Bacteria in Soil IV

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     The diversity of species in bacterial communities is often studied by phenotypic characterization. A problem with this method is that phenotypic methods can be used only on bacteria which can be isolated and cultured, and most soil bacteria that have been observed by fluorescence microscope cannot be isolated and cultured.
     DNA can be isolated from bacteria in soil to obtain genetic information about the nonculturable bacteria therein. The heterogeneity of this DNA is a measure of the total number of genetically different bacteria, or the number of species. DNA heterogeneity can be determined by thermal denaturation and reassociation. In general, renaturation of homologous single-stranded DNA follows second-order reaction kinetics. In other words, the fraction of DNA that has renatured within a given time period is proportional to the genome size or the complexity of DNA, defined as the number of nucleotides in the DNA of a haploid cell, without repetitive DNA. The genetic diversity of a bacterial community can be inferred in a similar manner.
     Vigdis Torsvik, Jostein Goksøyr, and Frida Lise Daae used this process to analyze soil samples taken from the soil from a beech forest north of Bergen, Norway. The reassociation curves for the main DNA fraction did not follow ideal second-order reaction kinetics, so the half-life values gave only approximate, underestimated values for the number of genomes present. Nevertheless, the soil bacterium DNA was very heterogeneous; the diversity corresponded to about 4,000 distinct genomes of a size typical of standard soil bacteria. This diversity was about 200 times as many species as could have been isolated and cultured.
     Various procedures for isolating DNA from river sediments and seawater are known. This opens up the possibility of applying the thermal denaturation method to systems other than soil. The results of the Norway study indicated that the genetic diversity of the total bacterial community in a deciduous-forest soil is so high that heterogeneity can be determined only approximately. In environments with pollution or extreme conditions, the genetic diversity might be easier to determine precisely.                

The author mentions that renaturation of the sample taken in Bergen, Norway did not follow ideal second-order kinetics in order to

Review: Bacteria in Soil IV


Explanation

This question touches on a comment by the author, one we've already noted, that the application of the thermal technique in Norway "did not follow ideal second-order kinetics." The overall point of the paragraph was that the technique was successful (otherwise, for example, the entire fourth paragraph would be nonsensical), so let's look for an answer choice that is consistent with that notion. Based on that fact, answer choice (A) is out. Choice (B) is either unsupported or redundant; the only support we can give to (B) is the fact itself that the kinetics were not followed, so we haven't answered why the author has mentioned that fact. In other words, (B) does not describe an overall objective to mentioning the detail, which the question asks for. Choice (C) can be ruled out swiftly, because it certainly wasn't desirable that the sample failed to follow the expected kinetics. Choice (D) is correct in that the value obtained by the technique is "underestimated," but it is inaccurate that attributing the author's point. In this line, the author is expressing a drawback of the findings--the "nevertheless" (31) indicates this point, for example, as the author goes on to make a positive claim--not emphasizing the large number of species. So (D) is out. We are down to (B) and (E). Choice (E) is most appropriate on the basic point of the identifying a limitation. Is the usefulness of the renaturation method really limited by the point in question? Sure; because the kinetics were not followed exactly, the results of the method were "approximate" (line 30) and therefore not as useful as they otherwise would have been.

The correct answer is (E).


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