Bis 2C, Pre-Lab #2
Bacteria and Archaea are often collectively referred to as prokaryotes because they lack a
nucleus (pro=before, karyon=nucleus). But, as you can see from figure 2.1, they are not each
other’s closest relatives. Because bacteria and archaea are so diverse, they can be difficu...
Bacteria and Archaea are often collectively referred to as prokaryotes because they lack a
nucleus (pro=before, karyon=nucleus). But, as you can see from figure 2.1, they are not each
other’s closest relatives. Because bacteria and archaea are so diverse, they can be difficult to
characterize. However, when compared to eukaryotes, they have significant differences in their
general biology including, reproduction, organization of genetic material, and a lack of
membrane-bound organelles. In contrast, eukaryotes house their genetic material within a
nucleus and have membrane-bound organelles such as mitochondria and chloroplasts.
While eukaryotes include all of the plants and animals that you are most familiar with, we use
the term microbe to refer to microscopic organisms in any of the domains and viruses. Be sure
to watch this language carefully as you work through the prelab.
1) Based on what you learned in lab 1, and assuming the relationships shown in figure 2.1 are
correct, do ‘prokaryotes’ form a monophyletic group?
Yes
No
Phylogenomics
In lab 1, we discussed the different types of data that are used to build phylogenetic trees,
including morphology, behavior, and genetic data in the form of DNA nucleotide sequences.
Rapid and steady improvements in generating nucleotide sequence data have made it possible
to quickly and cheaply sequence large portions of entire genomes; even for organisms that are
not routinely studied. These methods have helped lay the foundation for a field of study called
genomics. Currently, there are hundreds of thousands of complete genome sequences available
publicly for organisms from all across the tree of life. Most of these however are from bacteria
and archaea due to the fact that their genomes are relatively small (1-5 million base pairs in
length, on average) when compared to eukaryotes (which can have genomes of > 100 billion
base pairs in length). Although these genomes have many uses, one benefit has been the ability
to develop genome-scale data matrices for phylogenetic analysis. Using genomic data to build
phylogenies is sometimes referred to as phylogenomics.
Figure 2.1
Two Domains
Several recent phylogenomic studies have focused on exploring relationships among the three
domains and also trying to better understand the origins of the eukaryotic cell. The analysis of
1000s to hundreds of thousands of genomes in such studies including data from both cultured
and uncultured organisms from a wide sampling of habitats worldwide has fundamentally shifted
our view of relationships on the Tree of Life. In contrast to the three-domain tree (Figure 2.1),
current studies have shown some support for an alternative “two domain” Tree of Life (Figure
2.2). The key difference between these two hypotheses is that in the two domain tree
Eukaryotes are sister to some, but not all, Archaea. Instead, the sister group of eukaryotes is a
subset of Archaea called Asgard which were originally discovered near deep-sea hydrothermal
vents and are presently known only from genetic data. In this tree the “two domains” are the
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, bacteria (on one side of the tree) and the archaea (including the eukaryotes as a subgroup) on
the other side of the tree.
2) Based on figure 2.2, what can we conclude about the relationships of Archaea to
Eukaryotes? Are the groups labeled Archaea monophyletic in the “two-domain” hypothesis?
Eukaryotes originated from an ancestral Archaea and are sister taxa to an evolutionarily
modified Archaea. The groups labeled Archaea would be monophyletic.
Diversity
Question 3 (a-e). As an introduction to some of the organisms that will be discussed this week,
use clues from the scientific names of Bacteria and Archaea listed below to match the species
at left with the correct description at right.
3a. Bacillus anthracis
d. This bacterium produces a toxin known as anthrax toxin and causes the disease anthrax.
3b. Vibrio cholerae
f. This water-borne bacterium causes cholera.
3c. Chlamydia trachomatis
e. This sexually transmitted bacterium infects 2.3 million people younger than age 40 in the United
States.
3d. Lokiarchaeota
c. This group was originally discovered from samples near a deep sea hydrothermal vent called
Loki’s Castle.
3e. Yersinia pestis
b. Spread by rats and fleas, this bacterium decimated human populations in the Middle Ages.
3f. Thermus aquaticus
g. This bacterium is a thermophile and is a source of a heat resistant enzyme used in PCR.
3g. Staphylococcus aureus
a. This common bacterium causes boils and other infections; a highly drug-resistant strain of this
species, called MRSA is a major emerging global threat.
Morphology
Morphology
Although there is variation in body forms among Bacteria and Archaea, three morphologies are
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