Chapter 25

RECAP 25.1

  1. Before DNA sequencing was developed, biologists usually grouped all prokaryotes together, emphasizing the differences between eukaryotes and prokaryotes. But the characteristics that differentiated these two “groups” (such as the presence of a nucleus, or the various organelles) are all derived features of eukaryotes. When gene sequences were compared across all of life (especially the ribosomal RNA genes, which are easily compared across all living organisms), it became clear that the diversity among “prokaryotes” was far greater than the diversity among eukaryotes. Indeed, it soon became apparent that the ribosomal RNA genes of prokaryotic archaea were actually more similar to the ribosomal genes of eukaryotes than they were to the ribosomal RNA genes of bacteria, and Archaea was proposed as a domain separate from Bacteria. As biologists studied Archaea in more detail, they discovered that many other features were also distinct from Bacteria.

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  3. The genomes of eukaryotes contain mostly genes that are more closely related to prokaryotic archaea than to bacteria. This leads biologists to conclude that an ancestral prokaryotic archaean lineage first acquired the features that are characteristic of eukaryotes (such as the nucleus). These early eukaryotes then acquired an endosymbiotic proteobacterium, which was eventually incorporated as the eukaryote mitochondrium. Later, one group of eukaryotes acquired another endosymbiont, this time an early cyanobacterium, which became the chloroplast of photosynthetic eukaryotes.

RECAP 25.2

  1. Similarities between any two groups shown in the table can occur for three reasons: (1) the similar feature between two groups is ancestral to life, and the third group has a derived character; (2) the similar feature is a derived character, indicative of a shared ancestry (such as between prokaryotic archaea and their eukaryotic relatives), and the third group (bacteria) has the ancestral condition; or (3) the two endosymbioses of bacteria within eukaryotes may have led to similarities between bacteria and eukaryotes. An example of the first category is that the two prokaryotic groups lack a nucleus, whereas eukaryotes have a nucleus (a derived character). The similarity of the RNA polymerases of prokaryotic archaea and eukaryotes is likely an example of the second category (a derived feature that indicates an evolutionary relationship between these two groups). A possible example of the third category is the ester-linked membrane lipids of bacteria and eukaryotes, since the prokaryotic archaea have ether-linked membrane lipids.

  2. All organisms that are alive today are descendants of a common ancestor of life. Many changes have occurred in all these different species, including prokaryotes as well as eukaryotes. Many prokaryotes have undergone radical changes that allow them to live in extreme environments or in unusual ways. Numerous examples could be used, such as the following: One group of euryarchaeotes, the extreme halophiles (salt lovers), live exclusively in very salty environments, and some can live in lakes with pH values as high as 11.5. They have many adaptations that allow them to live in these environments, and so they are more “derived” in this respect than is any eukaryote. As another example, several groups of bacteria, such as chlamydias, are highly derived intercellular parasites. They have many derived changes that allow them to have very small cells than can live within the cells of other species. Thus the terms “primitive” and “derived” make sense only with respect to a particular feature of the organism, and no living organisms can be considered to be primitive overall (i.e., the common ancestor of life was very different from all organisms that are alive today).

RECAP 25.3

  1. Biofilms represent a complex community of microbial organisms, living together in a gel-like polysaccharide matrix. Many free-living prokaryotes that come into contact with a solid surface bind to the surface and secrete a sticky polysaccharide, which protects the cells. These cells may then secrete signal molecules that attract other microorganisms to the matrix, which develops into a complex community of organisms over time. This community may become highly resistant to attack and become very difficult to remove. Biofilms are of considerable interest to human health and industry, as they may form on any solid surface (e.g., teeth, contact lenses, artificial joints, the inside of pipes), resulting in decay. Biofilms were also critical to the evolution of many multicellular communities, such as stromatolites.

  2. Bacteria are essential for healthy digestion, and only a very few types of bacteria are pathogens. Humans use some of the metabolic products, such as vitamins B12 and K, that are produced by bacteria that live in the large intestine. Large communities of bacteria also line human intestines with a dense biofilm, which aids nutrient transfer from the gut into the human body. Thus our gut microbiome is essential to human health.

  3. Nitrogen-fixing prokaryotes convert nitrogen from the atmosphere into a chemical form that is usable by living organisms. In addition, denitrifying bacteria release organic nitrogen back into the atmosphere as nitrogen gas, keeping nitrogen from eventually leaching into the oceans. Thus these two groups of bacteria (nitrogen fixers and denitrifiers) allow the cycling of nitrogen and make life on land possible.

RECAP 25.4

  1. The greatly reduced genomes of most viruses provide few sequences that can be compared with other organisms. Also, the genomes of many viruses evolve very quickly, making comparisons even more difficult. The reduced nature of viruses provides few morphological clues to their relationships, and their tiny size means they do not produce fossils. Viruses have evolved many times throughout the history of life, so they are related to organisms across the tree of life. For all of these reasons, it is often difficult to place viruses precisely on the tree of life.

  2. Many viruses probably represent escaped components of cellular organisms that now evolve independently of their hosts. Other viruses are likely to represent highly reduced, parasitic organisms that evolved from cellular ancestors but lost their cellular structures as they became independent of their cellular hosts.

  3. Viruses called bacteriophages, or “phages” for short, infect and kill bacterial cells. Phage therapy, first developed during World War I, involves applying these phages to kill pathogenic bacteria. Phage therapy was largely replaced by the use antibiotics in the 1930s and 1940s. With the increase in evolution of bacterial resistance to antibiotics, however, phage therapy is once again an active area of research.

WORK WITH THE DATA, P. 538

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  2. 105°C, where growth is fastest (generation time is lowest).

  3. Simply lower the temperature of these cell cultures to below 120°C and look for cell growth.

FIGURE QUESTIONS

Figure 25.4 Lateral gene transfers are most likely to occur when there is a selective advantage to the transfer. One species may receive genes from many others, but the chances are smaller that a substantial portion of the genome of one species will be transferred into another. In contrast, the stable core of genes controls critical metabolic functions of the cell, so all of these genes are expected to be inherited from ancestors to descendants together.

Figure 25.24 Parasitic bacteria can depend on the gene products of their hosts, so some of their genes can be lost without loss of function. Small genomes allow smaller cell size, and small size is beneficial for a parasite that lives within other cells.

APPLY WHAT YOU’VE LEARNED

  1. As a denitrifier, Paracoccus denitrificans would be most appropriate to reduce nitrate concentrations. Its thermal range would also be appropriate under most environmental conditions.

  2. As an obligate anaerobe, Clostridium novyi would be appropriate to use in hypoxic conditions. Its thermal range is also suitable for mammalian body temperatures.

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  3. Trichodesmium thiebautii. Because the addition of ammonium temporarily increased the productivity of the ecosystem, one can infer that the ecosystem is nitrogen-limited. As a nitrogen fixer, T. thiebautii converts atmospheric nitrogen into a form other organisms can use.

  4. Clostridium novyi. Vancomycin targets bacteria with thick peptidoglycan-filled cell walls. That is the defining characteristic of Gram-positive bacteria, and C. novyi is the only Gram-positive bacterium in the table.