Deck 19: Archaeal Diversity

Question 1

All types of methanogenesis are poisoned by ________ and therefore require extreme ________.

A) carbon dioxide; aerobiosis
B) oxygen; anaerobiosis
C) heat; cold
D) pressure; vacuum
E) high salinity; freshwater

Answer 1

B

Question 2

The energy-yielding process of ________ occurs only in the archaea.

A) fermentation
B) sulfur oxidation
C) hydrogen oxidation
D) methanogenesis
E) anaerobic respiration

Answer 2

D

Question 3

Which archaea uses light energy to drive a retinal-based ion pup to establish a proton potential?

A) all archaea
B) hyperthermophilic Crenarchaeota
C) Methanobacteriales
D) Haloarchaea
E) Sulfolobales

Answer 3

D

Question 4

What causes the black color emitted from black smokers?

A) ammonia dissolution
B) steep temperature gradients
C) iron sulfide precipitation
D) elemental sulfur precipitation
E) denitrification

Question 5

Archaeosine is a guanosine analog found in archaeal

A) rRNA.
B) mRNA.
C) DNA.
D) msRNA.
E) tRNA.

Question 6

The Haloarchaea, extreme ________, are the only form of life to grow in concentrated brine.

A) thermophiles
B) psychrophiles
C) methanophiles
D) halophiles
E) acidophiles

Question 7

________-branched chains increase membrane stability.

A) Isoprenoid
B) Ester
C) Ether
D) Diether
E) Phospholipid

Question 8

Which organism has a periplasmic space containing membrane vesicles?

A) Desulfurococcus sp.
B) Ignicoccus sp.
C) Methanosarcina sp.
D) Methanothermus sp.
E) Pyrodictium sp.

Question 9

Some hyperthermophilic archaea contain genomes with positive supercoiling generated by ________, which protect DNA from melting at high temperatures.

A) helicase
B) polymerase
C) primase
D) reductase
E) reverse gyrase

Question 10

Why do most hyperthermophiles tend to be anaerobic?

A) Heated water dissolves high concentrations of sulfides and other reduced minerals.
B) The pH of high temperature water prohibits aerobic respiration.
C) All hyperthermophilic environments are deep beneath the sea.
D) At higher temperatures, the oxygen concentration of water declines.
E) Methanogenesis can only be performed anaerobically.

Question 11

Pyrodictium species grow as networks interconnected by glycoprotein tubules called

A) cannulae.
B) pili.
C) fimbriae.
D) flagella.
E) actin filaments.

Question 12

The Sulfolobales includes species that respire by oxidizing

A) sulfate.
B) carbon dioxide.
C) ammonia.
D) methane.
E) sulfur.

Question 13

With respect to pH, the ________ show the widest range of any clade.

A) crenarchaeotes
B) euryarchaeotes
C) Ancient Archaeal Group
D) nanoarchaeotes
E) methanogens

Question 14

Which of the following is unique to archaea?

A) pseudopeptidoglycan
B) S-layers
C) supercoiled DNA
D) infection by double-stranded DNA viruses
E) methanotrophs

Question 15

The ________ have/has such divergent SSU rRNA that its/their sequence fails to amplify with "standard" PCR primers.

A) Crenarchaeota
B) Euryarchaeota
C) Thaumarchaeota
D) Ancient Archaeal Group
E) Haloarchaea

Question 16

Which of the following species is aerobic?

A) Aeropyrum
B) Thermococci
C) Thermosphera
D) Pyrococcus
E) Sulfolobus

Question 17

What novel adaptation would you expect undersea vent archaea to have versus archaea growing at a similar temperature in terrestrial hot springs?

A) barophily
B) thermophily
C) bacteriorhodopsin phototrophy
D) pseudopeptidoglycan
E) positively supercoiled genome

Question 18

Which of the following is a glycerol diphytanyl diether containing a six-membered cyclic ring?

A) Crenarchaeol
B) Euryarchaeol
C) Nanoarchaeol
D) Korarchaeol
E) Methanoarchaeol

Question 19

Members of order ________ in the human gut may couple with methanogens to provide the hydrogen gas for methanogenesis.

A) Desulfurococcales
B) Thermococcales
C) Clostridiales
D) Rhizobiales
E) Enterobacteriales

Question 20

The coupling of energy-spending electron transfer via CO₂ reduction to an energy-yielding electron transfer via CoM-S-S-CoB reduction is called

A) autotrophy.
B) thermophily.
C) methanogenesis.
D) electron bifurcation.
E) methanotrophy.

Question 21

In the haloarchaea, the red pigment bacterioruberin protects cells from damage by

A) light.
B) salt.
C) heat.
D) acid.
E) cold.

Question 22

In methanogenesis from CO₂ and H₂, ________ is hydrogenated and deoxygenated in a stepwise fashion.

A) hydrogen
B) methane
C) oxygen
D) carbon dioxide
E) carbon

Question 23

Which of the following uses light to generate a proton gradient in the haloarchaeotes?

A) bacteriorhodopsin
B) bacterioruberin
C) halorhodopsin
D) methanofuran
E) ferredoxin

Question 24

Methanogenesis includes a unique pathway of carbon fixation, called the carbon monoxide ________ pathway, because the key enzyme can fix CO as well as CO₂.

A) gyrase
B) helicase
C) polymerase
D) reductase
E) dismutase

Question 25

In methanogenesis from CO₂ and H₂, the initial incorporation of H₂ requires a coupled gradient of which ion?

A) sodium
B) potassium
C) iron
D) magnesium
E) molybdenum

Question 26

Which is the model haloarchaeon for molecular biology education?

A) Haloarcula
B) Haloquadra
C) Halorubrum
D) Halobacterium
E) Halococcus

Question 27

Which of the following contains saturated salts of essentially the same ionic proportions as the ocean?

A) thalassic lakes
B) athalassic lakes
C) solar salterns
D) undersea brine pools
E) underground salt deposits

Question 28

The Sulfolobus species maintains an internal pH ________ that of its habitat.

A) equivalent to
B) higher than
C) lower than
D) variable enough that it cannot be measured against
E) not determined to be different to

Question 29

In wastewater, the bacteria are packed together by filamentous ________ to form sludge.

A) halophiles
B) thermophiles
C) methanogens
D) psychrophiles
E) acidophiles

Question 30

Which of the following Crenarchaeota grows as disks linked by cannulae?

A) Aeropyrum pernix
B) Desulfurococcus mobilis
C) Ignicoccus islandicus
D) Thermosphaera aggregans
E) Pyrodictium brockii

Question 31

Which of the following coenzymes is NOT specific for methanogenesis?

A) methanofuran (MFR)
B) tetrahydromethanopterin (H4MPT)
C) cofactor F420 (F420)
D) nicotinamide adenine dinucleotide (NAD+)
E) coenzyme M (CoM)

Question 32

Sulfolobus species are referred to as double ________, meaning they require high temperature and high acidity simultaneously.

A) extremophiles
B) thermophiles
C) acidophiles
D) hyperthermophiles
E) thermoacidophiles

Question 33

Species of ________ secrete toxins deadly to other strains of the same genus.

A) Sulfolobus
B) Halobacterium
C) Nanoarchaeum
D) Methanococcus
E) Thermoplasma

Question 34

The exceptionally small cell in the image shown below is an obligate symbiont to another archaeon and a member of the genus

A) Archaeoglobus.
B) Ignicoccus.
C) Pyrococcus.
D) Ferroplasma.
E) Nanoarchaeum.

Question 35

The thaumarcheal ammonia oxidizers contribute to the global cycling of

A) phosphorus.
B) nitrogen.
C) sulfur.
D) oxygen.
E) hydrogen.

Question 36

The major environmental location of methanogens is

A) landfills.
B) ruminant digestive tracts.
C) human digestive tracts.
D) anaerobic wetlands soil.
E) marine floor sediment.

Question 37

Methanogens are classified within how many major orders?

A) one
B) two
C) three
D) four
E) five

Question 38

Bovine ________ not only make a significant contribution to global methane, but also divert carbon from meat production.

A) halophiles
B) acidophiles
C) autotrophs
D) thermophiles
E) methanogenes

Question 39

Which of the following influences the fermentation efficiency of the gut flora?

A) pathogens
B) bacteria
C) eukarya
D) methanogens
E) halophiles

Question 40

Nitrosopumilus maritimus is able to oxidize

A) nitrate.
B) ammonia.
C) sulfide.
D) sulfate.
E) methane.

Question 41

All of the rhodopsins in the haloarchaeotes have how many alpha helical transmembrane domains?

A) one
B) three
C) five
D) seven
E) nine

Question 42

Crenarchaeol is a biosignature for Thaumarchaeota. Describe its structure.

Question 43

Haloarchaea can regulate their buoyancy through the production of

A) contractile vacuoles.
B) pigments.
C) salt.
D) gas vesicles.
E) carbon dioxide.

Question 44

Describe two possible explanations for the deep branching position of multiple methanogenic clades in the euryarchaeotes.

Question 45

What is the function of the device shown in the following figure? Describe what major challenges this instrument overcomes.

Question 46

Compare and contrast the supercoiling in hyperthermophilic archaeal species with bacteria and eukaryotes. What is responsible for this feature, and what does it accomplish for these archaea?

Question 47

Commercial evaporation pools for salt production benefit from the presence of red ________, whose light absorption accelerates heating and evaporation.

A) methanogens
B) Sulfolobus
C) acidophiles
D) haloarchaea
E) thermophiles

Question 48

Bacteriorhodopsin absorbs light and pumps H⁺ ________ the cell, whereas light-activated halorhodopsin pumps chloride ________ the cell.

A) into; out of
B) out of; into
C) into; into
D) out of; out of
E) through; across

Question 49

Which of the following is an extreme acidophile found anchored to deposits of pyrite ore in mines?

A) Thermus aquaticus
B) Pyrococcus abyssi
C) Ferroplasma acidarmanus
D) Picrophilus torridus
E) Thermoplasma acidophilum

Question 50

Thermococcales can utilize elemental sulfur as a terminal electron acceptor for anaerobic respiration, yielding ________ as a by-product.

A) H₂SO₄
B) S0
C) H₂S
D) thiosulfate
E) ammonia

Question 51

Describe some of the unique metabolic pathways found in archaea but not bacteria or eukarya.

Question 52

Which of the following is responsible for movement away from DNA-damaging light?

A) bacteriorhodopsin
B) halorhodopsin
C) sensory rhodopsin I
D) sensory rhodopsin II
E) sensory rhodopsin III

Question 53

Why has Sulfolobus been studied so much more extensively than many archaea, and what is known about it?

Question 54

Nanoarchaeum equitans is a hyperthermophilic symbiont of

A) Ignicoccus.
B) Sulfolobus.
C) Halobacterium.
D) Methanococcus.
E) Thermoplasma.

Question 55

Most organisms of the order ________ lack both a cell wall and an S-layer.

A) Archaeoglobales
B) Thermoplasmatales
C) Halobacteriales
D) Methanobacteriales
E) Methanococcales

Question 56

Why are hot springs and geysers important habitats for many crenarchaeotes?

Question 57

Archaeoglobus fulgidus conserves energy by sulfate respiration, which drives a unique acetyl-CoA degradation pathway involving the reversal of

A) methanogenesis.
B) glycolysis.
C) flagella rotation.
D) the TCA cycle.
E) electron transport.

Question 58

Elizabeth Hansen and colleagues suggested which two factors contribute to methanogen presence in human gut microbiomes? What evidence supports these claims?

Question 59

Why are the archaea so difficult to classify?

Question 60

What are some of the unique features of archaeal gene regulation?

Question 61

If a species of Ferroplasma is cultured on pyrite ore, what will they do to their surrounding environment?

Question 62

Discuss the genome and morphology of known archaeal viruses. Why are their genomes all similar in structure?

Question 63

What are "vent polymerases," why are they better than previously used polymerases, and from where are they acquired?

Question 64

If archaea are distinct from bacteria, why is the major haloarchaeal order called Halobacteriales, and why do most contain bacteriorhodopsin?

Question 65

Describe the physiological adaptations found in haloarchaea that compensate for the high internal potassium chloride concentrations.

Question 66

Discuss the role of the four different types of rhodopsins found in the Halobacterium species (bacteriorhodopsin, halorhodopsin, and sensory rhodopsins I and II).

Question 67

Explain how ammonia-oxidizing Thaumarchaeota gain energy and state the habitats in which they are found.

Question 68

Where are methanogens found in nature? What are some of the problems they can cause in these habitats?

Question 69

What is the Ancient Archaeal Group and what is known about these organisms?

Question 70

What are methane gas hydrates and where are they found? Discuss the idea of benthic mining.