Humans And The Ecology Of Bacteria And Viruses Flashcards
what are bacteria?
microscopic unicellular living organisms
-> most > 0.5 < 5m0 um w/ no organelles
what are viruses?
they are microorganisms )< 0.2um) with no capacity to generate their own energy
what do viruses lack?
complete set of RNA
What virus is an exception in terms of size?
mimivirus - large DNA phage
what environments can support bacterial growth?
almost every one, even extreme ones
what are the 6 main characteristics of bacteria?
- self feeding
- self replication
- differentiation (sporulaton)
- chemical signaling
- movement
- evolution
describe autotrophic organisms
use energy from light or chemical oxidation. gets carbon from co2 or cabonate
describe heterotrophic organisms
energy from oxidation of organic molecules, carbon from metabolic intermediates
most pathogens are….
heterotrophic
what does liebigs law state?
growth is not controlled by the total amount of resources available, but the scarcest resource (limiting factor)
what is a real world example of liebigs law?
plant growth often is not limited by water or sunlight, but by nitrogen or phosphate in the soil
what did liebig wrongly think about nitrogen?
he thought that plants assimilated N via gaseous ammonia in a similar fashion to how they do CO2 via photosynethsis
what was proven about how plants assimilate N?
do so as mineral NH4 or NO3-
what was martin’s experiment?
Experiment in which they introduced varying levels of iron to the natural environment & observed increased photosynthetic productivity (via chlorophyll)
what did martin’s experiment find?
the limiting factor was iron, when Fe was added plants grew more
-> increased production of chlorophyll
how does iron act as a limiting factor?
is critical for several metalloproteins in the body, and several bacteria have evolved iron carriers to take advantage of ferric iron in the body
what are siderophores?
Small, high-affinity iron-chelating compounds secreted by microorg’s that serve to transport iron across cell membranes.
-> have high affinity to iron
what has a great # of spiderophores?
e coli
how do siderophores work
Hydroxamate group of molecule binds to ferric iron, Fe3+ (not soluble at neutral pH) –> Ferric hydroxamate. Binds to cytoplasmic receptor on bacteria –> Brought into bacterial cell. Reduction process –> Fe2+. Hydroxamate leaves cytoplasm.
Fe2+ converted into Ferredoxin, then Heme (via Porphyrin)
what are the 2 principles constraining liebigs law?
- Only applicable under steady-state conditions (non-transitioning ecosystem)
- Limiting factor may change according to interaction of environmental variables
what does shelfords law stipulate?
Success of an organism relies not only on the availability of nutrient but also that organism’s tolerance to the environment. Optimal and minimal conditions exist.
optimum growth
the range of physical factors that allow max growth of a given organism
what differentiates eurytypic and stenotypic organisms?
Eury: grow within a wide range of a specific condition (ex: temp)
Steno: grow only in a narrow range of a specific condition (ex: dont tolerate change in temp)
what is meant by quorum sensing
cells reach a certain density and can start expressing proteins which affect surrounding population
what is meant by diauxic growth?
cells grow in 2 phases, caused by the organism switching from one nutrient source to another more beneficial one
what are 4 examples of environments that might affect bacteria growth?
water, sodium, light, temperature
The discovery of what process of chemical reduction of what form of nitrogen led to the used of chemical fertilizer in agriculture?
Discovery of the Haber-Bosch process of chemical reduction of N2 to NH3
enterobactin
a high affinity siderophore that acquires iron for microbial systems.
- Is primarily found in Gram-negative bacteria, such as Escherichia coli and Salmonella typhimurium.
what is the most important factor for life on earth
water
water availability and prokaryotes
some have developed molecular adaptations to support low availability of water
what decreases water activity
salt and sugar
resistance to water stress order
staph > pseudo, vibrio > strep, escherichia
Example of S. aureus vs. E. coli as a halotolerant or euryhaline organism
S. aureus can support higher ccn of sodium than E. coli.
Therefore, S. aureus is euryhaline or halotolerant compared to E. coli, which is stenohaline or non-halophile
Non-halophile vs. Halotolerant vs. Halophile vs. Extreme halophile (diagram)
importance of light
- energy source
- direct source of energy
- indirect source of energy
- source of UV rays
- drives thermal processes
- sterilization
in what 3 ways does temperature affect the growth and survival of organisms?
- rate of chemica rxns
- denaturation of proteins
- climate
different enzymes may have varying ______ to _____
tolerance, temperature changes
what is an example of temp and its effects on rate of chemical rxn’s?
- can lead to greater accumulation of certain by-product
- increased N2O from denitrifying bacteria at low temperatures
what are high temperatures usually assocaited with?
geothermal activities in hot springs, hydrothermal vents, or volcanoes (solfarata)
what temperatures can no phototrophic organisms grow at?
temps > 73 degrees
what can grow at temperatures above 73 degrees?
chemolithotrophic bacteria, those who use sulfide, elemental sulfur or ferrous iron as energy source
what adaptations to prokaryotes have to avoid inactivation of proteins are high temperature?
- subtle changes in hydrophobic interactions, H bonds
- extra salt bridges
at what temps do mesophilic bacteria thrive?
~39C
at what temperatures do thermophilic bacteria thrive?
~60C
what temperatures do hyperthermophilic bacteria thrive?
~88C or even greater (108C)
what temperature range do pathogenic bacteria usually prefer?
mesophiles who prefer narrow range of ~37C (normal temp of human body)
e. coli and temperature constraints
e coli OH157:H7 need environment below 25C while retinaing competitiveness at 37C
-> usually grows less at 20C than 37C (challenge for survival)
what kind of bacteria can use a temperature switch?
francisella tularensis in the development of a vaccine
obligate aerobe
organism that requires a constant supply of oxygen in order to live
Performs aerobic respiration
e.g. Micrococcus luteus (commensal)
Typically found on the skin
facultative aerobe
organism that can live with or without oxygen, but has optimal growth w/ oxygen
Can perform aerobic/anaerobic respiration or fermentation
e.g. Escherichia coli
Often found in mammalian sm intestine
microaerophilic aerobe
Oxygen is required but at levels lower than atmospheric (20%) - typically 5%
Perform aerobic respiration
e.g. Magnetospirillum magnetotacticum
Often found in sediment/soil in environment
aerotolerant anerobes
do not utilize oxygen but can survive and grow (less optimally) in its presence
Typically undergo fermentation
e.g. Streptococcus pyogenes (–> Strep throat)
Can be found in upper respiratory tract
e.g. Clostridium dittani
obligate anaerobes
Oxygen is harmful or lethal to them
Can perform fermentation or anaerobic respiration
e.g. Methanobacterium formicicum
Can be foundn in anoxic lake sediment, sewage sludge, etc.
what did oxygen appear
~2 billion years ago
what were living organisms most likely before oxygen?
chemoautotrophic or fermentative
anaerobic respiration
when the bacteria will use another compound, besides oxygen, (e.g. nitrate, or sulphate) as a terminal electron acceptor
what can we understand because we study populations?
nutrient limitations, tolerance factors
biological population
Anthropologic: All the inhabitant of a particular place
Ecological: Organisms of the same spp living in the same place and time
TB outbreak in Vancouver example
Pathogen species: Mycobacterium tuberculosis;
- Population could be those growing in a particular patient
- Could differ genetically from host to host; replicate by binary fission. Therefore, should be all the same/identical population in a single host.
Could also regard humans (host) living in Greater Vancouver that were affected w/ this pathogen during the study period.
Place: Vancouver
Time: Early 2000
population in regards to statistics
The totality of individual observations about which inferences are to be made, existing anywhere in the world or at least within a definitely specified sampling area limited in space and time
how can we study a biological population?
Need to determine…
a) What constitutes an individual (a cell, spore, etc.)
b) How it will be observed (cell under microscope, colony on petri dish, gene, protein, etc.)
c) How it will be treated for statistical analysis
example of how to study a population of plants
a) Determine…
i. Number of individuals of each group per surface area. Biomass determined by diameter of tree at breast height (DBH)
ii. Age of trees by drilling a core & counting # of rings = age.
b) Use mathematical procedure to determine size & characteristic of population
c) Presentation of data: Plot # of trees (y) in relation to age classes (x)
Oak-Hickory population example: regression analysis
measures the impact of a set of variables on another variable
An analytic technique where a series of input variables are examined in relation to their corresponding output results in order to develop a mathematical or statistical relationship.
what is stability of populations determined by?
the degree of variance from a given value or average point
what differentiates a stable population from an unstable one?
Stable: population does not change over time
Unstable: population fluctuates over time according to other factors
What are two very important parameters/characteristics of Populations (Hint: think of what affects numbers)
a) Reproduction - recruitment, offspring, seeds, spores, colonies bacteria
b) Death - e.g. decrease in # of trees w/ age
Since prokaryotes cannot be counted directly, what are some tools/devices to count cells?
1) Microscope (direct count) (Leeuwenhoek, 17th c.)
- Electron
- Epifluorescence (Barry & Evelyn Sherr)
2) Petri dishes (viable count) (Pasteur, Koch, 19th c.)
- Selective & differential media
3) Spectrophotometer (Monod, 1940-50)
4) Quantitative PCR & Molecular probing (Mullis et al., 1990-2010)
what is the problem with direct counting of bacteria using microscope?
There’s no way of knowing which cells are alive or dead –> inaccurate numbers
Therefore, should compare to a viable count for a more accurate representation
how do we count bacterial cells growing on media?
Can be counted as colony forming units (cfu) b/c one colony is typically derived from a single bacterial cell
May need to calculate actual number if performed serial dilutions
turbidimetry
Developed by Monod
The accurate measurement of turbidity as quantified by light transmitted through a suspension of particles
what do you need to be careful with when using turbidimetry?
the amount of cells that you are counting. i.e. you have to relate your optical density to the actual numbers. May need to dilute sample if optical density is too high, in order to get a more accurate number.
describe “monad’s experiments”
Jacques Monod used E. coli as an experimental model to understand bacterial populations
Grew E. coli with glucose as the limiting factor - i.e. Used diff concentrations of glucose & lactose (requires an inducible enzyme)
what are the 6 growth phases describe by monads experiments?
- lag -
- acceleration - growth rate increases
- exponential - growth rate Is constant (cell division)
- retardation - growth rate decreases
- stationary - growth rate is null (equal rates of exponential growth and lysis)
- declining - growth rate negative (rate of lysis exceeds rate of growth)
which phase is used to define a population in bacteriology?
exponential phase, constate rate of growth rather than an actual count
what components of a bacteria start to increase first during cell replication?
Found that the first thing to start increasing was the levels of RNA, followed by protein, DNA, then cell numbers.
Therefore, RNA is first required, which will then drive protein synthesis (e.g. DNA polymerase), then replication of DNA (along with other cellular components), leading to increase in cell numbers.
These processes are what account for the Lag phase
how did monod find the growth rate (umax)
Monod looked at the initial growth rate at differing [glucose]’s…
Observed a parabolic fn in relation to the growth rate and [substrate] –> Suggested to Monod an equation in which umax is the ‘plateau’. And half the umax (umax/2) is equivalent to the Ks (equilibrium constant)
what is the growth rate equation?
u=umax(s/(ks+s)
where, µ = specific growth rate (1/time)
µmax = maximum specific growth rate (1/time) for the culture
S = substrate concentration (mass/volume)
Ks = half-saturation constant (mass/volume) aka: the affinity constant.
what is k?
carrying capacity or limiting density,
the theoretical equilibrium population size at which a particular population will stabilize when its supply of resources remains constant
as k goes down…
s (susceptibles) does too
what is an example of how to measure bacterial populations in nature?
using serial dilutions for a viable count
-The number of dilutions you have depends on the number of expected bacteria in the sample.
how do you count colonies accurately? what sample size?
The colony cultured will originate from single cell. Must ensure that the colonies are well-separated. Ideal plate is one that has between 30 and 300 colonies. >300 is too many to count and likely inaccurate. <30 b/c, statistically speaking, an acceptable sample size is >30.
what is another aspect you need to take into account with serial dilution?
Also need to repeat the serial dilution in order to ensure accurate numbers. Triplicates are the minimum in order to have a sense of confidence in the number obtained. Have a greater sense of ‘freedom’ with at least triplicate dilutions.
quantitative PCR
used to quantify the amount of DNA in each cycle and thus the starting amount; usually uses a fluorescent dye or probe that binds to DNA and measures its concentration each cycle
what is the advantage of PCR?
can be very specific and does not require growth
what effects can mixing populations in natural systems have on population growth and survival?
positive, negative or no effect on growth and survival
what is the definition of a biological community?
a system of organisms living together and linked by the effect they have on each other and their shared environment.
what are the 8 interactions that can occur between populations?
Neutralism
Commensalism
Synergism (protocooperation)
Mutualism (symbiosis)
Competition
Amensalism
Predation
Parasitism
define neutralism
lack of interactions between two populations
-> more likely between populations w extremely different metabolic capabilities, spatially distance, or frozen
define commensalism
one organism lives off the leftover nutrients of another
example of commensalism
m. vaccae, by oxidizing cyclohexane to cyclohexanol provides a carbon source to Pseudomonas
What are 3 examples of bacteria inhabiting the human colon that participate in a commensal relationship?
1) Bacteriodes - obligate anaerobe 7 saccharophile
2) Escherichia coli - facultative anaerobe; can perform anaerobic respiration
3) Lactobacillus sp. - facultative anaerobe; uses glucose to produce lactate. Only 26% of people
define synergism
two populations both benefit from a non-obligatory relationship
example of synergism
Methanogens like Methanosaeta produce methane from fermentation of acetate or reduction of CO₂ with H₂ from the oxidation of propionate (Syntrophobacter) or butyrate & caproate (Syntrophomonas)
- Methanogens provide H₂ sink for syntrophic bacteria
define mutualism
two populations benefit eachother and depend on one another for survival
example of mutualism
e.g. Lichens: Cyanobacteria (or algae) w/ a fungus.
e.g. Rhizobium & Leguminosae (peas)
define competition
two populations use the same limiting resource. both are negatively affected
competitive exclusion principle
Two populations cannot occupy exactly the same niche.
Competition brings ecological separation of closely-related populations
i.e. One population will win the competition & the other will be eliminated
Streptococcus pneumoniae Heptavalent vaccine (PCV-7)
Covers 7 strains of the most important Strep. pneumoniae
Led to strain replacement - i.e. Observed a decrease in the prevalence of those pneumococcal cases caused by the 7 serotypes covered by vaccine
BUT the non-vaccine serotype (red) is INCREASING with time due to no competition with the eradication of the other 7.
Most strains are commensals, but some can be pathogenic
Can cause: Otitis media, pneumonia, bacteremia and even meningitis
how can competition be measured
experimentally between pure ultures -> look at growth rate and substrate concentration
what are the two possibilities of competitions for substrates?
a) Strain A always wins
b) At a low ccn, strain c wins, but at a high ccn, strain d wins. i.e. Varying ccn’s of substrate may affect strain’s success.
define amensalism
one population produces a substance toxic to competing populations, and gains advantage
what is amensalism also called?
allelopathy or antibiosis
what is an example of amensalism?
e.g. Production of lactic acid or similar low MW fatty acids are inhibitory to many bacterial populations
e.g. Production of sulfuric acid by Thiobacillus thiooxidans, creates a lower pH (1 or 2) and causes acid mine drainage, which precludes growth of other microorganisms
What are two examples of bacteria that produce antibiotics as a form of Amensalism?
Penicillium produce beta lactam
Streptomyces produce streptomycin
how do bacteriocins display amensalism?
they are small peptides that suppress the growth of nisin-sensitive closely related bacterial strains by destabilizing/disrupting cell membrane functions
-> are encoded on plasmids, may confer a competitive advantage
-> eg nisin - prevents e coli growth (disrupts cell membrane)
what is parasitism?
A relationship between two organisms of different species in which the parasite benefits by deriving its nutritional requirements from the host, which is harmed in the process
what are the two kinds of parasitism?
ectoparasites, endoparasites
what is an ectoparasite?
remains outside the cells of the host population
what is an endoparasites?
parasiites that can dwell within the host cell
-> viruses
what are bacteriophages?
viruses that infect bacteria
describe viral infections
- Virus docks at bacterial cell surface
- Injects its DNA (or RNA) into host,
- Genetic material is first replicated, then proteins are synthesized (using host cell’s resources) & precipitate around viral genome to form new viruses
what is yersinia pestis?
pathogen that causes bubonic plague, an opportunistic pathogen comes from rats or marmots
What is an example of a microbe who’s only parasitic when its host is a human
chlamydia
define predation
one population consumes members of another for energy
what are the two types of strategists of microorganisms?
r and k
r-strategist microorganisms
Success may be related to better molecular machinery for macromolecular synthesis
Fast-growing –> high numbers = more success!
Reproductive strategy in which organisms reproduce early, bear many small, unprotected offspring (ex. insects, mice).
High reproductive rate
k-strategist
Success may be related to a better use or a more efficient extraction of the energy & matter in the immediate environment
Live at the carrying capacity of the immediate environment
Slow-growing, but will expend more energy building up a better organism
reproductive strategy in which organisms reproduce late, bear few, cared for offspring (ex. humans, elephants).
what is the logistic equation for growth from which r and k were derived?
dX/dt x 1/X = r - (r/K x X)
r = per capita rate of population increase
K = carrying capacity of the environment
X = population density as either a number or mass
When X (population density) is LOW, what type of strategist dominates the rate of population change?
r
When X (population density) is LOW, what type of strategist dominates the rate of population change?
k
What is the assumption made with an r-K scheme?
That there is a continuum w/ evolution favouring either adaptation to….
a) High rates of reproduction (r strategists) or
b) Optimal utilization (conservation) of environmental resources (K strategists)
define ecological niche
The activity range of each species along every dimension of the environment, including…
- Physical & chemical factors (temp, humidity, salinity, oxygen ccn)
- Biological factors (syntrophism, amensalism, competition, etc.)
hutchinson niche 1957
An “n-dimensional hypervolume”, where the dimensions are environmental conditions and resources, that define the requirements of an individual or a species to practice its way of life for its population to persist.
Involves multivariate statistics in order to understand the relationship between multiple variables.
You can find the niche by quantifying the number of organisms in the sample
what drives formation of communities?
population succession
- Pop’s of plants, animals, or microorg’s are found in nature in environments that are suitable for their growth & reproductive success
e.g. As you go up in altitude, you can observe a change in the plants & groups of plants
What creates niches in aquatic environments such as the Sooke Lake Reservoir or the Saanich Inlet?
Light decreases as you go down the water column
Such gradients of light creates different masses of water at different temperatures w/ much reduced diffusion between layers
Different pop’s of organisms are thus found in the different layers of water.
examples of abiotic factors
light, temp, oxygen, salinity
examples of biotic factors
syntrophy, competition, amensalism
What are two environments/substrates in which succession can be found along spatial gradients
a) In sediment: Strong vertical gradient created by diffusion dissolved gases (O2, CH4, H2S, etc.) and solutes (NO3, NH4, dissolved organic carbon, etc.)
b) In intertidal marsh or sediment: Strong horizontal gradient associated w/ salinity
What are some species diversity indexes?
- species richness (d)
-shannon-weaber index of diversity (h)
What is often used to figure out the number of prokaryotic species (S) - b/c you can’t necessarily quantify visually
analysis of 16s rRNA
Describe the experiment by Torsvik et al. 1990
Started with samples of soil from the Beech Forest in Norway.
Consisted of 2 sets of experiments:
1) Counts & isolation of soil prokaryotes using classical methods of plating
2) Extraction of DNA from soil
Were able to ID 4000 genomes (which rep 1% of the diversity in the environment)
Describe set 1) Counts & isolation of soil prokaryotes using classical methods of plating
- Had serial dilutions of soil, which were then plated –> quantified # of isolates
- Performed phenotypic ID of bacterial isolates using API strip
- Similarity coefficients were calculated btwn each
isolate - Groupings of isolates organized into Operating Taxonomic Unit (OTU)
- Number of different genomes = (OTU)(species) that exhibited at least 0.8 similarity (or 16 identical tests out of 20)
Describe set 2) Extraction of DNA from soil
- Isolated 16S rRNA
- Denatured DNA at 94 deg Celsius
- ssDNA & dsDNA do not absorb UV at the same w.l.
- Monitored reassociation of DNA by UV spectrophotometry
- Cooled DNA at ~60 deg Celsius
- If DNA very different, time of reassociation will
take much longer than if DNA very similar –> Can compare with a single genome of E. coli
what factors support a community?
- Energy for individual organisms
- Nutrients
- Organisms that are adapted to climate & environmental conditions
- Other organisms as direct or indirect sources of food
define ecosystem
A community & its environment treated together as a functional system of complementary relationship, and transfer & circulation of energy and matter
who first defined an ecosystem
arthur tanslet in 1935
What are the 4 phylodynamic categories of RNA viruses?
- Short infection w/ strong cross immunity - measles
- Short infection w/ partial cross immunity - influenza
- Infection w/ immune enhancement - dengue
- Persistent infection - hiv
