and microbiological processes in the subsurface region is crucial to understanding the underlying forces that shape a landscape2. Future climate perturbation scenarios further confound the predictability and pattern of landscape evolution5. It thus becomes a challenge to link small-scale processes to their large-scale manifestation on the landscape-scale6. Traditional short-run laboratory experiments or experiments in natural landscapes with unknown initial conditions and time-variable forcing fall short in capturing the intrinsic heterogeneity of landscape evolution. Also, due to strong nonlinear coupling, it is difficult to predict biogeochemical changes from hydrological modeling in heterogeneous systems7. Here, we describe a novel experimental method to excavate a fully controlled and monitored soil hillslope with known initial conditions. Our excavation and sampling procedure is aimed at capturing the developing heterogeneity of the hillslope along its length and depth, with the goal of providing a comprehensive dataset to investigate hydro-bio-geochemical interactions and their impact on soil formation processes.
Hydrologic systems found in nature are far from being static in time, with changes in hydrological responses taking place over a wide range of spatial and temporal scales3. The spatial structure of flow pathways along landscapes determines the rate, extent and distribution of geochemical reactions and biological colonization that drive weathering, the transport and precipitation of solutes and sediments, and the further development of soil structure. Thus, incorporating knowledge from pedology, geophysics, and ecology into theories and experimental designs to assess hydrologic processes and improve hydrologic predictions has been suggested8,9. Landscape evolution is also impacted by subsurface biogeochemical processes in conjunction with water dynamics, elemental migration during soil development, and by mineralogical transformations brought about by reaction of mineral surfaces with air, water, and microorganisms10. Consequently, it is important to study development of geochemical hotspots within an evolving landscape. Additionally, it is critical to relate geochemical weathering patterns to hydrological process and microbiological signatures during incipient soil formation in order to understand the dynamics of complex landscape development. The specific processes of soil genesis are governed by the combined influence of climate, biological inputs, relief and time on a specific parent material. This experiment was designed to address heterogeneities in the weathering of parent material governed by hydrological and geochemical variations associated with relief (including slope and depth) and the associated variability in microbial activity that is driven by environmental gradients (i.e., redox potential) under conditions where parent material, climate and time are held constant. With respect to microbial activity, soil microorganisms are critical components and have a profound impact on landscape stability11. They play a crucial role in soil structure, biogeochemical cycling of nutrients, and plant growth. Therefore, it is necessary to understand the significance of these organisms as drivers of weathering, soil genesis, and landscape formation processes, while simultaneously identifying the reciprocal effects of hydrological flow-paths and geochemical weathering on microbial community structure and diversity. This can be achieved by studying spatial heterogeneity of microbial community diversity over an evolving landscape whose hydrological and geochemical characteristics are also being studied in parallel.
Here, we present an excavation procedure of a soil lysimeter, operationally named miniLEO, designed to mimic the large-scale zero-order basin models of the Landscape Evolution Observatory (LEO) housed at Biosphere 2 (University of Arizona). The miniLEO was developed to identify small-scale landscape evolution patterns arising from cumulative heterogeneous hydro-bio-geochemical processes. It is a lysimeter 2-m in length, 0.5-m in width, and 1-m in height, and slope of 10&#176; (Figure 1). Additionally, the walls of the lysimeter are insulated and coated with non-biodegradable two-part epoxy primer and an aggregate filled aliphatic urethane coat to avoid potential contamination or leaching of metals from the lysimeter frame into the soil. The lysimeter was filled with crushed basalt rock that was extracted from a deposit of late Pleistocene tephra associated with Merriam Crater in northern Arizona. The loaded basalt material was identical to the material used in the much larger LEO experiments. The mineral composition, particle size distribution, and hydraulic properties are described by Pangle et al.12. The downslope seepage face was lined with a perforated plastic screen (0.002-m diameter pores, 14% porosity). The system is fitted with sensors such as water content and temperature sensors, two types of water potential sensors, soil-water samplers, hydraulic weight balance, electrical conductivity probes, and pressure transducers to determine water table height. The lysimeter was irrigated for 18 months prior to the excavation.
The excavation was meticulous in its approach and was aimed at answering two broad questions: (1) what hydrological, geochemical, and microbial signatures can be observed across the length and depth of the slope with respect to simulated rainfall conditions and (2) whether relationships and feedbacks between hydro-bio-geochemical processes occurring on the hillslope can be deduced from the individual signatures. Alongside the experimental setup and excavation procedure, we present representative data and suggestions on how to apply similar excavation protocols for researchers interested in studying coupled earth-system dynamics and/or soil development processes.

<table border="0" cellpadding="0" cellspacing="0" width="1632">
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Measuring tape</td>
			<td style="width:71px;">Any</td>
			<td style="width:153px;">Any</td>
			<td style="width:1192px;">Preventing cross-contamination of samples&#160; is crucial. Therefore, it is helpful to have multiple putty knives to isolate voxel boundary.</td>
		</tr>
		<tr height="60">
			<td height="60" style="height:60px;width:216px;">Brilliant Blue dye</td>
			<td style="width:71px;">Waldeck GmBH &#38;Co&#160;</td>
			<td style="width:153px;">B0770</td>
			<td>Rulers can be used to draw grids. The sampling strategy can be modified based on individual experiments.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Soil Corer</td>
			<td style="width:71px;">AMS</td>
			<td style="width:153px;">56975</td>
			<td>Any commercially manufactured Brilliant Blue dye can be used.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">75% Ethanol</td>
			<td style="width:71px;">Any</td>
			<td style="width:153px;">Any</td>
			<td>A Nikon D90 camera and 50mm lens were used for photography. Any high resolution camera and lens can be used for this purpose.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Spray Bottle</td>
			<td style="width:71px;">Any&#160;</td>
			<td style="width:153px;">Any</td>
			<td>Use of dye and color card is subjective to individual experiments and/or research questions.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Spatula</td>
			<td style="width:71px;">Any&#160;</td>
			<td style="width:153px;">Any</td>
			<td>Gardening gloves may be used if handling of corer becomes tedious.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Gloves</td>
			<td style="width:71px;">Any&#160;</td>
			<td style="width:153px;">Any</td>
			<td>Ensure microbiology samples are kept in ice during sampling and frozen as soon as possible.</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;width:216px;">KimWipes</td>
			<td style="width:71px;">KimTech Science</td>
			<td style="width:153px;">Any</td>
			<td>Water can be used to wash soil corer, prior to sanitizing with ethanol.</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;width:216px;">Sterile Sample bags</td>
			<td style="width:71px;">Fisher Scientific&#160;</td>
			<td style="width:153px;">Whirl-Pak 4 OZ. 24 OZ</td>
			<td>Keep buckets and dustpans handy to facilitate removal of waste soil.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Color Card</td>
			<td style="width:71px;">Any</td>
			<td style="width:153px;">Any</td>
			<td>The original design of miniLEO has various sensors embedded in the lysimeter. Such sensors may or may not be necessary based on the scope of individual experimental design.</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;width:216px;">X-ray Fluoresce Spectrophotmeter</td>
			<td style="width:71px;">XRF, OLYMPUS</td>
			<td style="width:153px;">DS-2000 Delta XRF</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:216px;">Polypropylene cores</td>
			<td style="width:71px;">Any</td>
			<td style="width:153px;">Any</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:216px;">Metal cores&#160;</td>
			<td style="width:71px;">Any&#160;</td>
			<td style="width:153px;">Any</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:216px;">Caps for polypropylene cores</td>
			<td style="width:71px;">Any</td>
			<td style="width:153px;">Any</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:216px;">Hammer</td>
			<td style="width:71px;">Any&#160;</td>
			<td style="width:153px;">Any</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:216px;">Plastic putty knives</td>
			<td style="width:71px;">Any&#160;</td>
			<td style="width:153px;">Any</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Face masks</td>
			<td style="width:71px;">Any&#160;</td>
			<td style="width:153px;">Any</td>
			<td></td>
		</tr>
	</tbody>
</table>

soil lysimeter excavation for coupled hydrological, geochemical, and microbiological investigations

Studying co-evolution of hydrological and biogeochemical processes in the subsurface of natural landscapes can enhance the understanding of coupled Earth-system processes. Such knowledge is imperative in improving predictions of hydro-biogeochemical cycles, especially under climate change scenarios. We present an experimental method, designed to capture sub-surface heterogeneity of an initially homogeneous soil system. This method is based on destructive sampling of a soil lysimeter designed to simulate a small-scale hillslope. A weighing lysimeter of one cubic meter capacity was divided into sections (voxels) and was excavated layer-by-layer, with sub samples being collected from each voxel. The excavation procedure was aimed at detecting the incipient heterogeneity of the system by focusing on the spatial assessment of hydrological, geochemical, and microbiological properties of the soil. Representative results of a few physicochemical variables tested show the development of heterogeneity. Additional work to test interactions between hydrological, geochemical, and microbiological signatures is planned to interpret the observed patterns. Our study also demonstrates the possibility of carrying out similar excavations in order to observe and quantify different aspects of soil-development under varying environmental conditions and scale.

The dimensions of voxels ensured collection of samples for hydrological, geochemical, and microbiological measurements. The excavation procedure yielded 324 cores for microbiological analysis, 972 pXRF data points, 324 geochemical sample bags, 180 Ksat samples (128 vertical and 52 horizontal), and 311 bulk density samples. Preferential flow of Brilliant Blue dye was also observed to a depth of 30 cm below the surface. A representative set of 81 samples from a single vertical slice of the ...

Watch this Scientific Journal Video about Soil Lysimeter Excavation for Coupled Hydrological, Geochemical, and Microbiological Investigations at JoVE.com

Soil Lysimeter Excavation for Coupled Hydrological, Geochemical, and Microbiological Investigations

This study presents an excavation method for investigating subsurface hydrological, geochemical, and microbiological heterogeneity of a soil lysimeter. The lysimeter simulates an artificial hillslope which was initially under homogeneous condition and had been subjected to approximately 5,000 mm of water over eight cycles of irrigation in an 18-month period.

Studying co-evolution of hydrological and biogeochemical processes in the subsurface of natural landscapes can enhance the understanding of coupled ...

Studying Coevolution of Hydrological and Biogeochemical processes in the subsurface of natural landscapes can enhance the understanding of coupled earth system processes. The overall goal of this method is to excavate a soil Lysimeter to understand subsurface hydrological, geochemical and microbiological heterogeniety. This method can help answer key questions in the field of coupled earth system processes.Such as, how do hydrological and biogeochemical processes coevolve in the subsurface of natural ecosystems. The main advantage of this tactic is that it can capture the spacial heterogeneity of hydrological, geochemical and microbiological properties of soil in your sampling scale. Divide the Lysimeter into Voxels of fixed length, width and depth using Euclidean space coordinate system.Divide the total distance along each direction into an adequate number of equally spaced intervals. Assign each sample a unique XYZ location and identify it as a Voxel. In this excavation, X denotes the location along the width of the slope, Y denotes the location along the length of the slope and Z denotes the location along the depth of the slope.The size of the intervals within each dimension determines the width, length and depth of the Voxels. Shown here is the division of the Lysimeter after determining spacing intervals, along with the chosen origin for the XYZ system. The division in the current excavation scheme has nine intervals along both the Y and Z directions, and four intervals along the X direction producing a total of 324 Voxels.For demarcation of Voxels, attach measuring tape along the length of the slope to provide an insight to your reference system for guidance during demarcation of Voxels. Mark the dimension of each soil Voxel with the help of the measuring tape. Draw grid lines for each layer using aluminum blade shields and plastic putty knives.Discard the boundary materials five centimeters from each wall to prevent boundary effects. Collect microbiology samples aseptically from each Voxel prior to hydrological and geochemical analyses, to prevent cross-contamination of samples. Ensure that new gloves are worn by all members carrying out the excavation to reduce contamination from human skin.Use a soil corer of one centimeter diameter and 20 centimeters height, and a thin spatula for microbiological sample collection. Clean the corer and the spatula with distilled water. Wipe them dry with clean wipes, and rinse them with 75%ethanol using a spray bottle.Before allowing the corer and spatula to air dry. Core to a depth of 10 centimeters at each Voxel location. Then, use the spatula to empty the soil sample into pre-sterilized plastic bags that have been opened just prior to depositing the sample.Note the collection time of each sample. Homogenize the sample pouches by hand. Store the sample bag in an ice cooler during sampling, and transfer it as soon as possible to the minus 80 degrees Celsius freezer.Place the portable X-ray Fluorescence Spectrometer on the holder and point the beam window directly to the factory metal bead. Select cal and wait for 30 seconds to allow the calibration to be completed. Clean the beam window before taking every measurement.Measure the surface of each Voxel in triplicate at three different locations. Place the instrument on the soil surface and wait for 90 seconds to allow the measurement to be completed. Clean Metallic cores for bulk densities of desired Voxels.Clean polycarbonate cores for hydraulic conductivity measurements or KSAT of desired Voxels. Vertically insert metal cores and polycarbonate cores into the desired Voxels. Take care not to damage the sensors or sensor wires by gently hammering the cores into the soil using a flat surface, like a block of wood, between the core and the hammer to minimize disturbance to the soil.Additionally, once the core is halfway into the soil, place a second core on top of the first core. Place the wooden block on top of the second core and gently hammer the block until the first core is embedded in the soil with the core rims still visible. Take care to ensure that the Voxel being sampled is isolated from boundaries and neighboring Voxels prior to geochemical sample collection.To achieve this, use plastic putty knives followed by hand held trowels to collect soil samples around metal or polypropylene cores into labeled geochemical sample bags, until the cores can be easily removed. Remove the polypropylene cores and cover both sides with red plastic caps. Label the vertical polypropylene core as V and the horizontal polypropylene core as H, followed by the sample ID.Remove the metallic core, brush off excess material from both ends, and transfer the sample from the core to a labeled bulk density sample bag.Weigh each sample bag with sample and record the total weight. Collect the remaining material from the Voxel into the geochemical sample bag, leaving behind a couple of centimeters of soil at all four sides to prevent cross-contamination with the next Voxel. Repeat these steps for each Voxel.Insert the cores for horizontal KSAT as the lateral face of the Voxel opens up with sequential excavation. Use the wooden block and second core, as before, to minimize compaction, and collect the soil core. Shown here is a three dimensional schematic view of soil Lysimeter Voxels along the length, depth and width of the slope.A schematic view of one Voxel along the XYZ plane of the Lysimeter is shown here with examples of the types of collected cores. These cores can be seen in a representative Voxel showing the microbiological core, the horizontal and vertical hydraulic conductivity cores, a bulk density core and the remaining sample from the Voxel being used for geochemical analysis. Shown here is a two dimensional isopleth heat map of representative Bulk Density samples.Bulk density values were obtained by transferring samples to aluminum weighing dishes and oven drying them. Cells left blank represent Voxels where sample collection was not possible due to the presence of sensors and the lack of space to accommodate bulk density cores. A two dimensional DNA concentration heat map is shown here.For microbiological cores, two grams of soil was sub-sampled to extract the microbial DNA representative of each Voxel. After watching this video, you should have a good understanding on how to excavate a soil Lysimeter for the intensive hydrological, microbiological, and geochemical sample collection. This procedure is expected to produce significant insight on the studies of soil development and landscape evolution.While attempting this procedure it's important to remember that estimation of Voxel size and scale of quarry will determine the time and effort needed for sample collection. Visual demonstration of this method is critical, because microbiological, hydrological and geochemical sampling has to be done in a systematic manner, without destroying or contaminating samples. We believe that an intensive sampling scheme allows us to capture the scale effects on hydro, bio, geochemical properties in a very fine and detailed way.The implication of this technique, it stands toward the possibilities of carrying out similar excavation, in order to observe and quantify different aspects of soil development and their varying environmental conditions and scale. Don't forget that microbiological samples have to be excavated with extreme caution. Follow sterile procedure, including the use of gloves and mask, to prevent contamination.The techniques outlined are simple, repeatable and flexible to accommodate multiple research questions. Thereby, allowing implementation of alternate experimental designs.

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