LABS Flashcards
what are the two chemicals we added to the winogradsky column and why?
cellulose (a carbon source)
calcium sulfate (a sulfur source)
what does clostridium do in the winogradsky column?
breaks down cellulose to glucose and then ferments this for energy producing ethanol and organic acids as by-products
what does desulfovibrio do in the winogradsky column?
uses organic molecules produced by clostridium as carbon sources
uses sulfate as final e acceptor in respiration producing hydrogen sulfide creating an H2S gradient in the column (high at bottom low at top)
what does chlorobium do in the winogradsky column?
green sulfur bacteria which can tolerate higher H2S conc than purple sulfur bacteria
photosynthetic and can use calcium carbonate as carbon source, H2S from desulfovibrio as electron donor and light as energy to produce organic molecules
what does chromatium do in the winogradsky column?
purple sulfur bacteria (tolerates lower conc of H2S than green sulfur bacteria)
photosynthetic and can use calcium carbonate as carbon source, H2S from desulfovibrio as electron donor and light as energy to produce organic molecules
what does rhodomicrobium do in the winogradsky column?
purple non-sulfur bacteria
low sulfur levels, low oxygen but in presence of light they carry out photosynthesis like chromatium. They use organic acids or ethanol as electron donors (rather than H2S)
what does beggiatoa do in the winogradsky column?
uses H2S as energy source and oxidises it to sulphuric acid. The energy released by this process is used to fix carbon and produce organic molecules
what does cyanobacteria (and algae) do in the winogradsky column?
in pond water, aerobic photosynthetic microbes abound. They harvest light energy and release O2 as by-product. With energy from sunlight, the microbes fix CO2 and produce organic molecules
most microorganisms are…
cehmotrophs (gain energy from chemical sources)
what are autotrophs?
carbon source from inorganic CO2
generate new organic compounds from CO2
what are photoautotrophs?
energy source = light
what are chemoautotrophs?
energy source = chemical compounds
what are heterotrophs?
carbon source = organic compounds
uses carbon fixed by autotrophs
what are photoheterotrophs?
energy source = light
what are chemoheterotrophs?
energy source = chemical compounds
which way does the oxygen gradient go in a typical winogradsky column?
aerobic at top anaerobic at bottom microaerophilic in middle
what is a cross-inoculation group?
a group of rhizobia that infect a group of related legumes
how does rhizobia infection of a legume occur?
rhizobia enters root hair and grows within an infection thread which spreads through root hair to root. Tetraploid cells in root are stimulated to divide and form nodule. Bacterial cells bud off from infection thread surrounded by membrane of plant origin into tetraploid cell cytoplasm where they divide and become branched cells called bacteroids. Bacteroids fix nitrogen but can’t divide. When nodule deteriorates the few untransformed rhizobia inside will be released to soil to infect other roots or just be free
what is leghaemoglobin?
made by plants and serves as ‘oxygen buffer’ supplying oxygen to bacteroids for production of ATP and at the same time protecting oxygen-sensitive nitrogenase system. Gives nodule red-brown colour
why do we see irregular staining in rhizobium gram-stain?
due to internal storage granules
what might a pink smear behind the cell indicate in the rhizobium gram-stain?
due to polysaccharide layer around outside of the cells
how do you calculate the number of bacteria in an undiluted culture (from a serial dilution)?
number of colonies X 1/vol plated (ml) X dilution factor
how do you calculate what dilution factor is required to get a countable number of colonies (from undiluted CFU/ml)?
number of desiredcolonies / CFU/ml X 1 / volume plated (ml) = target dilution
what is the negative control?
diluent only (check sterility)
what is the positive control?
undiluted culture (check viability)
can a single bacteriological medium support growth of all the diverse populations in soil?
nah g
“the culturing method used may exert its own ____ (sometimes deliberately) on the population of microorganisms present in the sample”
selective pressure
how many soil microorganisms are culturable?
not many (1-10%)
why do we use molten plate count agar (PCA) for estimating microbial populations in environmental samples?
it was devised as a nutritive agar capable of culturing a wide range of microorganisms (still can’t do most in soil)
what are the cellulases and ligninases of fungi responsible for in forest and pastoral ecosystems?
the breakdown of much of the plant material
why are many of the specific close associations between plants and fungi considered mutualistic?
the fungus receives fixed carbohydrate from the plant and the plant receives minerals and water from the fungus
why is sabouraud dextrose agar the preferred medium to use when isolating fungi?
sabouraud agar has a low pH (5.6) that favours fungal growth (fungi grow at lower pH than bacteria)
why were penicillin and streptomycin added to the Sabouraud dextrose agar when estimating the number of fungi present?
as some soil bacteria (e.g. Pseudomonas) can also grow under these conditions of low pH, antibiotics are added to suppress their growth
when estimating the number of endospores present in a sample, why was the soil heated to 80 degrees celsius for 20 minutes?
to kill vegetative cells (this occurs at 65 degrees celsius)
heating the soil sample to 80 degrees celsius for 20 minutes will kill almost all vegetative cells (only extreme thermophile could withstand and unlikely to be any in soil sample)
so this treatment selects for endospores
the outcome of competition among microorganisms may depend on…
rates of nutrient uptake, inherent metabolic rates and growth rates
what is an antagonistic interaction?
one microorganism may produce metabolic products inhibitory to the growth of other microorganisms
why are microorganisms in pure cultures able to achieve growth rates dependent solely on their own genetic abilities and the given growth conditions?
because in a laboratory pure culture they do not have the pressures of having to compete with other species for nutrients or other limiting factors
what happens if another species is introduced to a pure culture and the two compete for resources?
the growth rate of one or both species may be compromised
what are the twelve compounds required to make a microbial cell called?
prescursor metabolites
which bacteria has the catabolic pathways to make all twelve precursor metabolites?
E. coli (via about 25 chemical reactions)
no single catabolic pathway produces all twelve precursor metabolites, what is the minimum number of pathways (and what are they) to make them all?
three (glycolysis, TCA/Krebs cycle, pentose phosphate pathway)
what happens to the twelve precursor metabolites after their production?
they enter biosynthetic pathways to produce the building blocks of macromolecules
what does eosin methylene blue (EMB) agar select for?
selective for growth of E. coli
what does blood agar + streptomycin (BA + s) select for?
selective for growth of streptococcus equi
what is antagonism?
implies a relationship characterised by the advantage to one partner and a disadvantage to the other partner e.g. microbe producing antibiotics to fuck up the other microbes
why are bacteriocins fundamentally different from other inhibitory molecules?
because they are ribosomally translated products, meaning the information encoding their primary structure is directly encoded in the DNA of the producer strain
what is an example of a bacteriocin producing bacteria?
Streptococcus equi subsp. zooepidemicus
what is commensalism?
symbiotic relationship in which one of the participants (typically the symbiont) benefits but the other organism (typically the host) neither benefits nor is harmed
what are some microbial examples of commensalism?
production of extracellular depolymerases (monomers released provide substrate for producer and other microbes by degrading polysaccharides, proteins and nucleic acids (and other macromolecules))
facultative anaerobe removing oxygen from confined environment as resultant anaerobic environment sustains strict anaerobes (E. coli does this in human gut)
how is an antibiotic sensitive organism being grown in the presence of an antibiotic resistant organism an example of commensalism?
E coli strain (XL1-Blue) carries plasmid which confers ampicillin resistance. Plasmid codes for production of beta lactamase enzyme which is exported to extracellular environment where it degrades any antibiotic with a beta lactam ring. By doing this the antibiotic is destroyed before it has a chance to reach bacterial cell and interfere with cell wall synthesis. This means ampicillin sensitive bacteria can grow close to resistant E coli strain as the antibiotic got fucked up
what gram reaction and cell morphology do most endospore-formers share?
gram positive rod
staining may be observed as irregular or beaded due to the endospore developing inside the cell
most often bacillus genera
what conclusion would you make if your negative control plate has no colonies?
the diluent and media were sterile
aseptic technique was good
what conclusion would you make if your negative control plate has a few surface colonies?
the plate was contaminated, probably by poor aseptic technique
what conclusion would you make if there were many subsurface and surface colonies on your negative control plate?
the diluent and media were not sterile
why does streptococcus equi die in minimal salts broth (MSB)?
cause S. equi can’t synthesise the precursor molecules required for growth and they are not provided in MSB
why is E. coli able to grow in minimal salts broth (MSB)?
cause E. coli can synthesise the essential precursors not provided in the MSB
why can both S. equi and E. coli grow in Todd Hewitt Broth (THB)?
THB is a complex medium meaning all growth requirements are provided in the medium so both organisms can grow
why does E. coli grow better in THB than S. equi?
E. coli is better at competing for nutrients than S. equi
what factors alter the growth patterns of microorganisms and how can microorganisms deal with them?
salinity, temperature, pH and UV light
mechanisms can be developed to detoxify the factor or to exclude the factor from the organisms structure. Some microorganisms simply adapt to living with the factors
what has studying the processes and mechanisms that enable microorganisms to survive in extreme conditions taught us much about?
how different protein structures function
what are the groups microorganisms can be grouped into based on which degree of salinity they grow best at?
non halophile (up to 0.3% NaCl)
mild halophile (1-4% NaCl)
moderate halophile (5-10% NaCl)
extreme halophile (12-35% NaCl)
what type of halophile is E. coli?
non/mild halophile
what type of halophile is listonella anguillarum?
moderate halophile (also likes cold temps cause marine microbe)
what type of halophile is staphylococcus epidermis?
extreme halophile
what are the groups microorganisms are categorised in based on which temperature range they grow best at?
psychrophiles
mesophiles
thermophiles
hyper thermophiles
what are psychrophiles?
prefer 0-20 degrees celsius
very important in food preservation
some pathogens e.g. listeria can grow at 4 degrees
what are mesophiles?
prefer 20-45 degrees celsius
many soil organisms and all human pathogens grow well in this range
e.g. S. aureus, E. coli
what are thermophiles?
prefer 45-80 degrees celsius
thermal pools and some soils in summer reach these temperatures
e.g. thermus aquaticus
what are hyper thermophiles?
prefer 80 degrees celsius or more
hot springs and marine hydrothermal vents
pyrolobus fumarii requires a temperature of above 90 degrees celsius to sustain growth
what are thermoduric organisms?
organisms which can survive high temperatures for long periods of time but are unable to grow
endospore formers are considered thermoduric cause their spores can survive at temps. where their vegetative cells rapidly destroyed
can many bacteria survive outside of their optimal growth ranges?
yes! they just might not be able to grow much or at all
what is bacillus stearothermophilus?
thermophile
what are the three forms of sunlight?
visible light (used for photosynthesis and most life dependent on this in some way)
ultraviolet radiation (UV) (can kill many microorganisms due to short wavelength and high energy, most lethal is wavelength of 260nm as easiest absorbed by DNA, causes thymine dimer formation in DNA)
infrared rays
in regards to the sun, what do microbes isolated from the environment often show increased tolerance to?
exposure to UV radiation
after the effect of UV light experiment, why did we cover the agar plates in aluminium foil AFTER exposure?
so that the repair process of photo reactivation cannot take place (visible light is required for photoreactivation)
why did we remove the lids of the petri dish when putting the agar under UV light in exposure to UV experiment?
UV light does not penetrate the plastic lid
why is acidity more common in nature than alkalinity?
because acidity develops in oxidising environments and the biosphere is predominantly aerobic
also human intervention has increased acidity a lot
what are acidophiles?
microbes which prefer acidic environments
what are alkaliphiles?
microbes which prefer alkaline environments
what does the term rhizobia mean?
rhizobia are a group of alpha-proteobacterial genera containing species that are able to form nitrogen-fixing nodules with legumes
what is Rhizobium?
the best studied genera of rhizobia
what are bacteroids?
they are differentiated. bacterial cells within the root nodule cells of legumes. They carry out nitrogen fixation in this form
what does it mean when people say bacteroids are ‘terminally differentiated’?
it means that the bacterial cells can neither divide or revert back to the non-differentiated state
what is leghaemoglobin and what is its function?
it is a protein that protects the nitrogenase enzyme. It does this by binding oxygen and helps maintain micro aerobic conditions within the mature nodule
what is leghaemoglobin and what is its function?
it is a protein that protects the nitrogenase enzyme. It does this by binding oxygen and helps maintain micro aerobic conditions within the mature nodule
how is the relationship between the bacteroid and the plant mutualistic?
the plant provides certain amino acids to the bacteroids and the bacteroids then shuttle amino acids (bearing fixed nitrogen) back to the plant. The bacteroids also receive carbon and energy from the host plant
how did the results of the biological communities plate exhibit antagonism?
antagonism means one microorganism has growth advantage over another. The S. equi subsp zooepidemicus (vertical strip) produced a bacteriocin which inhibits the growth of closely related species - for example, the S. pyogenes species (zone of inhibition between vertical strip and horizontal)
why was the Micrococcus luteus strain that was sensitive to ampicillin capable of growing in the presence of E. coli XL1-Blue/pBluescript?
The E. coli XL1-Blue (ampR) produces and excretes beta lactamase enzyme into medium which cleaves beta lactam ring of ampicillin. This means where the enzyme has diffused into the agar (close to E. coli growth) the ampicillin is degraded and M. luteus (ampS) is able to grow
why does Bacillus subtilis have increased resistance to UV exposure?
it is an endospore producer and a soil microbe
why is E coli very sensitive to UV light?
its normal environment is in the gut so no UV resistance and also no endospores
