Final Exam - MB 409 Microbial Diversity - Fall 1996

1. What are the three main evolutionary branches of living things? (5 points)

Bacteria, Archaea, and Eukarya

2. List the three phenotypic groups of Archaea, and give an example habitat where each are abundant. (5 points)

Sulfur-dependent thermophiles - hot springs
Methanogens - anaerboic sediments
Halophiles - salt lakes

3. How do the membrane lipids of Archaea differ from those of Bacteria and Eukarya? (5 points)

Archaeal membrane lipids are glycerol-phosphate ethers of isoprenoid alcohols. Bacterial and eukaryal membrane lipids are glycerol-phosphate esters of fatty acids.

4. Most of the Archaea are autotrophic. Most of those that are not autotrophic are 'sulfur respirers' - what does this mean? (5 points)

Sulfur respirers are heterotrophic organisms that use sulfur, rather than oxygen, as their terminal electron acceptor.

5. How does promoter recognition by archaeal RNA polymerase compare to that of Bacteria and Eukarya? (10 points)

Archaeal RNA polymerases recognize promoters in the same way that eukaryal RNA polymerases do - by recognition of transcription factors bound to the DNA. Bacterial RNA polymerases, on the other hand, recognize promoters directly via their sigma subunit.

6. Describe the phenotype, habitat, and metabolism of any particular Archaeal species, genus, or group you find interesting. (10 points)

Example answer :

Pyrodictium occultum

7. Photosynthesis in eukaryotic algae and plants is very similar to photosynthesis in cyanobacteria, but not green or purple Bacteria. What is the reason for this similarity? (5 points)

Because plants and algae are photosynthetic because of their chloroplasts, which are the descendants of cyanobacterial, not purple or green bacterial, endosymbionts.

8. Describe the phenotype, habitat, and morphology of any particular unicellular eukaryote you find interesting. (10 points)

 Example answer:


  • A member of the diplomonads
  • binucleated, flagellated
  • anaerobic - no mitochondria
  • gut symbionts - cause dysentery
  • not primative - just distantly related to us!

9. Lichens are symbiotic organisms composed of a fungus and an alga. In some cases, such as Reindeer moss, the algae are eukaryotic rather than cyanobacteria. How many different small-subunit ribosomal RNA sequences could you clone from this lichen, and where would they come from? (5 points)

2 from the fungus (1 from the nucleus & 1 from the mitochondrion)
3 from the alga (1 each from the nucleus, mitochondrion, and chloroplast)
total = 5

10. The root of any tree is determined by an outgroup. How is it possible, then, to root a 'universal' evolutionary tree (i.e. one that contains any organism)? (10 points)

A universal tree can be rooted by using sequences from a gene family in which the different genes diverged before the last common ancestor (e.g. EF-Tu/EF-G). The sub-tree for one member of the gene family (e.g. EF-Tu) serves to root the sub-tree for the other (e.g. EF-G):

11. Describe one case where an organism that could be seen but not cultivated was identified by molecular phylogenetic analysis. (10 points)

Example answer:

Epulopiscium fishelsonii

These organisms were thought to be protists (i.e. eukaryotes) because of their size, but seemed to lack the typical eukaryotic internal structures, e.g. nuclear envelop, mitochondria, Golgi, centrioles, etc. Although they could not (and still cannot) be cultivated, some were collected directly by micromanipulation, washed, and PCR was used to get ssu-rRNA gene sequences. These proved to be relatives of the anaerobic spore-forming Gram-positive Bacteria (Clostridium). To prove that the sequences they got were really from Epulopiscium, a fluorescently-labeled oligonucleotide that was complementary only to the Epulopiscium rRNA was used in direct hybridizations with fish gut contents, & sure enough only the Epulopiscium cells were fluorescently-labeled.

12. Describe one case where a natural microbial community was characterized by molecular microbial ecology. (10 points)

Example answer:

Anarctic pelagic sea water

Fluorescently-labeled ssu-rRNA probes that were specific for Bacteria, Archaea and Eukarya were used to ennumerate each of these groups in picoplancton (0.2 - 1.0 microns) collected from pelagic antarctic sea water. Surprizingly, there were large numbers of archaeal and even eukaryal species present - averaging about 20% of the total for archaeal cells and 10-20% for eukaryal cells (the remainder being bacterial). These species must account for a large fraction of the earths biomass, but the archaeal species must not be of any ofthe cultivated species phenotype, since they are growing in cold, aerobic, low-saline water. What that phenotype might be is as yet unknown. Also, they were lots of small, prokaryotic-looking cells that seem actually to be eukarya - what these are is also not yet known.

13. The complete DNA sequences of the genomes of Haemophilus influenza (a purple bacterium), Mycoplasma genitalium and Mycoplasma pneumoniae (Gram-positive bacteria), Synechocystis lividans PCC6301 (a cyanobacterium), Methanococcus jannaschii (a euryarchaeon), and Saccharomyces cerevisiae (a yeast) are now available. How would you determine which genes were present in the last common ancestor of the three main evolutionary groups? (5 points)

Although you could never determine the entire set of genes in the last common ancestor, you could compile a list of many of them by just looking for those genes that have been identified in any one of the bacterial species and either M. jannaschii or S. cerevisiae - since these genes are present in both branches that diverged from the last common ancestor, they must have been present in that last common ancestor.