Bacteria in Soil V

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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 passage suggests that the whether the thermal denaturation method can be applied in a specific environment depends primarily on which of the following considerations?

Review: Bacteria in Soil V


Explanation

This question asks for the prerequisite conditions for using the thermal denaturation method. The passage mentions a couple, and one is fresh in our mind from the previous question: following second-order reaction kinetics. There it is, in answer choice (D). Can life be so simple on this question? We can review the other answers. Choice (A) is inaccurate. The passage states in the last line that pollution and extreme conditions might help the method, and they were not present in this case, so they are not a precondition. Choice (B) might sound plausible if complex DNA make for a complex problem to solve, but there is no support in the passage for this idea. Choice (C) is exactly wrong, in a way, the "whole point" is that we can use the thermal method to count the species without culturing them. Choice (E) does touch on a relevant point, because we do need to be able to isolate the bacteria--this is indicated in lines 8 and 37. If we can't isolate the bacteria, we can't get started with the method. That leaves us with (D) and (E) as contenders--which is correct? One must have an objective defect. Looking back at (D), we see that it says that the bacteria in that environment follow second-order reaction kinetics. This is nonsensical, as it's the reassociation of the bacterial DNA, not "the bacteria," that must follow second-order reaction kinetics. Another point is that it has been presented to us as fact in the passage that bacterial DNA does tend to follow second-order kinetics in reassociating, if only approximately. Meanwhile, it is not a given that the bacterial DNA can be isolated. Therefore (D) is out and (E) is in.

The correct answer is (E).


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