Lecture 6/7

Question 1

what is a progenote?

Answer 1

• hypothetical organisms that carry cellular information on DNA maintained as unlinked genes
• genes NOT linked on chromosomes
• genetic rather than genomic system
• genetic rather than genomic system
• genomes evolved after the domains split

Question 2

so what happened to progenotes? was LUCA a progenote?

Answer 2

• grouping of genes over time lead to genomic life
• it was easier to pass on a complete set of genes to the next generation

Question 3

so what was Woese contribution to biology?

Answer 3

he reversed taxonomy so that kingdom is not the highest taxonomic level

Question 4

whats the central dogma of molecular biology as applied in microbial ecology

Answer 4

genetics –> physiology –> ecological niche –> niche

Question 5

what is niche?

Answer 5

where mutant strains evolve to the point at which they can no longer be considered to be the same species, thus increasing microbial diversity.

Question 6

what are the 3 ways that Bacteria Reproduce?

Answer 6

• transformation (free-floating DNA)
• transfection/transduction (virus)
• conjugation (Sex pilus)

Question 7

what is DNA vs DNA hybridization (DDH)

Answer 7

• calculate % homology between genomes by comparison of melting temps of pure vs mixed DNA samples
• more mutational differences between genomes, the less tightly the hybrid duplexes will bind, therefore lowering the melting temperature of the hybrid vs pure DNA

Question 8

Can DDH be used as the sole evidence that two organisms belong to the same species?

Answer 8

DDH cannot be used as sole evidence that two organisms belong to the same species.

Question 9

what sequence identity do bacterial strains need to have to be considered identical?

Answer 9

for two bacterial strains to be considered possible the same species they must have a minimum of 98.7% 16s rRNA gene sequence identity.

Question 10

why can 16s rRNA sequencing not be used as sole evidence that two organisms belong to the same species, why or why not?

Answer 10

• no because the sequence could be from artificial chimera

Question 11

define habitat vs culturability

Answer 11

• the vast majority of bacteria and archaeal cells observed under a microscope cannot be grown in culture
• some can be culturable, but viable-but-non-culturable (VBNC).

Question 12

why would a known and previously cultured species not grow in any given experiment

Answer 12

• cells may have entered non-culturable state

or

• cultivation techniques are known but were not used.

Question 13

Why would an uncharacterized species not grow in any given experiment?

Answer 13

• cells may have entered VBNC state or
• cultivation techniques that would have allowed them to grow were not used

we are currently unable to culture them)

Question 14

what is VBNC state

Answer 14

• viable but not culturable
• controversial
• possibly a dormant state

Question 15

examples of known pathogens that enter VBNC?

Answer 15

• salmonella
• vibrio cholerae

Question 16

how do we know when microbes are in VBNC and not dead?

Answer 16

• they retain the ability to infect and cause disease in host, even if they fail to grow in culture

Question 17

how do we prevent infection with VBNC?

Answer 17

chlorinate/ disinfect drinking water

Question 18

can we learn anything about non-culturable species ?

Answer 18

If we know they are present in the environment, we can use a fluorescent probe to detect them using a technique like FISH. But it is very hard to learn anything about its physiology, therefore it is very hard to determine its ecology (interactions with the environment abiotic and biotic factors). But depending on where we find the microorganism, we can guess its physiology its physiology.

Question 19

what is Epulopiscium fishelsoni?

Answer 19

found inside tropical surgeon fish

Question 20

what do we know about E. Fishelsoni ? (Ecology, phylogeny, reproduction)

Answer 20

• heterotroph
• firmicutes, Gram-positive

Question 21

brief lifecycle/ reproduction of E.Fishelsoni

Answer 21

Only eats when its awake, digests when sleeping.

- DNA is found all over the cell, as night time approaches, the genome segregates to the poles to mimic something similar to binary fission. 

• The cell starts to grow and forms two cells within mother cell
• They form a tough coating and exit the original cell in the morning.

Essentially, two cells start to form within an original cell and then they burst out after developing the external coating.

Question 22

E.fishelsoni genome and DNA replication

how can a single copy of a genome control such a large volume of cytoplasm spread over great distances?

Answer 22

it can’t. large cells need to make many copies of the genome that can be distributed throughout the cytoplasm (extreme polyploidy).

Question 23

Turbulence vs upwelling

Answer 23

Turbulence:
- if you have a might puddle and you stir up the mud.
- Stirring the upper part of the dirt.
- Always getting resuspended and settling down

Upwelling
- Currents come from deep in the ocean and come up to the surface
- Big driver of biogeochemical cycling: stuff in the ocean dies and sinks down
- At the bottom of the ocean it decomposes
- There is oxygen at the bottom of the sea, allowing aerobes to live.
- Nitrate can build up at the bottom of the sea
○ Upwelling pushes it up
Where it comes up, life flourishes

Question 24

What is thiomargarita ecophysiology?

Answer 24

• Sediments are rich in H2S
  
  • H2S is a waste product of sulfate-reducing bacteria that consumes organic compounds in anaerobic environments via respiration of SO42-
  • Thiomargarita oxidizes sulfide and reduces nitrate
    It needs to be able to travel between H2S and NO3- zones in order to survive.