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BIOL 322: Diversity and Evolution of Microbial Life > Unit 3 Review > Flashcards

Unit 3 Review Flashcards

Review for Quiz 2

1
Q

Microorganisms in the sulfur cycle can perform 2 types of metabolism. Give and define them

A
  1. Assimilative= oxidation of sulfur compounds; create organic sulfur compounds for organism
  2. Dissimilative= reduction of sulfur compounds; getting energy from sulfur compounds (respiration)
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2
Q

The 5 groups of bacteria and Archaea that control the sulfur cycle are:

A
  1. Purple sulfur bacteria
  2. green sulfur bacteria
  3. sulfate reducers
  4. sulfur reducers
  5. sulfur oxidizers
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3
Q

Green sulfur bacteria and purple sulfur bacteria are ______ phototrophs, meaning

A

anoxygenic
they can perform photosynthesis without oxygen

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4
Q

Sulfate Reducers

Energy sources (2):
Produce:

A

Sulfate Reducers

Use H2 & organic compounds (lactate) as energy sources

Produce H2S via sulfate respiration

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5
Q

Which bacteria (2) and archaea (1) are sulfate reducers?

A

Bacteria: proteobacteria (1 group) and firmicutes

Archaea: Euryarchaeota

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6
Q

Sulfate reducers are ____ anaerobes, meaning they perform sulfate respiration in the absence of oxygen

A

obligatory

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7
Q

Give 2 alternative metabolisms that sulfate reducers can use

A
  1. nitrite reduction
  2. fermentation (products= H2, CO2, acetate)
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8
Q

List the 7 famous sulfate reducers (6 bacteria, 1 archaea)

A

Bacteria:
- Desulfomonas
- Desulfotomaculum
- Desulfobacter
- Desulfovibrio
- Thermodesulfobacterium
- Thermodesulfovibrio

Archaea:
- Archaeoglobus

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9
Q

Sulfur reducers use what as an energy source? (2)

these act as the electron ___

A
  • H2
  • Organic compounds

these act as the electron donor

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10
Q

Which bacteria (1) and archaea (1) are sulfur reducers?

A

3 groups of proteobacteria
and
crenarchaeota (archaea)

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11
Q

Sulfur reducers are typically _____ anaerobes, but can use ____aerobic strategies as an alternative metabolism

A

anaerobes
facultative

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12
Q

Sulfur oxidizers use ___ and ___ as their energy source (ie electron donor)

A

H2S
S

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13
Q

Which bacteria and archaea are sulfur oxidizers?

A

3 subgroups of proteobacteria

crenarchaeota

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14
Q

Is Acidithiobacillus ferrooxidans a sulfur oxidizer or a sulfur reducer?

A

oxidizer

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15
Q

Acidithiobacillus ferrooxidans uses ___ as its electron donor

A

FeS2

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16
Q

How can Acidithiobacillus ferrooxidans be beneficial for mining?

A
  • it oxidizes FES2, releasing iron from sulfur
  • This is bioleaching= metal extraction from ores via microorganisms
  • helps humans with the mining process
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17
Q

How can Acidithiobacillus ferrooxidans be harmful for mining?

A

Bioleaching (caused by oxidation of FeS2) can cause unwanted acidification and can release toxic metals (eg cadmium, aluminum)

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18
Q

It’s possible for many oxidizers to use H2S and O2 together because of the evolution of ecological strategies. List these 3 potential strategies.

Why are these strategies needed?

A
  1. O2 dependent positioning
  2. Anaerobic vacuole
  3. Symbiotic association

Needed because H2S and O2 are VERY reactive together

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19
Q

Describe the hypothesis of O2 dependent positioning to explain how sulfur oxidizers can use both H2S and O2

A
  • cyanobacteria produce O2 via photosynthesis in the daytime (on top of microbial mats)
  • Beggiatoa (a bacteria) stays on the bottom of the mats during the day, and comes up for O2 at night

Both H2S= oxidized and O2= reduced –> produces energy

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20
Q

Describe the hypothesis of the anaerobic vacuole to explain how sulfur oxidizers can use both H2S and O2

A
  • bacteria “thiomargarita” uses this
  • Bacteria uses H2S and NO3- (nitrate resp) –> makes S and NH4+
  • this process occurs in a vacuole, where the S and NH4+ is stored
  • Bacteria uses S and O2 for energy generation instead of H2S and O2
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21
Q

Describe the hypothesis of symbiotic association to explain how sulfur oxidizers can use both H2S and O2

A
  • eukaryotic host= yeti crab
  • this host regulates the levels of H2S and O2 (balances)
  • bacterium fixes CO2 for the host
    = symbiosis
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22
Q

_______ is the enzyme that completes nitrogen fixation (it’s O2 sensitive)

A

nitrogenase

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23
Q

T/F

Many diazotrophs evolved the ability to protect nitrogenase from oxygen (cyanobacteria)

A

true

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24
Q

What are the 3 main groups of organisms that control the nitrogen cycle?

A
  1. diazotrophs
  2. nitrifiers
  3. denitrifiers
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25
Q

Bacteria have __ phyla of diazotrophs, and archaea has __

A

9
1

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26
Q

T/F

LUCA was likely a sulfur oxidizer

A

False

LUCA was most likely a nitrogen-fixing bacteria (Diazotroph)

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27
Q

The diversity of diazotrophs is through the ___ gene, NOT _____

Why?

A

nifH gene (nitrogenase)
NOT
16S r RNA

Inconsistent b/c of horizontal gene transfer

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28
Q

How many unique nifH gene sequences have been described?

A

more than 30,000!

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29
Q

List 3 famous diazotrophs

A
  1. Azotobacter (free living)
  2. Azospirillim (free living)
  3. Rhizobium (symbiont)
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30
Q

How do diazotrophs protect dinitrogenase? List & briefly explain the 4 main ways

A
  1. Microaerophillic lifestyle: N fixation only if O2 level is less than 2%
  2. Specialized protective cells: heterocysts in cyanobacteria, spatial separation of N2 fixation
  3. Increased respiration and conformational protection : high O2 levels triggers synthesis of Shethna proteins, which shield nitrogenase
  4. Alternative Nitrogenase: regular nitrogenase uses molybdenum as cofactor (or vanadium or iron) –> two genes b/c of duplication = paralogs
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31
Q

What are shethna proteins?

A

A strategy for diazotrophs to protect dinitrogenase
- high O2 level triggers the synthesis of these

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32
Q

“nitrifiers” generate __

A

nitrite/ nitrate

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33
Q

What are the 3 groups of nitrifiers?

A
  1. Oxidize ammonia to nitrite (NO2-)
    - Ammonia oxidizing bacteria (AOB) and ammonia oxidizing archaea (AOA)
  2. Oxidize nitrite to nitrate (NO3-)
    - nitrite oxidizing bacteria (NOB)
  3. Comammox
    - oxidize ammonia to nitrate completely
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34
Q

Nitrification=
___ –> ____–> ____

A

NH3 –> NO2- –> NO3-
(ammonia to nitrite to nitrate)

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35
Q

AOB/AOA + ___= complete nitrification

A

NOB

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36
Q

Lift 5 famous nitrifiers

A
  • Nitrosomonas multiformis
  • Nitrosomonas europea
  • Nitrosomonas communis
  • Nitrospira
  • Nitrobacter
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37
Q

AOB genus name begins with “___”
NOB genus name begins with “___”

A

Nitroso
Nitro

38
Q

T/F

Nitrifiers are anaerobes and fix nitrogen via the Calvin cycle

A

False

Nitrifiers= aerobics
- Fix CO2 via the Calvin cycle

39
Q

Denitrifiers use ___ respiration, and produce gaseous forms of ____ when respiring

A

anaerobic
nitrogen

40
Q

Denitrifier path:
___–>___–>___–>____

A

NO3- –> NO2- –> NO –> N2O (& sometimes even N2)

41
Q

Nitrifier denitrification= ____ in AOB that creates __ and ___

A

NirK (nitrite reductase)
NO and N2O

42
Q

Nitrifier denitrification produces ___ nitrogen species and may ___(inc/dec) the availability of nitrite for NOB

A

reactive nitrogen species (RNS)
decrease

43
Q

__________ __________ does nitrifier denitrification in low and high O2 conditions

A

nitroaomonas europea

44
Q

It’s suggested that N2 fixation was developed in the early stages of evolution. Is this likely true? Explain why or why not

A

Fe and molybdenum were abundant on early earth- these are components of N2 fixing enzyme nitrogenase
BUT
The gene complexity for nitrogen fixation and high energy cost of it suggests this could not be the early form of life

45
Q

Give 4 types of enzymes that are abundant in early anoxic earth

A
  1. hydrogenases (nickel)
  2. cytochromes c proteins (iron and sulfur)
  3. formate dehydrogenase (molybdenum)
  4. nitrate reductase (molybdenum)
46
Q

T/F
nitrifiers are good methanotrophs

A

FALSE
they are not

47
Q

If an enzyme had a class B transition metal (eg copper, zinc, cadmium) in early anoxic earth, was it functional?

A

No
The ocean was very sulfidic: sulfides reacted with transition metals, so they were not available for enzymes

48
Q

T/F
methanotrophs are good nitrifiers

A

true!
- oxidase ammonia and hydroxylamine
- the opposite is not true though (nitrifiers are bad methanotrophs)

49
Q

MOB: Use methane monooxygenase activated by oxygen to make _____ and create ____

A

CH3OH and H2O

50
Q

AOB: use ammonia monooxygenase activated by oxygen to make ____ and create ___

A

NH2OH
H2O

51
Q

What is the difference between MOB and AOB in terms of NH2OH oxidation?

A
  • AOB evolved the ability to use e- from hydroxylamine oxidation via cytochromes c552 and c554= drive energy production
  • Methanotrophs cannot use e- from NH2OH oxidation because they don’t have c552 and c554
52
Q

T/F
MOB and AOB have different catabolic lifestyles but connection illustrating prokaryotic diversity created by modular evolution of catabolism

A

true

53
Q

List the 7 groups of chemotrophic organisms we covered in class

A
  • Iron (Fe3+) reducers
  • Iron (Fe2+) oxidizers
  • Manganese (Mn4+) reducers
  • Manganese (Mn2+) oxidizers
  • Predatory bacteria
  • stalked bacteria
  • bioluminescent bacteria
54
Q

Iron reducing bacteria evolved the ability to respire solid materials

A

true

55
Q

For iron reducing bacteria, __ is the electron acceptor.

A

Metal Fe3+
- insoluble external e- acceptor

56
Q

T/F
Iron respiration likely existed in LUCA

A

true

& then was lost in some lineages

57
Q

Iron reducers contain outer membrane ______. What do these do?

A

cytochromes
- facilitate e- transfer to insoluble minerals (nanowires)

58
Q

List 3 famous iron reducing microorganisms

A
  • thermus
  • thermotoga
  • geobacter
59
Q

In Manganese (Mn4+) reducing microorganisms, ___ is the electron acceptor

A

Metal Mn4+

60
Q

Anaerobic methane oxidation is coupled to manganese reduction by members of the ____ family “____________”

A

ANME
Methanoperedenaceae

61
Q

ANME=

A

archaea that reduce manganese (but they can also use iron!)
- methane oxidation coupled to manganese reduction

62
Q

Microbial fuel cell=

A

the use of metal respiration in biotechnology (metal reducers)

63
Q

What are the 2 compartments of microbial fuel cell?

A

Anoxic
- anode
- Fe3+ oxides
- Iron oxides build anode

Oxic
- cathode

64
Q

Explain the process of microbial fuel cells

A
  • microbes grow in anoxic compartment using organic compounds
  • e- are extracted
  • e- end up on anode
    = reduction of iron (Fe3+ reduced to Fe2+)
65
Q

In microbial fuel cells, the e- are driven through the anode to the ____ (oxic area).
- In the oxic compartment, ___ is created
- The remaining energy can be captured in the __ compartment and used (to turn on light bulbs etc!)

A

cathode
H2O
oxic

66
Q

T/F

Iron oxidation trait evolved quite late in earth history

A

false
early

67
Q

Iron oxidizing microorganisms use __ as the e- donor. They’re strongly affected by ___ and ____

A

Fe2+
pH and O2

68
Q

Iron oxidizers can be divided into 4 functional groups. List and briefly describe each

A
  1. Aerobic, acidophillic iron oxidizers
    - respire S, live in very low pH
  2. Aerobic, neutrophillic iron oxidizers
    - oxidation of iron creates stalk; eg Gallionella
  3. Anaerobic chemotrophic iron oxidizers
    - iron-nitrate pair; potential metabolism on mars
  4. Anaerobic phototrophic iron oxidizers
    - purple and green non-sulfer iron oxidizing bacteria (Rhodobacter ferriixidans and Chlorobium ferroxidans)
69
Q

There are genes that encode for enzymes involved in iron oxidation and the creation of _________

A

magnetosomes

70
Q

Explain what magnetosomes are and what they do

A

= intracellular structures that contain a lipid bilayer and have their own transporters
- function= oxygen sensing
- Magnetosomes orient themselves towards earth’s magnetic pool (=aerotaxis or magneto-aerotaxis)

Thanks to the iron oxides in magnetosomes, cells are aligning and migrate together toward specific oxygen gradient

71
Q

Manganese (Mn2+) oxidizing organisms:
-Oxidize _____ (electron donor)
- Reduce _____ (electron acceptor)

A

manganese is oxidized, oxygen is reduced

72
Q

What is the purpose of Mn oxidation?

A

to make their own TEA

73
Q

The famous Mn oxidizer is sporulating ____

A

bacillus

74
Q

How do Mn oxidizing organisms make their own TEA?

A
  • Have a multicopper oxidase enzyme
  • the result is Mn-oxide, which serves as a protective coat
75
Q

List 3 famous predatory bacteria

A

Vampirococcus

Bdellovibrio

Myxococcus

76
Q

Vampirococcus is a(n) _______ predator

Bdellovibrio is a(n) _______ predator

Myxococcus is a(n) _______ predator

Options: Intracellular, periplasmic, social

A

Vampirococcus is an intracellular predator

Bdellovibrio is a periplasmic predator

Myxococcus is a social predator

77
Q

Explain how the predatory bacteria “Bdellovibrio” functions

A
  • invades periplasmic of prey cells
    = periplasmic predator
77
Q

Explain how the predatory bacteria “Vampirococcus” functions

A
  • attaches to the surface of their prey
  • acquires nutrients from prey’s cytoplasm and periplasm (intracellular)
78
Q

Explain how the predatory bacteria “Myxococcus” functions

A
  • lyse prey and feed on their nutrients
    = social predators
79
Q

Stalked bacteria produced cytoplasmic extrusions, collectively called “__________”. Give 3 examples

A

prosthecae

  • stalks
  • hyphae
  • appendages
80
Q

What do prosthecae do?

A
  • allow organisms to attach to particulate matter, plant material, or other microorganisms in aquatic habitats
  • can reduce cell sinking
81
Q

Give 2 examples of famous stalked bacteria

A
  • Caulobacter
  • Gallionella
82
Q

Caulobacter is a ___ bacteria that’s a chemoorganotroph. It’s ____ is filled with cytoplasm

A

stalked
stalk

83
Q

Gallionella is a famous ___ bacteria. It’s a(n) _____ oxidizer, and has a stalk composed of ___

A

stalked
iron
Fe3+

84
Q

Give 3 famous genera of bioluminescent bacteria

A
  • vibrio
  • aliivibrio
  • photobacterium
85
Q

Most bioluminescent bacteria live in __ enviros and some of them colonize special light organs in ___ and ___

A

marine
fish and squids

86
Q

T/F
Bioluminescent bacteria produce light that animals often use for signaling to avoid predators/ attract prey

A

true

87
Q

Luciferase enzyme=

A

found in bioluminescent bacteria
- produces light, alcohol, and water

88
Q

luminescence in bacteria requires the gene ____ for luciferase

A

luxCDABE

89
Q

T/F
luminescence in many bioluminescent bacteria only occurs at low population density

A

False
the opposite is true (only at high pop)

90
Q

Transcription of luciferase genes is controlled via ___ ____ molecules. How do they do that?

A

AHL inducer molecules

  • they cross cell membranes of other cells and induce luciferase expression
91
Q
A

BIOL 322: Diversity and Evolution of Microbial Life (12 decks)

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