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Bio 322 > Unit 3 > Flashcards

Unit 3 Flashcards

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1
Q

what are the 2 ways microbial diversity can be considered?

A
  • phylogenetic diveristy
  • functional diversity
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2
Q

phylogenetic diversity

A

genetic diversity if evolutionary lineage
- based on rRNA gene

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3
Q

functional diversity

A

diversity of form and function
- physiological/metabolic
- ecological

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4
Q

why are there discrepancies between phylogenetic and functional diversity?

A
  • gene loss: trait present in common ancestor of many lineages
  • convergent evolution: trait evolved independently in 2 or more lineages
  • HGT: gene encodes certain trait is exchanged between distantly related lineages
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5
Q

which phyla’s have anoxygenic photosynthesis?

A

Acidobacteria
Chlorobi
Chloroflexi
Firmicutes
Proteobacteria

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6
Q

which phyla has oxygenic photosynthesis?

A

cyanobacteria

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7
Q

what are the 5 morphological groups of cyanobacteria?

A

Unicellular(1)
Unicellular(2)
Filamentous(1)
Filamentous(2)
Filamentous(3)

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8
Q

Chroococcales

A
  • unicellular
  • Binary fission
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9
Q

Pleurocapsales

A
  • multiple fissions
    Unicellular
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10
Q

Oscillatoriales

A

Filamentous
- no heterocysts

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11
Q

Nostocales

A

Filamentous
- cellular differentiation

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12
Q

Stigonematales

A
  • filamentous
  • branching cells
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13
Q

cyanobacteria

A

not coherent
- Pleurocapsales is only one coherent

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14
Q

multiple fissions

A

feature arose only ONCE in evolution

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15
Q

which group of cyanobacteria does multiple fissions?

A

Pleurocapsales

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16
Q

which 3 cyanobacteria share common ancestor?

A

Oscillatoriales
Nostocales
Stigonematales
- single origin of differentiation
- filamentous

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17
Q

which cyanobacteria is the only one with branching?

A
  • stigonematales
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18
Q

how many times did branching arise in evolution?

A

once

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19
Q

major characteristics of cyanobacteria

A
  • filament (gliding motility)
  • gas vesicles (floating in water)
  • mucilaginous envelopes (bound filaments)
  • hormogonia (dispersion)
  • akinetes (protection)
  • storage structures (cyanophycin, heterocysts)
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20
Q

gliding motility

A
  • cell filament makes contact with solid surface or with another filament
  • junctional pore complex (prokaryotic secretion organelle) is molecular motor underlying gliding motility in cyanobacteria
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21
Q

gas vesicles (floating in water)

A
  • adjust to light intensity for photosynthesis
  • gas vesicles regulate position of cells in water
  • proteins as decor on surface
  • GvpA + GvpC = intercrosses net of proteins on vesicles
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22
Q

mucilaginous envelopes (bound filaments)

A
  • bind group of cells or filaments together
  • polysaccharidic material released during growth
  • protection from desiccation, antibacterial agents and predators
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23
Q

hormogonia (dispersion)

A
  • disperse in time of stress
  • short motile filament separated easily from longer filament
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24
Q

akinetes (protection)

A
  • cells with thickened outer walls
  • cells germinate from akinetes when conditions are better
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25
Q

storage structures

A
  • cyanophycin: copolymeric strucutre made of aspartate and arginine, nitrogen storage product
  • heterocysts: specialized structures for N fixation
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26
Q

what enzyme does nitrogen fixation and where?

A

nitrogenase in hetercysts

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27
Q

t or f: nitrogenase is oxygen sensitive?

A

true

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28
Q

how can cyanobacteria do anaerobic and aerobic process?

A

regulatory mechanism
- heterocysts- specialized cell with lost PSII (no O2 making)
- temporal separation of nitrogen fixation and photosynthesis (fix N at night)
- suppress photosynthesis during nitrogen fixation

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29
Q

how does unicellular cyanobacteria fix N?

A

during night when photosynthesis not happening

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30
Q

what suppresses photosynthesis when N fixation occurs?

A

Trichodesmus

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31
Q

when did nitrogenase arise?

A

before oxidation of atmosphere by oxygenic photoautotrophs
- oxygen-protective mechanisms developed

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32
Q

purple sulfur bacteria

A
  • H2S to run photosynthesis
  • S^0 granules inside cell
  • CO2 fixation
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33
Q

purple non-sulfur bacteria

A
  • light = source of energy
  • organic compounds source of C
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34
Q

2 families of purple sulfur bacteria

A
  • chromatiaceae- granules inside, vesicular photosynthetic membrane
  • ectothiorhodospiraceae- granules outside, lamellar photosynthetic membrane
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35
Q

how do purple non-sulfur bacteria conserve energy?

A
  • fermentation
  • anaerobic respiration
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36
Q

what is the key genera of purple non-sulfur bacteria?

A
  • Rhodobacter
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37
Q

green sulfur bacteria

A
  • H2S as e donor for phototrophic growth
  • generate S^0 oxidized to sulfate if needed
  • S granules are deposited outside cell
  • Phylum Chlorobi
  • bacteriochlorophylls c,d,e
  • pigements chlorosomes
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38
Q

green non-sulfur bacteria

A
  • lack of cultivation = not metabolically characterized
  • filamentous and perform gliding motility
  • Phylum Chloroflexi
  • photoheterotrophs - organic C source or sometimes inorganic
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39
Q

what are chlorosomes?

A

pigment-rich bodies bound by thin membrane attaches to cytoplasmic membrane at the periphery of cell

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40
Q

exception organisms in green non-sulfur bacteria

A
  • heliothrix - no chlorosomes and bacteriochlorophylls, more carotenoids
  • thermomicrobium- unique membrane lipids (1,2- dialcohols), no ester or ether, cell wall made or proteins
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41
Q

what are the two type of metabolism done by microorganisms?

A
  • assimilative
  • dissimilative
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42
Q

assimilative

A

oxidation of sulfur compounds
- create organic sulfur compounds

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43
Q

dissimilative

A

reduction of sulfur compounds
- getting energy from sulfur compounds (respiration)

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44
Q

what organisms control the sulfur cycle?

A
  • purple sulfur
  • green sulfur
  • sulfate reducers
  • sulfur reducers
  • sulfur oxidizers
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45
Q

sulfate reducers

A
  • energy sources: H2, organic compounds
  • bacteria: proteobacteria, firmicutes
  • archaea: euryarchaeota
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46
Q

physiology of sulfate reducers

A
  • obligate anaeroabes
  • H2 or lactate
  • use hydrocarbons
  • produce H2S
  • alternative metabolism: nitrate reduction, fermentation
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47
Q

famous sulfate reducers

A
  • desulfomonas
  • desulfotomaculum
  • desulfotomaculum
  • desulfobacter
  • thermodesulfobacterium
  • thermodesulfovibrio
  • archea: archaeglobus
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48
Q

sulfur reducers

A
  • energy source: H2, organic compounds
  • Bacteria: Proteobacteria (3 groups)
  • Archaea: Crenarchaeota
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49
Q

physiology of sulfur reducers

A
  • obligatory anaerobes- H2 or organic compounds
  • use formate, ethanol, propanol
  • produce H2S
  • alternative metabolism: aerobic (facultative)
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50
Q

sulfur oxidizer

A
  • energy source: H2S and S^0
  • bacteria: proteobacteria (3 groups)
  • archaea: Crenarchaeota
51
Q

famous sulfur oxidizers

A
  • Acidithiobacillus ferrooxidans
  • uses FeS2 as e donor
52
Q

benefit of Acidithiobacillus ferrooxidans for mining

A
  • oxidation of FeS2 releases iron
  • bioleaching process
  • bioleaching used for other metals
53
Q

harmful effect of Acidithiobacillus ferrooxidans for mining

A
  • bioleaching causes acidification and release toxic metals
54
Q

what do many sulfur oxidizer use together?

A

H2S and O2

55
Q

why can sulfur oxidizers use H2S and O2 together?

A

O2 dependent positioning
Anaerobic vacuole
Symbiotic association

56
Q

O2 dependent positioning

A
  • Beggiatoa
  • cyanobacteria produce O2 in photosynthesis in daylight
  • Beggiata on bottom in daylight
  • during night photosynthesis drops
  • glide to top for O2
  • H2S oxidized- O2 reduced to produce energy (oxidation of sulfur compounds)
57
Q

anaerobic vacuole

A
  • thiomargarita
  • uses H2S and NO3- and makes S^0 nad NH4+
  • occurs in vacuole
  • storage of S^0 and NH4+
  • S^0 and O2 - better couple for energy generation
58
Q

symbiotic association

A
  • Yeti crab
  • eukaryotic host
  • regulates levels of H2S and O2
  • bacterium fixes CO2 for host
59
Q

which organisms control nitrogen cycle?

A
  • diazotrophs
  • nitrifiers
  • denitrifiers
60
Q

what enzyme completes nitrogen fixation?

A
  • nitrogenase
  • O2 sensitive
61
Q

which bacteria evolved ability to protect nitrogenase from o2?

A

diazotrophs

62
Q

diazotrophs

A
  • LUCA was N2 fixator
  • Bacteria - 9 phyla
  • Archaea - 1 phylum
  • diversity determined through nirF gene (16s r RNA too unreliable)
  • inconsistent bc of HGT
63
Q

famous diazotrophs

A
  • azotobacter (free)
  • azospirillum (free)
  • rhizobium (symbiont)
64
Q

how diazotrophs protect dinotrogenase?

A
  • microaerophilic lifestyle
  • specialized protective cells
  • increased respiration and conformational protection
  • alternative nitrogenase
65
Q

microaerophilic lifestyle

A
  • nitrogen fixation only if O2 level less than 2%
66
Q

specialized protective cells

A
  • heterocysts in cyano
  • spatial separation of N2 fixation
67
Q

increased respiration and conformational protection

A
  • high O2 levels trigger synthesis of complex proteins (Shethna proteins)
  • specialized proteins from shield around nitrogenase as protection
68
Q

alternative nitrogenase

A
  • regular nitrogenase uses Molybdenum as cofactor
  • alternative uses Vanadium or iron
  • two genes - results of duplication event (paralogs)
69
Q

nitrifiers

A
  • AOB and AOA
  • NOB
  • Commamox
70
Q

AOB and AOA process

A

oxidize ammonia to nitrite

71
Q

NOB process

A

oxidize nitrite ro nitrate

72
Q

Comammox process

A
  • oxidize ammonia to nitrate completely
73
Q

_____ + _______ = complete nitrification

A

AOA/AOB + NOB

74
Q

what is the process of nitrification?

A

NH3 > NO2 > NO3

75
Q

physiology of nitrifiers

A
  • aerobic
  • fix CO2 via calvin cycle
  • AOB begins with Nitroso-
  • NOB begins with Nitro-
76
Q

famous nitrifiers

A
  • Nitrosomonas multiformis
  • Nitrosomonas europea
  • Nitrosomonas communis
  • Nitrospira
  • Nitrobacter
77
Q

who performs anaerobic respiration?

A
  • denitrifiers
78
Q

what do denitrifiers produce?

A

gaseous forms of nitrogen

79
Q

set of reductases

A

NO3 > NO2 > NO > N2O

80
Q

nitrifier denitrification

A

NirK in AOB creates NO and N2O
- produces reactive nitrogen species (RNS) and may reduce availability for nitrite for NOB

81
Q

Nitrosomonas europea

A

nitrifier denitrification in O2 low and O2-high conditions

82
Q

what was abundant on early earth?

A

iron
molybdenum

83
Q

what was the purpose of iron and molybdenum?

A

components of N2 fixing enzyme nitrogenase

84
Q

what was one suggestion that nitrogen was not part of early form of life?

A
  • gene complexity for nitrogen fixation
  • high energy cost
85
Q

what are the abundant enzymes for anoxic earth?

A
  • hydrogenases
  • cytochrome c proteins
  • formate dehydrogenase
  • nitrate reductase
86
Q

were enzymes with class B transition metals functional?

A

no

87
Q

what happened when sulfides reacted with transition metals?

A

no available for enzymes

88
Q

MOB

A

use methane monooxygenase activated by oxygen to make CH3OH and create H2O

89
Q

AOB

A

use ammonia monooxygenase activated by oxygen to make NH2OH and create H2O

90
Q

what are great nitrifiers?

A

methanotrophs
- oxidase ammonia and hydroxylamine

91
Q

how are MOB and AOB different in terms of NH2OH oxidation?

A
  • AOB evolved ability to use electrons from hydroxylamine oxidation via cytochromes c552 and c554 to quinone pool to drive energy production and cellular growth
  • methanotrophs cannot use electrons from NH2Oh oxidation bc no c552 and c554
92
Q

what created modular evolution of catabolism?

A

different catabolic lifestyle

93
Q

what are the types of chemotrophic organisms?

A
  • iron reducers (3+)
  • iron oxidizers (2+)
  • manganese reducers (4+)
  • manganese oxidizers(2+)
  • predatory bacteria
  • stalked bacteria
  • bioluminescent bacteria
94
Q

iron reducers

A
  • couple reduction of oxidized metal to cell growth
  • Fe3+: e acceptor
  • evolved ability to respire solid materials
95
Q

iron respiration in early life

A
  • prob existed in LUCA
  • prob evolved early in history life
  • some lineages, iron respiration was lost
96
Q

characteristics of iron reducers

A
  • insoluble external electron acceptor
  • contain outer membrane cytochromes
  • outer membrane cytochromes facilitate electron transfer to insoluble minerals (nanowires)
97
Q

famous iron reducing microoganisms

A
  • thermus
  • thermotoga
  • geobacter
98
Q

geobacter

A
  • contain pili that facilitate electron transfer to solid acceptors
  • pili have cytochromes that interacts with solid iron oxide
99
Q

manganese reducing microoganisms

A
  • coupling reduction of Mn4+ to cell growth
  • Mn4+ is electron acceptor
100
Q

who couple anaerobic methane oxidation to manganese reduction?

A

ANME family Methanoperedenaceae
- archaea reduce manganese (also use iron)

101
Q

microbial fuel cell

A

use metal respiration in biotech

102
Q

what are the two compartments of MFC?

A

anoxic and oxic

103
Q

anoxic compartment components of MFC

A
  • anode
  • fe3+ oxides
  • iron oxides build anode
  • microbes grow using organic compound
104
Q

oxic compartment components of MFC

A

cathode
- create H2O
- energy captured by oxic compartment and used to turn on light bulbs

105
Q

iron oxidizing microorganisms

A
  • evolved early in history
  • Fe2+ as electron donor
  • strongly affected by pH and O2
    stable iron pH = 6.4
    with O2 iron precipitates pH = 7.7
106
Q

what are the 4 functional groups of iron oxidizers?

A
  • aerobic, acidophilic
  • aerobic, neutrophilic
  • anaerobic chemotrophic
  • anaerobic phototrophic
107
Q

aerobic acidophilic iron oxidizer

A
  • repsire S^0
  • v low pH
  • Acidithiobacillus
  • Ferroplasma
108
Q

aerobic neutrophilic iron oxidizer

A

oxidation of iron creates stalk
- Gallionella

109
Q

anaerobic chemotrophic iron oxidizers

A
  • iron-nitrate pair potential metabolism
  • Aquabacterium
110
Q

anaerobic phototrophic iron oxidizers

A
  • purple and green non-sulfur iron oxidizing bacteria
  • Rhodobacter ferrooxidans
  • Chlorobium ferrooxidans
111
Q

magnetotactic bacteria

A
  • iron oxidizing
  • large cassette of genes that encode for enzymes involved in iron oxidation and creation of magnetosomes
112
Q

magnetosomes

A

intracellular structures that contain lipid bilayer and have own transporters
- oxygen sensing
- orient themselves toward Earth magnetic pool (aerotaxis, magneto-aerotaxis)
- cells align and migrate toward specific oxygen gradient

113
Q

manganese oxidizing microogranisms

A
  • reaction between Mn and O2
  • Mn oxidizing (e donor)
  • O2 reduced (e acceptor)
  • make own TEA
114
Q

how is TEA made?

A

multicopper oxidase (enzyme)
- makes Mn-oxide
- Mn oxide = protective coat
- Bacillus = famous Mn oxidizer

115
Q

predatory bacteria

A
  • vampirococcus (intracellular)
  • bdellovibrio (periplasmic)
  • myxococcus (social)
116
Q

Vampirococcus

A
  • attach to surface of prey
  • acquire nutrients from cytoplasm and periplasm
117
Q

Bdellovibirio

A

periplasmic predators
invade periplasmic of prey cells

118
Q

Myxococcus

A

social
- lyse prey and feed on their nutrients

119
Q

stalked bacteria

A
  • produce cytoplasmic extensions
  • stalks
  • hyphae
  • appendages
  • extrusions = prosthecae
120
Q

prosthecae

A

allow organisms to attach to particulate matter, plant material or other microoganisms in aquatic habitats
- reduce cell sinking

121
Q

Caulobacter

A

stalk bacteria
chemoorganotroph
stalk filled w cytoplams

122
Q

Gallionella

A

stalked bacteria
iron oxidizer
stalk composed of Fe3+

123
Q

bioluminescent bacteria

A
  • light emission - bioluminescence
  • marine enviro
  • some colonize special light organs of certain fishes and squids
  • produce light that animal uses for signaling, avoid predators and attracting prey
  • luminescence requires luxCDABE for luciferase
  • high population density only
124
Q

luciferase

A
  • produces light, alcohol and water
  • transcription of genes controlled via AHL inducer molecules
  • cross cell membrane of other cells and induce luciferase expression

Bio 322 (11 decks)

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