Author
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Sims, Gerald |
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Submitted to: Research Signpost: Research Developments in Agricultural and Food Chemistry
Publication Type: Book / Chapter Publication Acceptance Date: 2/21/2007 Publication Date: N/A Citation: N/A Interpretive Summary: The majority of approaches used to identify soil microorganisms cannot determine the organism’s role in its ecological community. However, stable isotope probing (SIP) has the advantage of being able to provide more definitive evidence that a microbial population takes part in a specific process, providing that the process results in the incorporation of carbon or nitrogen into the microbes’ cellular components. In SIP, a stable, heavy isotope substrate is made available to the microbial population under investigation. If the organism can use the substrate for growth, it will take up the isotope, which in turn will be incorporated into its cellular structures, including DNA, RNA, and phospholipid fatty acids (PFLAs), which can be recovered from the organism by various techniques. If the organism is not active, the cellular components will remain unchanged. The sequences of DNA and RNA and the mixture of materials that make up the PFLAs are characteristic of a particular organism, so any of these materials can be used to identify (or at least narrow down the identity) of the experimental organism. As a result, with SIP, you can know that an organism is active and potentially identify it among thousands of other kinds of organisms that may be present, but inactive. For use of SIP to study soils, it will be important to verify the availability of the test substance to the microorganism, since soil contains a complex array of pore space and chemicals do not necessarily mix throughout the soil readily. The impact of this new technology is that it facilitates research on organisms involved in organic matter turnover, biodegradation of organic pollutants, nitrification, nitrogen fixation, and plant-microbe interactions, each of which is important to agricultural production and management. Technical Abstract: Most approaches for in situ phylogenetic characterization of soil microorganisms lack the ability to establish a causal relationship to function within the community. Recently, the use of stable isotopes to label phylogenetically informative biomolecules (phospholipid fatty acids, DNA, or RNA), typically referred to as stable isotope probing (SIP) has the advantage of providing more definitive evidence that a detected population is active in a specific process, if that process results in assimilation of C or N into cellular constituents. Carbon labeling is considerably more sensitive than N labeling, and is thus more generally useful. Application of SIP techniques to unsaturated soils should be treated with the same caution as other attempts to address function in soils. Of particular concern is the issue of bioavailability of the test substance, which is often neglected in ecological studies. Processes that appear to be amenable to SIP approaches include, but are not limited to, organic matter turnover, biodegradation of organic pollutants, nitrification, nitrogen fixation, and plant-microbe interactions. |
