1
Q
what are the 2 ways microbial diversity can be considered?
A
- phylogenetic diveristy
- functional diversity
2
Q
phylogenetic diversity
A
genetic diversity if evolutionary lineage
- based on rRNA gene
3
Q
functional diversity
A
diversity of form and function
- physiological/metabolic
- ecological
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
5
Q
which phyla’s have anoxygenic photosynthesis?
A
Acidobacteria
Chlorobi
Chloroflexi
Firmicutes
Proteobacteria
6
Q
which phyla has oxygenic photosynthesis?
A
cyanobacteria
7
Q
what are the 5 morphological groups of cyanobacteria?
A
Unicellular(1)
Unicellular(2)
Filamentous(1)
Filamentous(2)
Filamentous(3)
8
Q
Chroococcales
A
- unicellular
- Binary fission
9
Q
Pleurocapsales
A
- multiple fissions
Unicellular
10
Q
Oscillatoriales
A
Filamentous
- no heterocysts
11
Q
Nostocales
A
Filamentous
- cellular differentiation
12
Q
Stigonematales
A
- filamentous
- branching cells
13
Q
cyanobacteria
A
not coherent
- Pleurocapsales is only one coherent
14
Q
multiple fissions
A
feature arose only ONCE in evolution
15
Q
which group of cyanobacteria does multiple fissions?
A
Pleurocapsales
16
Q
which 3 cyanobacteria share common ancestor?
A
Oscillatoriales
Nostocales
Stigonematales
- single origin of differentiation
- filamentous
17
Q
which cyanobacteria is the only one with branching?
A
- stigonematales
18
Q
how many times did branching arise in evolution?
A
once
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)
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
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
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
23
Q
hormogonia (dispersion)
A
- disperse in time of stress
- short motile filament separated easily from longer filament
24
Q
akinetes (protection)
A
- cells with thickened outer walls
- cells germinate from akinetes when conditions are better
25
storage structures
- cyanophycin: copolymeric strucutre made of aspartate and arginine, nitrogen storage product
- heterocysts: specialized structures for N fixation
26
what enzyme does nitrogen fixation and where?
nitrogenase in hetercysts
27
t or f: nitrogenase is oxygen sensitive?
true
28
how can cyanobacteria do anaerobic and aerobic process?
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
29
how does unicellular cyanobacteria fix N?
during night when photosynthesis not happening
30
what suppresses photosynthesis when N fixation occurs?
Trichodesmus
31
when did nitrogenase arise?
before oxidation of atmosphere by oxygenic photoautotrophs
- oxygen-protective mechanisms developed
32
purple sulfur bacteria
- H2S to run photosynthesis
- S^0 granules inside cell
- CO2 fixation
33
purple non-sulfur bacteria
- light = source of energy
- organic compounds source of C
34
2 families of purple sulfur bacteria
- chromatiaceae- granules inside, vesicular photosynthetic membrane
- ectothiorhodospiraceae- granules outside, lamellar photosynthetic membrane
35
how do purple non-sulfur bacteria conserve energy?
- fermentation
- anaerobic respiration
36
what is the key genera of purple non-sulfur bacteria?
- Rhodobacter
37
green sulfur bacteria
- 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
38
green non-sulfur bacteria
- lack of cultivation = not metabolically characterized
- filamentous and perform gliding motility
- Phylum Chloroflexi
- photoheterotrophs - organic C source or sometimes inorganic
39
what are chlorosomes?
pigment-rich bodies bound by thin membrane attaches to cytoplasmic membrane at the periphery of cell
40
exception organisms in green non-sulfur bacteria
- heliothrix - no chlorosomes and bacteriochlorophylls, more carotenoids
- thermomicrobium- unique membrane lipids (1,2- dialcohols), no ester or ether, cell wall made or proteins
41
what are the two type of metabolism done by microorganisms?
- assimilative
- dissimilative
42
assimilative
oxidation of sulfur compounds
- create organic sulfur compounds
43
dissimilative
reduction of sulfur compounds
- getting energy from sulfur compounds (respiration)
44
what organisms control the sulfur cycle?
- purple sulfur
- green sulfur
- sulfate reducers
- sulfur reducers
- sulfur oxidizers
45
sulfate reducers
- energy sources: H2, organic compounds
- bacteria: proteobacteria, firmicutes
- archaea: euryarchaeota
46
physiology of sulfate reducers
- obligate anaeroabes
- H2 or lactate
- use hydrocarbons
- produce H2S
- alternative metabolism: nitrate reduction, fermentation
47
famous sulfate reducers
- desulfomonas
- desulfotomaculum
- desulfotomaculum
- desulfobacter
- thermodesulfobacterium
- thermodesulfovibrio
- archea: archaeglobus
48
sulfur reducers
- energy source: H2, organic compounds
- Bacteria: Proteobacteria (3 groups)
- Archaea: Crenarchaeota
49
physiology of sulfur reducers
- obligatory anaerobes- H2 or organic compounds
- use formate, ethanol, propanol
- produce H2S
- alternative metabolism: aerobic (facultative)
50
sulfur oxidizer
- energy source: H2S and S^0
- bacteria: proteobacteria (3 groups)
- archaea: Crenarchaeota
51
famous sulfur oxidizers
- Acidithiobacillus ferrooxidans
- uses FeS2 as e donor
52
benefit of Acidithiobacillus ferrooxidans for mining
- oxidation of FeS2 releases iron
- bioleaching process
- bioleaching used for other metals
53
harmful effect of Acidithiobacillus ferrooxidans for mining
- bioleaching causes acidification and release toxic metals
54
what do many sulfur oxidizer use together?
H2S and O2
55
why can sulfur oxidizers use H2S and O2 together?
O2 dependent positioning
Anaerobic vacuole
Symbiotic association
56
O2 dependent positioning
- 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
anaerobic vacuole
- 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
symbiotic association
- Yeti crab
- eukaryotic host
- regulates levels of H2S and O2
- bacterium fixes CO2 for host
59
which organisms control nitrogen cycle?
- diazotrophs
- nitrifiers
- denitrifiers
60
what enzyme completes nitrogen fixation?
- nitrogenase
- O2 sensitive
61
which bacteria evolved ability to protect nitrogenase from o2?
diazotrophs
62
diazotrophs
- 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
famous diazotrophs
- azotobacter (free)
- azospirillum (free)
- rhizobium (symbiont)
64
how diazotrophs protect dinotrogenase?
- microaerophilic lifestyle
- specialized protective cells
- increased respiration and conformational protection
- alternative nitrogenase
65
microaerophilic lifestyle
- nitrogen fixation only if O2 level less than 2%
66
specialized protective cells
- heterocysts in cyano
- spatial separation of N2 fixation
67
increased respiration and conformational protection
- high O2 levels trigger synthesis of complex proteins (Shethna proteins)
- specialized proteins from shield around nitrogenase as protection
68
alternative nitrogenase
- regular nitrogenase uses Molybdenum as cofactor
- alternative uses Vanadium or iron
- two genes - results of duplication event (paralogs)
69
nitrifiers
- AOB and AOA
- NOB
- Commamox
70
AOB and AOA process
oxidize ammonia to nitrite
71
NOB process
oxidize nitrite ro nitrate
72
Comammox process
- oxidize ammonia to nitrate completely
73
_____ + _______ = complete nitrification
AOA/AOB + NOB
74
what is the process of nitrification?
NH3 > NO2 > NO3
75
physiology of nitrifiers
- aerobic
- fix CO2 via calvin cycle
- AOB begins with Nitroso-
- NOB begins with Nitro-
76
famous nitrifiers
- Nitrosomonas multiformis
- Nitrosomonas europea
- Nitrosomonas communis
- Nitrospira
- Nitrobacter
77
who performs anaerobic respiration?
- denitrifiers
78
what do denitrifiers produce?
gaseous forms of nitrogen
79
set of reductases
NO3 > NO2 > NO > N2O
80
nitrifier denitrification
NirK in AOB creates NO and N2O
- produces reactive nitrogen species (RNS) and may reduce availability for nitrite for NOB
81
Nitrosomonas europea
nitrifier denitrification in O2 low and O2-high conditions
82
what was abundant on early earth?
iron
molybdenum
83
what was the purpose of iron and molybdenum?
components of N2 fixing enzyme nitrogenase
84
what was one suggestion that nitrogen was not part of early form of life?
- gene complexity for nitrogen fixation
- high energy cost
85
what are the abundant enzymes for anoxic earth?
- hydrogenases
- cytochrome c proteins
- formate dehydrogenase
- nitrate reductase
86
were enzymes with class B transition metals functional?
no
87
what happened when sulfides reacted with transition metals?
no available for enzymes
88
MOB
use methane monooxygenase activated by oxygen to make CH3OH and create H2O
89
AOB
use ammonia monooxygenase activated by oxygen to make NH2OH and create H2O
90
what are great nitrifiers?
methanotrophs
- oxidase ammonia and hydroxylamine
91
how are MOB and AOB different in terms of NH2OH oxidation?
- 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
what created modular evolution of catabolism?
different catabolic lifestyle
93
what are the types of chemotrophic organisms?
- iron reducers (3+)
- iron oxidizers (2+)
- manganese reducers (4+)
- manganese oxidizers(2+)
- predatory bacteria
- stalked bacteria
- bioluminescent bacteria
94
iron reducers
- couple reduction of oxidized metal to cell growth
- Fe3+: e acceptor
- evolved ability to respire solid materials
95
iron respiration in early life
- prob existed in LUCA
- prob evolved early in history life
- some lineages, iron respiration was lost
96
characteristics of iron reducers
- insoluble external electron acceptor
- contain outer membrane cytochromes
- outer membrane cytochromes facilitate electron transfer to insoluble minerals (nanowires)
97
famous iron reducing microoganisms
- thermus
- thermotoga
- geobacter
98
geobacter
- contain pili that facilitate electron transfer to solid acceptors
- pili have cytochromes that interacts with solid iron oxide
99
manganese reducing microoganisms
- coupling reduction of Mn4+ to cell growth
- Mn4+ is electron acceptor
100
who couple anaerobic methane oxidation to manganese reduction?
ANME family Methanoperedenaceae
- archaea reduce manganese (also use iron)
101
microbial fuel cell
use metal respiration in biotech
102
what are the two compartments of MFC?
anoxic and oxic
103
anoxic compartment components of MFC
- anode
- fe3+ oxides
- iron oxides build anode
- microbes grow using organic compound
104
oxic compartment components of MFC
cathode
- create H2O
- energy captured by oxic compartment and used to turn on light bulbs
105
iron oxidizing microorganisms
- 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
what are the 4 functional groups of iron oxidizers?
- aerobic, acidophilic
- aerobic, neutrophilic
- anaerobic chemotrophic
- anaerobic phototrophic
107
aerobic acidophilic iron oxidizer
- repsire S^0
- v low pH
- Acidithiobacillus
- Ferroplasma
108
aerobic neutrophilic iron oxidizer
oxidation of iron creates stalk
- Gallionella
109
anaerobic chemotrophic iron oxidizers
- iron-nitrate pair potential metabolism
- Aquabacterium
110
anaerobic phototrophic iron oxidizers
- purple and green non-sulfur iron oxidizing bacteria
- Rhodobacter ferrooxidans
- Chlorobium ferrooxidans
111
magnetotactic bacteria
- iron oxidizing
- large cassette of genes that encode for enzymes involved in iron oxidation and creation of magnetosomes
112
magnetosomes
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
manganese oxidizing microogranisms
- reaction between Mn and O2
- Mn oxidizing (e donor)
- O2 reduced (e acceptor)
- make own TEA
114
how is TEA made?
multicopper oxidase (enzyme)
- makes Mn-oxide
- Mn oxide = protective coat
- Bacillus = famous Mn oxidizer
115
predatory bacteria
- vampirococcus (intracellular)
- bdellovibrio (periplasmic)
- myxococcus (social)
116
Vampirococcus
- attach to surface of prey
- acquire nutrients from cytoplasm and periplasm
117
Bdellovibirio
periplasmic predators
invade periplasmic of prey cells
118
Myxococcus
social
- lyse prey and feed on their nutrients
119
stalked bacteria
- produce cytoplasmic extensions
- stalks
- hyphae
- appendages
- extrusions = prosthecae
120
prosthecae
allow organisms to attach to particulate matter, plant material or other microoganisms in aquatic habitats
- reduce cell sinking
121
Caulobacter
stalk bacteria
chemoorganotroph
stalk filled w cytoplams
122
Gallionella
stalked bacteria
iron oxidizer
stalk composed of Fe3+
123
bioluminescent bacteria
- 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
luciferase
- 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
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