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Chapter 66 : Drilling, Coring, and Sampling Subsurface Environments

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Abstract:

Sampling of subsurface solids requires specialized techniques for drilling (advancing the borehole) and coring (collecting samples of subsurface materials). The goal of this chapter is to provide background information and general guidelines necessary for obtaining representative samples of subsurface solids and groundwater for microbiological and geochemical analyses. To this end, approaches for collecting representative solid and groundwater samples, processing of subsurface solids to reduce and assess microbiological and geochemical alterations during coring, and evaluating the quality of subsurface samples are described. The major advantages of coring through hollow-stem augers are that it is relatively simple, commonly available, and economical to use for obtaining nearly undisturbed unsaturated or saturated subsurface samples. A major source of microbial and solute contamination during hollow-stem auger coring beneath the water table is from sediment and water in the borehole. Selection of tracer type and deployment method is dependent upon the goals of the sampling, the types of lithologies being sampled, the type and source(s) of contaminants being traced, and the drilling and coring methods being used. The chapter provides background information and general guidelines for obtaining representative samples from subsurface environments for microbiological and geochemical analyses.

Citation: Kieft T, Phelps T, Fredrickson J. 2007. Drilling, Coring, and Sampling Subsurface Environments, p 799-817. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch66

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Microbial Ecology
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Restriction Fragment Length Polymorphism
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Figures

Image of FIGURE 1
FIGURE 1

Diagram of split-spoon core barrel containing tracers and core liner for sampling saturated subsurface sediments using cable tool, hollow-stem auger, or rotary drilling methods.

Citation: Kieft T, Phelps T, Fredrickson J. 2007. Drilling, Coring, and Sampling Subsurface Environments, p 799-817. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch66
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Image of FIGURE 2
FIGURE 2

Photograph of a hollow-stem auger drill rig used for obtaining core samples from relatively shallow (<100 m) subsurface sediments.

Citation: Kieft T, Phelps T, Fredrickson J. 2007. Drilling, Coring, and Sampling Subsurface Environments, p 799-817. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch66
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Image of FIGURE 3
FIGURE 3

Simplified diagram of below-ground portion of coring process for collection of subsurface materials during hollow-stem auger, cable tool, and wireline rotary drilling.

Citation: Kieft T, Phelps T, Fredrickson J. 2007. Drilling, Coring, and Sampling Subsurface Environments, p 799-817. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch66
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Image of FIGURE 4
FIGURE 4

Photograph of a cable tool drill rig.

Citation: Kieft T, Phelps T, Fredrickson J. 2007. Drilling, Coring, and Sampling Subsurface Environments, p 799-817. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch66
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Image of FIGURE 5
FIGURE 5

Diagram of assembly used for rotary drilling with wireline coring.

Citation: Kieft T, Phelps T, Fredrickson J. 2007. Drilling, Coring, and Sampling Subsurface Environments, p 799-817. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch66
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Image of FIGURE 6
FIGURE 6

Transport of Br, bacteria, and clay associated with drill muds through an intact core of aquifer sand (A) and distribution of these components over the length of the core after collection of approximately 1 pore volume (B). C/Co, ratio of the concentration at a given pore volume or distance to the starting concentration.

Citation: Kieft T, Phelps T, Fredrickson J. 2007. Drilling, Coring, and Sampling Subsurface Environments, p 799-817. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch66
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Image of FIGURE 7
FIGURE 7

Photomicrograph of fluorescent microparticles among sediment particles, demonstrating easy detection of such particles when used as tracers. The photomicrograph was taken by using a combination of epifluorescent and phase-contrast microscopy.

Citation: Kieft T, Phelps T, Fredrickson J. 2007. Drilling, Coring, and Sampling Subsurface Environments, p 799-817. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch66
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Image of FIGURE 8
FIGURE 8

(A) Diagram of bailer with check-valve for introducing tracers into a borehole for vadose- and saturated-zone coring. (B) The bailer is lowered to the bottom of the borehole on a cable, and the dry tracer is released, covering the exposed sediment.

Citation: Kieft T, Phelps T, Fredrickson J. 2007. Drilling, Coring, and Sampling Subsurface Environments, p 799-817. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch66
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Image of FIGURE 9
FIGURE 9

Diagram of hydraulic core splitter (A) and rock crusher (C) used for sampling consolidated subsurface materials. Careful paring of the discs produced by splitting of the core is required to produce rock fragments (B) from which outer, potentially contaminated materials have been removed. Reprinted from reference with permission from the publisher.

Citation: Kieft T, Phelps T, Fredrickson J. 2007. Drilling, Coring, and Sampling Subsurface Environments, p 799-817. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch66
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Image of FIGURE 10
FIGURE 10

Diagram of a packer and manifold system designed to collect groundwater samples from flowing boreholes in mines or tunnels. The system enables aseptic, anaerobic sampling without exposing the samples to air. The manifold allows collection of multiple samples simultaneously and for different purposes.

Citation: Kieft T, Phelps T, Fredrickson J. 2007. Drilling, Coring, and Sampling Subsurface Environments, p 799-817. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch66
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Image of FIGURE 11
FIGURE 11

(A) Diagram of sand-trap sampling apparatus used to collect bacteria from the flow from an artesian well (reprinted from reference with permission of the publisher). (B) Cutaway view of hollow-fiber tangential-flow filter (reprinted, in part, from reference with permission of the publisher).

Citation: Kieft T, Phelps T, Fredrickson J. 2007. Drilling, Coring, and Sampling Subsurface Environments, p 799-817. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch66
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Tables

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TABLE 1

Comparison of various drilling methods

Citation: Kieft T, Phelps T, Fredrickson J. 2007. Drilling, Coring, and Sampling Subsurface Environments, p 799-817. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch66
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TABLE 2

Techniques used to evaluate potential biological contamination of cored subsurface sediments

Citation: Kieft T, Phelps T, Fredrickson J. 2007. Drilling, Coring, and Sampling Subsurface Environments, p 799-817. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch66
Generic image for table
TABLE 3

Tracers used to evaluate chemical contamination in cores of subsurface sediments

Citation: Kieft T, Phelps T, Fredrickson J. 2007. Drilling, Coring, and Sampling Subsurface Environments, p 799-817. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch66

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