The diversity of species in bacterial communities is often studied by

Question

New Project RC Butler 2019  -  Practice 2 RC Passages Everyday   
Passage # 365, Date : 02-Oct-2019
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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.   1 
 B 
 1. According to the passage, the primary reason that thermal denaturation and reassociation gives information about the genetic diversity in a soil sample is that

A. the process has been demonstrated to manifest second-order reaction kinetics exactly
B. the time it takes the genetic material to reassociate reflects the diversity in the sample
C. the level of genetic diversity in a typical soil sample is sufficiently high for the process to work ideally
D. the genetic material in such a soil sample does not contain repetitive DNA
E. the ecosystem under study is not subject to extreme climatic conditions

2 
 D 
2. The passage suggests that, in the context of thermal denaturation and reassociation, a bacterial community is comparable to

A. A snapshot taken by fluorescence microscope
B. A multiple of 200 of the number of species that can be cultured
C. A sample of repetitive DNA from non-bacterial organisms
D. A single haploid cell
E. A single species

3 
 A 
 3. With which of the following statements would the author of the passage most likely agree?

A. Isolating and culturing specific bacteria is an inferior method of determining the number of species in a soil sample, but it may be useful to study certain culturable species more directly than is possible by thermal denaturation.
B. Isolating and culturing specific bacteria no longer has any useful application, especially in environments with pollution or extreme conditions.
C. Isolating and culturing specific bacteria is a superior but unfeasible method of studying bacteria communities.
D. Isolating and culturing specific bacteria might be useful to obtain a basic estimate of the number of species in a sample that can then be confirmed through the thermal denaturation method.
E. Isolating and culturing specific bacteria, while not always possible, might be useful to give estimates of the number of species in bacteria communities that fail to exhibit second-order reaction kinetics.

4 
 E 
 4. The author mentions that renaturation of the sample taken in Bergen, Norway did not follow ideal second-order kinetics in order to

A. highlight that aspects of the renaturation method remain unproven
B. point out a difference between the expected and the actual characteristics of the genetic material in the sample
C. emphasize the superiority of the renaturation method over isolating and culturing bacteria
D. imply that the genetic diversity in the sample might be even higher than the reported value
E. identify a limitation of the usefulness of the renaturation method

5 
 E 
 5. 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?

A. Whether the environment is free of pollution and extreme conditions
B. Whether the average DNA complexity of the species present is sufficiently low
C. Whether a majority of the bacteria in that environment can be cultured
D. Whether the bacteria in that environment follow second-order reaction kinetics
E. Whether the bacterial DNA in a terrestrial or water sample from that environment can be isolated

6 
 C 
 6. The passage suggests that employing the thermal denaturation and reassociation method entails assuming a value for which of the following?

A. the average frequency, by mass, of pollutants present in a sample
B. the maximum half-life of reassociation for the bacterial community
C. the average size of the genome of a species in the community
D. the number of nonrepeating nucleotides in the DNA of a haploid cell
E. the percentage of species in the community that are culturable

Source:  GMAT Free  (26)
Difficulty Level:   700

mimishyu · Accepted Answer

para1: introduce into the main theme the author intend to talk about “diversity of species in bacterial communities” and the isolation method, which cannot apply to certain bacteria, relate to it

para2: following the isolation method in para1 we could extend our scope of study to DNA heterogeneity, and it is in this heterogeneity which lead to the study other than the isolation method, that is—thermal denaturation & reassociation

para3: the application of the process of thermal denaturation & reassociation to analyze soils, and though the reassociation curves not follow the specific kinetic order, as most renatural DNA do, it is still a very useful method to the study of heterogeneity as well as species diversity

para4: the potential to apply the denatural method to landscape other than soils, to which studies confirm that different environment will certainly influence the result of heterogeneity

summary: discuss several methods in studying diversity of species in bacterial communities, about its use and advantage、limitation and potentials

1. According to the passage, the primary reason that  thermal denaturation and reassociation  gives  information  about the genetic diversity in a soil sample is that

refer to para2 &3
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.

A. the process has been demonstrated to manifest second-order reaction kinetics exactly

though this option can be the information to be offered, its not as good as option (B) to be the answer

B. the time it takes the genetic material to reassociate reflects the diversity in the sample

….correct
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,
--->here we compare the given time period in renaturing the fraction of DNA to genome size or the complexity of DNA, this part of the sentence offer explicit clue/information about the genetic diversity in a soil sample

C. the level of genetic diversity in a typical soil sample is sufficiently high for the process to work ideally

…out of scope

D. the genetic material in such a soil sample does not contain repetitive DNA

…..though this can be the info offered by denaturation and reassociation, “non-repetitive DNA” should better be serve as additional supplement to the info be offered

E. the ecosystem under study is not subject to extreme climatic conditions

…out of scope

2. The passage suggests that, in the context of thermal denaturation and reassociation, a bacterial community is comparable to
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.

A. A snapshot taken by fluorescence microscope

….not within the context

B. A multiple of 200 of the number of species that can be cultured

….out of scope
…see last sentence in para3
This diversity was about 200 times as many species as could have been isolated and cultured.

C. A sample of repetitive DNA from non-bacterial organisms
 
 repetitive DNA….wrong

D. A single haploid cell

….correct
…see second last sentence in para2

E. A single species

….out of scope, nowhere in the passage raise this phrase ever

3. With which of the following statements would the author of the passage most likely agree?

A. Isolating and culturing specific bacteria is an inferior method of determining the number of species in a soil sample, but it may be useful to study certain culturable species more directly than is possible by thermal denaturation.

correct, “isolating and culturing specific bacteria is an inferior method of determining the number of species in a soil sample”, this can easily be inferred from para1

method to isolate and culture specific bacteria:
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.

method of denaturation and reassociation:
 DNA heterogeneity can be determined by thermal denaturation and reassociation.  In general, renaturation of homologous single-stranded DNA follows second-order( not direct) 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(we had to infer, thus not as direct as isolation method in para1)  in a similar manner.

B. Isolating and culturing specific bacteria no longer has any useful application, especially in environments with pollution or extreme conditions.

no, see sentence in the last sentence of para4 “In environments 
with pollution or extreme conditions, the genetic diversity 
might be easier to determine precisely” we can infer that “isolating and culturing specific bacteria” still very useful

C. Isolating and culturing specific bacteria is a superior but unfeasible method of studying bacteria communities.

no, still feasible, this can be infer from first &last sentence in para2

D. Isolating and culturing specific bacteria might be useful to obtain a basic estimate of the number of species in a sample that can then be confirmed through the thermal denaturation method.

….incorrect, I was wrong at this point to which “isolating and culturing specific bacteria” is a method different from “thermal denaturation method”

E. Isolating and culturing specific bacteria, while not always possible, might be useful to give estimates of the number of species in bacteria communities that fail to exhibit second-order reaction kinetics.

….no, “fail to exhibit second-order reaction kinetics.” is wrong
see sentence in para2:
In general, renaturation of homologous single-stranded DNA follows second-order reaction kinetics.
…..the heterogeneity of this DNA is a measure of the total number of genetically different bacteria, or the number of species.

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

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.

A. highlight that aspects of the renaturation method remain unproven

no, it is still hold and proved

B. point out a difference between the expected and the actual characteristics of the genetic material in the sample

incorrect, trap choice, “the expected general condition(not sample)” which follow the order show up in para2 while “actual sample” is in para3

C. emphasize the superiority of the renaturation method over isolating and culturing bacteria

opposite, the author mention this is aim at posing the disadvantage to renaturation

D. imply that the genetic diversity in the sample might be even higher than the reported value

no, sample might be lower than “reported value”
see sentence: so the half-life values gave only approximate, underestimated values for the number of genomes present.

E. identify a limitation of the usefulness of the renaturation method

Correct, best fit to the purpose of this section which deviate from the general pattern of renaturation

5. 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?

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.

A. Whether the environment is free of pollution and extreme conditions

…..incorrect
this is just one of the multiple environment to be consider

B. Whether the average DNA complexity of the species present is sufficiently low

….out of scope

C. Whether a majority of the bacteria in that environment can be cultured

….out of scope

D. Whether the bacteria in that environment follow second-order reaction kinetics

….out of scope

E. Whether the bacterial DNA in a terrestrial or water sample from that environment can be isolated

correct, see sentence:” ….various procedures for isolating DNA 
from river sediments and seawater are known.” We can infer this 
would be critical point in applying the thermal denaturation method

6. The passage suggests that employing  the thermal denaturation and reassociation method  entails assuming a  value  for which of the following?

para3:
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.

A. the average frequency, by mass, of pollutants present in a sample

….out of scope
“pollutant” appear only in the last sentence of para4, see 
sentence: …..In environments with pollution or extreme 
conditions, the genetic diversity might be easier to determine precisely.

B. the maximum half-life of reassociation for the bacterial community

C. the average size of the genome of a species in the community

“genome size” appear in para2, not match to what the question intend to ask
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.

D. the number of  nonrepeating nucleotides  in the DNA of a haploid cell

….out of scope
para2:
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.

E. the percentage of species in the community that are culturable

…. totally out of scope, nowhere in the passage concern about “percentage”

pogod · Answer

Can someone explain why #5 is not D? Even though E seems reasonable too, but shouldn't the feasibility of this method depends on how well a bacteria react to Kinetic Reaction? Is it because the Kinetic Reaction is more related to the DNA and not bacteria?

Sajjad1994 · Answer

Is it because the Kinetic Reaction is more related to the DNA and not bacteria?

Exactly!  You are perfect in your findings

(D)  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.

adityashikhar4 · Answer

In question 4, the line "..., so the half life values gave only approximate, underestimated values for the number of genomes present." This line clearly indicates that the genetic diversity might be more than the reported value which makes option (d) the suitable answer in my opinion. I don't get why option (e) should be referred to as the answer.

Sajjad1994 · Answer

Official Explanation

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

Difficulty Level:   700

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"  and therefore not as useful as they otherwise would have been.

Answer: E

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