1
Q
What are the three major habits that most prokaryotes reside in?
A
Aquatic, soils, sediments in the subsurface
2
Q
How many prokaryotic cells are there on earth
A
10ˆ30
3
Q
What was Robert Hooke’s contribution to microbial ecology?
A
Published Micrographia. Used a 20 fold magnification microscope to look at and draw microorganism
4
Q
What was Van Leeuwenhoek’s contribution to microbial ecology?
A
Discovered tiny organisms in an infusion of pepper and water. Using 300 magnification microscope, examined scrapings from his body
5
Q
Who disproved spontaneous generation and how?
A
Louis Pasteur. Pasteurization. Using a flask with a bend in the neck, so only fresh air could get in (no microbes). Heat up solution, no microbial growth until turning flask so contaminated air could get in.
6
Q
What are Koch’s postulates
A
- The organism must always be present in the case of disease
- The organism must be isolated from a host containing the disease and grown in pure culture
- Samples of the organism taken from pure cylytre myst cause the same disease when inoculated into healthy host
- Organism must be isolated from inoculated animal and identified as same original organism
7
Q
What are some challenges of Koch’s postulates
A
Asymptomatic infections, contextuality, culturability, multifactorial disease, pathogenicity present only in some strains, in host evolution
8
Q
What was Ferdinand Cohen’s contribution to microbial ecology?
A
Tried to classify microbes based on shapes, liquid cultures, discovered spores
9
Q
What is the benefit of 16s sequencing?
A
Allows to sequence prokaryotes using ribosomes
10
Q
Why do we use ribosomes to study life?
A
All organisms have them, sequences generally conserved, perform sone key functions, adequate length in evolutionary history
11
Q
When was the GOE
A
2.4 bya
12
Q
When did anoxygenic photosynthesis evolve
A
3.4 bya
13
Q
When did oxygenic photosynthesis evolve?
A
2.7. bya
14
Q
H2 can be reduced to…..
A
H2O
15
Q
H2O can be reduced to
A
1/2 O2
16
Q
What is some evidence for an RNA world
A
RNA chains found in all life today, free pairing of nucleotides in water, selection acts on RNA nucleotides, ribozymes
17
Q
What are the goals of catabolism and anabolism (jointly)
A
Extract electrons, store energy, and use it to build cellular components
18
Q
What are chemoorganotrophs
A
Organisms that get their energy/electrons from organic compounds
19
Q
What are chemolithotrophs
A
Organisms that get their energy/electrons from inorganic compounds
20
Q
What is a TPC
A
Thermal performance curve. Curve that tells us how well/poorly microbes grow (fitness) at certain temperatures
21
Q
What is Topt on a thermal performance curve?
A
Optimal temperature for growth. Temperature at which fitness is highest
22
Q
At low temperatures, do fast growers or slow growers win?
A
Fast
23
Q
At medium temperatures, do fast growers or slow growers win?
A
Coexistence
24
Q
At high temperatures, do fast growers or slow growers win?
A
Slow
25
What are mechanisms that move valuable metabolites out of the cell?
Cell lysis, cell envelope metabolism, EC degradation of complex molecules, passive/facilitated diffusion, active transport
26
What is the difference between gram + and gram - bacteria
Gram positive bacteria have a thicker layer of peptidoglycan that surrounds the whole cell. There is only 1 membrane, plus the peptidoglycan layer.
Gram negative bacteria have a thinner layer of peptidoglycan between 2 membranes.
27
What are the three types of community interaction?
Pairwise, interaction chain, higher order interaction
28
What is the difference between the per capita effect and the density effects?
Per capita effect describes how much an individual affects another, while the density effect describes how changing the # of species affects a community
29
What are the assumptions of the consumer-resource model
Species only interact through resources, no interactions between resources
30
What is the difference between a state and controlling variable
A controlling variable is the environmental driver, state variable is continuous and affected by state variable
31
What are the 2 contexts that can be described as alternative stable states
1) Environment fixed, but communities can exist under multiple possible configurations
2) Environment changes impacting state of the community
32
What are some examples of state variables?
Abundance of species, species richness, biomass, spatial coverage, respiration rate
33
How can a community shift from one state to another?
Shift in state variable, or shift in environmental driver (control variable)
34
How does a shift in the state variable affect a community?
More than one state simultaneously exists under same environmental conditions
Community moves from one state to another by a sufficiently large perturbation to the state variable
35
How does a shift in the controlling variable affect a community?
Community moves to the other state because environmental variable controlling the state variable changes. Not all states have to be present at all times.
36
What is resilience, and what affects resilience (graphically)
Steepness of slope - affects return time of ball to lowest point of basin. the slower the ball returns to the bottom (shallow basin), the higher the probability that even a small perturbation pushes it to other basin.
Area of basin - size of perturbations. The larger the basin, the bigger the perturbation needed to push the ball outside the basin. Changes in basin size only possible in case of changes in environmental controlling variable
37
What does it mean to have high resilience
High recovery rate to small perturbations
38
What is hysteresis
When a system's history influences its current state. Response is folded backwards for a range of conditions. System shows 2 alternative states separated by an unstable region.
39
What are priority effects
Notion that the order and timing of species arrival (assembly history) in communities affects species composition and interactions
40
What does assembly history effect?
Diversity, community structure
41
What is assembly history
The order and timing of species arrival
42
What is niche preemption
early-arriving microbes use up resources (like nutrients or space), leaving less for later arrivals and limiting their abundance or preventing them from colonizing
43
When are the oldest rocks + life dated to? How?
3.8-4 bya. Using carbon isotopic ratios
44
What is the most likely first metabolic pathway?
Chemolithoautrophy --> using inorganic compounds for energy and carbon fixation
45
What were the likely electron donors and carbon sources in the first metabolic pathway?
H2 as an electron donor, and CO2 as a source of carbon
46
Why dow e think that H2 and CO2 were part of the first metabolic pathways?
Early earth (hydrothermal vents) had abundant H2, CO2, Fe2+, and sulfure compounds
Modern, deep branching archaea and bacteria use these metabolisms
47
Is anoxygenic photosynthesis considered the first most probably metabolism
No
48
When did anoxygenic photosynthesis evolve?
Between 3.5 and 3.4 bya
49
Which evolved first, anoxygenic or oxygenic photosynthesis
Anoxygenic
50
What is evidence for oxygenic photosynthesis developing from anoxygenic photosynthesis?
PSII is closely related to the reaction center found in purple bacteria. It has an additional protein that uses manganese atoms (oxygen evolving complex) to split water
The structure of PS1 is similar to that of green sulfur bacteria
Some algae and cyanobacteria can carry out cyclic phosphorylation using only PS1 (aka anoxygenic photosynthesis)
51
When was the great oxygenation event?
Between 2.5 and 2.3 bya
52
What is some evidence for the GEO in rock record
Red soils on land and disappearance of easily oxidized minerals from anccient stream beds
Disappearance of NMD sulfure isotope fractionations in sedimentary rocks deposited after 2.3-2.4 bya. For signals to be generated and preserved in rock record requires very low atmospheric oxygen levels (<.001% of present atmospheric level)
53
What is the evidence that oxygenic photosynthesis predates the GOE?
Banded iron formation (oxidized iron)
Microbial fossils and stromatolites (simple morphologies, hard to link them to specific metabolisms like oxygen producing photosyntheisis)
Biomarker records --> cyanobacteria 2.7 bya. molecular fossils of lipids appear in 2.7bya rocks
54
Other than oxygen, what other electron donors could have powered the production of organic carbon to marine sediments
H2S, Fe2+, H2
55
Why did it take so long for O2 to build up to .1% PAL
Initially bio O2 production was offset by abiotic and biotic consumption (rxns with reduced compounds from interior of earth). Delivery of these compounds to the ocean and atmosphere must have decreased, becoming subordinate to O2 production.
56
What are the metabolic requirements of all microbes?
H2O to perform metabolic reactions.
Sources of carbon and other nutrients (nitrogen, phosphorous) with which they can make macromolecules
Free energy, that s available to do work
Reducing power (source of e-) to generate free energy and fuel biosynthetic reactions
57
E- acceptors get...
Reduced
58
E- donors get...
Oxidized
59
What is catabolism
Employing exergonic rxns to drive the synthesis of ATP. Couples ATP synthesis with release of reducing equivalents from a redox
60
What is anabolism
Consumes ATP and anabolic substrates to produc cellular components
61
Metabolism relies on the movement of ________ from ______ ____ to ______ ________
electrons, electron donors, electron acceptors
62
How is change in free energy expressed
deltaG nought
63
What is generated by catabolic reactions
Free energy
64
What are common carriers for electron transfer?
NAD+ (NADH is reduced compound)
65
Even exergonic reactions will sometimes not proceed spontaneously. How do we get over this energy barrier?
Catalysts, such as enzymes
66
Name two common redox couples
2H+/H2
(1/2 O2)/H2O
67
What are the redox couples involved in photosynthesis?
CO2/C6H12O6
(1/2 O2) / H2O
68
What are standard conditions
ph 7, 1 atm, T= 25 C, all solutes at molar concentrations
69
Are favorable reactions endergonic or exergonic
Exergonic
70
What is bacterial growth rate
Flux of mass through these (cellular) processes
71
What are the three processes/categories that the cell must allocate resources towards
Ribosomes (translation), metabolism, and everything else (housekeeping)
72
What are the assumptions of growth rate laws?
Cell is in stead exponential growth, phiQ (housekeeping biomass) is condition-independent
73
Describe each part of the following equation:
phiR = phiMax - gamma/Kn
phiR : Fraction of mass allocated to ribosomes
phiMax: 1- phiQ (phiQ = mass allocated to housekeeping)
gamma: growth rate
Kn: Nutrient quality
74
What growth equation can help us predict results of experiments (with E coli)
phiR = phiMax - gamma/Kn
75
What are some complications of the growth rate equation for e coli that we learned in class?
Tested only on e coli. Slow growers might behave differently
Valid only in exponential growth
Nutrient quality not an intrinsic property of a nutrient, but a self determined property
Proteins that dont generate flux in current conditions might be produced in prep for next condition
76
How do we infer growth rate from genomes
rRNA operon copy number
Codon usage bias (fast growers preferably use codons that are translated by more abundant tRNAs)
77
What happens at temperatures higher than Tops
Denaturation of proteins sets in, causing irreversible damage to cellular structures and a sharp decline in growth rate
78
Which life forms are found at temperatures above 100C
Bacteria and archaea
79
What are the different classifications for prokaryotes based on temperature
Psychrophiles, mesophiles, thermophiles, hyperthermophiles
80
What is the relationship between Topt and r (growth rate)
Hotter is better. Species adapted to higher temperatures show higher max growth rates
81
What is the relationship between thermal niche and environmental niche
Species that grow in more temperate regions have wider TPCs
82
What is the arrhenius growth equation
r(T) = ae^(-Ea/KbT)
83
At high growth rates, in the presence of oxygen, does e coli favor fermentation or respiration
Fermentation --> faster rate of ATP production
84
Which species benefit from temp increase
Slow growers. Fast growers Win at low temps, coexistence at temperate temps, slow wins at higher temps
85
What are the different kinds of species interactions (based on positive vs negative)
Mutualism, Commensalism, neutralism, amensalism, exploitation (parasitism), competition
86
Evidence for positive interactions dominating?
Large amounts of auxotrophs, who rely on crossfeeding
Parasitism is common, and parasitism benefits one species
87
Evidence for negative interactions dominating?
Foster and Bell: vast majority of the species in pairwise interactions had very low productivity as compared to that of their respective monocultures. This suggests a high occurrence of competitive interactions, because fitness is decreasing after being paired with other microbes.
Granato et al: bacterial warfare; the diversity of bacterial weapons (releasing toxins, antibiotics, physical “weapons” that harm other bacteria), the evolution of these weapons, and the broad range of methodology when it comes to combat (suicide, reciprocation, etc.)
88
Why do we mostly detect negative interactions in pairwise coculture studies?
Isolation techniques favor phototrophic bacteria, disruption of networks based on diffusion over small spatial scales, storage effects, context dependency, dynamism of interactions
89
How does crossfeeding occur
Metabolite externalized by producer and consumed by recipient, metabolite assimilated or participates in energy transformation, fitness of recipient / consumed altered by the transfer of the metabolite, transfer occurs between genotypically or phenotypically distinct (sub)populations
90
What colors do gram positive and negative bacteria stain as?
Gram positive - blue
gram negative - red
91
Why are metabolites leaked/externalized?
Crossfeeding, physiological role (maintain homeostasis broadly)
92
What is a bottom up model for community assembly?
Pairwise interactions should predict community assembly. AKA if two species can be cocultured and survive, they should be able to coexist in a multispecies community
93
What is a top down model for community assembly?
Larger communities should inform pairwise interactions. AKA all species living in a multispecies community should survive when cocultured.
94
What is the assembly rule
Species A will exclude species B in community assembly if A excludes B in pairwise competition (top down
95
How do we define a resource
Factor that leads to higher population growth rates as its availability is increased. Its consumed by a population
96
What are the key ingredients of a consumer resource model?
Dynamics of species: growth rate as function of resources - (mortality rate)
Dynamics of resources: supply rate - consumption rate
97
In a consumer resource model, which two variables are constant
Death rate and supply rate
98
What are the assumptions of a consumer resource model
Species only interact through resources, resources not interactive
99
What is the ZNGU for a species
The set of nutrient/resource conditions at which growth rate and death rate are equal
100
What are different ways of measuring diversity
Species richness, Shannon wiener (entropy), Simpson
101
How do we quantify the relationship between simpson and shannon wiener?
Hill numbers. Hill number of q= 1 is shannon wiener, q = 2 is inverse simpson
102
If q=0 is the hill number what does this mean?
Species richness. Counting species without weighing species by their abundance
103
What is the difference between shannon wiener and simpson?
Shannon wiener tells you about how even the diversity is, while simpson tells you about species dominance
104
For hill numbers, if D=S, what does this mean?
All species are equally abundant
105
What are good graphic tools for measuring diversity
Species abundance distribution and rank abundance distribution
106
What is the difference between SAD and RAD
Species abundance distribution: Abundance vs. # of species
Rank abundance distribution: rank vs. p
RAD better to explore patterns of commonness and rarity
107
What are some major environmental variables that shape microbial diversity
Salinity, temperature, nutrients
108
When quantifying diversity, what do we count?
OTU - operational taxonomic unity; organisms with 16S rRNA genes that are > 97% similar
ASV - amplicon sequence variant - Any one of inferred single DNA sequences recovered from a high throughput analysis of marker genes: oligotypes. Two sequences (organisms) can differ by as little as 1 nucleotide
109
What is the paradox of the plankton
a limited number of resources in aquatic environments support an unexpectedly large diversity of plankton species
110
What are some explanations of LDG gradients?
Physiological tolerance hypothesis, kinetic energy hypothesis, productivity/resources hypothesis, environmental stability hypothesis
microbial ecology
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