Topic 3: Archaea to Know

Question 1

What are the main groups?

Answer 1

Euryarchaeota
TACK
DPANN

Question 2

Euryarchaeota

Answer 2

Methanogens

Question 3

Haloarchaea

Answer 3

Euryarchaeota
- tree shows lots of gene transfer and many varying roles with functional implications 
- most relatives are methanogens
- ancestor is a methanogen 
- aerobes, heterotrophs 
- vesicles for vaccine delivery 
?
  engineered haloarchaea to pack antibiotics inside the vesicles.  Then you can dry up the salty culture, with salt crystals containing halobacteria.  Could have salt and get antibiotics that way.  Important in poor areas, an example of how these weird things can have a positive effect somewhere else.  Same was true for Taq polymerase that was heat resistant in Yellowstone National park that had large unexpected benefits elsewhere

Question 4

Methanopyrus kandleri

Answer 4

eukaraeota

highest growth temp

Question 5

Methanosaeta concilii

Answer 5

lowest growth temp

Question 6

Altiarchaea

Answer 6

anoxic freshwater springs

commensal with suffice oxidizing bacteria, carbon fixing (chemoautotrophs)

Question 7

Haloquadratum walsbyi

Answer 7

Haloarchaea, Euryarchaeota

• square shape
• have gas vacuole inside to float around
• hard to cultivate (doubling time is 2 days)
• abundant
• extreme halophile
• very big (40um x 40 um)
• strict aerobe
• optimal growth = 37 C, 20% NaCl
• normally lives in salters, brine pools
• famous for being square and hard to cultivate
• can form sheets (like stamps)
• carotenoids

Question 8

gas vesicle genomic island

Answer 8

can be transferred from archaea to bacteria

Question 9

Thermoplasma

Answer 9

taxonomic group = euryarcheota

• facultative anaerobe
• optimal growth = 55-60 C, pH 0.5-4
• motile (monotrichous flagella)
• normally lives in h0t springs, coal waste piles
• famous for changing shape, living at low pH
• no proper cell wall -> can change shape easily

Question 10

DPANN

Answer 10

DPANN superphyla are all small, not all are obligate symbionts/parasites, they are not all fermenters, they are not all genomes of <1 Mbp, but htey do all have small size

Question 11

sulfolobales

Answer 11

crenarchaeota 
aka TACK
- aerobe 
- optimal growth temp : 80 C pH 3
- normally lives in hot springs 
- famous of: DNA repair, living at low pH, viruses 
- first CAD genome sequenced (at Dalhousie)
    - took 10 years 
- model to study archaea viruses 
- sulfur oxidizing chemoautotrophs 
- special pili for DNA change and repair

Question 12

TACK

Answer 12

super phyla 
Thaumarchaeota 
Aigarchaeota
Crenarchaeota
Korarchaeota
(Lokiarchaeota)

Question 13

Pyrodictum obyssii

Answer 13

crenarchaeota
first ones from hydrothermal vents an hot springs
-share nutrients through canulae
- form biofilm and transfer nutrients through tubes. Mother cells areconnected to daughter cells, can
tell they’re alive
- sulfur oxidizing chemoautotroph
- Shrimps that live here are symbiotic with bacteria that feed them their sugars, crabs can grow long hairs to grow bacteria that they end up eating. Tube worms look like plants but are an animal that host sulfur oxidizing bacteria so they eat sugar. Water is above 100 degrees, quickly cools down because of pressure which creates different microniches

Question 14

thaumarchaeota

Answer 14

group in TACK

Question 15

Canditatus Korarchaeum cryptofilum

Answer 15

KORARCHAEOTA TACK
seen under microscope
small genome
freeliving 
feeds on syntrophic peptides 
- heterotroph

Question 16

Cenarchaeum symbiosis

Answer 16

thought to be chrenarchaeo but it is actually a korarchaota

• inhabits the sponge Axinella mexicana

Question 17

Crenarchian

Answer 17

first mesophilic archaeote

Question 18

Lokiarchaeota

Answer 18

TACK

clusters with Korarchaeota but that could be LBA

Question 19

Bacteriarchaeota

Answer 19

part of TACK 
many groups 
sediments found
anoxic 
some warm, some cold 
now called Bathyarchaeota
- BA1 BA2 have entire genomes sequence, have been able to reverse the process of methanogenesis.  can probably oxidize methane which makes sense of where they live (close to methane sources, good energy source), can't prove it because we haven't cultured them yet and can't run other experiments

Question 20

DPANN super phyla

Answer 20

Diapherotrites 
Parvachaeota 
Aenigmarchaeota 
Nanoarchaeota 
Nanohaloarchaeota 

• DPANN can be like candidate phyla radiation, small genome, fermenter, parasite, endosymbiont. Cannot grow without specific nutrients or marker, so we haven’t been able to culture and study it

Question 21

Nanoarchaeota

Answer 21

DPANN

• Nanoarchaeota first discovered by Carl Stedter, first archaeal parasites found at the time, 1/2 million base pairs. Had co-evolved with crenarchaeal host
• co-evolved with Ignococcus Hospitalis (TACK). Clearly associated with a host, only one species of Ignococcus would it work. Eventually separated by centrifugation and then sequenced it.
• it’s 16s rRNA gene cannot be amplified using typical archaea primers
• Ignicoccus hasn’t been found without nanoarchaea in nature, in lab grows better without it, not sure what the problem is in nature. Could be a very good parasite, but confusing as it only attaches to the one species.
• nanoarchaea has no base metabolism, completely dependent on the host, building blocks are homologous, likely transfer through vesicles, hooked through fibrular structures, not sure if they are transfer structure. Have found some lateral gene transfer

Question 22

batheriophyle (Diaptherotrites)

Answer 22

batheriophyle is bigger, has pathway for utilizing glucose, no ETC, has peptide pathway, some genes to H utilization, has ATPase, proper fermentation, probably free-living. Limited growth, needs to find someone to provide organic molecules