Evolution of microbial life Flashcards
1
Q
what are the 3 types of primary nutritional categories?
A
- photo-organo-autrotroph
- photo-litho-heterotroph
- chemo-organo-autotroph
2
Q
Why is the calvin cycle common in aerobes?
A
- common in aerobic autotrophs despite RuBiscCO being sensitive to O2
- requires 12 NADPH and 18ATP to reduce 6 CO2 to 1 glucose: LOT’S OF ENERGY
3
Q
what type of microbes use the calvin cycle?
A
organisms that have a high energy yield from chemo- or photo-lithotrophy
4
Q
best energy yield for chemolithotroph?
using what as TEA/pathway
A
using O2 as terminal electron acceptor
5
Q
best energy yield for photolithotroph
using what pathway?
A
oxygenic Z pathway
6
Q
Explain the earth’s early history:
-atmosphere
- what kind of trophes would we see rn?
- where would the living world be
A
- Atmosphere had no oxygen
- The exact composition is up for debate
- Most gases are coming from volcanic and geothermal activity.
- There is an abundance of metals, acting as an abundance of metals.
- There was no ozone (no oxygen), therefore no protection to UV.
○ Life probably would not be on the surface of the planet, therefore there was subsurface organisms that were not exposed to the light§ Likely an autotroph.
7
Q
what is the Miller-Urey experiment?
A
when energy is added, organic compounds can be formed.
- if you keep cycling the gasses around and give constant energy to primordial soup , organic compounds can be formed (prebiotics). `
8
Q
How do we take the prebiotic molecules (organic molecules) and condensing them in one place where a cell would be?
A
- Early organic molecules would be floating freely when primordial soup gets zapped with energy
- Macro-macromolecule interactions are more favourable than macromolecule-water interactions,
○ Under the right conditions, macromolecules will prefer to associate with one another than with water
§ Leads to liquid-liquid phase separation
○ You’ll get clumps of macromolecules separate from the water.
Under microscope, kind of looks like cells.
- Macro-macromolecule interactions are more favourable than macromolecule-water interactions,
9
Q
How are coacervates built and broken down?
A
- If you add more nutrients, the coacervates get bigger.
- When you apply a shear stress (movement of water, tides, in the ocean)…
○ The coacervates divide into smaller bits
○ You add nutrients and they get big again, they shear into small bits again, etc. - Based on physical processes only, we can see growth and division of coacervates.
- When you apply a shear stress (movement of water, tides, in the ocean)…
10
Q
why would metabolism evolve?
A
- When you think about early earth and prebiotic soup, there was probably a limited supply of spontaneously formed molecules.
- The protocell figured out how it can make more of these molecules by itself so that it can have an advantage compared to other things in the environment, because if you need something and it is limited in the environment, if you make it yourself then you will no longer run out and you can keep living.
11
Q
what is LUCA
A
LUCA: the last common ancestor among bacteria and eukaryota/archaea
12
Q
What are the 2 criteria for including proteins in LUCA?
A
- Present in at least two higher taxa of bacteria and archaea
- Its tree must recover bacterial and archaeal monophyly
13
Q
What is LUCA like then?
A
- LUCA has a membrane
- It will acquire carbon from Wood-Ljungdahl pathway for a source of carbon
- With our understanding of the carbon source… we know that LUCA has enzymes (CoA and Acetyl-Coa) for the Wood-Ljungdahl pathway.
- Took nitrogen gas for biosynthesis
- LUCA had DNA.
- Cofactors are there to help store the oxygen
- Energy: acetyl-phosphate (like ATP) that came from membrane bound ATP synthase.
LUCA is run on s
14
Q
Evidence that hydrothermal vents are a good source for life
A
Spontaneous thioester synthesis (common bond in biological molecules)
- H2 is abundant (for the Wood-Ljundhal pathway)
- Environment is acidic, so natural PMF
- Salt water (so you get this sodium proton system)
○ Get energy from bringing Na+ in, and then you send sodium out and proton in
§ Forming a natural PMF.
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15
Q
criteria for including proteins in LUCA (2)
A
- Present in at least two higher taxa of bacteria and archaea respectively
- Its tree must recover bacterial and archaea monophyly
16
Q
Why is there no evidence for metabolic pathways in LUCA?
A
- The Wood Ljungdahl pathway produces acetyl-CoA, so we don’t really need catabolic pathways to break down larger carbon molecules
- What we think of today as catabolic pathways likely evolved in reverse
- LUCA would synthesize acetyl-CoA and the cell eventually had to find a way to store the acetyl-CoA as a carbon storage (which is modernly known as catabolic pathways to build up thinks like glucose, sugars, etc.).
`
17
Q
Which three of the metabolic pathways might have evolved first?
A
- Start with little energy
Lower energy options for catabolism is: ED
18
Q
What are the three true catabolic pathways:
A
EMP, ED, PPP
19
Q
What is a problem with genome-based reconstruction?
A
- Horizontal gene transfer
- It is more likely that rather than one super cell that we all came from, LUCA as we think about it was likely a community of cells exchanging ATP, metabolites, etc and this community essentially evolved into life as we know it.
Not one super cell!
- It is more likely that rather than one super cell that we all came from, LUCA as we think about it was likely a community of cells exchanging ATP, metabolites, etc and this community essentially evolved into life as we know it.
20
Q
LUCA might be the last universal ancestor of all organisms, but because of HGT
A
It is not the last ancestor of all genes.
21
Q
At some point, the early community of cells needed to separate into archaea and bacteria domains.
How were bacteria and archaea hypothesized to differentiate into two domains?
A
- Wood-Ljungdahl pathway produces acetate, but a small change will cause it to produce methane rather than acetate.
- If you just swap a few enzymes, methane can be made from the WL pathway
- So some community of cells made acetyl-CoA and some made methane (Archaea)
- Therefore, we have distinguished archaea and bacteria
22
Q
How are stromatolites formed?
A
- cyanobacteria grow in a mat or biofilm, creating a layer of cells
- sediments deposit on top of the biofilm (biofilms are sticky) and/or cells cause minerals to precipitate, creating a layer of sediment
- cells migrate to the surface of the sediments for better access to sunlight, creating a new layer of cells
- the process continues indefinitely…
23
Q
Explain banded iron formations:
A
- Increase in iron, decrease in iron, cycling
- Dark bands form from iron deposition
- The light bands’ form from non-iron mineral deposition
Oxygenic photosynthesis evolved before cells evolved mechanisms for oxygen tolerance.
24
Q
What does banded iron formations tell us?
A
That oxygenic photosynthesis evolved before cells evolved mechanisms for oxygen tolerance.
25
Do stromatolites still roam the earth?
They still form in a select few places but are very uncommon.
26
Do banded iron formations still roam the earth?
No because we have an oxygen rich environment and iron is not rich in the ocean to produce enough solid layers of rock.
but there are still some stromatolites.
27
What is the great oxidation event?
- When the atmosphere went from very little oxygen to lot's of oxygen
- This was 2.2 billion years ago
- Oxygen slowly accumulated and was neutralized by iron in the ocean for 1 billion years
But life evolved to use it once it became available.
28
Where did eukaryotes come from?
- Endosymbiosis theory
- Eukaryotes arose when a pre-eukaryote engulfed a bacterial endosymbiont, which became the mitochondrion.
- Driven by bioenergetics and survival necessity : O2 concentrations were increasing globally, a heterotrophic anaerobe engulfed an aerobic bacterium.
One lineage of eukarotes later engulfed a cyanobacteria, which became the chloroplast.
29
what archaeon swallowed the bacteria? and why?
asgard archaea
carry many eukaryotic signature proteins (ESPs)
30
Why is the eukaryotic cell line metabolically limited?
- Because eukaryotes arose from one archaeal group that engulfed ONE bacterial group (or two for chloroplasts)
Therefore, their metabolism is limited
31
Why is this not a problem in terms of energy?
- The mitochondria allows eukaryotes to access a massively larger energy supply
More energy= more possibility for growth = multicellularity
32
Summary: early microbial evolution was a quest for energy
- LUCA needed to harvest energy (hydrothermal vents)
- Phososystems provide a great way to obtain abundant energy
- Oxygenic photosystems produced more energy than anoxygenic photosystems and quickly became more favourable
- When O2 was available, it was better terminal electron acceptor and became more favourable than anaerobic metabolisms
Mitochondria enabled early eukaryotes to adapt to oxygen and increasing available amounts of energy.
33
what is the purpose of taxonomy?
- ensures that scientists around the world use a universal label for every organism they discuss or study
- organizes vast amounts of information about different microbial species with diverse metabolic abilities
34
what are the 3 parts/ systematics of taxonomy?
1. classification (arranging of organisms into groups (taxa))
2. nomenclature (assigning names to taxa)
3. identification (determining the taxon to which a new isolate belongs)
35
what system are microbes named by?
difference between naming animals and microbes?
- follows traditional Linnean taxonomy
- microorganisms are not classed by physical trait, but metabolic (bioenergetic) traits.
36
what 3 steps were followed to historically name organisms by taxonomy?
1. isolate a species
2. perform numerous biochemical tests and microscopy techniques to determine:
- cell morphology
- colony morphology
- C, N and energy
- Cell wall/membrane composition
- Motility
3. compare the Bergey's Manual of Determinative Bacteriology
INCREDIBLY LABOR-INTENSIVE!
37
Today, how do we normally name organisms ?
- phylogenetic approach
- usually comparing 16s rRNAn sequences
38
what indicates a species match vs novel species?
>97% similarity to existing sequence indicates species match
<95% similarity to an existing sequence indicates a NOVEL species
39
what is the Shine- Digarno Sequence in mRNA
why is 16s rRNA gene required for translation?
- 16s binds the Shina Dalgarno sequence in mRNA
-16s gene help mRNA bind to ribosome
- 16s rRNA gene is highly conserved because its required for translation in all bacteria and archaea
40
are all parts of the 16s rRNA gene equally important?
no. he hypervariable regions have mutation rates that are higher (less important for translation).
41
is the 16s rRNA gene fully conserved?
- conserved enough to easily find and sequence
- different enough to provide taxonomic information
42
what are 4 common genotypic analysis?
1. GC content
2. Multicocus sequence typing (MLST)
3. DNA DNA hybridization
4. whole genome sequencing
43
how is GC content used for genotypic analysis
- comparing the percentage of GC base pairs
44
what is multilocus sequence typing (MLST)
- you compare housekeeping genes
45
what is DNA DNA hybridization
take the DNA from species A and B
mix the DNA
heat it up to denature, lower temp to anneal
different species wont anneal together properly due to lots of bp mismatching
46
what is the best approach for genotypic analyses?
whole genome sequencing
47
what is the gold standard in taxonomy?
polyphasic taxonomy.
using both phenotypic and genotypic methods
48
which 4 phylums are the most specious?
1. proteobacteria
2. bacteroidetes
3. actinobacteria
4. firmcutes
49
what are two thermophilic phyla?
Aquifae and thermotogae
50
where to find thermophilic bacteria?
hot springs, sulfur pools, thermal ocean vents
51
what are Deinococcus Thermus
they have thick cell walls and two membranes , therefore HIGHLY RESISTANT TO ENVIRONMENTAL HAZARDS
52
what are cyanobacteria?
abundant, windespread carbon fixers that use oxygenic photosynthesis coupled to the calvin cycle. many species can fix nnitrogen.
53
what is chlamydiae
obligate intracellular parasite of eukaryotes.
cannot synthesize its own ATP even
54
what is special about spirochaetes?
unique cell morphology and mode of motility.
55
what are actinobacteria?
high GC, gram-positive phylum. Originally belived to be fungi because they grow MYCELIA
56
what are firmicutes?
low GC_ Gram positive phylum. Metabolically diverse.
57
what are bacteroidetes?
Gram negative, heterotrophic.
58
what phylum is the anammox phylum?
planctomycetes
59
Green bacteria: chlorobi vs chloroflexi
chlorobi: green sulfur bacteria
- anoxygenic photosystem 1
chloroflexi: green non - sulfur bacteria
- anoxygenic phososystem II
- 3 hydroxyproprionate bicycle.
60
what are green bacteria?
use chlorosomes as their light harvesting structure. this is an efficient mechanism for absorbing light at lower intensities than other prototrophs
61
what are the 3 classes of proteobacteria?
alphaproteobacteria
betaproteobacteria
gammaproteobacteria
62
what type of bacteria (phylum) is peligabacterales (SAR11)
what do you know about them?
- Alphaproteobacteria
-heterotrophic clade that accounts for one quarter to one half of all bacterial cells int eh ocean.
63
what type of phylum does Rhizobium belong to.
what is rhizobium?
belongs to alphaproteobacteria
nitrogen-fixing symbiont of plant roots
64
what type of phylum does copiotrophs, Burkholderia and thiobacillus belong to
belongs to betaproteobacteria
65
who is found in gammaproteobacteria?
many enteric bacteria, like E.coli
66
proteobacteria: Chromatiales vs Rhodospirillacaea
chromatiales: purple sulfur bacteria
rhodospirillacaea: purple non-sulfur bacteria
67
what is the candidate phyla?
extremely large group of uncultured microorganisms
most members have a relatively small genome, small cell size and restricted metabolic capacities.
68
Archaean DPANN: noticeable features
DPANN is extremely small
as small as could be while still being a live cell.
69
what are Asgard Archaea?
the most "eukaryote-like" prokaryotes
70
what are TACK archaea?
1- thaumarchaeota
2- Aigarchaeota
3- Crenarchaeota
4- korarchaeota
71
archaea: TACK
thaumarchaeota notable features
chemolithoautotrophic "ammonia oxidizing archaea", mostly marine
72
archaea: TACK
crenarchaeota
abundant, thermohillic archaea
73
what are the noticeable features of Archaea: Euryaarchaeota?
- diverse bioenergetic abilities:
- methanogens (methano-, common in diverse anaerobic habitats)
-halophiles (haloarchaea), common in salty areas.
74
what are 3 eukaryotic supergroups?
Archaeaplastida: green algae, red algae, plants
Amorphea: animals, fungi, amoebe
TSAR: mixed bag: cilliates, brown algae, diatoms,
75
what are arbuscular mycorrhizae?
fungi found in 80% of plant roots
help the plant bring nutrients into the plant, gives it carbon sources.
