Biol 407 Final Exam

24. What is the difference when extracting gold via bioleaching?

Cyanide is used, so it must be contained.

6. Understand soil as a habitat

Soil is a complex habitat with numerous microenvironments and niches. Microorganisms in the soil primary attach to soil particles. Surface soil = H2O limits m/o's. Deep soil = nutrients limit.

15. Of what value is the squid-Alivibrio symbiosis to the squid? To the bacterium?

Squid produces NO, which is consumed by the bacteria. The bacteria trigger developmental chances in the squid and provide fluorescence, which the squid then uses as protection (protects both).

9. What region of soil is the most microbially active?

Subsurface, because nutrients are available from the ground water.

36. What is STAT?

Subtherapeutic antibiotic therapy.

5. What was the importance of exchanging gut microbes between Hawaiian goats and Australian goats?

The Hawaiian goats received a fecal transplant from the Australian goats, which provided tolerance to legumes.

6. How are microbial symbionts inherited? (examples)

Vertical, horizontal (squid), or heritable (Wolbachia) transmission.

8. What factors govern the extent and type of microbial activity in soils?

Water availability, nutrient sources, oxygen presence, soil type, geographical location

27. How can environmental conditions change the quantity and quality of the normal skin microflora? (What are examples of changes?)

Weather (temp and moisture INCREASE flora), age, and personal hygiene

39. Are there really "FAT" microbes?

Yes, they allow more nutrient absorption.

15. How does pressure change with depth in a water column?

Pressure increases the further down you go. Increase 1 ATM per 10m. (Increased archaea ~ decreased bacteria)

21. What are the two mechanisms of Symbiodinium transfer to developing corals?

1) ingestion (horizontal). 2) reproduction (vertical)

b. What happens with change in osmolarity?

An increase in osmolarity can lead to biofilm formation, because OmpR gets phosphorylated.

32a. What is vinyl chloride (VC)?

A known carcinogen that is found in groundwater and comes from PVC production plants.

13. What are the characteristics of marine bacteria (general)?

Aerobic anoxygenic phototroph. No CO2 fixation, light to ATP synthase.

20. How do leeches transmit symbionts to their progeny?

Aeromonas is vertically transmitted via the crop. The remaining bacteria are horizontally transmitted.

2. Why form a biofilm

Aids in cell communication, nutrient trapping, and surface adherence - all of which act to improve survival, growth, and defense. A biofilm allows cells to remain in a favorable niche and to live in close association with each other.

23. What is the importance to the two types of Symbiodinium (Type C1b-c Vs Types D1)?

Allows coral to survive in different conditions. C1= low temp. D1= high temp.

3. What physical and chemical conditions prevail in the rumen?

Anoxic environment and VFA's which produce vitamins, AA's, and proteins. Rumen contains CH4 and CO2.

38. How do you think antibiotics affect bacterial number and SCFA formation?

Antibiotics decrease bacterial count, causing anaerobic fermentation, causing more SCFA.

9. How are anoxic conditions maintained in the termite hindgut?

Bacteria around the gut walls consumer a lot of oxygen.

18. How do giant tube worms receive their nutrition?

Bacterial chemoautotrophic symbionts.

16. What does it mean to be a barophile, barotolerant or extreme barophile.

Barophile: Grow best under pressure. Barotolerant: Can grow under elevated pressure, but grow best @ atm pressures. Extreme barophile: obtained from greatest depths, requires high pressure for growth

10. What is BOD? How do we measure it, what does it tell us?

Biochemical Oxygen Demand: a measure of the oxygen-consuming properties of a water sample. Steps: 1) Collect Water 2) Aerate 3) Bottle 4) Incubate 5) Measure O2

21. What is bioremediation, why is it important? bioleaching, xenobiotics?

Bioremediation is a way to clean up oil, toxic chemicals, or other pollutants by microorganisms. Bioleaching is the removal of valuable metals from low grade ores via microbial activities. Xenobiotics are synthetic chemicals.

26. Describe the properties of microorganisms that grow well on the skin.

Dry: Beta- proteobacteria. Moist: Corynebacteria. Wet: Staphylococcus

a. Know the Cpx system

E. Coli uses the cpx system to promote stable cell-surface interactions. There are 2 components to the cpx system: 1) CpxA, the sensor kinase/phosphatase (increases biomass). 2) CpxR, the response regulator. (increases stability). When E. Coli interacts with a hydrophobic surface, the cpx system is turned on. Pili formation is positively regulated via the cpx system.

31. Identify several essential compounds made by indigenous intestinal microorganisms.

Enzymes and AA's.

3. Know how a biofilm forms (info from paper helps here)

Expression of biofilm-specific genes initiate cell attachment to a surface. These genes encode proteins that synthesize intercellular signaling molecules, initiating matrix formation. The matrix is first initiated by colonization of cells, leading to growth and polysaccharide formation. It then develops as more growth occurs and more polysaccharides form. Some bacteria then disperse, to repeat the process again and form another biofilm elsewhere. 1) Adhesion 2) Slime Excretion 3) Increased Growth 4) Detachment

22. What is required to oxidize CuS under anaerobic conditions?

Fe3+

d. How did the authors determine the vinyl chloride mutation was stable?

Fed VC for 30 days, then didn't feed them for 30 days, then fed them again - and they consumed VC.

28. Which major phyla of bacteria dominate the human gut?

Firmicutes and Bacteroides

17. What molecular adaptations are found in bacteria that allow them to grow optimally under high pressure?

Folding is different, decreasing the binding capacity of enzymes. Transport is also affected because membranes have unsaturated fatty acids. OmpH (porin) is synthesized under pressure.

1. How do animals with foregut and hindgut fermentation differ in recovery of nutrients from plants?

Foregut: fermentation before small intestine. Hindgut: fermentation before cecum and large intestine.

34. What is GABA, what does it do?

Gamma aminobutyric acid - it reduces neuron function.

26. Why is immobilization a good strategy for dealing with uranium pollution?

Groundwater contamination can still occur via water soluble uranium (U6+).

4. Why is the metabolism of Streptococcus bovis of special concern to ruminant nutrition?

Grows well on starches and produces lactic acid, if too fast of a diet change is made.

22. What are the major environmental factors contributing to coral bleeching?

High heat and high light.

13. What happens when MASC RNA in injected into a Wolbachia-infected embryonic Ostrinia? (What is MASC?)

In males, MASC Rna will decrease, as its formation is inhibited by Wolbachia.

12. What factors might account for the prokaryotic diversity of freshwater lakes?

Increase in organic matter concentrations, salinity, average temperature, depth, oxygen conc

11. Will addition of organic matter to water samples increase or decrease its BOD?

Increase, because more bacteria use more O2 to consumer organic matter.

37. How does STAT affect mice?

Increased fat deposits.

29. How might increased numbers of methanogens in the gut contribute to obesity?

Increased methanogens = obesity. Low H2 promotes fermentation, allowing more nutrient absorption.

30. Why might the addition of inorganic nutrients stimulate oil degradation whereas the addition of glucose would not?

Inorganic nutrients are needed to balance the influx of carbon from the oil itself. Adding glucose would only add more carbon, it would be counterproductive.

4. What is quorum sensing

Intercellular communication crucial to developing and maintaining the biofilm.

14. What is proteorhodopsin? Why might proteorhodopsin make a bacterium such as Pelagibacter more competitive in its habitat?

It is a bacterial rhodopsin that provides some energy to Pelagibacter, because carbon is limited. It increased the competitiveness in lower nutrient conc's.

35. What did we learn on how lactobacillus affects brain function?

It reduces stress by modulating the stress response and immune system.

23. What key role does Acidothiobacillus ferroxidans play in the copper leaching process?

It reoxidizes Fe2+ to Fe3+ and gets rid of the acid byproduct.

12. How does Wolbachia lead to male lethality in the moth?

It selects for female hosts by manipulating the sex of males by splicing the doublesex gene.

30. Why might the small intestine be more suitable for growth of facultative aerobes than the large intestine?

Large intestine is anoxic.

18. Mercury and its problems, Pseudomonas

Mercury is not a biological nutrient and can be toxic in high conc (methylmercury). Pseudomonas has mercury resistance genes, encoded by the mer operon, controlled by the MerR regulatory protein.

19. What forms of mercury are most toxic to organisms?

Methyl mercury (Ch3Hg+) (it's 100x more toxic)

31. What main advantage do microbial plastics have over synthetic plastics?

Microbial plastics can be degraded by existing enzymes, synthetic plastics can not.

19. What is a trophosome? How does it become infected with bacteria?

Modified GI tract of spongy tissue; Fill with sulfur granules which are loaded with bacteria. New theory: symbionts infect larvae skin.

25. At what body sites are microflora found? How are these sites different?

Mouth, skin, gut, excretory and reproductive systems, mucous membranes. They are different in pH, temp, and osmotic pressure.

2. How does retention time affect microbial digestion of food in a gut compartment?

Nutrient absorption is increased.

7. What factors stabilize the presence of a secondary insect symbiont?

Nutrient availability, protection from the environment and pathogens, via living intra or extracellularly, and changing the host's reproductive system.

1. Why might a biofilm be a good habitat for bacterial cells living in a flowing system?

Nutrients are constantly flowing, becoming trapped. The cells do not detach easily.

25. Which reaction, oxidation or reduction, is key to uranium bioremediation?

Oxidation (of U4+ → U6+)

e. How did they check for contaminants?

PCR and other genetic tests.

17. How is the correct bacterial symbiont selected in the squid-aliivibrio symbiosis?

PG of G+ bacteria causes squid to secrete mucus, causing G- bacteria to aggregate. A. fischeri outcompetes the remaining G-.

28. What is needed to break down an oil spill?

Petroleum, which is the hydrocarbon source.

7. Which phylum of Bacteria dominates bacterial diversity in vegetated soil?

Proteobacteria

27. What is the importance of melanin in dealing with radioactivity.

Radiation → change in electron property of melanin → enhance fungi growth

11. What do we know about the symbiosis between the leaf cutting ants and their fungus? How is the fungus maintained without contamination?

The ants harvest the lead, the garden fungus grows on the lead, the ants eat the fungus. The garden fungus has a parasitic fungus, which is weakened by actinobacteria.

10. What do we know about the bacteria that live within the protozoan within the termite hindgut?

The bacteria contain pseudogenes, which repair/replicate DNA, act in transportation, and lipid synthesis.

16. What features of the squid-Alivibrio symbiosis make it an ideal model for studying symbiosis?

The experiment can be run under lab conditions and genetic information can be collected.

32. Why might microbes be altering our eating habits?

They generate cravings, suppress food competitors may need, and induce dysphoria.

8. What are the consequences of symbiont genome reduction?

They lose catabolic genes and some pathogens lose anabolic genes.

29. Why do petroleum-degrading bacteria need to attach to surface of oil droplets?

The oil is their carbon source.

b. Why would organisms that grow on ethane be likely to grow on vinyl chloride?

They are structurally similar.

20. How is mercury detoxified by bacteria? What is the regulation?

They use an enzyme from a plasmid, called mercuric reductase, to reduce Hg2+ → Hg0. Regulatory protein (merP) stops transcription (it acts as a repressor) and can also activate transcription (acts as an activator). In absence of Hg2+, merR binds promoter and stops transcription. If Hg2+ present, merR activates transcription via a confirmational change. MerT transports the toxin in, which meets the reductase and converts Hg2+ → Hg0. Mer → mercuric reductase → Hg2+ → Hg0

c. What did the author's do to find an organism that can utilize vinyl chloride?

They used mycobacterium strains that haven't been reported to use VC, but use ethene.

33. An example of mood altering by microbes

Toxoplasma gondii - rat's fear suppression

24. Identify factors necessary to support colonization of body surfaces by normal microflora.

pH, temp, and osmotic pressure

14. Know the squid story (how you establish the symbiosis), tube worm, termites, leaf cutting ants

squid= A. fischeri enters juvenile squid through ducts, to cause squid to developmentally change. Tubeworm = trophosome. Termites = bacteria (inside of protozoa) make AA's and fixes nitrogen (for the protozoan). The protozoan (inside the termite) breaks down wood via cellulase. Leaf Cutting ants = vertical transmission