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

Published: September 11th, 2016



1Biosphere 2, University of Arizona, 2Department of Soil, Water and Environmental Science, University of Arizona, 3Department of Hydrology and Water Resources, University of Arizona

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 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.

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

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1. Devise a Sampling Matrix to Ensure Systematic and Comprehensive Sampling of Lysimeter

  1. Divide lysimeter into voxels of fixed length, width, and depth.
    1. 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.......

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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 .......

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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 "time zero" conditions. Literature reports on.......

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We thank Ty P.A. Ferré, 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.


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Name Company Catalog Number Comments
Measuring tape Any Any Preventing cross-contamination of samples  is crucial. Therefore, it is helpful to have multiple putty knives to isolate voxel boundary.
Brilliant Blue dye Waldeck GmBH &Co  B0770 Rulers can be used to draw grids. The sampling strategy can be modified based on individual experiments.
Soil Corer AMS 56975 Any commercially manufactured Brilliant Blue dye can be used.
75% Ethanol Any Any A Nikon D90 camera and 50mm lens were used for photography. Any high resolution camera and lens can be used for this purpose.
Spray Bottle Any  Any Use of dye and color card is subjective to individual experiments and/or research questions.
Spatula Any  Any Gardening gloves may be used if handling of corer becomes tedious.
Gloves Any  Any Ensure microbiology samples are kept in ice during sampling and frozen as soon as possible.
KimWipes KimTech Science Any Water can be used to wash soil corer, prior to sanitizing with ethanol.
Sterile Sample bags Fisher Scientific  Whirl-Pak 4 OZ. 24 OZ Keep buckets and dustpans handy to facilitate removal of waste soil.
Color Card Any Any 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.
X-ray Fluoresce Spectrophotmeter XRF, OLYMPUS DS-2000 Delta XRF
Polypropylene cores Any Any
Metal cores  Any  Any
Caps for polypropylene cores Any Any
Hammer Any  Any
Plastic putty knives Any  Any
Face masks Any  Any

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