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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Design and Operation of a Continuous 13C and 15N Labeling Chamber for Uniform or Differential, Metabolic and Structural, Plant Isotope Labeling

Tracing rare stable isotopes from plant material through the ecosystem provides the most sensitive information about ecosystem processes; from CO2 fluxes and soil organic matter formation to small-scale stable-isotope biomarker probing. Coupling multiple stable isotopes such as 13C with 15N, 18O or&#160;2H has the potential to reveal even more information about complex stoichiometric relationships during biogeochemical transformations. Isotope labeled plant material has been used in various studies of litter decomposition and soil organic matter formation1-4. From these and other studies, however, it has become apparent that structural components of plant material behave differently than metabolic components (i.e. leachable low molecular weight compounds) in terms of microbial utilization and long-term carbon storage5-7. The ability to study structural and metabolic components separately provides a powerful new tool for advancing the forefront of ecosystem biogeochemical studies. Here we describe a method for producing 13C and 15N labeled plant material that is either uniformly labeled throughout the plant or differentially labeled in structural and metabolic plant components.
Here, we present the construction and operation of a continuous 13C and 15N labeling chamber that can be modified to meet various research needs. Uniformly labeled plant material is produced by continuous labeling from seedling to harvest, while differential labeling is achieved by removing the growing plants from the chamber weeks prior to harvest. Representative results from growing Andropogon gerardii Kaw demonstrate the system&#39;s ability to efficiently label plant material at the targeted levels. Through this method we have produced plant material with a 4.4 atom%13C and 6.7 atom%15N uniform plant label, or material that is differentially labeled by up to 1.29 atom%13C and 0.56 atom%15N in its metabolic and structural components (hot water extractable and hot water residual components, respectively). Challenges lie in maintaining proper temperature, humidity, CO2 concentration,&#160;and light levels in an airtight 13C-CO2 atmosphere for successful plant production. This chamber description represents a useful research tool to effectively produce uniformly or differentially multi-isotope labeled plant material for use in experiments on ecosystem biogeochemical cycling.

Design and Operation of a Continuous 13C and 15N Labeling Chamber for Uniform or Differential, Metabolic and Structural, Plant Isotope Labeling

This method explains how to build and operate a continuous 13C and 15N isotope labeling chamber for uniform or differential plant tissue labeling. Representative results from metabolic and structural labeling of Andropogon gerardii are discussed.

Tracing rare stable isotopes from plant material through the ecosystem provides the most sensitive information about ecosystem processes; from CO2 fluxes ...

Integrated Field Lysimetry and Porewater Sampling for Evaluation of Chemical Mobility in Soils and Established Vegetation

Potentially toxic chemicals are routinely applied to land to meet growing demands on waste management and food production, but the fate of these chemicals is often not well understood. Here we demonstrate an integrated field lysimetry and porewater sampling method for evaluating the mobility of chemicals applied to soils and established vegetation. Lysimeters, open columns made of metal or plastic, are driven into bareground or vegetated soils. Porewater samplers, which are commercially available and use vacuum to collect percolating soil water, are installed at predetermined depths within the lysimeters. At prearranged times following chemical application to experimental plots, porewater is collected, and lysimeters, containing soil and vegetation, are exhumed. By analyzing chemical concentrations in the lysimeter soil, vegetation, and porewater, downward leaching rates, soil retention capacities, and plant uptake for the chemical of interest may be quantified. Because field lysimetry and porewater sampling are conducted under natural environmental conditions and with minimal soil disturbance, derived results project real-case scenarios and provide valuable information for chemical management. As chemicals are increasingly applied to land worldwide, the described techniques may be utilized to determine whether applied chemicals pose adverse effects to human health or the environment.

Field lysimetry and porewater sampling allow researchers to evaluate the fate of chemicals applied to soils and established vegetation. The goal of this protocol is to demonstrate how to install required instrumentation and collect samples for chemical analysis during integrated field lysimetry and porewater sampling experiments.

Potentially toxic chemicals are routinely applied to land to meet growing demands on waste management and food production, but the fate of these chemicals ...

A Protocol for Collecting and Constructing Soil Core Lysimeters

Leaching of nutrients from land applied fertilizers and manure used in agriculture can lead to accelerated eutrophication of surface water. Because the landscape has complex and varied soil morphology, an accompanying disparity in flow paths for leachate through the soil macropore and matrix structure is present. The rate of flow through these paths is further affected by antecedent soil moisture. Lysimeters are used to quantify flow rate, volume of water and concentration of nutrients leaching downward through soils. While many lysimeter designs exist, accurately determining the volume of water and mass balance of nutrients is best accomplished with bounded lysimeters that leave the natural soil structure intact. 
Here we present a detailed method for the extraction and construction of soil core lysimeters equipped with soil moisture sensors at 5 cm and 25 cm depths. Lysimeters from four different Coastal Plain soils (Bojac, Evesboro, Quindocqua and Sassafras) were collected on the Delmarva Peninsula and moved to an indoor climate controlled facility. Soils were irrigated once weekly with the equivalent of 2 cm of rainfall to draw down soil nitrate-N concentrations. At the end of the draw down period, poultry litter was applied (162 kg TN ha-1) and leaching was resumed for an additional five weeks. Total recovery of applied irrigation water varied from 71% to 85%. Nitrate-N concentration varied over the course of the study from an average of 27.1 mg L-1 before litter application to 40.3 mg L-1 following litter application. While greatest flux of nutrients was measured in soils dominated by coarse sand (Sassafras) the greatest immediate flux occurred from the finest textured soil with pronounced macropore development (Quindocqua).

A detailed method for extraction and assembly of intact soil core lysimeters and their use for study of leachate and associated loss of nutrients from surface applied poultry litter is demonstrated.

Leaching of nutrients from land applied fertilizers and manure used in agriculture can lead to accelerated eutrophication of surface water. Because the ...

A Gusseted Thermogradient Table to Control Soil Temperatures for Evaluating Plant Growth and Monitoring Soil Processes

Thermogradient tables were first developed in the 1950s primarily to test seed germination over a range of temperatures simultaneously without using a series of incubators. A temperature gradient is passively established across the surface of the table between the heated and cooled ends and is lost quickly at distances above the surface. Since temperature is only controlled on the table surface, experiments are restricted to shallow containers, such as Petri dishes, placed on the table. Welding continuous aluminum vertical strips or gussets perpendicular to the surface of a table enables temperature control in depth via convective heat flow. Soil in the channels between gussets was maintained across a gradient of temperatures allowing a greater diversity of experimentation. The gusseted design was evaluated by germinating oat, lettuce, tomato, and melon seeds. Soil temperatures were monitored using individual, battery-powered dataloggers positioned across the table. LED lights installed in the lids or along the sides of the gradient table create a controlled temperature chamber where seedlings can be grown over a range of temperatures. The gusseted design enabled accurate determination of optimum temperatures for fastest germination rate and the highest percentage germination for each species. Germination information from gradient table experiments can help predict seed germination and seedling growth under the adverse soil conditions often encountered during field crop production. Temperature effects on seed germination, seedling growth, and soil ecology can be tested under controlled conditions in a laboratory using a gusseted thermogradient table.

Traditional thermogradient tables create a range of temperatures across the surface. Welding gussets perpendicular to the surface of a thermogradient table will control temperature in depth increasing possible research applications.

Thermogradient tables were first developed in the 1950s primarily to test seed germination over a range of temperatures simultaneously without using a ...

Protocols for Quantifying Transferable Pesticide Residues in Turfgrass Systems

Plant canopies in established turfgrass systems can intercept an appreciable amount of sprayed pesticides, which can be transferred through various routes onto humans. For this reason, transferable pesticide residue experiments are required for registration and re-registration by the United States Environmental Protection Agency (USEPA). Although such experiments are required, limited specificity is required pertaining to experimental approach. Experimental approaches used to assess pesticide transfer to humans including hand wiping with cotton gloves, modified California roller (moving a roller of known mass over cotton cloth) and soccer ball roll (ball wrapped with sorbent strip) over three treated turfgrass species (creeping bentgrass, hybrid bermudagrass and tall fescue maintained at 0.4, 5 and 9 cm, respectively) are presented. The modified California roller is the most extensively utilized approach to date, and is best suited for use at low mowing heights due to its reproducibility and large sampling area. The soccer ball roll is a less aggressive transfer approach; however, it mimics a very common occurrence in the most popular international sport, and has many implications for nondietary pesticide exposure from hand-to-mouth contact. Additionally, this approach may be adjusted for other athletic activities with limited modification. Hand wiping is the best approach to transfer pesticides at higher mowing heights, as roller-based approaches can lay blades over; however, it is more subjective due to more variable sampling pressure. Utility of these methods across turfgrass species is presented, and additional considerations to conduct transferable pesticide residue research in turfgrass systems are discussed.

Transferable pesticide residue experiments in turfgrass systems are integral components of human risk exposure assessments. Experimental approaches to measure transferable residues should be adjusted to the human interaction of interest and turfgrass system dynamics. Three transferable pesticide residue protocols are presented and the suitability across three turfgrass systems is discussed.

Plant canopies in established turfgrass systems can intercept an appreciable amount of sprayed pesticides, which can be transferred through various routes ...

Nanopore DNA Sequencing for Metagenomic Soil Analysis

This article describes the steps for construction of a DNA library from soil, preparation and use of the nanopore flow cell, and analysis of the DNA sequences identified using computer software. Nanopore DNA sequencing is a flexible technique that allows for rapid microbial genome sequencing to identify bacterial and viral species, to characterize bacterial strains, and to detect genetic mutations that confer resistance to antibiotics. The advantages of nanopore sequencing (NS) for life sciences include its low complexity, reduced cost, and rapid real-time sequencing of purified genomic DNA, PCR amplicons, cDNA samples, or RNA. NS is an example of "strand sequencing" which involves sequencing DNA by guiding a single stranded DNA molecule through a nanopore that is inserted into a synthetic polymer membrane. The membrane has an electrical current applied across it, so as the individual bases pass through the nanopore the electrical current is disrupted to varying degrees by the four nucleotide bases. The identification of each nucleotide occurs by detecting the characteristic modulation of the electrical current by the different bases as they pass through the nanopore. The NS system consists of a handheld, USB powered portable device and a disposable flow cell that contains a nanopore array. The portable device plugs into a standard laptop computer that reads and records the DNA sequence using computer software.

Nanopore technology for sequencing biomolecules has wide applications in the life sciences, including identification of pathogens, food safety monitoring, genomic analysis, metagenomic environmental monitoring, and characterization of bacterial antibiotic resistance. In this article, the procedure for metagenomic soil DNA sequencing for species identification using the nanopore sequencing technology is demonstrated.

This article describes the steps for construction of a DNA library from soil, preparation and use of the nanopore flow cell, and analysis of the DNA ...

Measuring and Mapping Patterns of Soil Erosion and Deposition Related to Soil Carbonate Concentrations Under Agricultural Management

Spatial patterns of soil erosion and deposition can be inferred from differences in ground elevation mapped at appropriate time increments. Such changes in elevation are related to changes in near-surface soil carbonate (CaCO3) profiles. The objective is to describe a simple conceptual model and detailed protocol for repeatable field and laboratory measurements of these quantities. Here, accurate elevation is measured using a ground-based differential global positioning system (GPS); other data acquisition methods could be applied to the same basic method. Soil samples are collected from prescribed depth intervals and analyzed in the lab using an efficient and precise modified pressure-calcimeter method for quantitative analysis of inorganic carbon concentration. Standard statistical methods are applied to point data, and representative results show significant correlations between changes in soil surface layer CaCO3 and changes in elevation consistent with the conceptual model; CaCO3 generally decreased in depositional areas and increased in erosional areas. Maps are derived from point measurements of elevation and soil CaCO3 to aid analyses. A map of erosional and depositional patterns at the study site, a rain-fed winter wheat field cropped in alternating wheat-fallow strips, shows the interacting effects of water and wind erosion affected by management and topography. Alternative sampling methods and depth intervals are discussed and recommended for future work relating soil erosion and deposition to soil CaCO3.

Spatial patterns of soil erosion and deposition can be inferred from differences in ground elevation mapped at appropriate time increments. Such changes in elevation are related to changes in near-surface soil carbonates. Repeatable methods for field and laboratory measurements of these quantities and data analysis methods are described here.

Spatial patterns of soil erosion and deposition can be inferred from differences in ground elevation mapped at appropriate time increments. Such changes ...

Wastewater Irrigation Impacts on Soil Hydraulic Conductivity: Coupled Field Sampling and Laboratory Determination of Saturated Hydraulic Conductivity

Since the early 1960s, an alternative wastewater discharge practice at The Pennsylvania State University has been researched and its impacts monitored. Rather than discharging treated wastewater to a stream, and thereby directly impacting the stream quality, the effluent is applied to forested and cropped land managed by the University. Concerns related to reductions in soil hydraulic conductivity occur when considering wastewater reuse. The methodology described in this manuscript, matching soil sample size with the size of the laboratory-based hydraulic conductivity measurement apparatus, provides the benefits of a relatively rapid collection of samples with the benefits of controlled laboratory boundary conditions. The results suggest that there may have been some impact of wastewater reuse on the soil&#39;s ability to transmit water at deeper depths in the depressional areas of the site. Most of the reductions in the soil hydraulic conductivity in the depressions appear to be related to the depth from which the sample was collected, and by inference, associated with the soil structural and textural differences.

Here we present a methodology which matches a soil sample size and a hydraulic conductivity measurement device to prevent the so-called wall flow along the inside of the soil container from being erroneously included in water flow measurements. Its use is demonstrated with samples collected from a wastewater irrigation site.

Since the early 1960s, an alternative wastewater discharge practice at The Pennsylvania State University has been researched and its impacts monitored. ...

Use of Principal Components for Scaling Up Topographic Models to Map Soil Redistribution and Soil Organic Carbon

Landscape topography is a critical factor affecting soil formation and plays an important role in determining soil properties on the earth surface, as it regulates the gravity-driven soil movement induced by runoff and tillage activities. The recent application of Light Detection and Ranging (LiDAR) data holds promise for generating high spatial resolution topographic metrics that can be used to investigate soil property variability. In this study, fifteen topographic metrics derived from LiDAR data were used to investigate topographic impacts on redistribution of soil and spatial distribution of soil organic carbon (SOC). Specifically, we explored the use of topographic principal components (TPCs) for characterizing topography metrics and stepwise principal component regression (SPCR) to develop topography-based soil erosion and SOC models at site and watershed scales. Performance of SPCR models was evaluated against stepwise ordinary least square regression (SOLSR) models. Results showed that SPCR models outperformed SOLSR models in predicting soil redistribution rates and SOC density at different spatial scales. Use of TPCs removes potential collinearity between individual input variables, and dimensionality reduction by principal component analysis (PCA) diminishes the risk of overfitting the prediction models. This study proposes a new approach for modeling soil redistribution across various spatial scales. For one application, access to private lands is often limited, and the need to extrapolate findings from representative study sites to larger settings that include private lands can be important.

Landscape processes are critical components of soil formation and play important roles in determining soil properties and spatial structure in landscapes. We propose a new approach using stepwise principal component regression to predict soil redistribution and soil organic carbon across various spatial scales.

Landscape topography is a critical factor affecting soil formation and plays an important role in determining soil properties on the earth surface, as it ...

Combined Size and Density Fractionation of Soils for Investigations of Organo-Mineral Interactions

Combined size and density fractionation (CSDF) is a method used to physically separate soil into fractions differing in particle size and mineralogy. CSDF relies on sequential density separation and sedimentation steps to isolate (1) the free light fraction (uncomplexed organic matter), (2) the occluded light fraction (uncomplexed organic matter trapped in soil aggregates) and (3) a variable number of heavy fractions (soil minerals and their associated organic matter) differing in composition. Provided that the parameters of the CSDF (dispersion energy, density cut-offs, sedimentation time) are properly selected, the method yields heavy fractions of relatively homogeneous mineral composition. Each of these fractions is expected to have a different complexing ability towards organic matter, rendering this a useful method to isolate and study the nature of organo-mineral interactions. Combining density and particle size separation brings an improved resolution compared to simple size or density fractionation methods, allowing the separation of heavy components according to both mineralogy and size (related to surface area) criteria. As is the case for all physical fractionation methods, it may be considered as less disruptive or aggressive than chemically-based extraction methods. However, CSDF is a time-consuming method and furthermore, the quantity of material obtained in some fractions can be limiting for subsequent analysis. Following CSDF, the fractions may be analyzed for mineralogical composition, soil organic carbon concentration and organic matter chemistry. The method provides quantitative information about organic carbon distribution within a soil sample and brings light to the sorptive capacity of the different, naturally-occurring mineral phases, thus providing mechanistic information about the preferential nature of organo-mineral interactions in soils (i.e., which minerals, what type of organic matter).

Combined size and density fractionation (CSDF) is a method to physically separate soil into fractions differing in texture (particle size) and mineralogy (density). The purpose is to isolate fractions with different reactivities towards soil organic matter (SOM), in order to better understand organo-mineral interactions and SOM dynamics.

Combined size and density fractionation (CSDF) is a method used to physically separate soil into fractions differing in particle size and mineralogy. CSDF ...