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

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.