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Chapter 2.6.3 : Soil Sampling for Microbial Analyses

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Soil Sampling for Microbial Analyses, Page 1 of 2

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Abstract:

Environmental microbiology is wrought with difficult to sample environments, not least of which is soil. Soil is a dynamic environment, ripe with changing viral, prokaryotic, and eukaryotic populations, all awaiting assay. Soil sampling, depending on the assay, experiment, or project can vary from simple probes, deep cores, to soil slurry collections. Atop of this, soils must be collected from a statistically sound perspective as well as considerations made for physiological, cultivation, or molecular analysis. This chapter will focus on the use of soil sampling equipment, schemes, assays, and case studies aimed at introducing the reader to the various caveats and potential pitfalls associated with soil sampling. No one chapter can attempt to cover all potential characteristics of a specific soil sampling situation; therefore, this chapter will focus on general trends in microbial soil sampling.

Citation: Brooks J. 2016. Soil Sampling for Microbial Analyses, p 2.6.3-1-2.6.3-11. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch2.6.3
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Image of FIGURE 1
FIGURE 1

(a) Common experimental designs, including (1) complete randomized; (2) complete randomized block; and (3) split-plot randomized block designs. (b) Typical sampling regimes which can be applied in each of the experimental designs in part (a). doi:10.1128/9781555818821.ch2.6.3.f1

Citation: Brooks J. 2016. Soil Sampling for Microbial Analyses, p 2.6.3-1-2.6.3-11. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch2.6.3
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Image of FIGURE 2
FIGURE 2

(a) Banded poultry litter (dark spot in soil profile and core) as an example of localized, concentrated nutrients and microbial activity. In this example the treatment (e.g., litter) is applied in a band which concentrates all litterborne bacteria and nutrients into a small section of the applied row. (b) A sample collection template used to identify the litter band and locations flanking the band; thus ensuring a reproducible and representative sample. Sample cores would be collected from atop the band (top through the middle of the triangle) and flanking the band; in this case one band soil core would represent 1/13 of the sample assuming all flanking cores were collected (six on each side). Alternatively, if the study is associated with pathogen die-off in the band, soil cores could be collected exclusively from the middle of the triangle. Photos courtesy of Dr. Haile Tewolde. doi:10.1128/9781555818821.ch2.6.3.f2

Citation: Brooks J. 2016. Soil Sampling for Microbial Analyses, p 2.6.3-1-2.6.3-11. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch2.6.3
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Image of FIGURE 3
FIGURE 3

Soil cores collected with a (a) core sampler mounted to a tractor capable of reaching approximately 1 m, and a (b) standard soil probe capable of reaching approximately 30–45 cm. Photos courtesy of Drs. Karamat Sistani and Ardeshir Adeli. doi:10.1128/9781555818821.ch2.6.3.f3

Citation: Brooks J. 2016. Soil Sampling for Microbial Analyses, p 2.6.3-1-2.6.3-11. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch2.6.3
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Image of FIGURE 4
FIGURE 4

Soil core samples collected from a drainage ditch in the Mississippi Delta. The soil was collected shortly following large rain events; hence, collecting intact soil cores using a soil probe is not feasible. Soil core liners, in this case, can be pushed through the soil (inset) and capped at the either end. Alternatively sludge samplers could be used if the soil is too moist to maintain profile integrity. Photos courtesy of Dr. Beth Baker. doi:10.1128/9781555818821.ch2.6.3.f4

Citation: Brooks J. 2016. Soil Sampling for Microbial Analyses, p 2.6.3-1-2.6.3-11. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch2.6.3
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