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Micro 450 > Unit 2 > Flashcards

Unit 2 Flashcards

1
Q

define ecology

A

oikos: family household
logos: study
not environmentalism and not natural history

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2
Q

natural history versus ecology

A

nat his: direct observations, purely descriptive

Eco: tests a hypothesis, is a science

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3
Q

why is understanding ecology important (5)

A
  1. understand how the world works
  2. responsibility as earth’s gaurdians
  3. sustainability, ecosystem services
  4. applications
  5. human health-microbiome, emerging diseases
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4
Q

ecophysiology

A

deals with the function and performance of organisms ni their environment
attempts to understand the physiological mechanisms by which organisms confront constraints in the environment

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5
Q

Niche

A

environmental conditions that allow a species to satisfy its means.
pattern of living/job not a habitat
determined by metabolic properties of the organism

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6
Q

2 components of niche

A

requirements

impact to the ecosystem

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7
Q

fundamental niche

A

conditions under which an organism can live without competition

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8
Q

realized niche

A

conditions in which the organism actually does live
narrower than fundamental niche
also called competitive refuge

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9
Q

environmental constraints of niches

A 
nutrients (N, C, S)
electron acceptors
temperatures
osmotic pressure
intensities of light
pH
bile acids (toxic to bugs, antimicrobial)
host-produced antimicrobials
pressure
salinity
fluctuation in nutrients (hibernating animals)
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10
Q

adaptations to temperature

A

cold-tolerant microbes: very flexible enzymes because of lots of alpha helixes, few beta sheets
heat-tolerant microbes: different protein structures that make the enzymes more rigid at lower temperatures and functional at high temperatures.

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11
Q

methanogens and SRB

A

both consume H2 gas
rarely coexist because availability of electron acceptors is the limiting factor. If sulfate is present, SRB will outcompete.

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12
Q

antimicrobial peptides

A

AMPs
part of innate immune response
kill gram negative and positive bacteria, envelope viruses and fungi, and transform cancerous cells.

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13
Q

specialists versus generalists

A

specialists: narrower niche. B. thetaiotamicron
generalists: able to adapt better to changing conditions E. rectale

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14
Q

Rhodopseudomonas palustris

A

member Rhizobiales, alphaproteobacteria

model organism to study metabolic diversity and adaptations to changing environments

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15
Q

How to determine potential niche of a new species of bacteria from Lake Mendota?

A

sequences genome to determine possible functions based on proteins/enzymes it forms to determine fundamental niche
sample many other places in lake to see if the organism is there to determine realized niche

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16
Q

Culture-dependent approach

A

advantages:
inexpensive, have stock to work with in the future
disadvantages:
not yet culturable organisms, difficult to distinguish species based on morphology or chemical traits

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17
Q

16S rRNA sequences with Sanger

A

1.5kb gene, Sanger output 700-900 bases
low-throughput (one sequence at a time)
high accuracy
shallow sequencing of a sample

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18
Q

16S rRNA with high-throughput gene sequencing (Illumina)

A

Pros: inexpensive, relatively simple, high throughput
Cons: short reads=low resolution, requires access to computer cluster, PCR bias, sequencing errors create artificial diviersity

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19
Q

How to find culturable fraction of community?

A
  1. sequence all DNA of a sample to determine what is there
  2. grow sample on plates and collect DNA from each colony
  3. compare number of types between two thigns
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20
Q

Community Fingerprinting: Denaturing Gradient Gel ELectrophoresis (DGGE)

A

extract DNA–>PCR 16S using primers with GC clamp–>electrophoresis PCR products (which also have clamp) on vertical gel.
high concentration GC fragments denature later, low concentration GC fragments denature earlier in gel.
used for comparison of samples. each lane is one organism’s gene (does not need to be 16S rRNA) fragment
can cut out band and sequence it to determine identity.

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21
Q

Terminal Restriction Fragment Length Polymorphism Analysis (TRFLPA)

A

extract DNA–>PCR 16S with labeled primers–>cut DNA with restriction enzymes–>run on RFLP gel
also used for comparision.

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22
Q

limitations to 16S methods

A

dead cells’ DNA still matters
extra steps are required to learn the species (band methods)
no insights into functions, interactions, or structural organization of communities

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23
Q

FISH

A

you know dis.

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24
Q

laser capture microdisection

A

FISH first
can collect single cell of interest to isolate DNA
incredibly time consuming

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25
Q

Pros and Cons of FISH

A

Pros: tells relative abundance and potential interactions
Cons: low through-put, laborious and time consuming, dead cells count

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26
Q

method metatranscriptomics and purpose

A 
isolate RNA 
remove rRNA
make cDNA of remaining mRNA
sequence and remove low quality reads
functional analysis (BLAST, KEGG, CAZy)
Annotated reads

learn about metabolic activities. to analyze compare abundance of expressed functions in the microbiota for different samples

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27
Q

Limitations of metagenomics

A 
DNA from dead cells counts
presence of gene does not mean there is activity from it
costly 
requires a lot more sequence than 16S
we dont know what most genes do.
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28
Q

Transcriptomics limitations

A

most expensive method
method works well for E. coli but not other things
large dynamic range of mRNA in cell=must sequence really deep to get information on genes expressed at low levels
we dont know what most RNA do.

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29
Q

TnSeq

A

identifies genetic determinants of growth at a large scale
insert plasmid into a population of cells.
determine where transposon inserted.
put cells with transposon insertions into different conditions and see how levels of levels of Tn inserts change.
used to determine realized niche

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30
Q

Dantas method

A

chop of genome of euk. cell
insert each piece into Tn and put into E. coli cells
expose cells to trait you are trying to find
cells that survive, sequence all DNA to see what euk. DNA is there.

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31
Q

RNA-seq

A

compares RNA levels in two separate conditions and sees what changes.
determines niches i think.

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32
Q

Symbiosis

A

relationship between two organisms that live in an intimate association.
no implications about outcome

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33
Q

Commensalism

A

no benefits, other unaffected.
hard to document/have cryptic costs and benefits
microbe-animal associations frequently

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34
Q

Microbe commensalism example

A

B. thetaiomicron produce acetate

E. ractale uses acetate to make butyrate

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35
Q

importance of Parasitism

A

influence host fitness by taking resources
mediate competition/influence community ecology
selection agent favoring sexual recombination: makes offsprings genetically unique, harder to parasitize

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36
Q

endoparasites

A

inside body of the host

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37
Q

ectoparasite

A

live outside body of host

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38
Q

Bdellovibrio

A

predatory, parasitic and bacteriolytic microorganism
parasite of other G-bacteria
modified host cell wall to enter and replicate.

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39
Q

Mutualism

A

relationship results in net positive for all organisms

services cost organisms but result in benefit=mutual exploitation

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40
Q

effects of mutualism on populations, individuals

A

increase birth rate
decrease death rate
increase carrying capacity for population

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41
Q

Types of goods/services exchanged in mutualism

A

food (energy and nutrients)
protection from predators, parasites
shelter
dispersal (seeds)

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42
Q

Mutualism degrees of dependence

A

obligate: cant survive without relationship
facultative: relationship not required but is beneficial

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43
Q

Degrees of specialization in mutualism

A

specialist: associates with only 1 or a few species
generalist: no species specificity
* *one partner could be specialist and the other generalist**

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44
Q

Context specifics for mutualism

A

density dependence: more benefit if higher density of one partner
abiotic conditions: especially for shelter

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45
Q

why cooperation should not exist

A

evolution selects for cheating not for altruism

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46
Q

viral mutualistic symbioses

A

some viruses provide essential functions to host (bacteria, insects, plants, fungi, and animals)

reasons:
1. long association has made virus essential
2. viruses attenuate diseases caused by other viruses/pathogens
3. helpful to kill competitors
4. help host adapt to extreme environments

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47
Q

wasp-virus mutualism

A

virus in wasp genome suppresses larva immune system allowing wasp eggs to hatch
virus gets to replicate

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48
Q

conditional mutualism/natural weapons

A

many bacteria contain lysogenic virus that fends of lytic forms of virus=helpful
if lysogenic virus goes lytic, it kills host

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49
Q

Dichanthelium grass

A

can grow above 50C

requires fungi Curvularia prouberata

50
Q

Syntrophy

A

microorganisms cooperate to metabolize compounds that neither partner could alone
chemical outcome of cooperation different from what organisms could do on their own.
Examples:
Hydrogen metabolizers use H2 to other bacteria can produce acetate.

51
Q

Sulfur syntrophy

A

Desulfuromonas acetoxidans: use acetate and elemental S, produce S2- which is poison to it
Green sulfur bacteria (Chlorobium): use S2- and CO2 to make elemental sulfur and acetate

52
Q

Symbiosis as a continuum

A

categories are not discrete
all relationships have costs to each partner, despite benefits
costs and benefits change over space and time

53
Q

H. pylori continuum

A

prevalence greatest in less developed countries, low in developed nations
small amount of infected get cancer but presence also reduces risk of allergies, IBS

54
Q

why should we care about symbiosis?

A

ecosystem function
agriculture production
diversity
human health

55
Q

What is an individual?

Why is that important?

A

in plant and animal ecology: easy. can determine niches, interactions, densities based on individuals.
In microbial ecology: must consider filament-forming, biofilm-forming clones, swarms. How to count?
important to determine fitness and health, abundance, distribution, interactions and for medicine, agriculture, and industry

56
Q

3 concepts of the individual

A
  1. numerical
  2. genetic
  3. ecological
57
Q

numerical individuals in microbiology

A

discrete, countable independent unit
CFUs: 1 cell forms a colony, uncultured microbes can’t be counted this way
Florescent stains: chains of cells–how to count?

58
Q

genetic individuals in microbiology

A

Genet=a single genetic unit. best for macroorganisms because implies that genotype is stable over time. not true for bacteria
Ramets=individual colony or clone

59
Q

ecological individual in microbiology

A

follows individual through its life cycle from birth to death
binary fission: identical offspring-who is parent who is offspring?
important to demonstrate major changes in morphology, ploidy, or other

60
Q

strain versus isolate

A

isolate: an individual population, strain, or culture obtained by or resulting from selection or separation
Strain: a genetic variant

61
Q

define population

A

collection of individuals of same group/species that inhabit a specific geographic location at a specific time.

62
Q

why care about populations

A 
fisheries/wildlife management
combat parasites, pests
conservation
detect, control epidemics
understand dynamics of infections
63
Q

properties of a population

A

size
density
patterns of distribution
age structure

64
Q

Geometric growth/per capita growth/constant growth

A

leads to exponential growth
expected in ideal conditions with ample resources
invasive species, population recovery, viral/bacterial populations during infection, disease outbreaks,

65
Q

carrying capacity

A

K
equilibrium population size.
maximum number of individuals an environment can support
is a line but populations oscillate around it

66
Q

why does per capita growth decrease with population density?

A

stronger competition for resources
increase death rate
reduction of birth rate

67
Q

logistic growth

A

accounts for carrying capacity

describes bacteria in liquid culture well

68
Q

delayed density regulation

A

increases in population density cause population to crash when there is competition for resources

69
Q

population dispersion patterns

A

clumped: patchy distribution of resources or attraction between individuals
uniform: territorial or antagonistic interactions between individuals
Random: random distribution of resources

70
Q

Why is colony growth not exponential?

A

only bacteria near edge of colony divide

resources near edge of colony farther away and high concentration of waste products there=slow growth.

71
Q

Allee effect

A

decrease in growth rate per capita at low population densities
difficult to find mate/little contact of free gametes
cooperation within populations=at low density makes more work for individuals
per capita risk of predation is smaller in large prey populations
cooperative defenses not active at low population
N: critical density to support positive growth.

72
Q

catastrophic transition

A

small change in conditions causes a sudden, large and not easily reversible change in the system.

73
Q

community

A

consists of all organisms in a geographic area

surface of tooth, forest, drop of rain, etc.

74
Q

community ecology

A

studies distribution abundance and interactions between coexisting populations
interactions between species in a community

75
Q

why study community ecology

A

depend on ecosystems for oxygen, food, waste degradation
human activity affects natural communities
helps us understand how we affect stability and function of communities
engineer microbial communities

76
Q

species richness

A

number of species in a community
problem because microbial species are not well defined.
rarefaction curves estimate species richness fro sampled communities

77
Q

Species-area rule

A

tenfold increase in the size of a habitat to produce a doubling of the number of species.

78
Q

species diversity

A

limitation of richess: rare species are given the same weight as abundant species
Shannon index is a measure of how even species are-high index equals a more even community

79
Q

rank-abundance distribution

A

few abundant species

many rare species=fat tail/rare biosphere

80
Q

spatial structure

A

can use imaging mass spec.

some species create habitat for others

81
Q

temporal structure

A

timing of the appearance and activity of species.

ex: desert plants and animals are dormant until seasonal rains.

82
Q

factors that determine community stability/maintenance of species coexistence

A

competitive exclusion principle/paradox of the plankton
resources partitioning/character displacement
predator/prey oscillations
trophic cascades

83
Q

competitive exclusion principle

paradox of the plankton

A

two species with similar requirements cannot coexists in same community. one will outcompete the other.
two populations can coexist only if their needs are sufficiently different
-How do so many species exist in a relatively unstable environment when competing for the same resources, especially in waters?

84
Q

resource partitioning

A

instead of one species going exist as a result of competition, resources used will diverge
either the species will use different resources of they will use different part of the same resource.
Ex: five species of warblers live in different parts of the same tree/bacteria that grow at different levels in liquid culture.

85
Q

temporal partitioning example

A

different types of phytoplankton bloom at different times of the year
diatoms: spring and fall
green algae: early summer
blue-green algae: late summer

86
Q

character displacement

A

tendency of characters to be more divergent in sympatric populations (same location, different niches) of two species, as compared to allopatric populations (geographically isolated) of the same two species
consequence of resource partitioning

87
Q

predator-prey/consumer-resource relationships

A

consumer doesn’t decimate all resources because food web is more complex than a single interaction, natural selection changes prey and predators must adapt, prey has defense mechanisms

88
Q

kill-the-winner

A

more abundant microbial strains are more efficiently predated so they are the losers
Ex: phages can lead to diversity of bacteria in the ocean.
slower growing strains are hunted less easily but they grow slower so also losers.
nobody wins, everyone is equal.

89
Q

trophic cascades

A

top-down control
predators mediate the activity of the prey, protecting primary producers. though there may be only a few of the keystone species, their presence changes the behavior of the prey.

90
Q

Top-down vs bottom-up effects

A

bottom-up: organisms at each trophic level are food limited

top-down: top level is food limited, lower levels are alternately predator vs. food limited.

91
Q

ecosystem ecology

A

study of community and nonliving surroundings to understand how systems operate as a whole

  • amount of energy produced by photosynthesis?
  • how energy/materials flow along the food chain?
  • what controls the rate of nutrient cycling?
92
Q

invasive species

A

non-native organisms in an ecosystem. introduction likely causes harm because it has no predators.
Burmese pythons in the Everglades, ferrel dogs, emerald ash borer

93
Q

role of microorganisms in ecosystems

A

contribute to all trophic levels
act as primary producers, decomposers
also act as symbiots

94
Q

Carbon Cycle

A

CO2 fixed by photosynthetic land plants and marine microbes.
CO2 returned to atmosphere by respiration, decomposition, and anthropogenic activities
greatest carbon reservoir is in rocks and sediments (inorganic)

95
Q

nitrogen cycle

A

78% of atmosphere mostly in form of N2 (unusable)

often the limiting factor for growth.

96
Q

microbes and the nitrogen cycle

A

only organisms able to fix nitrogen (anoxically)
energy generated from NH4 oxidation
NO2–>N2: AMAMMOX bacteria gain energy (form 30-50% of N2 gas produced.

97
Q

Nitrogen fixation

A

done by bacteria that live in root nodules of legumes on land
marine: filamentous cyanobacteria

98
Q

Humans and nitrogen

A

humans fix twice as much terrestrial nitrogen fixation than microbes, 45% of the total useful nitrogen on Earth.
Haber-Bosch process: invented for fertilizer

99
Q

Hydrothermal vents

A

chemosynthetic bacteria are primary producers, using sulfur compounds for energy
life may have originated here.
not reliant on sun energy

100
Q

Cold seeps

A

chemical energy derived from methane or H2S

bacteria are primary producers

101
Q

biodegradation

A

break down of organic matter by microbes

102
Q

bioremediation

A

engineering technique applied by people to clean up organic matter by helping microbes with the biodegradation process
used to clean up oil, toxic chemicals, other pollutants
cost-effective and practical.

103
Q

xenobiotics

A

synthetic compounds that do not occur naturally
degrade extremely slowly
microorganisms can break them down.
example: degradation of plastics.

104
Q

define cooperation and its problem

A

individuals forgo some of their reproductive potential to help one another.
Problem: natural selection implies survival of the fittest

105
Q

Fruiting body formation pros and cons

A

benefits: spores can get dispersed farther and better ensuring survival of the species
cons: many cells must die to form the stalk and non-spore parts of body

106
Q

biofilm formation pros and cons

A

pros: it is difficult to reach the cells. film gives protection from antibiotics, other organisms, dessication
cons: energy had to be expended to for biofilm. takes away from energy used for reproduction

107
Q

public good generation and examples

A

products produced by one organism but used by all.
secretion of enzymes that degrade cellulose (yeast cells)
production of antibiotics (good for resistant bacteria)
siderophore production (iron sequestration
biofilm matrix production
secretion of antibiotic degradation enzymes
quorum sensing signal production

108
Q

tragedy of the commons

A

cheaters/defectors obtain benefits from a collectively produced public good that are larger than the cheaters’ contributions.
selfish genotypes can readily invade cooperative populations in the absence of mechanisms to exclude them.

109
Q

classical game theory

A

study of mathematical models of conflict and cooperation between intelligent, rational decision-makers.

110
Q

evolutionary game theory

A

study of mathematical models of conflict and cooperation in evolving populations
mostly concerned with the fate of different genetically-encoded strategies within a population

111
Q

prisoner’s dilemma

A

no direct benefit from ones own cooperation. one only benefits from the cooperation of others.
best strategy is to defect/cheat despite low payoff
end result: cooperators get extinct in well mixed communities with random interactions. community only successful if everyone cooperates

112
Q

snow drift theory

A

it is worth cooperating even if others do not cooperate
it is worth cheating if others are cooperating
end result: frequency dependent selection leads to coexistence between cooperators and defectors.

113
Q

hawk-dove example

A

hawk: cheater/aggressor
dove: cooperator/passive

114
Q

mechanisms promoting cooperation

A
  1. preferential access to a public good
  2. globally, mixed populations grow more in size than populations of either separately, despite subpopulations being dominated by cheaters.
  3. kin selection
115
Q

preferential access to a public good, unpacked.

A

sucrose utilization story:
though there is a cost to sucrose degradation to cooperator (enzyme producers)
cooperator has 1% preferential access to glucose, producing snow drift game.
99% of good available to public

116
Q

growth-rate yield tradeoff

A

yeast can eat glucose by fermentation (cheaters) or by respirations (cooperators)
cheaters can grow much more quickly so they perpetuate the species by being very competitive
cooperators grow more slowly but generate a lot more energy so they perpetuate the species for the long haul.

117
Q

kin selection

A

there is no conflict in isogenic populations

Streptomyces colonies originate from a single original cell so they’re all related. conflict is avoided because genome is shared by all. some cells produce antibiotics and other cells undergo PCD to form fruiting bodies and exospores.

118
Q

other factors that help cooperation

A

there is no conflict in isogenic populations
spatial structure-cooperators are clustered
reciprocity: repeated interactions–must keep a good reputation
recognition and discrimination of partners-only cooperate with other cooperators.

119
Q

Dantas paper: INSeq (TnSeq) applications, pros and cons

A
  1. randomly insert Tn with restriction site into population
  2. mutant population passed through experimental system (germ-free mouse gut)
  3. genomic DNA collected and cut with enzyme to determine what gene it inserted into
    purpose: identifies genes required for survival in different conditions by removing function of gene.
    Pro: discovery of gene is tied to a function
    Con: we don’t know what most genes do (?)
120
Q

Dantas paper: functional metagenomics applications, pros and cons

A
  1. DNA extraction
  2. shotgun sequencing
  3. insert pieces into hosts and searching for a specific function.
    Purpose: genes needed for survival in toxic environments and use of substrates
    Pro: Gene discovered is tied to a function.
    Con: difficult to tell if survival of cell is due to natural capacity or because of added DNA.

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