Choose one of the phylogenetic schemes in Figure 10.5 and explain why you feel this one is preferable to the others. Figure XXXXXXXXXXUse the information given in Table 10.3 to answer questions (a)...

ESSAY

ESSAY. The following should be answered in essay form. Each essay should be at least 300 words.
1. Choose one of the phylogenetic schemes in Figure 10.5 and explain why you feel this one is preferable to the
others.
Figure 10.5
Ans. Phylogenetic scheme shown in figure a is most appropriate according to me. Scheme d is not correct and
excepted because the kingdom Protista is the least homologous and hardest to define. Protists are eukaryotes
with unicellular organization of the body and can be present singly or in colonies lacking true tissues. They may
have ingestive, absorptive, or photoautotrophic nutrition, and they include most of the microorganisms known
as algae, protozoa, and many of the simpler fungi. Thus kingdom protista is too diverse to be taxonomically
useful. The boundaries between kingdoms protista, plantae and fungi cannot be defined properly. Phylogenetic
scheme b cannot be considered appropriate because Prokaryota can be further divided into Eubacteria and
Archaebacteria and again there is no specific distinction between other kingdoms. Scheme c is also invalid
kindom Fungi and Animalia are shown to have common node and Fungi has been shown more closely related to
animals but actually they are more closely related to plants. Thus, Scheme a is the correct representation. Like
the bacteria, Archae also contains diverse types of micro-organisms and are generally present in extreme
environments. (Prescott, Sherwood, Woolverton, & Prescott, 2007)
2. Use the information given in Table 10.3 to answer questions (a) and (b). Note A=Pseudomonas;
B=Escherichia; C=Staphylococcus; D=Neisseria; E=Alcaligenes.
Table 10.3
Organism
Characteristic A B C D E
Morphology Rod Rod Coccus Coccus Rod
Motile Yes Yes No No Yes
Gram Reaction - - + - -
Glucose Utilization Oxid. Ferm. Ferm. Ferm. None
% G+C 58-70 50-51 30-40 47-52 58-70
Cytochrome oxidase Present Absent Absent Present Present
a. Which organisms are most closely related? On what did you base your answer?
Ans. According to me Pseudomonas (A) and Alcaligenes (E) are closely related. The first criterion is that
they both are non-fermenters. It has been mentioned that Pseudomonas can carry out oxidation of glucose
and thus it does not ferment glucose. Alcaligenes can neither oxidize nor ferment glucose. Other organisms
(B,C,D) are all glucose fermenters. This is the first evidence which shows that A and E are closely related.
Both Pseudomonas and Alcaligenes are gram negative, rod-shaped, motile, contain cytochrome oxidase and
have same G+C content. Although same G+C content does not prove that they are closely related but it can
be said that they might be closely related. If two organisms differ in their G+C content by about more than
10%, their genomes have quite different base sequences. On the other hand, it is not safe to assume that
organisms with very similar G+C contents also have similar DNA sequences. Only if two microorganisms
are also alike phenotypically does their similar G+C content indicate close relatedness. Thus, these
characteristics help to determine that Pseudomonas and Alcaligenes are closely related.
b. DNA from which organisms will probably hybridize?
Ans. It is likely that DNA from Pseudomonas (A) and Alcaligenes will hybridize together and DNA from
Escherichia (B) and Neisseria (D) will also hybridize together because their G+C content are closely related
which will help them to hybridize. The similarity between genomes can be compared more directly by the
use of nucleic hybridization studies. If a mixture of single-stranded DNA (ss DNA) formed by heating a
double stranded DNA (ds DNA) is cooled and held at a temperature about 25 degree Celsius below the
melting temperature, strands with complementary base sequences will re-associate to form stable ds DNA,
whereas non complementary strands will remain unpaired. The G+C content often is determined by melting
Temperature (Tm). If DNA molecules are very different in sequence, they will not form a stable, detectable
hybrid. Therefore DNA-DNA hybridization is used to study only closely related organisms. (Prescott,
Sherwood, Woolverton, & Prescott, 2007)
3. One of the advantages of some newly developed rapid identification tools is that pure cultures aren't needed.
Why is a pure culture necessary for biochemical tests such as the Enterotube, but not for DNA probes?
Ans. For biochemical tests, such as the Enterotube, if the culture contains any unwanted organisms, it could
lead to an error of the results of the biochemical test potentially producing false-positive or false-negative
results of the test. Enterotube test is used for identification of microorganisms belonging to Enterobactereacea
family. In natural habitats microorganisms usually grow in complex, mixed populations with many species.
This presents a problem for microbiologists because single type of microorganism cannot be studied adequately
in a mixed culture. Thus a pure culture which is a population of cells arising from a single cell is required so
that biochemical identification can be done with most accuracy.
On the other hand, when it is difficult to get pure culture of Microorganisms, a DNA probe can be used. Each
organism has its unique genome sequence. A probe is a sequence of single stranded DNA which can be used for
identification of an organism. DNA probes bind directly to predefined nucleic acid sequences, which basically
identifies the microbe even when surrounded by other microorganisms. It forms a hybrid with complementary
DNA or rRNA sequences which is unique for every species. Probe is particular for a species and is
radioactively labeled which makes its detection and identification easier. Radioactive labeling is usually done
using radioactive P-32. Thus using this molecular biology identification tool it is now possible to identify
different microorganisms from a mixed culture including soil, water and faeces. This is because about 70% of
16S rRNA of microbes is conserved.
4) Discuss the use of Bergey's Manual as a tool of (1) classification and (2) identification.
Ans. There has been enormous progress in prokaryotic taxonomy since the first volume of Bergey’s manual of
Systemic Bacteriology. In particular, the sequencing of rRNA, DNA and proteins has made phylogenetic
analysis of prokaryotes feasible. Bergey’s Manual has now been separated into two books i.e. Bergey’s Manual
of Determinative Bacteriology and Bergey’s Manual of Systematic Bacteriology. The first book serves as a tool
for identification of organisms. This book helps to identify bacteria on the basis of their phenotype. The results
of Gram staining, shapes and sizes of the cells, arrangement of cells as well as the formation of spores is taken
into account for identification. Even the motility of bacteria, their growth temperature, other growth conditions
and biochemical assays have also been used in the manual for identification of bacteria.
The second book i.e. Bergey’s Manual of Systematic Bacteriology is used for classification of bacteria. It
provides phylogenetic relationship between bacteria and archae. In the new edition this classification has been
done using molecular techniques which includes using 16S rRNA sequences. The second edition of this book
has more ecological information about the individual taxa and organisms are arraged in five volumes:
Volume 1: It includes Archae and the deeply brancing phototrophic bacteria.
Voolume 2: It includes Proteobacteria.
Volume 3: Gram-positive bacteria having low G+C
Volume 4: Gram positive bacteria having...