L11: Thiomargarita namibiensis

Question 1

NO: Thiomargarita namibiensis (what, nutrients, habitat, growth, appearance)

Answer 1

• sulfur pear of Namibia, largest bacteria by volume, G+
  *lives in marine sediments from the upwelling zone
  Nutrients: NO3- from ocean depth and H2S from sediments, SOB

*grows in an unattached chain in a sheath
*appears white because of central vacoule and cytoplasm is a narrow band around it
*has S0 granules making it white
*G+ with cell wall on outside

Question 2

NO: Thiomargarite ecophysiology, where, sediments

Answer 2

*inhabits upper 10cm of turbulent marine sediments in upwelling zones
*sediments have low O2
*upwelling brings NO3- to seawater above sediments

Question 3

NO: What is upwelling

Answer 3

not turbulence, current from the deep ocean where there is decomposed shit, so there is a lot Nitrate and upwelling brings it up

Question 4

NO: T. n culturability

Answer 4

*cannot be cultured must use microcosm

Question 5

Describe temperature, oxygen and dead things availability in the ocean.

Answer 5

temp
* is higher at top and drops towards bottom, colder at the bottom of the ocean

oxygen
*will diffuse from the atmopshere, more light, more oxygen
* in water coloum there is minimum zone, less photosyntheiss but still a lot of nutrients so organisms are consuming it still so there is a drop
* then the oxygen will increase again

Dead things
*dead things fall to the bottom, poop from birds
*PN (dead things) will break down. ammonification will break down ammonia, be oxidised for food and NO3- is the byproduct
==> PN ⇒ NH4+ ⇒ NO2- ⇒ NO3-
* this bottom water is forced up perdiodically (upwelling) which brings the NO3 up
*brings relativley high concentrations of nitrate up and thats where it lives

Question 6

NO: Nutrients in the env, What does Tm do with nutrients, motility

Answer 6

The sediments are rich in H2S, which is a SRB waste product.

*H2S and NO3 cannot exist in the sample place, so microbial metabolism creates gradients
*Thio oxidised sulfide (SOB) and reduces nitrate so it needs to be able to travel between H2S and NO30 zones but is non-motile
*Must use passive movement mediated by turbulence

Question 7

What do SRBs do

Answer 7

Consume organic compounds in anaerobic environments via SO4 2- respiration

*two kinds:aneorobic and facultative aneronic

Question 8

NO: Describe the motility more in depth

Answer 8

• sulfur perals move up and down because the much is turblance because of waves, when tey go up the suck up nitrate ONLY into vacule
  
  • concentrate it to 800mM ⇒ very concentrated (its their liquid air)
  • only get nitrate when they are up there
  • if they took oxygen they would float up
  • when they go down they get closer to SRB, SRB use sulfate as e- acceptor ⇒ SRB produce H2S as byproduct
  • competition for H2S because its good energy source
• the upwelling is not because of turbulance, its just marine phenomimuon

Question 9

NO: Explore Thio energy metabolism, what does this reveal

Answer 9

*H2S oxidation
*NO3- reduction (TEA) - maybe O2, SO4
C source : CO2

In the upper zone
*cells accumulate 0.8M NO3- in vacuoles, could also do oxygen so may be facultative aerobic but does not prefer it

*afterwards they carriy own NO3- supply to lower zone, allowing cells to oxidising H2S, results in elemental sulfur

• large sizes needed to store NO3- as the cells are non motile, spends a lot of time in H2S zones so needs big size. Large polymers can help to store it

Question 10

NO: Thio granules

Answer 10

• suflur granules that reflect white light
• also have granules of polyPhosphate
  
  • phosphate when u break those bonds to get energy
  • when u have a lot it forms a plastic wrap and they can use it as phophate source
  • need a lot of phosphate for DNA too
• glycogen
  
  • carbon energy e- storage
• SOB

Question 11

NO: Draw and understand

Answer 11

slide 208

Question 12

NO: How did we try maintain thio in the lab

Answer 12

*microcosm
* to oxidie added H2S
* reduce added NO3-/SO4-
*added C sources like glucose, acetate
did not work => maybe it is an autotroph vs hetetroph
*added granule ingredients

*uses Calvin cycle to fix CO2?

Question 13

NO: Thio phylogenetics

Answer 13

performed 16s analysis revealing its in gamma proteaobacteria class
*related to Thioplce and other nitrrate storing bacteria

*related to Beggiatoa and other SOBs (thio…) which are similar to endosymbionts of marine animals

Question 14

NO: Thio genetics

Answer 14

• mystery solved with single cell genome sequencing
  *has CO2 fixatation pathway so they are chemolithotrophic with CO2 as C source
  *has O2 and NO3- TEA
  *has H2S and H2 as energy source genes