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Chapter 6 : Stable Isotope Probing Techniques Using H O

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Stable Isotope Probing Techniques Using H O, Page 1 of 2

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Abstract:

This chapter reviews the use of O-water in stable isotope probing (SIP) studies. Research groups made important contributions to understanding of adenosine triphosphate (ATP) production in mitochondria and bacteria. Richards and Boyer, employing O-water, showed that oxygen atoms from water can be transferred to DNA inside cells. Subsequently, it was shown that O-water may also be used to label DNA formed in soil. Water is a small molecule and therefore can rapidly diffuse throughout the soil environment, so that the label is relatively homogenously distributed throughout the sample and all soil organisms are exposed to similar concentrations of label. However, it is unlikely that the label will be completely homogenously distributed in soil. SIP with O-water may also be used to study the impact of environmental conditions such as temperature or pH on microbial population dynamics in soil. Finally, SIP with O-water is suitable for studies on the impact of complex nutrient sources on microbial population dynamics in soil. For instance, it is well known that plant litter quality, often gauged by measuring the lignin to nitrogen ratio, affects decomposition rates and therefore multiple nutrient cycles in soil.

Citation: Schwartz E. 2011. Stable Isotope Probing Techniques Using H O, p 115-128. In Murrell J, Whiteley A (ed), Stable Isotope Probing and Related Technologies. ASM Press, Washington, DC. doi: 10.1128/9781555816896.ch6

Key Concept Ranking

Restriction Fragment Length Polymorphism
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Denaturing Gradient Gel Electrophoresis
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Figures

Image of FIGURE 1.
FIGURE 1.

Separation of O-labeled DNA from nonlabeled DNA on a cesium chloride gradient. (A) DNA extracted from grown in O-water; (B) DNA extracted from grown in H O DNA (top band) and DNA extracted from grown in 47.5 atom% O-water (bottom band); (C) DNA extracted from grown in O-water (top band) and DNA extracted from grown in 23.75 atom% O-water (bottom band).

Citation: Schwartz E. 2011. Stable Isotope Probing Techniques Using H O, p 115-128. In Murrell J, Whiteley A (ed), Stable Isotope Probing and Related Technologies. ASM Press, Washington, DC. doi: 10.1128/9781555816896.ch6
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Image of FIGURE 2.
FIGURE 2.

results of soil incubated with O-water for 6 days (A), with O-water for 6 days (B), or with O-water for 21 days (C).

Citation: Schwartz E. 2011. Stable Isotope Probing Techniques Using H O, p 115-128. In Murrell J, Whiteley A (ed), Stable Isotope Probing and Related Technologies. ASM Press, Washington, DC. doi: 10.1128/9781555816896.ch6
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Image of FIGURE 3.
FIGURE 3.

Experimental design of a SIP experiment with three replicates. The time = 0 soil sample, control sample, and treatment sample are linked within each replicate before the SIP experiment is initiated so that growth or mortality indices may late5pr be calculated.

Citation: Schwartz E. 2011. Stable Isotope Probing Techniques Using H O, p 115-128. In Murrell J, Whiteley A (ed), Stable Isotope Probing and Related Technologies. ASM Press, Washington, DC. doi: 10.1128/9781555816896.ch6
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Image of FIGURE 4.
FIGURE 4.

Close-up of DNA bands in centrifuge tube after isopycnic centrifugation. On the left is the time = 0 DNA, obtained from the soil prior to incubation with O-water, while on the right are shown two DNA bands, the top nonlabeled DNA band and the bottom labeled DNA band, retrieved from a soil incubated with O-water for 7 days.

Citation: Schwartz E. 2011. Stable Isotope Probing Techniques Using H O, p 115-128. In Murrell J, Whiteley A (ed), Stable Isotope Probing and Related Technologies. ASM Press, Washington, DC. doi: 10.1128/9781555816896.ch6
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Image of FIGURE 5.
FIGURE 5.

Non-metric multidimensional scaling analysis of TRFLP patterns generated from subsamples taken from centrifuge tubes with DNA extracted from a soil incubated with O-water for 21 days. Patterns were generated from the bottom DNA band (□), from the middle DNA band (●), and from the top DNA band (○).

Citation: Schwartz E. 2011. Stable Isotope Probing Techniques Using H O, p 115-128. In Murrell J, Whiteley A (ed), Stable Isotope Probing and Related Technologies. ASM Press, Washington, DC. doi: 10.1128/9781555816896.ch6
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